Console Output
Skipping 1,027 KB..
Full LogTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTest
+ 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
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