Started by user Miriam Baglioni Obtained BETA_aggregation/Jenkinsfile from git gitea@code-repo.d4science.org:D-Net/dnet-hadoop-deployment.git [Pipeline] Start of Pipeline [Pipeline] node Running on ip-90-147-167-168.ct1.garrservices.it in /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation [Pipeline] { [Pipeline] stage [Pipeline] { (Declarative: Checkout SCM) [Pipeline] checkout The recommended git tool is: NONE using credential dnet-hadoop-deployment-credentials Cloning the remote Git repository Cloning repository gitea@code-repo.d4science.org:D-Net/dnet-hadoop-deployment.git > git init /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation # timeout=10 Fetching upstream changes from gitea@code-repo.d4science.org:D-Net/dnet-hadoop-deployment.git > git --version # timeout=10 > git --version # 'git version 2.17.1' using GIT_SSH to set credentials User for CI/CD Verifying host key using known hosts file > git fetch --tags --progress -- gitea@code-repo.d4science.org:D-Net/dnet-hadoop-deployment.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch Checking out Revision 8b2f52f3272e2231ba7a8feaada684f75579403c (refs/remotes/origin/master) Commit message: "Merge pull request '[BETA] added the deployment instruction in the jenkins file for beta related to the creation of the action set to include the results tagged with FoS without a doi' (#8) from fosNoDoiExtention into master" > git config remote.origin.url gitea@code-repo.d4science.org:D-Net/dnet-hadoop-deployment.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f 8b2f52f3272e2231ba7a8feaada684f75579403c # timeout=10 > git rev-list --no-walk 8b2f52f3272e2231ba7a8feaada684f75579403c # timeout=10 [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Setup) [Pipeline] script [Pipeline] { [Pipeline] readFile [Pipeline] sh + date +%Y-%m-%d + echo /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 [Pipeline] pwd [Pipeline] } [Pipeline] // script [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-QvYhVJ23mDqN/agent.19420 SSH_AGENT_PID=19422 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_2739366930730902536.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl rm -rf /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && mkdir -p /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 + scp -r /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/deploy_release.sh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl:/tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 19422 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Checkout) [Pipeline] dir Running in /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop [Pipeline] { [Pipeline] git The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://code-repo.d4science.org/D-Net/dnet-hadoop > git init /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop # timeout=10 Fetching upstream changes from https://code-repo.d4science.org/D-Net/dnet-hadoop > git --version # timeout=10 > git --version # 'git version 2.17.1' > git fetch --tags --progress -- https://code-repo.d4science.org/D-Net/dnet-hadoop +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch Checking out Revision 4f0a04424562f64bb3989fff7e1a391933a274bd (refs/remotes/origin/beta) > git config remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/beta^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f 4f0a04424562f64bb3989fff7e1a391933a274bd # timeout=10 > git branch -a -v --no-abbrev # timeout=10 > git checkout -b beta 4f0a04424562f64bb3989fff7e1a391933a274bd # timeout=10 Commit message: "Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta" > git rev-list --no-walk 4bb504e693927a2e3aae2cb65ca9d91833e8111a # timeout=10 [Pipeline] } [Pipeline] // dir [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Install) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config2215950293747603192tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config2215950293747603192tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sh + cd dnet-hadoop + mvn clean install -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] dhp-code-style [jar] [INFO] dhp [pom] [INFO] dhp-build [pom] [INFO] dhp-build-assembly-resources [jar] [INFO] dhp-build-properties-maven-plugin [maven-plugin] [INFO] dhp-pace-core [jar] [INFO] dhp-common [jar] [INFO] dhp-workflows [pom] [INFO] dhp-workflow-profiles [jar] [INFO] dhp-aggregation [jar] [INFO] dhp-actionmanager [jar] [INFO] dhp-graph-mapper [jar] [INFO] dhp-dedup-openaire [jar] [INFO] dhp-enrichment [jar] [INFO] dhp-graph-provision [jar] [INFO] dhp-blacklist [jar] [INFO] dhp-stats-actionsets [jar] [INFO] dhp-stats-hist-snaps [jar] [INFO] dhp-stats-monitor-irish [jar] [INFO] dhp-stats-monitor-update [jar] [INFO] dhp-stats-update [jar] [INFO] dhp-stats-promote [jar] [INFO] dhp-usage-stats-build [jar] [INFO] dhp-usage-raw-data-update [jar] [INFO] dhp-broker-events [jar] [INFO] dhp-doiboost [jar] [INFO] dhp-impact-indicators [jar] [INFO] dhp-swh [jar] [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-code-style >-------------------- [INFO] Building dhp-code-style 1.2.5-SNAPSHOT [1/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-code-style --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-code-style --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources [INFO] [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ dhp-code-style --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-code-style --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-code-style/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ dhp-code-style --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ dhp-code-style --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ dhp-code-style --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-code-style/target/dhp-code-style-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-code-style --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-code-style/target/dhp-code-style-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-code-style/1.2.5-SNAPSHOT/dhp-code-style-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-code-style/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-code-style/1.2.5-SNAPSHOT/dhp-code-style-1.2.5-SNAPSHOT.pom [INFO] [INFO] -------------------------< eu.dnetlib.dhp:dhp >------------------------- [INFO] Building dhp 1.2.5-SNAPSHOT [2/28] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp --- [INFO] Total Files Processed: 0 in 00:00.004 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp/1.2.5-SNAPSHOT/dhp-1.2.5-SNAPSHOT.pom [INFO] [INFO] ----------------------< eu.dnetlib.dhp:dhp-build >---------------------- [INFO] Building dhp-build 1.2.5-SNAPSHOT [3/28] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-build --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-build --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-build --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-build --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-build --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-build --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-build --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build/1.2.5-SNAPSHOT/dhp-build-1.2.5-SNAPSHOT.pom [INFO] [INFO] ------------< eu.dnetlib.dhp:dhp-build-assembly-resources >------------- [INFO] Building dhp-build-assembly-resources 1.2.5-SNAPSHOT [4/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-build-assembly-resources --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-build-assembly-resources --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-build-assembly-resources --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-build-assembly-resources --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-build-assembly-resources --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-build-assembly-resources --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-build-assembly-resources --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-build-assembly-resources --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-build-assembly-resources --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-build-assembly-resources --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-build-assembly-resources --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-build-assembly-resources --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/target/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-build-assembly-resources --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/target/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-assembly-resources/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.pom [INFO] [INFO] ----------< eu.dnetlib.dhp:dhp-build-properties-maven-plugin >---------- [INFO] Building dhp-build-properties-maven-plugin 1.2.5-SNAPSHOT [5/28] [INFO] ----------------------------[ maven-plugin ]---------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-build-properties-maven-plugin --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-build-properties-maven-plugin --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-build-properties-maven-plugin --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-build-properties-maven-plugin --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 4 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 4 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-build-properties-maven-plugin --- [INFO] Total Files Processed: 4 in 00:00.401 [INFO] Already Sorted: 4 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-build-properties-maven-plugin --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-build-properties-maven-plugin --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/classes [INFO] [INFO] --- maven-plugin-plugin:3.3:descriptor (default-descriptor) @ dhp-build-properties-maven-plugin --- [INFO] Using 'UTF-8' encoding to read mojo metadata. [INFO] Applying mojo extractor for language: java [INFO] Mojo extractor for language: java found 2 mojo descriptors. [INFO] Applying mojo extractor for language: bsh [INFO] Mojo extractor for language: bsh found 0 mojo descriptors. [INFO] Applying mojo extractor for language: java-annotations [INFO] Mojo extractor for language: java-annotations found 0 mojo descriptors. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-build-properties-maven-plugin --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-build-properties-maven-plugin --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-build-properties-maven-plugin --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-build-properties-maven-plugin --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-build-properties-maven-plugin --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-plugin-plugin:3.3:addPluginArtifactMetadata (default-addPluginArtifactMetadata) @ dhp-build-properties-maven-plugin --- [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ dhp-build-properties-maven-plugin --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-build-properties-maven-plugin --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-properties-maven-plugin/1.2.5-SNAPSHOT/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-properties-maven-plugin/1.2.5-SNAPSHOT/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-build/dhp-build-properties-maven-plugin/target/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT-sources.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-properties-maven-plugin/1.2.5-SNAPSHOT/dhp-build-properties-maven-plugin-1.2.5-SNAPSHOT-sources.jar [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-pace-core >-------------------- [INFO] Building dhp-pace-core 1.2.5-SNAPSHOT [6/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-pace-core --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-pace-core --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-pace-core --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-pace-core --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-pace-core --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 2 Scala sources and 93 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/classes ... [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkDeduper.scala:125: non-variable type argument Any in type pattern scala.collection.mutable.WrappedArray[Any] is unchecked since it is eliminated by erasure [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala:107: non-variable type argument String in type pattern Seq[String] (the underlying of Seq[String]) is unchecked since it is eliminated by erasure [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala:115: non-variable type argument String in type pattern Seq[String] (the underlying of Seq[String]) is unchecked since it is eliminated by erasure [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala:122: non-variable type argument String in type pattern Seq[String] (the underlying of Seq[String]) is unchecked since it is eliminated by erasure [WARNING] four warnings found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/config/DedupConfig.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/config/DedupConfig.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-pace-core --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 100 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 100 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-pace-core --- [INFO] Total Files Processed: 100 in 00:00.748 [INFO] Already Sorted: 100 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-pace-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 13 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-pace-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 93 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/AbstractComparator.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/AbstractComparator.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-pace-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 13 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-pace-core --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 7 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/test-classes ... [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-pace-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-pace-core --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-pace-core --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-pace-core --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/dhp-pace-core-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-pace-core --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/target/dhp-pace-core-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-pace-core/1.2.5-SNAPSHOT/dhp-pace-core-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-pace-core/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-pace-core/1.2.5-SNAPSHOT/dhp-pace-core-1.2.5-SNAPSHOT.pom [INFO] [INFO] ---------------------< eu.dnetlib.dhp:dhp-common >---------------------- [INFO] Building dhp-common 1.2.5-SNAPSHOT [7/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-common --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-common --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/scala IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 4 were unformatted Details: Correctly formatted: ScholixUtils.scala Correctly formatted: DedupLogModel.scala Correctly formatted: DedupLogWriter.scala Correctly formatted: SparkScalaApplication.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-common --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-common --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-common --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 4 Scala sources and 87 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-common --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 104 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 104 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-common --- [INFO] Total Files Processed: 104 in 00:00.272 [INFO] Already Sorted: 104 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-common --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-common >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-common --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/scala IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 4 were unformatted Details: Correctly formatted: ScholixUtils.scala Correctly formatted: DedupLogModel.scala Correctly formatted: DedupLogWriter.scala Correctly formatted: SparkScalaApplication.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-common --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-common --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-common --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-common --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 104 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 104 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-common --- [INFO] Total Files Processed: 104 in 00:00.286 [INFO] Already Sorted: 104 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-common <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-common --- model contains 128 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-common --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 87 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-common --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 33 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-common --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 17 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/test-classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-common --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 17 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-common --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-common --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-common --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/dhp-common-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-common --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/target/dhp-common-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-common/1.2.5-SNAPSHOT/dhp-common-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-common/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-common/1.2.5-SNAPSHOT/dhp-common-1.2.5-SNAPSHOT.pom [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-workflows >-------------------- [INFO] Building dhp-workflows 1.2.5-SNAPSHOT [8/28] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-workflows --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-workflows --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-workflows --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-workflows --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-workflows --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-workflows --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-workflows --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/target/dhp-workflows-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-workflows --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-workflows/1.2.5-SNAPSHOT/dhp-workflows-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/target/dhp-workflows-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-workflows/1.2.5-SNAPSHOT/dhp-workflows-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-workflow-profiles >---------------- [INFO] Building dhp-workflow-profiles 1.2.5-SNAPSHOT [9/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-workflow-profiles --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-workflow-profiles --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-workflow-profiles --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-workflow-profiles --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-workflow-profiles --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-workflow-profiles --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 22 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-workflow-profiles --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-workflow-profiles --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-workflow-profiles --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-workflow-profiles --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-workflow-profiles --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-workflow-profiles --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/target/dhp-workflow-profiles-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-workflow-profiles --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/target/dhp-workflow-profiles-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-workflow-profiles --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/target/dhp-workflow-profiles-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-workflow-profiles/1.2.5-SNAPSHOT/dhp-workflow-profiles-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-workflow-profiles/1.2.5-SNAPSHOT/dhp-workflow-profiles-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-workflow-profiles/target/dhp-workflow-profiles-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-workflow-profiles/1.2.5-SNAPSHOT/dhp-workflow-profiles-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [10/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 2 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 137 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.056 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 2 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.386 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-aggregation --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-aggregation/1.2.5-SNAPSHOT/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-aggregation/1.2.5-SNAPSHOT/dhp-aggregation-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-aggregation/1.2.5-SNAPSHOT/dhp-aggregation-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ------------------< eu.dnetlib.dhp:dhp-actionmanager >------------------ [INFO] Building dhp-actionmanager 1.2.5-SNAPSHOT [11/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-actionmanager --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-actionmanager --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-actionmanager --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-actionmanager --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 10 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 10 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-actionmanager --- [INFO] Total Files Processed: 10 in 00:00.031 [INFO] Already Sorted: 10 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-actionmanager --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 12 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-actionmanager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-actionmanager --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 35 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-actionmanager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-actionmanager --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-actionmanager --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-actionmanager --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/dhp-actionmanager-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-actionmanager --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/dhp-actionmanager-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-actionmanager --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/dhp-actionmanager-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-actionmanager/1.2.5-SNAPSHOT/dhp-actionmanager-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-actionmanager/1.2.5-SNAPSHOT/dhp-actionmanager-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-actionmanager/target/dhp-actionmanager-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-actionmanager/1.2.5-SNAPSHOT/dhp-actionmanager-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ------------------< eu.dnetlib.dhp:dhp-graph-mapper >------------------- [INFO] Building dhp-graph-mapper 1.2.5-SNAPSHOT [12/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-graph-mapper --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-graph-mapper --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 26 were unformatted Details: Correctly formatted: SparkApplyHostedByMapToResult.scala Correctly formatted: Aggregators.scala Correctly formatted: SparkApplyHostedByMapToDatasource.scala Correctly formatted: SparkPrepareHostedByInfoToApply.scala Correctly formatted: SparkProduceHostedByMap.scala Correctly formatted: CopyHdfsOafSparkApplication.scala Correctly formatted: SparkResolveEntities.scala Correctly formatted: SparkResolveRelation.scala Correctly formatted: SparkDataciteToOAF.scala Correctly formatted: SparkConvertDatasetToJsonRDD.scala Correctly formatted: SparkCreateScholix.scala Correctly formatted: SparkConvertObjectToJson.scala Correctly formatted: SparkCreateInputGraph.scala Correctly formatted: SparkCreateSummaryObject.scala Correctly formatted: SparkConvertRDDtoDataset.scala Correctly formatted: ORCIDAuthorMatchers.scala Correctly formatted: ORCIDAuthorEnricher.scala Correctly formatted: SparkEnrichGraphWithOrcidAuthors.scala Correctly formatted: TestApply.scala Correctly formatted: TestPreprocess.scala Correctly formatted: TestPrepare.scala Correctly formatted: ResolveEntitiesTest.scala Correctly formatted: RetrieveDataciteDeltaTest.scala Correctly formatted: ScholixGraphTest.scala Correctly formatted: EnrichOrcidTest.scala Correctly formatted: ORCIDAuthorMatchersTest.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-graph-mapper --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-graph-mapper --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-graph-mapper --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 51 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes ... [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala:114: abstract type T is unchecked since it is eliminated by erasure [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala:88: match may not be exhaustive. It would fail on the following inputs: datasource, organization, project [WARNING] two warnings found [WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE reason: class file for org.apache.http.annotation.ThreadingBehavior not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP [WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE reason: class file for org.apache.http.annotation.ThreadingBehavior not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP [WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE reason: class file for org.apache.http.annotation.ThreadingBehavior not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP [WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE reason: class file for org.apache.http.annotation.ThreadingBehavior not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP [WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE reason: class file for org.apache.http.annotation.ThreadingBehavior not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP [WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java:104: non-varargs call of varargs method with inexact argument type for last parameter; cast to java.lang.Object for a varargs call cast to java.lang.Object[] for a non-varargs call and to suppress this warning [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-graph-mapper --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 67 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 67 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-graph-mapper --- [INFO] Total Files Processed: 67 in 00:00.225 [INFO] Already Sorted: 67 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-graph-mapper --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 84 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-graph-mapper --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-graph-mapper --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 126 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-graph-mapper --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 8 Scala sources and 16 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-graph-mapper --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 16 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-graph-mapper --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-graph-mapper --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-graph-mapper --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-graph-mapper --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-graph-mapper --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-mapper/1.2.5-SNAPSHOT/dhp-graph-mapper-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-mapper/1.2.5-SNAPSHOT/dhp-graph-mapper-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-mapper/1.2.5-SNAPSHOT/dhp-graph-mapper-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] -----------------< eu.dnetlib.dhp:dhp-dedup-openaire >------------------ [INFO] Building dhp-dedup-openaire 1.2.5-SNAPSHOT [13/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-dedup-openaire --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-dedup-openaire --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/test/scala IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 1 were unformatted Details: Correctly formatted: ConnectedComponent.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-dedup-openaire --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-dedup-openaire --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-dedup-openaire --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 1 Scala source and 23 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-dedup-openaire --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 33 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 33 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-dedup-openaire --- [INFO] Total Files Processed: 33 in 00:00.083 [INFO] Already Sorted: 33 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-dedup-openaire --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 23 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-dedup-openaire --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-dedup-openaire --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 59 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-dedup-openaire --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 10 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/test-classes ... [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-dedup-openaire --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-dedup-openaire --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-dedup-openaire --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-dedup-openaire --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/dhp-dedup-openaire-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-dedup-openaire --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/dhp-dedup-openaire-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-dedup-openaire --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/dhp-dedup-openaire-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-dedup-openaire/1.2.5-SNAPSHOT/dhp-dedup-openaire-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-dedup-openaire/1.2.5-SNAPSHOT/dhp-dedup-openaire-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-dedup-openaire/target/dhp-dedup-openaire-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-dedup-openaire/1.2.5-SNAPSHOT/dhp-dedup-openaire-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-enrichment >-------------------- [INFO] Building dhp-enrichment 1.2.5-SNAPSHOT [14/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-enrichment --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-enrichment --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-enrichment --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-enrichment --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 97 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 97 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-enrichment --- [INFO] Total Files Processed: 97 in 00:00.175 [INFO] Already Sorted: 97 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-enrichment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 44 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-enrichment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 83 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/classes [WARNING] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java:[37,27] com.sun.media.sound.ModelInstrumentComparator is internal proprietary API and may be removed in a future release [WARNING] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java:[37,27] com.sun.media.sound.ModelInstrumentComparator is internal proprietary API and may be removed in a future release [WARNING] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java:[37,27] com.sun.media.sound.ModelInstrumentComparator is internal proprietary API and may be removed in a future release [WARNING] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java:[37,27] com.sun.media.sound.ModelInstrumentComparator is internal proprietary API and may be removed in a future release [WARNING] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java:[37,27] com.sun.media.sound.ModelInstrumentComparator is internal proprietary API and may be removed in a future release [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-enrichment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 130 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-enrichment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 14 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-enrichment --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-enrichment --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-enrichment --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/dhp-enrichment-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-enrichment --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/dhp-enrichment-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-enrichment --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/dhp-enrichment-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-enrichment/1.2.5-SNAPSHOT/dhp-enrichment-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-enrichment/1.2.5-SNAPSHOT/dhp-enrichment-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-enrichment/target/dhp-enrichment-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-enrichment/1.2.5-SNAPSHOT/dhp-enrichment-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] -----------------< eu.dnetlib.dhp:dhp-graph-provision >----------------- [INFO] Building dhp-graph-provision 1.2.5-SNAPSHOT [15/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-graph-provision --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-graph-provision --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-graph-provision --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-graph-provision --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-graph-provision --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 34 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java:-1: Some input files use or override a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-graph-provision --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 47 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 47 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-graph-provision --- [INFO] Total Files Processed: 47 in 00:00.137 [INFO] Already Sorted: 47 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-graph-provision --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-graph-provision --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 34 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-graph-provision --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-graph-provision --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 13 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/test-classes ... [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-graph-provision --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-graph-provision --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-graph-provision --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-graph-provision --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/dhp-graph-provision-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-graph-provision --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/dhp-graph-provision-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-graph-provision --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/dhp-graph-provision-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-provision/1.2.5-SNAPSHOT/dhp-graph-provision-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-provision/1.2.5-SNAPSHOT/dhp-graph-provision-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/dhp-graph-provision-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-graph-provision/1.2.5-SNAPSHOT/dhp-graph-provision-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-blacklist >-------------------- [INFO] Building dhp-blacklist 1.2.5-SNAPSHOT [16/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-blacklist --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-blacklist --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-blacklist --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-blacklist --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 5 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 5 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-blacklist --- [INFO] Total Files Processed: 5 in 00:00.021 [INFO] Already Sorted: 5 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-blacklist --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-blacklist --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-blacklist --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-blacklist --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-blacklist --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-blacklist --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-blacklist --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/dhp-blacklist-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-blacklist --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/dhp-blacklist-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-blacklist --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/dhp-blacklist-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-blacklist/1.2.5-SNAPSHOT/dhp-blacklist-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-blacklist/1.2.5-SNAPSHOT/dhp-blacklist-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-blacklist/target/dhp-blacklist-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-blacklist/1.2.5-SNAPSHOT/dhp-blacklist-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-stats-actionsets >----------------- [INFO] Building dhp-stats-actionsets 1.2.5-SNAPSHOT [17/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-actionsets --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-actionsets --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-actionsets --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 2 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 2 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-actionsets --- [INFO] Total Files Processed: 2 in 00:00.014 [INFO] Already Sorted: 2 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-actionsets --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-actionsets --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-actionsets --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-actionsets --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-actionsets --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/dhp-stats-actionsets-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-actionsets --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/dhp-stats-actionsets-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-actionsets --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/dhp-stats-actionsets-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-actionsets/1.2.5-SNAPSHOT/dhp-stats-actionsets-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-actionsets/1.2.5-SNAPSHOT/dhp-stats-actionsets-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/dhp-stats-actionsets-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-actionsets/1.2.5-SNAPSHOT/dhp-stats-actionsets-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-stats-hist-snaps >----------------- [INFO] Building dhp-stats-hist-snaps 1.2.5-SNAPSHOT [18/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-hist-snaps --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-hist-snaps --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-hist-snaps --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-hist-snaps --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-hist-snaps --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-hist-snaps --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-hist-snaps --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-hist-snaps --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-hist-snaps --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-hist-snaps --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-hist-snaps --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-hist-snaps --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/target/dhp-stats-hist-snaps-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-hist-snaps --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/target/dhp-stats-hist-snaps-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-hist-snaps --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/target/dhp-stats-hist-snaps-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-hist-snaps/1.2.5-SNAPSHOT/dhp-stats-hist-snaps-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-hist-snaps/1.2.5-SNAPSHOT/dhp-stats-hist-snaps-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-hist-snaps/target/dhp-stats-hist-snaps-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-hist-snaps/1.2.5-SNAPSHOT/dhp-stats-hist-snaps-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ---------------< eu.dnetlib.dhp:dhp-stats-monitor-irish >--------------- [INFO] Building dhp-stats-monitor-irish 1.2.5-SNAPSHOT [19/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-monitor-irish --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-monitor-irish --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-monitor-irish --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-monitor-irish --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-monitor-irish --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-monitor-irish --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-monitor-irish --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-monitor-irish --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-monitor-irish --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-monitor-irish --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-monitor-irish --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-monitor-irish --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/target/dhp-stats-monitor-irish-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-monitor-irish --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/target/dhp-stats-monitor-irish-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-monitor-irish --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/target/dhp-stats-monitor-irish-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-irish/1.2.5-SNAPSHOT/dhp-stats-monitor-irish-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-irish/1.2.5-SNAPSHOT/dhp-stats-monitor-irish-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-irish/target/dhp-stats-monitor-irish-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-irish/1.2.5-SNAPSHOT/dhp-stats-monitor-irish-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --------------< eu.dnetlib.dhp:dhp-stats-monitor-update >--------------- [INFO] Building dhp-stats-monitor-update 1.2.5-SNAPSHOT [20/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-monitor-update --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-monitor-update --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-monitor-update --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-monitor-update --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-monitor-update --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-monitor-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-monitor-update --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-monitor-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-monitor-update --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-monitor-update --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-monitor-update --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-monitor-update --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/target/dhp-stats-monitor-update-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-monitor-update --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/target/dhp-stats-monitor-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-monitor-update --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/target/dhp-stats-monitor-update-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-update/1.2.5-SNAPSHOT/dhp-stats-monitor-update-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-update/1.2.5-SNAPSHOT/dhp-stats-monitor-update-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-monitor-update/target/dhp-stats-monitor-update-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-monitor-update/1.2.5-SNAPSHOT/dhp-stats-monitor-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ------------------< eu.dnetlib.dhp:dhp-stats-update >------------------- [INFO] Building dhp-stats-update 1.2.5-SNAPSHOT [21/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-update --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-update --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-update --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-update --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-update --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 39 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-update --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-update --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-update --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-update --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-update --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/target/dhp-stats-update-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-update --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/target/dhp-stats-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-update --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/target/dhp-stats-update-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-update/1.2.5-SNAPSHOT/dhp-stats-update-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-update/1.2.5-SNAPSHOT/dhp-stats-update-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-update/target/dhp-stats-update-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-update/1.2.5-SNAPSHOT/dhp-stats-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ------------------< eu.dnetlib.dhp:dhp-stats-promote >------------------ [INFO] Building dhp-stats-promote 1.2.5-SNAPSHOT [22/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-promote --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-promote --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-promote --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-promote --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-promote --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-promote --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-promote --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-promote --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-promote --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-promote --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-promote --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-promote --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/target/dhp-stats-promote-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-stats-promote --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/target/dhp-stats-promote-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-stats-promote --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/target/dhp-stats-promote-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-promote/1.2.5-SNAPSHOT/dhp-stats-promote-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-promote/1.2.5-SNAPSHOT/dhp-stats-promote-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-promote/target/dhp-stats-promote-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-stats-promote/1.2.5-SNAPSHOT/dhp-stats-promote-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-usage-stats-build >---------------- [INFO] Building dhp-usage-stats-build 1.2.5-SNAPSHOT [23/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-usage-stats-build --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-usage-stats-build --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-usage-stats-build --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- git-commit-id-plugin:2.1.15:revision (default) @ dhp-usage-stats-build --- [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-usage-stats-build --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 7 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 7 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-usage-stats-build --- [INFO] Total Files Processed: 7 in 00:00.035 [INFO] Already Sorted: 7 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-usage-stats-build --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.1:compile (default-compile) @ dhp-usage-stats-build --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-usage-stats-build --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.1:testCompile (default-testCompile) @ dhp-usage-stats-build --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-usage-stats-build --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-usage-stats-build --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-usage-stats-build --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/dhp-usage-stats-build-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-usage-stats-build --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/dhp-usage-stats-build-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-usage-stats-build --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/dhp-usage-stats-build-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-stats-build/1.2.5-SNAPSHOT/dhp-usage-stats-build-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-stats-build/1.2.5-SNAPSHOT/dhp-usage-stats-build-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-stats-build/target/dhp-usage-stats-build-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-stats-build/1.2.5-SNAPSHOT/dhp-usage-stats-build-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --------------< eu.dnetlib.dhp:dhp-usage-raw-data-update >-------------- [INFO] Building dhp-usage-raw-data-update 1.2.5-SNAPSHOT [24/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-usage-raw-data-update --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-usage-raw-data-update --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-usage-raw-data-update --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- git-commit-id-plugin:2.1.15:revision (default) @ dhp-usage-raw-data-update --- [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-usage-raw-data-update --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 10 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 10 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-usage-raw-data-update --- [INFO] Total Files Processed: 10 in 00:00.080 [INFO] Already Sorted: 10 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-usage-raw-data-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.1:compile (default-compile) @ dhp-usage-raw-data-update --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-usage-raw-data-update --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.1:testCompile (default-testCompile) @ dhp-usage-raw-data-update --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-usage-raw-data-update --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-usage-raw-data-update --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-usage-raw-data-update --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/dhp-usage-raw-data-update-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-usage-raw-data-update --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/dhp-usage-raw-data-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-usage-raw-data-update --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/dhp-usage-raw-data-update-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-raw-data-update/1.2.5-SNAPSHOT/dhp-usage-raw-data-update-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-raw-data-update/1.2.5-SNAPSHOT/dhp-usage-raw-data-update-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-usage-raw-data-update/target/dhp-usage-raw-data-update-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-usage-raw-data-update/1.2.5-SNAPSHOT/dhp-usage-raw-data-update-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ------------------< eu.dnetlib.dhp:dhp-broker-events >------------------ [INFO] Building dhp-broker-events 1.2.5-SNAPSHOT [25/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-broker-events --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-broker-events --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-broker-events --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-broker-events --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 87 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 87 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-broker-events --- [INFO] Total Files Processed: 87 in 00:00.157 [INFO] Already Sorted: 87 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-broker-events --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 20 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-broker-events --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 80 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-broker-events --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-broker-events --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-broker-events --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-broker-events --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-broker-events --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/dhp-broker-events-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-broker-events --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/dhp-broker-events-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-broker-events --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/dhp-broker-events-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-broker-events/1.2.5-SNAPSHOT/dhp-broker-events-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-broker-events/1.2.5-SNAPSHOT/dhp-broker-events-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-broker-events/target/dhp-broker-events-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-broker-events/1.2.5-SNAPSHOT/dhp-broker-events-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-doiboost >--------------------- [INFO] Building dhp-doiboost 1.2.5-SNAPSHOT [26/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-doiboost --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-doiboost --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [INFO] Scalafmt results: 0 of 22 were unformatted Details: Correctly formatted: DoiBoostMappingUtil.scala Correctly formatted: SparkGenerateDoiBoost.scala Correctly formatted: ORCIDToOAF.scala Correctly formatted: SparkPreprocessORCID.scala Correctly formatted: SparkConvertORCIDToOAF.scala Correctly formatted: GenerateCrossrefDataset.scala Correctly formatted: Crossref2Oaf.scala Correctly formatted: CrossrefDataset.scala Correctly formatted: SparkMapDumpIntoOAF.scala Correctly formatted: UnpackCrtossrefEntries.scala Correctly formatted: SparkMapUnpayWallToOAF.scala Correctly formatted: UnpayWallToOAF.scala Correctly formatted: SparkGenerateDOIBoostActionSet.scala Correctly formatted: SparkImportMagIntoDataset.scala Correctly formatted: MagDataModel.scala Correctly formatted: SparkProcessMAG.scala Correctly formatted: MappingORCIDToOAFTest.scala Correctly formatted: DoiBoostHostedByMapTest.scala Correctly formatted: NormalizeDoiTest.scala Correctly formatted: CrossrefMappingTest.scala Correctly formatted: UnpayWallMappingTest.scala Correctly formatted: MAGMappingTest.scala [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-doiboost --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-doiboost --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 16 Scala sources and 32 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 37 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 37 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-doiboost --- [INFO] Total Files Processed: 37 in 00:00.136 [INFO] Already Sorted: 37 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 48 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 6 Scala sources and 5 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes ... [WARNING] [Warn] : there was one feature warning; re-run with -feature for details [WARNING] one warning found [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-doiboost --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-doiboost --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-doiboost --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-doiboost/1.2.5-SNAPSHOT/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-doiboost/1.2.5-SNAPSHOT/dhp-doiboost-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-doiboost/1.2.5-SNAPSHOT/dhp-doiboost-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-impact-indicators >---------------- [INFO] Building dhp-impact-indicators 1.2.5-SNAPSHOT [27/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-impact-indicators --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-impact-indicators --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-impact-indicators --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-impact-indicators --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 0 [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-impact-indicators --- [INFO] Total Files Processed: 0 in 00:00.000 [INFO] Already Sorted: 0 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-impact-indicators --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 9 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-impact-indicators --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-impact-indicators --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-impact-indicators --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-impact-indicators --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-impact-indicators --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-scm-plugin:1.8.1:checkout (checkout-bip-ranker) @ dhp-impact-indicators --- [INFO] Removing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker [INFO] Executing: /bin/sh -c cd /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app && git clone --branch v1.0.0 https://github.com/athenarc/Bip-Ranker.git /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker [INFO] Working directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app [INFO] Executing: /bin/sh -c cd /tmp && git ls-remote https://github.com/athenarc/Bip-Ranker.git [INFO] Working directory: /tmp [INFO] Executing: /bin/sh -c cd /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker && git fetch https://github.com/athenarc/Bip-Ranker.git [INFO] Working directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker [INFO] Executing: /bin/sh -c cd /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker && git checkout v1.0.0 [INFO] Working directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker [INFO] Executing: /bin/sh -c cd /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker && git ls-files [INFO] Working directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/oozie-package/oozie_app/bip-ranker [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-impact-indicators --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/dhp-impact-indicators-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-impact-indicators --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/dhp-impact-indicators-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-impact-indicators --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/dhp-impact-indicators-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-impact-indicators/1.2.5-SNAPSHOT/dhp-impact-indicators-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-impact-indicators/1.2.5-SNAPSHOT/dhp-impact-indicators-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-impact-indicators/target/dhp-impact-indicators-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-impact-indicators/1.2.5-SNAPSHOT/dhp-impact-indicators-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] -----------------------< eu.dnetlib.dhp:dhp-swh >----------------------- [INFO] Building dhp-swh 1.2.5-SNAPSHOT [28/28] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-swh --- [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-swh --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-swh --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 11 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 11 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-swh --- [INFO] Total Files Processed: 11 in 00:00.036 [INFO] Already Sorted: 11 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-swh --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-swh --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-swh --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-swh --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-swh --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/dhp-swh-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (integration-test-package) @ dhp-swh --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/dhp-swh-1.2.5-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ dhp-swh --- [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/dhp-swh-1.2.5-SNAPSHOT.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-swh/1.2.5-SNAPSHOT/dhp-swh-1.2.5-SNAPSHOT.jar [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/pom.xml to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-swh/1.2.5-SNAPSHOT/dhp-swh-1.2.5-SNAPSHOT.pom [INFO] Installing /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/dhp-swh-1.2.5-SNAPSHOT-tests.jar to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-swh/1.2.5-SNAPSHOT/dhp-swh-1.2.5-SNAPSHOT-tests.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for dhp 1.2.5-SNAPSHOT: [INFO] [INFO] dhp-code-style ..................................... SUCCESS [ 0.787 s] [INFO] dhp ................................................ SUCCESS [ 1.557 s] [INFO] dhp-build .......................................... SUCCESS [ 0.085 s] [INFO] dhp-build-assembly-resources ....................... SUCCESS [ 0.718 s] [INFO] dhp-build-properties-maven-plugin .................. SUCCESS [ 4.009 s] [INFO] dhp-pace-core ...................................... SUCCESS [ 14.859 s] [INFO] dhp-common ......................................... SUCCESS [ 30.865 s] [INFO] dhp-workflows ...................................... SUCCESS [ 0.949 s] [INFO] dhp-workflow-profiles .............................. SUCCESS [ 0.409 s] [INFO] dhp-aggregation .................................... SUCCESS [01:09 min] [INFO] dhp-actionmanager .................................. SUCCESS [ 2.227 s] [INFO] dhp-graph-mapper ................................... SUCCESS [ 46.346 s] [INFO] dhp-dedup-openaire ................................. SUCCESS [ 18.219 s] [INFO] dhp-enrichment ..................................... SUCCESS [ 3.526 s] [INFO] dhp-graph-provision ................................ SUCCESS [ 6.547 s] [INFO] dhp-blacklist ...................................... SUCCESS [ 1.573 s] [INFO] dhp-stats-actionsets ............................... SUCCESS [ 0.840 s] [INFO] dhp-stats-hist-snaps ............................... SUCCESS [ 0.169 s] [INFO] dhp-stats-monitor-irish ............................ SUCCESS [ 0.138 s] [INFO] dhp-stats-monitor-update ........................... SUCCESS [ 0.157 s] [INFO] dhp-stats-update ................................... SUCCESS [ 0.171 s] [INFO] dhp-stats-promote .................................. SUCCESS [ 0.135 s] [INFO] dhp-usage-stats-build .............................. SUCCESS [ 2.350 s] [INFO] dhp-usage-raw-data-update .......................... SUCCESS [ 1.434 s] [INFO] dhp-broker-events .................................. SUCCESS [ 2.625 s] [INFO] dhp-doiboost ....................................... SUCCESS [ 47.017 s] [INFO] dhp-impact-indicators .............................. SUCCESS [ 1.958 s] [INFO] dhp-swh ............................................ SUCCESS [ 1.812 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 04:22 min [INFO] Finished at: 2024-04-02T17:24:26Z [INFO] ------------------------------------------------------------------------ [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (metadata_collection) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8789135412839954939tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8789135412839954939tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-JZbruS6QCvdt/agent.20477 SSH_AGENT_PID=20479 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_8871641596993041738.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/collection -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:24:39+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.075 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:25:12+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.344 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/collection into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/collection/2024-04-02_17_24/oozie_app + hadoop fs -rm -r /user/git.dnet/collection 24/04/02 17:25:51 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/collection' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/collection + hadoop fs -mkdir -p /user/git.dnet/collection + hadoop fs -mkdir -p /user/git.dnet/collection/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/collection/2024-04-02_17_24/oozie_app /user/git.dnet/collection [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:33 min [INFO] Finished at: 2024-04-02T17:26:02Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh collection /lib/dnet/BETA collection + app_dir=collection + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=collection ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/collection/oozie_app + hdfs_target_dir=/lib/dnet/BETA/collection + hdfs dfs -rm -r -f /lib/dnet/BETA/collection 24/04/02 17:26:04 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/collection' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/collection + hdfs dfs -mkdir -p /lib/dnet/BETA/collection + hdfs dfs -mv /user/git.dnet/collection/oozie_app /lib/dnet/BETA/collection [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 20479 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (metadata_transformation) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config4367863764817909917tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config4367863764817909917tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-3bVFkWFo2ONj/agent.20747 SSH_AGENT_PID=20749 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_2952642692401758317.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/transformation -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:26:21+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.043 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:26:52+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.365 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/transformation into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/transformation/2024-04-02_17_26/oozie_app + hadoop fs -rm -r /user/git.dnet/transformation 24/04/02 17:27:30 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/transformation' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/transformation + hadoop fs -mkdir -p /user/git.dnet/transformation + hadoop fs -mkdir -p /user/git.dnet/transformation/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/transformation/2024-04-02_17_26/oozie_app /user/git.dnet/transformation [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:29 min [INFO] Finished at: 2024-04-02T17:27:40Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh transformation /lib/dnet/BETA transformation + app_dir=transformation + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=transformation ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/transformation/oozie_app + hdfs_target_dir=/lib/dnet/BETA/transformation + hdfs dfs -rm -r -f /lib/dnet/BETA/transformation 24/04/02 17:27:43 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/transformation' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/transformation + hdfs dfs -mkdir -p /lib/dnet/BETA/transformation + hdfs dfs -mv /user/git.dnet/transformation/oozie_app /lib/dnet/BETA/transformation [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 20749 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (crossref_download) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config72276608598213985tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config72276608598213985tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-NqFHr0qAZlU5/agent.20995 SSH_AGENT_PID=20997 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_551234224332241999.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-doiboost + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/doiboost/crossref_dump_reader -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-doiboost >--------------------- [INFO] Building dhp-doiboost 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-doiboost --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-doiboost --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf [INFO] Scalafmt results: 0 of 22 were unformatted Details: Correctly formatted: DoiBoostMappingUtil.scala Correctly formatted: SparkGenerateDoiBoost.scala Correctly formatted: ORCIDToOAF.scala Correctly formatted: SparkPreprocessORCID.scala Correctly formatted: SparkConvertORCIDToOAF.scala Correctly formatted: GenerateCrossrefDataset.scala Correctly formatted: Crossref2Oaf.scala Correctly formatted: CrossrefDataset.scala Correctly formatted: SparkMapDumpIntoOAF.scala Correctly formatted: UnpackCrtossrefEntries.scala Correctly formatted: SparkMapUnpayWallToOAF.scala Correctly formatted: UnpayWallToOAF.scala Correctly formatted: SparkGenerateDOIBoostActionSet.scala Correctly formatted: SparkImportMagIntoDataset.scala Correctly formatted: MagDataModel.scala Correctly formatted: SparkProcessMAG.scala Correctly formatted: MappingORCIDToOAFTest.scala Correctly formatted: DoiBoostHostedByMapTest.scala Correctly formatted: NormalizeDoiTest.scala Correctly formatted: CrossrefMappingTest.scala Correctly formatted: UnpayWallMappingTest.scala Correctly formatted: MAGMappingTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-doiboost --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-doiboost --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-doiboost --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-doiboost --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-doiboost --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:28:01+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/version.properties ] (for module dhp-doiboost )... [info] dhp-doiboost ] project dhp-doiboost [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-doiboost --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 16 Scala sources and 32 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 37 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 37 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-doiboost --- [INFO] Total Files Processed: 37 in 00:00.754 [INFO] Already Sorted: 37 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-doiboost --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 48 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 6 Scala sources and 5 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes ... [WARNING] [Warn] : there was one feature warning; re-run with -feature for details [WARNING] one warning found [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-doiboost --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-doiboost --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-doiboost --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-doiboost --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-doiboost --- [INFO] Priming eu/dnetlib/dhp/doiboost/crossref_dump_reader into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-doiboost --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-doiboost --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-doiboost --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-doiboost --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-doiboost --- [INFO] Executing tasks [copy] Copying 3 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 68 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-doiboost --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/doiboost/crossref_dump_reader/2024-04-02_17_27/oozie_app + hadoop fs -rm -r /user/git.dnet/doiboost/crossref_dump_reader 24/04/02 17:28:42 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/doiboost/crossref_dump_reader' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/doiboost/crossref_dump_reader + hadoop fs -mkdir -p /user/git.dnet/doiboost/crossref_dump_reader + hadoop fs -mkdir -p /user/git.dnet/doiboost/crossref_dump_reader/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/doiboost/crossref_dump_reader/2024-04-02_17_27/oozie_app /user/git.dnet/doiboost/crossref_dump_reader [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:01 min [INFO] Finished at: 2024-04-02T17:28:52Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh doiboost/crossref_dump_reader /lib/dnet/BETA actionmanager/crossref_dump_reader + app_dir=doiboost/crossref_dump_reader + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/crossref_dump_reader ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/doiboost/crossref_dump_reader/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/crossref_dump_reader + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/crossref_dump_reader 24/04/02 17:28:54 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/crossref_dump_reader' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/crossref_dump_reader + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/crossref_dump_reader + hdfs dfs -mv /user/git.dnet/doiboost/crossref_dump_reader/oozie_app /lib/dnet/BETA/actionmanager/crossref_dump_reader [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 20997 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (doiboost_preprocess_BETA) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8426696294396185417tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8426696294396185417tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-6px24FrmGnB8/agent.21208 SSH_AGENT_PID=21210 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_607194104194978270.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-doiboost + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/doiboost/preprocess -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-doiboost >--------------------- [INFO] Building dhp-doiboost 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-doiboost --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-doiboost --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf [INFO] Scalafmt results: 0 of 22 were unformatted Details: Correctly formatted: DoiBoostMappingUtil.scala Correctly formatted: SparkGenerateDoiBoost.scala Correctly formatted: ORCIDToOAF.scala Correctly formatted: SparkPreprocessORCID.scala Correctly formatted: SparkConvertORCIDToOAF.scala Correctly formatted: GenerateCrossrefDataset.scala Correctly formatted: Crossref2Oaf.scala Correctly formatted: CrossrefDataset.scala Correctly formatted: SparkMapDumpIntoOAF.scala Correctly formatted: UnpackCrtossrefEntries.scala Correctly formatted: SparkMapUnpayWallToOAF.scala Correctly formatted: UnpayWallToOAF.scala Correctly formatted: SparkGenerateDOIBoostActionSet.scala Correctly formatted: SparkImportMagIntoDataset.scala Correctly formatted: MagDataModel.scala Correctly formatted: SparkProcessMAG.scala Correctly formatted: MappingORCIDToOAFTest.scala Correctly formatted: DoiBoostHostedByMapTest.scala Correctly formatted: NormalizeDoiTest.scala Correctly formatted: CrossrefMappingTest.scala Correctly formatted: UnpayWallMappingTest.scala Correctly formatted: MAGMappingTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-doiboost --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-doiboost --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-doiboost --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-doiboost --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-doiboost --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:29:12+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/version.properties ] (for module dhp-doiboost )... [info] dhp-doiboost ] project dhp-doiboost [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-doiboost --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 16 Scala sources and 32 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 37 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 37 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-doiboost --- [INFO] Total Files Processed: 37 in 00:00.719 [INFO] Already Sorted: 37 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-doiboost --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 48 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 6 Scala sources and 5 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes ... [WARNING] [Warn] : there was one feature warning; re-run with -feature for details [WARNING] one warning found [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-doiboost --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-doiboost --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-doiboost --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-doiboost --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-doiboost --- [INFO] Priming eu/dnetlib/dhp/doiboost/preprocess into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-doiboost --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-doiboost --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-doiboost --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-doiboost --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-doiboost --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 68 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-doiboost --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/doiboost/preprocess/2024-04-02_17_29/oozie_app + hadoop fs -rm -r /user/git.dnet/doiboost/preprocess 24/04/02 17:29:58 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/doiboost/preprocess' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/doiboost/preprocess + hadoop fs -mkdir -p /user/git.dnet/doiboost/preprocess + hadoop fs -mkdir -p /user/git.dnet/doiboost/preprocess/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/doiboost/preprocess/2024-04-02_17_29/oozie_app /user/git.dnet/doiboost/preprocess [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:06 min [INFO] Finished at: 2024-04-02T17:30:08Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh doiboost/preprocess /lib/dnet/BETA actionmanager/doiboost_preprocess + app_dir=doiboost/preprocess + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/doiboost_preprocess ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/doiboost/preprocess/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/doiboost_preprocess + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/doiboost_preprocess 24/04/02 17:30:10 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/doiboost_preprocess' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/doiboost_preprocess + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/doiboost_preprocess + hdfs dfs -mv /user/git.dnet/doiboost/preprocess/oozie_app /lib/dnet/BETA/actionmanager/doiboost_preprocess [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 21210 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (doiboost_process_BETA) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5110163688620255648tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5110163688620255648tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-HFa67Ab092YB/agent.21390 SSH_AGENT_PID=21392 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_7377955896528486531.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-doiboost + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/doiboost/process -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-doiboost >--------------------- [INFO] Building dhp-doiboost 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-doiboost --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-doiboost --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf [INFO] Scalafmt results: 0 of 22 were unformatted Details: Correctly formatted: DoiBoostMappingUtil.scala Correctly formatted: SparkGenerateDoiBoost.scala Correctly formatted: ORCIDToOAF.scala Correctly formatted: SparkPreprocessORCID.scala Correctly formatted: SparkConvertORCIDToOAF.scala Correctly formatted: GenerateCrossrefDataset.scala Correctly formatted: Crossref2Oaf.scala Correctly formatted: CrossrefDataset.scala Correctly formatted: SparkMapDumpIntoOAF.scala Correctly formatted: UnpackCrtossrefEntries.scala Correctly formatted: SparkMapUnpayWallToOAF.scala Correctly formatted: UnpayWallToOAF.scala Correctly formatted: SparkGenerateDOIBoostActionSet.scala Correctly formatted: SparkImportMagIntoDataset.scala Correctly formatted: MagDataModel.scala Correctly formatted: SparkProcessMAG.scala Correctly formatted: MappingORCIDToOAFTest.scala Correctly formatted: DoiBoostHostedByMapTest.scala Correctly formatted: NormalizeDoiTest.scala Correctly formatted: CrossrefMappingTest.scala Correctly formatted: UnpayWallMappingTest.scala Correctly formatted: MAGMappingTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-doiboost --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-doiboost --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-doiboost --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-doiboost --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-doiboost --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:30:28+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/version.properties ] (for module dhp-doiboost )... [info] dhp-doiboost ] project dhp-doiboost [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-doiboost --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 16 Scala sources and 32 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 37 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 37 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-doiboost --- [INFO] Total Files Processed: 37 in 00:00.679 [INFO] Already Sorted: 37 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-doiboost --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 48 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 6 Scala sources and 5 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes ... [WARNING] [Warn] : there was one feature warning; re-run with -feature for details [WARNING] one warning found [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-doiboost --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-doiboost --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-doiboost --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-doiboost --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-doiboost --- [INFO] Priming eu/dnetlib/dhp/doiboost/process into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-doiboost --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-doiboost --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-doiboost --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-doiboost --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-doiboost --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 68 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-doiboost --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/doiboost/process/2024-04-02_17_30/oozie_app + hadoop fs -rm -r /user/git.dnet/doiboost/process 24/04/02 17:31:10 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/doiboost/process' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/doiboost/process + hadoop fs -mkdir -p /user/git.dnet/doiboost/process + hadoop fs -mkdir -p /user/git.dnet/doiboost/process/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/doiboost/process/2024-04-02_17_30/oozie_app /user/git.dnet/doiboost/process [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:02 min [INFO] Finished at: 2024-04-02T17:31:20Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh doiboost/process /lib/dnet/BETA actionmanager/doiboost_process + app_dir=doiboost/process + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/doiboost_process ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/doiboost/process/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/doiboost_process + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/doiboost_process 24/04/02 17:31:23 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/doiboost_process' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/doiboost_process + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/doiboost_process + hdfs dfs -mv /user/git.dnet/doiboost/process/oozie_app /lib/dnet/BETA/actionmanager/doiboost_process [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 21392 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (datacite_collect) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8353174359870224994tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8353174359870224994tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-pHzmQc0p1N50/agent.21595 SSH_AGENT_PID=21597 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_4454021233768292211.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/datacite/collection -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:31:41+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.174 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:32:12+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.359 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/datacite/collection into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/datacite/collection/2024-04-02_17_31/oozie_app + hadoop fs -rm -r /user/git.dnet/datacite/collection 24/04/02 17:32:50 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/datacite/collection' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/datacite/collection + hadoop fs -mkdir -p /user/git.dnet/datacite/collection + hadoop fs -mkdir -p /user/git.dnet/datacite/collection/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/datacite/collection/2024-04-02_17_31/oozie_app /user/git.dnet/datacite/collection [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:30 min [INFO] Finished at: 2024-04-02T17:33:01Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh datacite/collection /lib/dnet/BETA aggregation/datacite_collection + app_dir=datacite/collection + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/datacite_collection ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/datacite/collection/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/datacite_collection + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/datacite_collection 24/04/02 17:33:03 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/datacite_collection' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/datacite_collection + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/datacite_collection + hdfs dfs -mv /user/git.dnet/datacite/collection/oozie_app /lib/dnet/BETA/aggregation/datacite_collection [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 21597 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (datacite_transform) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3954601311088012428tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3954601311088012428tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-oN8GpHzR0ogg/agent.21878 SSH_AGENT_PID=21880 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_3248965502747041288.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/datacite/transformation -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:33:20+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.193 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:33:50+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.377 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/datacite/transformation into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/datacite/transformation/2024-04-02_17_33/oozie_app + hadoop fs -rm -r /user/git.dnet/datacite/transformation 24/04/02 17:34:29 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/datacite/transformation' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/datacite/transformation + hadoop fs -mkdir -p /user/git.dnet/datacite/transformation + hadoop fs -mkdir -p /user/git.dnet/datacite/transformation/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/datacite/transformation/2024-04-02_17_33/oozie_app /user/git.dnet/datacite/transformation [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:28 min [INFO] Finished at: 2024-04-02T17:34:39Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh datacite/transformation /lib/dnet/BETA aggregation/datacite_transformation + app_dir=datacite/transformation + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/datacite_transformation ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/datacite/transformation/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/datacite_transformation + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/datacite_transformation 24/04/02 17:34:41 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/datacite_transformation' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/datacite_transformation + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/datacite_transformation + hdfs dfs -mv /user/git.dnet/datacite/transformation/oozie_app /lib/dnet/BETA/aggregation/datacite_transformation [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 21880 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (biodb_aggregation) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3546242060819092122tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3546242060819092122tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-uBEeiX4Scgt7/agent.22126 SSH_AGENT_PID=22128 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_7476472350335765346.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/bio/db -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:34:59+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.940 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:35:32+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.334 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/sx/bio/db into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/sx/bio/db/2024-04-02_17_34/oozie_app + hadoop fs -rm -r /user/git.dnet/sx/bio/db 24/04/02 17:36:11 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/bio/db' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/bio/db + hadoop fs -mkdir -p /user/git.dnet/sx/bio/db + hadoop fs -mkdir -p /user/git.dnet/sx/bio/db/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/sx/bio/db/2024-04-02_17_34/oozie_app /user/git.dnet/sx/bio/db [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:32 min [INFO] Finished at: 2024-04-02T17:36:21Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh sx/bio/db /lib/dnet/BETA aggregation/biodb_aggregation + app_dir=sx/bio/db + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/biodb_aggregation ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/sx/bio/db/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/biodb_aggregation + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/biodb_aggregation 24/04/02 17:36:24 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/biodb_aggregation' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/biodb_aggregation + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/biodb_aggregation + hdfs dfs -mv /user/git.dnet/sx/bio/db/oozie_app /lib/dnet/BETA/aggregation/biodb_aggregation [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 22128 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (ebi_links_aggregation) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3897092020394378817tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3897092020394378817tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-YXO4h3KlaF9W/agent.22450 SSH_AGENT_PID=22452 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_1441695630770897921.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/bio/ebi -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:36:42+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.024 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:37:15+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.364 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/sx/bio/ebi into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/sx/bio/ebi/2024-04-02_17_36/oozie_app + hadoop fs -rm -r /user/git.dnet/sx/bio/ebi 24/04/02 17:37:54 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/bio/ebi' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/bio/ebi + hadoop fs -mkdir -p /user/git.dnet/sx/bio/ebi + hadoop fs -mkdir -p /user/git.dnet/sx/bio/ebi/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/sx/bio/ebi/2024-04-02_17_36/oozie_app /user/git.dnet/sx/bio/ebi [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:32 min [INFO] Finished at: 2024-04-02T17:38:04Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh sx/bio/ebi /lib/dnet/BETA aggregation/ebi_aggregation + app_dir=sx/bio/ebi + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/ebi_aggregation ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/sx/bio/ebi/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/ebi_aggregation + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/ebi_aggregation 24/04/02 17:38:07 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/ebi_aggregation' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/ebi_aggregation + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/ebi_aggregation + hdfs dfs -mv /user/git.dnet/sx/bio/ebi/oozie_app /lib/dnet/BETA/aggregation/ebi_aggregation [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 22452 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (pubmed_aggregation) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8695932564544890724tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8695932564544890724tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-aQvDCErcBczH/agent.22765 SSH_AGENT_PID=22767 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_5348492031337397922.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/bio/pubmed -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:38:25+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.221 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:38:53+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.369 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/sx/bio/pubmed into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/sx/bio/pubmed/2024-04-02_17_38/oozie_app + hadoop fs -rm -r /user/git.dnet/sx/bio/pubmed 24/04/02 17:39:32 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/bio/pubmed' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/bio/pubmed + hadoop fs -mkdir -p /user/git.dnet/sx/bio/pubmed + hadoop fs -mkdir -p /user/git.dnet/sx/bio/pubmed/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/sx/bio/pubmed/2024-04-02_17_38/oozie_app /user/git.dnet/sx/bio/pubmed [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:27 min [INFO] Finished at: 2024-04-02T17:39:42Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh sx/bio/pubmed /lib/dnet/BETA aggregation/pubmed_aggregation + app_dir=sx/bio/pubmed + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/pubmed_aggregation ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/sx/bio/pubmed/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/pubmed_aggregation + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/pubmed_aggregation 24/04/02 17:39:45 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/pubmed_aggregation' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/pubmed_aggregation + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/pubmed_aggregation + hdfs dfs -mv /user/git.dnet/sx/bio/pubmed/oozie_app /lib/dnet/BETA/aggregation/pubmed_aggregation [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 22767 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (collect_orcid) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config4939740270862603tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config4939740270862603tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-567zEbhxaUvg/agent.23006 SSH_AGENT_PID=23008 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_212598664110013742.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/collection/orcid/update -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:40:02+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.062 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:40:35+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.397 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/collection/orcid/update into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/collection/orcid/update/2024-04-02_17_39/oozie_app + hadoop fs -rm -r /user/git.dnet/collection/orcid/update rm: `/user/git.dnet/collection/orcid/update': No such file or directory + hadoop fs -mkdir -p /user/git.dnet/collection/orcid/update + hadoop fs -mkdir -p /user/git.dnet/collection/orcid/update/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/collection/orcid/update/2024-04-02_17_39/oozie_app /user/git.dnet/collection/orcid/update [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:33 min [INFO] Finished at: 2024-04-02T17:41:25Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh collection/orcid/update /lib/dnet/BETA aggregation/orcid_update + app_dir=collection/orcid/update + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/orcid_update ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/collection/orcid/update/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/orcid_update + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/orcid_update 24/04/02 17:41:28 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/orcid_update' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/orcid_update + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/orcid_update + hdfs dfs -mv /user/git.dnet/collection/orcid/update/oozie_app /lib/dnet/BETA/aggregation/orcid_update [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 23008 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (download_orcid_dump) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8410695355602921932tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config8410695355602921932tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-kV32tqG8np34/agent.23282 SSH_AGENT_PID=23284 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_8675443604357794.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/collection/orcid -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:41:45+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.070 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:42:16+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.359 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/collection/orcid into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/collection/orcid/2024-04-02_17_41/oozie_app + hadoop fs -rm -r /user/git.dnet/collection/orcid 24/04/02 17:42:55 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/collection/orcid' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/collection/orcid1712079775804 + hadoop fs -mkdir -p /user/git.dnet/collection/orcid + hadoop fs -mkdir -p /user/git.dnet/collection/orcid/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/collection/orcid/2024-04-02_17_41/oozie_app /user/git.dnet/collection/orcid [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:30 min [INFO] Finished at: 2024-04-02T17:43:06Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh collection/orcid /lib/dnet/BETA aggregation/orcid_dump + app_dir=collection/orcid + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=aggregation/orcid_dump ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/collection/orcid/oozie_app + hdfs_target_dir=/lib/dnet/BETA/aggregation/orcid_dump + hdfs dfs -rm -r -f /lib/dnet/BETA/aggregation/orcid_dump 24/04/02 17:43:08 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/aggregation/orcid_dump' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/aggregation/orcid_dump + hdfs dfs -mkdir -p /lib/dnet/BETA/aggregation/orcid_dump + hdfs dfs -mv /user/git.dnet/collection/orcid/oozie_app /lib/dnet/BETA/aggregation/orcid_dump [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 23284 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (update_actionset_statsdb) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config1397173559140880165tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config1397173559140880165tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-NKAYUSBAB0MF/agent.23562 SSH_AGENT_PID=23564 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_3293710527663554904.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-stats-actionsets + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/stats_actionsets -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] ----------------< eu.dnetlib.dhp:dhp-stats-actionsets >----------------- [INFO] Building dhp-stats-actionsets 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-stats-actionsets --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-stats-actionsets --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-stats-actionsets --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-stats-actionsets --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-stats-actionsets --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-stats-actionsets --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-stats-actionsets --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:43:19+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/oozie_app/version.properties ] (for module dhp-stats-actionsets )... [info] dhp-stats-actionsets ] project dhp-stats-actionsets [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 2 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 2 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-stats-actionsets --- [INFO] Total Files Processed: 2 in 00:00.390 [INFO] Already Sorted: 2 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-stats-actionsets --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-stats-actionsets --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-stats-actionsets --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-stats-actionsets --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-stats-actionsets --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-stats-actionsets --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-stats-actionsets --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-stats-actionsets --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-stats-actionsets --- [INFO] Priming eu/dnetlib/dhp/actionmanager/stats_actionsets into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-stats-actionsets --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-stats-actionsets --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-stats-actionsets --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-stats-actionsets --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/dhp-stats-actionsets-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-stats-actionsets --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-stats-actionsets --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/oozie_app/lib [copy] Copying 80 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-stats-actionsets/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-stats-actionsets --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-stats-actionsets --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-stats-actionsets --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/stats_actionsets/2024-04-02_17_43/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/stats_actionsets 24/04/02 17:43:35 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/stats_actionsets' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/stats_actionsets + hadoop fs -mkdir -p /user/git.dnet/actionmanager/stats_actionsets + hadoop fs -mkdir -p /user/git.dnet/actionmanager/stats_actionsets/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/stats_actionsets/2024-04-02_17_43/oozie_app /user/git.dnet/actionmanager/stats_actionsets [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 29.778 s [INFO] Finished at: 2024-04-02T17:43:45Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/stats_actionsets /lib/dnet/BETA actionmanager/stats_actionsets + app_dir=actionmanager/stats_actionsets + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/stats_actionsets ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/stats_actionsets/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/stats_actionsets + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/stats_actionsets 24/04/02 17:43:48 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/stats_actionsets' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/stats_actionsets + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/stats_actionsets + hdfs dfs -mv /user/git.dnet/actionmanager/stats_actionsets/oozie_app /lib/dnet/BETA/actionmanager/stats_actionsets [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 23564 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (update_actionset_usagestats) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config899347385331454472tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config899347385331454472tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-MiHcw5nwfjdD/agent.23690 SSH_AGENT_PID=23692 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_3210929742153602848.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/usagestats -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:44:06+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.086 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:44:38+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.413 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/usagestats into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/usagestats/2024-04-02_17_43/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/usagestats 24/04/02 17:45:18 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/usagestats' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/usagestats + hadoop fs -mkdir -p /user/git.dnet/actionmanager/usagestats + hadoop fs -mkdir -p /user/git.dnet/actionmanager/usagestats/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/usagestats/2024-04-02_17_43/oozie_app /user/git.dnet/actionmanager/usagestats [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:33 min [INFO] Finished at: 2024-04-02T17:45:29Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/usagestats /lib/dnet/BETA actionmanager/usagestats_actionset + app_dir=actionmanager/usagestats + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/usagestats_actionset ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/usagestats/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/usagestats_actionset + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/usagestats_actionset 24/04/02 17:45:31 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/usagestats_actionset' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/usagestats_actionset + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/usagestats_actionset + hdfs dfs -mv /user/git.dnet/actionmanager/usagestats/oozie_app /lib/dnet/BETA/actionmanager/usagestats_actionset [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 23692 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (update_actionset_orcidnodoi) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config111139214650747959tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config111139214650747959tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-FxY8sNOZG9WY/agent.23955 SSH_AGENT_PID=23957 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_4492604303552437896.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-doiboost + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/doiboost/orcidnodoi -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] --------------------< eu.dnetlib.dhp:dhp-doiboost >--------------------- [INFO] Building dhp-doiboost 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-doiboost --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-doiboost --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/.scalafmt.conf [INFO] Scalafmt results: 0 of 22 were unformatted Details: Correctly formatted: DoiBoostMappingUtil.scala Correctly formatted: SparkGenerateDoiBoost.scala Correctly formatted: ORCIDToOAF.scala Correctly formatted: SparkPreprocessORCID.scala Correctly formatted: SparkConvertORCIDToOAF.scala Correctly formatted: GenerateCrossrefDataset.scala Correctly formatted: Crossref2Oaf.scala Correctly formatted: CrossrefDataset.scala Correctly formatted: SparkMapDumpIntoOAF.scala Correctly formatted: UnpackCrtossrefEntries.scala Correctly formatted: SparkMapUnpayWallToOAF.scala Correctly formatted: UnpayWallToOAF.scala Correctly formatted: SparkGenerateDOIBoostActionSet.scala Correctly formatted: SparkImportMagIntoDataset.scala Correctly formatted: MagDataModel.scala Correctly formatted: SparkProcessMAG.scala Correctly formatted: MappingORCIDToOAFTest.scala Correctly formatted: DoiBoostHostedByMapTest.scala Correctly formatted: NormalizeDoiTest.scala Correctly formatted: CrossrefMappingTest.scala Correctly formatted: UnpayWallMappingTest.scala Correctly formatted: MAGMappingTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-doiboost --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-doiboost --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-doiboost --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-doiboost --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-doiboost --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:45:49+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/version.properties ] (for module dhp-doiboost )... [info] dhp-doiboost ] project dhp-doiboost [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-doiboost --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 16 Scala sources and 32 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes ... [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 37 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 37 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-doiboost --- [INFO] Total Files Processed: 37 in 00:00.757 [INFO] Already Sorted: 37 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-doiboost --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-doiboost --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 48 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-doiboost --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 6 Scala sources and 5 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes ... [WARNING] [Warn] : there was one feature warning; re-run with -feature for details [WARNING] one warning found [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-doiboost --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-doiboost --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-doiboost --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-doiboost --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-doiboost --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-doiboost --- [INFO] Priming eu/dnetlib/dhp/doiboost/orcidnodoi into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-doiboost --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-doiboost --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-doiboost --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-doiboost --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/dhp-doiboost-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-doiboost --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-doiboost --- [INFO] Executing tasks [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 68 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-doiboost/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-doiboost --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-doiboost --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/doiboost/orcidnodoi/2024-04-02_17_45/oozie_app + hadoop fs -rm -r /user/git.dnet/doiboost/orcidnodoi 24/04/02 17:46:37 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/doiboost/orcidnodoi' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/doiboost/orcidnodoi + hadoop fs -mkdir -p /user/git.dnet/doiboost/orcidnodoi + hadoop fs -mkdir -p /user/git.dnet/doiboost/orcidnodoi/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/doiboost/orcidnodoi/2024-04-02_17_45/oozie_app /user/git.dnet/doiboost/orcidnodoi [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:08 min [INFO] Finished at: 2024-04-02T17:46:47Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh doiboost/orcidnodoi /lib/dnet/BETA actionmanager/orcidnodoi_actionset + app_dir=doiboost/orcidnodoi + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/orcidnodoi_actionset ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/doiboost/orcidnodoi/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/orcidnodoi_actionset + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/orcidnodoi_actionset 24/04/02 17:46:50 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/orcidnodoi_actionset' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/orcidnodoi_actionset + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/orcidnodoi_actionset + hdfs dfs -mv /user/git.dnet/doiboost/orcidnodoi/oozie_app /lib/dnet/BETA/actionmanager/orcidnodoi_actionset [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 23957 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (update_actionset_ror) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5970643328490649272tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5970643328490649272tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-S03JpzxB70Rb/agent.24170 SSH_AGENT_PID=24172 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_1713212425687300806.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/ror -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:47:07+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.153 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:47:37+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.303 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/ror into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/ror/2024-04-02_17_46/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/ror 24/04/02 17:48:20 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/ror' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/ror + hadoop fs -mkdir -p /user/git.dnet/actionmanager/ror + hadoop fs -mkdir -p /user/git.dnet/actionmanager/ror/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/ror/2024-04-02_17_46/oozie_app /user/git.dnet/actionmanager/ror [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:33 min [INFO] Finished at: 2024-04-02T17:48:30Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/ror /lib/dnet/BETA actionmanager/ror + app_dir=actionmanager/ror + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/ror ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/ror/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/ror + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/ror 24/04/02 17:48:33 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/ror' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/ror + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/ror + hdfs dfs -mv /user/git.dnet/actionmanager/ror/oozie_app /lib/dnet/BETA/actionmanager/ror [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 24172 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (update_actionset_opencitations) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5713667815450367129tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5713667815450367129tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-4Wy2bWBLbWCb/agent.24445 SSH_AGENT_PID=24447 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_4483290013137513177.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/opencitations -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:48:50+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.183 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:49:18+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.288 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/opencitations into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 3 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/opencitations/2024-04-02_17_48/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/opencitations 24/04/02 17:49:58 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/opencitations' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/opencitations + hadoop fs -mkdir -p /user/git.dnet/actionmanager/opencitations + hadoop fs -mkdir -p /user/git.dnet/actionmanager/opencitations/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/opencitations/2024-04-02_17_48/oozie_app /user/git.dnet/actionmanager/opencitations [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:28 min [INFO] Finished at: 2024-04-02T17:50:09Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/opencitations /lib/dnet/BETA actionmanager/opencitations + app_dir=actionmanager/opencitations + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/opencitations ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/opencitations/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/opencitations + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/opencitations 24/04/02 17:50:11 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/opencitations' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/opencitations + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/opencitations + hdfs dfs -mv /user/git.dnet/actionmanager/opencitations/oozie_app /lib/dnet/BETA/actionmanager/opencitations [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 24447 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (h2020programmes) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3321995359380434494tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3321995359380434494tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-80itKhqtWEFk/agent.24689 SSH_AGENT_PID=24691 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_6465249764435269968.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/project -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:50:29+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.256 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:50:59+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.319 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/project into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 3 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/project/2024-04-02_17_50/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/project 24/04/02 17:51:38 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/project' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/project + hadoop fs -mkdir -p /user/git.dnet/actionmanager/project + hadoop fs -mkdir -p /user/git.dnet/actionmanager/project/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/project/2024-04-02_17_50/oozie_app /user/git.dnet/actionmanager/project [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:29 min [INFO] Finished at: 2024-04-02T17:51:48Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/project /lib/dnet/BETA actionmanager/project + app_dir=actionmanager/project + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/project ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/project/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/project + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/project 24/04/02 17:51:51 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/project' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/project + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/project + hdfs dfs -mv /user/git.dnet/actionmanager/project/oozie_app /lib/dnet/BETA/actionmanager/project [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 24691 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Software_Heritage) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config6397008548764611604tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config6397008548764611604tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-TQbwDpxn96s2/agent.24960 SSH_AGENT_PID=24962 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_6152188851173003552.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-swh + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/swh -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -----------------------< eu.dnetlib.dhp:dhp-swh >----------------------- [INFO] Building dhp-swh 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-swh --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-swh --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/.scalafmt.conf [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/scala [WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/test/scala [INFO] Scalafmt results: 0 of 0 were unformatted Details: [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-swh --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-swh --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-swh --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-swh --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-swh --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:52:02+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/oozie_app/version.properties ] (for module dhp-swh )... [info] dhp-swh ] project dhp-swh [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 11 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 11 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-swh --- [INFO] Total Files Processed: 11 in 00:00.416 [INFO] Already Sorted: 11 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 7 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-swh --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-swh --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java uses unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-swh --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-swh --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-swh --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-swh --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-swh --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-swh --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-swh --- [INFO] Priming eu/dnetlib/dhp/swh into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-swh --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-swh --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/primed/job.properties [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-swh --- [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-swh --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/dhp-swh-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-swh --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-swh --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/oozie_app/lib [copy] Copying 75 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-swh/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-swh --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-swh --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-swh --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/swh/2024-04-02_17_51/oozie_app + hadoop fs -rm -r /user/git.dnet/swh 24/04/02 17:52:19 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/swh' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/swh + hadoop fs -mkdir -p /user/git.dnet/swh + hadoop fs -mkdir -p /user/git.dnet/swh/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/swh/2024-04-02_17_51/oozie_app /user/git.dnet/swh [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 30.045 s [INFO] Finished at: 2024-04-02T17:52:28Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh swh /lib/dnet/BETA actionmanager/swh + app_dir=swh + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/swh ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/swh/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/swh + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/swh 24/04/02 17:52:31 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/swh' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/swh + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/swh + hdfs dfs -mv /user/git.dnet/swh/oozie_app /lib/dnet/BETA/actionmanager/swh [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 24962 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (bipFinder_affiliations) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config177124331853708687tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config177124331853708687tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-SQwV0WLj2fYh/agent.25088 SSH_AGENT_PID=25090 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_735085180735874709.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/bipaffiliations -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:52:48+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.203 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:53:17+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.339 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/bipaffiliations into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/bipaffiliations/2024-04-02_17_52/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/bipaffiliations 24/04/02 17:54:02 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/bipaffiliations' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/bipaffiliations + hadoop fs -mkdir -p /user/git.dnet/actionmanager/bipaffiliations + hadoop fs -mkdir -p /user/git.dnet/actionmanager/bipaffiliations/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/bipaffiliations/2024-04-02_17_52/oozie_app /user/git.dnet/actionmanager/bipaffiliations [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:33 min [INFO] Finished at: 2024-04-02T17:54:12Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/bipaffiliations /lib/dnet/BETA actionmanager/bipfinder_affiliations + app_dir=actionmanager/bipaffiliations + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/bipfinder_affiliations ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/bipaffiliations/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/bipfinder_affiliations + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/bipfinder_affiliations 24/04/02 17:54:14 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/bipfinder_affiliations' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/bipfinder_affiliations + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/bipfinder_affiliations + hdfs dfs -mv /user/git.dnet/actionmanager/bipaffiliations/oozie_app /lib/dnet/BETA/actionmanager/bipfinder_affiliations [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 25090 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (create_unresolved_entities) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config2057674368553854740tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config2057674368553854740tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-6qXaerGvEWrq/agent.25365 SSH_AGENT_PID=25367 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_7428651187404110775.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/createunresolvedentities -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:54:32+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.054 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:55:03+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.343 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/createunresolvedentities into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/createunresolvedentities/2024-04-02_17_54/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/createunresolvedentities 24/04/02 17:55:47 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/createunresolvedentities' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/createunresolvedentities + hadoop fs -mkdir -p /user/git.dnet/actionmanager/createunresolvedentities + hadoop fs -mkdir -p /user/git.dnet/actionmanager/createunresolvedentities/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/createunresolvedentities/2024-04-02_17_54/oozie_app /user/git.dnet/actionmanager/createunresolvedentities [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:35 min [INFO] Finished at: 2024-04-02T17:55:58Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/createunresolvedentities /lib/dnet/BETA actionmanager/unresolvedentities + app_dir=actionmanager/createunresolvedentities + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/unresolvedentities ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/createunresolvedentities/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/unresolvedentities + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/unresolvedentities 24/04/02 17:56:00 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/unresolvedentities' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/unresolvedentities + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/unresolvedentities + hdfs dfs -mv /user/git.dnet/actionmanager/createunresolvedentities/oozie_app /lib/dnet/BETA/actionmanager/unresolvedentities [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 25367 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (open_apc_transformative_agreement) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3013808106527491744tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config3013808106527491744tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-uCeyHDaCQtKX/agent.25635 SSH_AGENT_PID=25637 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_2354212305873429062.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/transformativeagreement -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:56:18+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.302 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:56:51+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.364 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/transformativeagreement into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 3 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/transformativeagreement/2024-04-02_17_56/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/transformativeagreement 24/04/02 17:57:33 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/transformativeagreement' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/transformativeagreement + hadoop fs -mkdir -p /user/git.dnet/actionmanager/transformativeagreement + hadoop fs -mkdir -p /user/git.dnet/actionmanager/transformativeagreement/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/transformativeagreement/2024-04-02_17_56/oozie_app /user/git.dnet/actionmanager/transformativeagreement [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:36 min [INFO] Finished at: 2024-04-02T17:57:44Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/transformativeagreement /lib/dnet/BETA actionmanager/transformativeagreement + app_dir=actionmanager/transformativeagreement + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/transformativeagreement ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/transformativeagreement/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/transformativeagreement + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/transformativeagreement 24/04/02 17:57:46 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/transformativeagreement' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/transformativeagreement + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/transformativeagreement + hdfs dfs -mv /user/git.dnet/actionmanager/transformativeagreement/oozie_app /lib/dnet/BETA/actionmanager/transformativeagreement [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 25637 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (fos_no_doi) [Pipeline] configFileProvider provisioning config files... copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5424505926679787335tmp [Pipeline] { [Pipeline] load [Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/config5424505926679787335tmp) [Pipeline] } [Pipeline] // load [Pipeline] tool [Pipeline] tool [Pipeline] withEnv [Pipeline] { [Pipeline] sshagent [ssh-agent] Using credentials git.dnet (User for CI/CD) [ssh-agent] Looking for ssh-agent implementation... [ssh-agent] Exec ssh-agent (binary ssh-agent on a remote machine) $ ssh-agent SSH_AUTH_SOCK=/tmp/ssh-Ib4tN5f9hciS/agent.25923 SSH_AGENT_PID=25925 Running ssh-add (command line suppressed) Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/private_key_8154135170264394698.key (git.dnet) [ssh-agent] Started. [Pipeline] { [Pipeline] sh + cd dnet-hadoop/dhp-workflows/dhp-aggregation + mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/actionmanager/fosnodoi -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2 [INFO] Scanning for projects... [INFO] [INFO] -------------------< eu.dnetlib.dhp:dhp-aggregation >------------------- [INFO] Building dhp-aggregation 1.2.5-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-aggregation --- [INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:58:04+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala [INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/scala [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 18 Scala sources and 103 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ... [WARNING] [Warn] : there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java:-1: Recompile with -Xlint:deprecation for details. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Some input files use unchecked or unsafe operations. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java:-1: Recompile with -Xlint:unchecked for details. [INFO] Done compiling. [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 1s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:01.228 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 97 resources [INFO] [INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-aggregation --- [INFO] Executing tasks [unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/eu/dnetlib/dhp/dhp-build-assembly-resources/1.2.5-SNAPSHOT/dhp-build-assembly-resources-1.2.5-SNAPSHOT.jar into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/assembly-resources [INFO] Executed tasks [INFO] [INFO] >>> scala-maven-plugin:4.0.1:doc (scala-doc) > generate-resources @ dhp-aggregation >>> [INFO] [INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-aggregation --- [INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf [INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf IndentOperator: top-level presets deprecated; use 'preset' subsection DanglingParentheses: top-level presets deprecated; use 'preset' subsection [INFO] parsed config (v2.7.5): /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf [INFO] Scalafmt results: 0 of 21 were unformatted Details: Correctly formatted: SparkRetrieveDataciteDelta.scala Correctly formatted: PubMedToOaf.scala Correctly formatted: PMParser.scala Correctly formatted: BioDBToOAF.scala Correctly formatted: SparkCreateBaselineDataFrame.scala Correctly formatted: SparkEBILinksToOaf.scala Correctly formatted: SparkDownloadEBILinks.scala Correctly formatted: SparkTransformBioDatabaseToOAF.scala Correctly formatted: DataciteModelConstants.scala Correctly formatted: ImportDatacite.scala Correctly formatted: DataciteAPIImporter.scala Correctly formatted: AbstractRestClient.scala Correctly formatted: SparkDownloadUpdateDatacite.scala Correctly formatted: GenerateDataciteDatasetSpark.scala Correctly formatted: DataciteToOAFTransformation.scala Correctly formatted: CollectionUtils.scala Correctly formatted: SparkApplyUpdate.scala Correctly formatted: SparkGenerateORCIDTable.scala Correctly formatted: BioScholixTest.scala Correctly formatted: DataciteToOAFTest.scala Correctly formatted: DataciteUtilityTest.scala [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-aggregation --- [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-aggregation --- [INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation@tmp/.m2/org/jacoco/org.jacoco.agent/0.7.9/org.jacoco.agent-0.7.9-runtime.jar=destfile=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/jacoco.exec,excludes=**/schemas/*:**/com/cloudera/**/*:**/org/apache/avro/io/**/* [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-connection-properties-file-existence) @ dhp-aggregation --- [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-aggregation --- [INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/connection-properties/iis-cdh5-test-gw.properties [INFO] [INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-aggregation --- [info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/.git [info] git.build.user.name null [info] git.build.user.email null [info] Using environment variable based branch name. GIT_BRANCH = origin/master [info] git.branch origin/master [info] Tag refs [ [Ref[refs/tags/1.0.1=26bd6211a3c51d2d2358b6cc72004808d8e318ce], Ref[refs/tags/archive/bipFinder_master_test=d6686dd7cf7b73d5efa8b333aca59c54e83fcf0a], Ref[refs/tags/archive/dedupTest=36f8f2ea66412f909cd8983cc0718b0ab6e10641], Ref[refs/tags/archive/islookup_timeout=2c4196ab22872046d6d7ae994d70a5dc57e47e19], Ref[refs/tags/archive/junit5=9dff4adbc3d4bbc2d1a4587f5424d7b7190ace4d], Ref[refs/tags/archive/master_pre_stable_ids=ef612105ba883c9a4b12a35f62eec420185db0ef], Ref[refs/tags/dhp-1.0.2=fdf024d17efe96629fdcafc00888429233e8a42b], Ref[refs/tags/dhp-1.0.3=d9fdf571c86cfdbd27e1153c587a1da7f2525e33], Ref[refs/tags/dhp-1.0.4=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1], Ref[refs/tags/dhp-1.1.5=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570], Ref[refs/tags/dhp-1.1.6=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10], Ref[refs/tags/dhp-1.1.7=cb5f978660ee4bc6f8d547caf7709a5736a3a24d], Ref[refs/tags/dhp-1.2.0=85c96bd95517be30d93692630f29806f39c68b8c], Ref[refs/tags/dhp-1.2.1=2b632494536e76ba5b190d8bda8841e79b7a4704], Ref[refs/tags/dhp-1.2.2=40bb2202a2df622928ce367d205d2a3c18ec4000], Ref[refs/tags/dhp-1.2.3=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd], Ref[refs/tags/dhp-1.2.4=fdbee9aadd3ee119c777c94b53d762ece6352061], Ref[refs/tags/september-2023=77a21998373e4bfe909faaec599202514cfd5daa]] ] [info] Resolved tag [ 1.0.1 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 11:47:41 2019 +0100] ], points at [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ] [info] Resolved tag [ dhp-1.0.2 ] [ PersonIdent[sandro.labruzzo, sandro.labruzzo@isti.cnr.it, Thu Oct 31 12:08:50 2019 +0100] ], points at [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ] [info] Resolved tag [ dhp-1.0.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Nov 4 12:34:47 2019 +0100] ], points at [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ] [info] Resolved tag [ dhp-1.0.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Nov 7 17:39:28 2019 +0100] ], points at [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ] [info] Resolved tag [ dhp-1.1.5 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Feb 13 18:11:32 2020 +0100] ], points at [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ] [info] Resolved tag [ dhp-1.1.6 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Mar 30 20:05:58 2020 +0200] ], points at [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ] [info] Resolved tag [ dhp-1.1.7 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri May 8 17:01:29 2020 +0200] ], points at [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ] [info] Resolved tag [ dhp-1.2.0 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 11 10:17:12 2020 +0200] ], points at [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ] [info] Resolved tag [ dhp-1.2.1 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon May 25 19:48:16 2020 +0200] ], points at [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ] [info] Resolved tag [ dhp-1.2.2 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Fri Jun 12 12:21:05 2020 +0200] ], points at [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ] [info] Resolved tag [ dhp-1.2.3 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Mon Jun 22 11:27:41 2020 +0200] ], points at [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ] [info] Resolved tag [ dhp-1.2.4 ] [ PersonIdent[Claudio Atzori, claudio.atzori@isti.cnr.it, Thu Apr 7 13:32:21 2022 +0200] ], points at [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ] [info] key [ commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------ ], tags => [ [DatedRevTag{id=cb5f978660ee4bc6f8d547caf7709a5736a3a24d, tagName='dhp-1.1.7', date=May 8, 2020 3:01:29 PM +00:00}] ] [info] key [ commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------ ], tags => [ [DatedRevTag{id=40bb2202a2df622928ce367d205d2a3c18ec4000, tagName='dhp-1.2.2', date=June 12, 2020 10:21:05 AM +00:00}] ] [info] key [ commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------ ], tags => [ [DatedRevTag{id=13ba91334cb0bc12d3d4f059f6f0e3f10de220e1, tagName='dhp-1.0.4', date=November 7, 2019 4:39:28 PM +00:00}] ] [info] key [ commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------ ], tags => [ [DatedRevTag{id=eb2af119a744c2cd8a7ccbea73e76ab0240de8fd, tagName='dhp-1.2.3', date=June 22, 2020 9:27:41 AM +00:00}] ] [info] key [ commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------ ], tags => [ [DatedRevTag{id=9d28b5d7c56b368e7a84efd1ada56b27ac55bb10, tagName='dhp-1.1.6', date=March 30, 2020 6:05:58 PM +00:00}] ] [info] key [ commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------ ], tags => [ [DatedRevTag{id=85c96bd95517be30d93692630f29806f39c68b8c, tagName='dhp-1.2.0', date=May 11, 2020 8:17:12 AM +00:00}] ] [info] key [ commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------ ], tags => [ [DatedRevTag{id=d9fdf571c86cfdbd27e1153c587a1da7f2525e33, tagName='dhp-1.0.3', date=November 4, 2019 11:34:47 AM +00:00}] ] [info] key [ commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------ ], tags => [ [DatedRevTag{id=fdbee9aadd3ee119c777c94b53d762ece6352061, tagName='dhp-1.2.4', date=April 7, 2022 11:32:21 AM +00:00}] ] [info] key [ commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------ ], tags => [ [DatedRevTag{id=1406b298f27fc42fd5aeaf5be1b92c7bd2a61570, tagName='dhp-1.1.5', date=February 13, 2020 5:11:32 PM +00:00}] ] [info] key [ commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------ ], tags => [ [DatedRevTag{id=2b632494536e76ba5b190d8bda8841e79b7a4704, tagName='dhp-1.2.1', date=May 25, 2020 5:48:16 PM +00:00}] ] [info] key [ commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------ ], tags => [ [DatedRevTag{id=26bd6211a3c51d2d2358b6cc72004808d8e318ce, tagName='1.0.1', date=October 31, 2019 10:47:41 AM +00:00}] ] [info] key [ commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------ ], tags => [ [DatedRevTag{id=fdf024d17efe96629fdcafc00888429233e8a42b, tagName='dhp-1.0.2', date=October 31, 2019 11:08:50 AM +00:00}] ] [info] Created map: [ {commit 6e47c724c6fdd9ed34c510af4e2e69ceb3e0dbc3 0 ------=[dhp-1.1.7], commit f0746a76055527b5b4855af4533bebe76f4e7c30 0 ------=[dhp-1.2.2], commit 58918967d9a8880bbd409b62e256b443f16e2d4d 0 ------=[dhp-1.0.4], commit 1e3dab06318516b1eda81fe42dd370aa2c726d0b 0 ------=[dhp-1.2.3], commit 76d9315129ba009ca020a79e34ff6ec07f0e2560 0 ------=[dhp-1.1.6], commit c267d958d5e82abe44680740533c7dcfb48057c0 0 ------=[dhp-1.2.0], commit 34b0e7b40a9a4bb21ab1df6263a7130422b1b8d3 0 ------=[dhp-1.0.3], commit 86585a6b274ad8e0beaa9e7f43d123b7320739be 0 ------=[dhp-1.2.4], commit 6ed9a15bc8319f1d19453f49119bd19a29defb46 0 ------=[dhp-1.1.5], commit 01c2e933958a17d6a23b150d5d8fdccf371baf09 0 ------=[dhp-1.2.1], commit 3150c7ce6d7607bbd302f0a4967aa165fddaef84 0 ------=[1.0.1], commit f224613b402ede31257601bdf7d81f30e081c4d3 0 ------=[dhp-1.0.2]} ] [info] HEAD is [ 4f0a04424562f64bb3989fff7e1a391933a274bd ] [info] Repo is in dirty state [ true ] [info] git.commit.id.describe dhp-1.2.4-1321-g4f0a044 [info] git.commit.id 4f0a04424562f64bb3989fff7e1a391933a274bd [info] git.commit.id.abbrev 4f0a044 [info] git.commit.user.name Miriam Baglioni [info] git.commit.user.email miriam.baglioni@isti.cnr.it [info] git.commit.message.full Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta Reviewed-on: https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/413 [info] git.commit.message.short Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta [info] git.commit.time 2024-04-02T15:33:38+0000 [info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop [info] git.tags [info] git.build.time 2024-04-02T17:58:34+0000 [info] git.commit.id.describe-short dhp-1.2.4-1321 [info] found property git.tags [info] found property git.commit.id.abbrev [info] found property git.commit.user.email [info] found property git.commit.message.full [info] found property git.commit.id [info] found property git.commit.id.describe-short [info] found property git.commit.message.short [info] found property git.commit.user.name [info] found property git.build.user.name [info] found property git.commit.id.describe [info] found property git.build.user.email [info] found property git.branch [info] found property git.commit.time [info] found property git.build.time [info] found property git.remote.origin.url [info] Writing properties file to [ /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/version.properties ] (for module dhp-aggregation )... [info] dhp-aggregation ] project dhp-aggregation [INFO] [INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-aggregation --- [INFO] [INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] [INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to format source files. [INFO] Number of files to be formatted: 139 [INFO] Successfully formatted: 0 file(s) [INFO] Fail to format: 0 file(s) [INFO] Skipped: 139 file(s) [INFO] Read only skipped: 0 file(s) [INFO] Approximate time taken: 0s [INFO] [INFO] --- impsort-maven-plugin:1.4.1:sort (sort-imports) @ dhp-aggregation --- [INFO] Total Files Processed: 139 in 00:00.343 [INFO] Already Sorted: 139 [INFO] Needed Sorting: 0 [INFO] [INFO] <<< scala-maven-plugin:4.0.1:doc (scala-doc) < generate-resources @ dhp-aggregation <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:4.0.1:doc (scala-doc) @ dhp-aggregation --- model contains 186 documentable templates [INFO] [INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 103 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Some input files use or override a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java: Recompile with -Xlint:deprecation for details. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Some input files use unchecked or unsafe operations. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-aggregation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 120 resources [INFO] [INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-aggregation --- [INFO] Using incremental compilation using Mixed compile order [INFO] Compiling 3 Scala sources and 36 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ... [WARNING] [Warn] : there were three deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP reason: class file for javax.persistence.TemporalType not found [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java:-1: Recompile with -Xlint:deprecation for details. [INFO] Done compiling. [INFO] [INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java uses or overrides a deprecated API. [INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-aggregation --- [INFO] Tests are skipped. [INFO] [INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-aggregation --- [INFO] Skipping JaCoCo execution due to missing execution data file. [INFO] [INFO] --- maven-dependency-plugin:3.6.0:copy-dependencies (copy dependencies) @ dhp-aggregation --- [INFO] [INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation --- [INFO] Skipping packaging of the test-jar [INFO] [INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation --- [INFO] Priming eu/dnetlib/dhp/actionmanager/fosnodoi into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-aggregation --- [INFO] Loading classpath:project-default.properties [INFO] [INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-aggregation --- [INFO] [INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-aggregation --- [INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/primed/job.properties' [INFO] Ignoring non-existent properties file 'job-override.properties' [INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/job.properties [INFO] [INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-aggregation --- [INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/dhp-aggregation-1.2.5-SNAPSHOT.jar [INFO] [INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-aggregation --- [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [INFO] Copying files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-antrun-plugin:1.3:run (default) @ dhp-aggregation --- [INFO] Executing tasks [copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app [mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 82 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib [tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package [delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_aggregation/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts [INFO] Executed tasks [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation --- [INFO] [INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation --- + '[' 0 = 0 ']' ++ pwd + target_dir_root=/home/git.dnet/oozie-packages/actionmanager/fosnodoi/2024-04-02_17_57/oozie_app + hadoop fs -rm -r /user/git.dnet/actionmanager/fosnodoi 24/04/02 17:59:18 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/actionmanager/fosnodoi' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/actionmanager/fosnodoi + hadoop fs -mkdir -p /user/git.dnet/actionmanager/fosnodoi + hadoop fs -mkdir -p /user/git.dnet/actionmanager/fosnodoi/working_dir + hadoop fs -put /home/git.dnet/oozie-packages/actionmanager/fosnodoi/2024-04-02_17_57/oozie_app /user/git.dnet/actionmanager/fosnodoi [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:34 min [INFO] Finished at: 2024-04-02T17:59:28Z [INFO] ------------------------------------------------------------------------ + ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl cd /tmp2/git.dnet/dnet-hadoop/BETA/2024-04-02 && sh deploy_release.sh actionmanager/fosnodoi /lib/dnet/BETA actionmanager/fosnodoi + app_dir=actionmanager/fosnodoi + hdfs_target_root_dir=/lib/dnet/BETA + app_target_dir=actionmanager/fosnodoi ++ whoami + user_name=git.dnet + export HADOOP_USER_NAME=hdfs + HADOOP_USER_NAME=hdfs + hdfs_app_source_dir=/user/git.dnet/actionmanager/fosnodoi/oozie_app + hdfs_target_dir=/lib/dnet/BETA/actionmanager/fosnodoi + hdfs dfs -rm -r -f /lib/dnet/BETA/actionmanager/fosnodoi 24/04/02 17:59:31 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/lib/dnet/BETA/actionmanager/fosnodoi' to trash at: hdfs://nameservice1/user/hdfs/.Trash/Current/lib/dnet/BETA/actionmanager/fosnodoi + hdfs dfs -mkdir -p /lib/dnet/BETA/actionmanager/fosnodoi + hdfs dfs -mv /user/git.dnet/actionmanager/fosnodoi/oozie_app /lib/dnet/BETA/actionmanager/fosnodoi [Pipeline] } $ ssh-agent -k unset SSH_AUTH_SOCK; unset SSH_AGENT_PID; echo Agent pid 25925 killed; [ssh-agent] Stopped. [Pipeline] // sshagent [Pipeline] } [Pipeline] // withEnv [Pipeline] } Deleting 1 temporary files [Pipeline] // configFileProvider [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [Pipeline] cleanWs [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] done [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline Finished: SUCCESS