Console Output
Skipping 174 KB..
Full LogTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTestTest
Deleting 1 temporary files
[Pipeline] // configFileProvider
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Scholexplorer_createFinalGraph)
[Pipeline] configFileProvider
provisioning config files...
copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config7843786049977258329tmp
[Pipeline] {
[Pipeline] load
[Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config7843786049977258329tmp)
[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-8f336I74k3Om/agent.27937
SSH_AGENT_PID=27939
Running ssh-add (command line suppressed)
Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/private_key_5423811756126419151.key (git.dnet)
[ssh-agent] Started.
[Pipeline] {
[Pipeline] sh
+ cd dnet-hadoop/dhp-workflows/dhp-graph-mapper
+ mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/graph/finalGraph -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/.m2
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------< eu.dnetlib.dhp:dhp-graph-mapper >-------------------
[INFO] Building dhp-graph-mapper 1.2.5-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-graph-mapper ---
[INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target
[INFO]
[INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-graph-mapper ---
[INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
[INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/.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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/.scalafmt.conf
[INFO] Scalafmt results: 0 of 21 were unformatted
Details:
Correctly formatted: SparkApplyHostedByMapToResult.scala
Correctly formatted: Aggregators.scala
Correctly formatted: SparkApplyHostedByMapToDatasource.scala
Correctly formatted: SparkPrepareHostedByInfoToApply.scala
Correctly formatted: SparkProduceHostedByMap.scala
Correctly formatted: CopyHdfsOafSparkApplication.scala
Correctly formatted: SparkResolveEntities.scala
Correctly formatted: SparkResolveRelation.scala
Correctly formatted: SparkDataciteToOAF.scala
Correctly formatted: SparkConvertDatasetToJsonRDD.scala
Correctly formatted: SparkCreateScholix.scala
Correctly formatted: SparkConvertObjectToJson.scala
Correctly formatted: SparkCreateInputGraph.scala
Correctly formatted: SparkCreateSummaryObject.scala
Correctly formatted: SparkConvertRDDtoDataset.scala
Correctly formatted: TestApply.scala
Correctly formatted: TestPreprocess.scala
Correctly formatted: TestPrepare.scala
Correctly formatted: ResolveEntitiesTest.scala
Correctly formatted: RetrieveDataciteDeltaTest.scala
Correctly formatted: ScholixGraphTest.scala
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-graph-mapper ---
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-graph-mapper ---
[INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/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-graph-mapper ---
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-graph-mapper ---
[INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties
[INFO]
[INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-graph-mapper ---
[info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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/scholexplorer_cleaning
[info] git.branch origin/scholexplorer_cleaning
[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]] ]
[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 [ 9c1df1507157c5fcbfa35842c67c8887b137dedc ]
[info] Repo is in dirty state [ false ]
[info] git.commit.id.describe dhp-1.2.4-345-g9c1df15
[info] git.commit.id 9c1df1507157c5fcbfa35842c67c8887b137dedc
[info] git.commit.id.abbrev 9c1df15
[info] git.commit.user.name michele.artini
[info] git.commit.user.email michele.artini@isti.cnr.it
[info] git.commit.message.full null values in date range conditions
[info] git.commit.message.short null values in date range conditions
[info] git.commit.time 2023-02-13T15:05:58+0000
[info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop
[info] git.tags
[info] git.build.time 2023-03-23T15:11:34+0000
[info] git.commit.id.describe-short dhp-1.2.4-345
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/version.properties ] (for module dhp-graph-mapper )...
[info] dhp-graph-mapper ] project dhp-graph-mapper
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-graph-mapper ---
[INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala
[INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/scala
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-graph-mapper ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 15 Scala sources and 53 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes ...
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala:113: abstract type T is unchecked since it is eliminated by erasure
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala:87: match may not be exhaustive.
It would fail on the following inputs: datasource, organization, project
[WARNING] two warnings found
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java:75: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Object for a varargs call
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: Recompile with -Xlint:deprecation for details.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java:-1: Some input files use unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to format source files.
[INFO] Number of files to be formatted: 69
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format: 0 file(s)
[INFO] Skipped: 69 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-graph-mapper ---
[INFO] Total Files Processed: 69 in 00:00.874
[INFO] Already Sorted: 69
[INFO] Needed Sorting: 0
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 91 resources
[INFO]
[INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-graph-mapper ---
[INFO] Executing tasks
[unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/assembly-resources
[INFO] Executed tasks
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-graph-mapper ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 53 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: Recompile with -Xlint:deprecation for details.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Some input files use unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 115 resources
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-graph-mapper ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 6 Scala sources and 16 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes ...
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-graph-mapper ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 16 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-graph-mapper ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-graph-mapper ---
[INFO] Skipping JaCoCo execution due to missing execution data file.
[INFO]
[INFO] --- maven-dependency-plugin:3.0.0:copy-dependencies (copy dependencies) @ dhp-graph-mapper ---
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-graph-mapper ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-graph-mapper ---
Downloading from ceon: https://maven.ceon.pl/artifactory/repo/log4j/log4j/maven-metadata.xml
Downloading from dnet4-releases: http://maven.research-infrastructures.eu/nexus/content/repositories/dnet4-releases/log4j/log4j/maven-metadata.xml
Downloading from iis-releases: https://maven.ceon.pl/artifactory/iis-releases/log4j/log4j/maven-metadata.xml
Progress (1): 892 B
Downloaded from ceon: https://maven.ceon.pl/artifactory/repo/log4j/log4j/maven-metadata.xml (892 B at 334 B/s)
[INFO] Priming eu/dnetlib/dhp/sx/graph/finalGraph into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/primed
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-graph-mapper ---
[INFO] Loading classpath:project-default.properties
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-graph-mapper ---
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-graph-mapper ---
[INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/primed/job.properties'
[INFO] Ignoring non-existent properties file 'job-override.properties'
[INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/job.properties
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-graph-mapper ---
[INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT.jar
[INFO]
[INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-graph-mapper ---
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package_shell_scripts
[WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/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-graph-mapper ---
[INFO] Executing tasks
[copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app
[mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[copy] Copying 81 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package.tar.gz
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package_shell_scripts
[INFO] Executed tasks
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-graph-mapper ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-graph-mapper ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-graph-mapper ---
+ '[' 0 = 0 ']'
++ pwd
+ target_dir_root=/home/git.dnet/oozie-packages/sx/graph/finalGraph/2023-03-23_15_11/oozie_app
+ hadoop fs -rm -r /user/git.dnet/sx/graph/finalGraph
23/03/23 15:12:28 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/graph/finalGraph' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/graph/finalGraph
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/finalGraph
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/finalGraph/working_dir
+ hadoop fs -put /home/git.dnet/oozie-packages/sx/graph/finalGraph/2023-03-23_15_11/oozie_app /user/git.dnet/sx/graph/finalGraph
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:25 min
[INFO] Finished at: 2023-03-23T15:12:49Z
[INFO] ------------------------------------------------------------------------
+ ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl
cd /tmp2/git.dnet/dnet-hadoop/BETA/2023-03-23 &&
sh deploy_release.sh sx/graph/finalGraph /lib/dnet/PROD/scholix sx/graph/finalGraph
+ app_dir=sx/graph/finalGraph
+ hdfs_target_root_dir=/lib/dnet/PROD/scholix
+ app_target_dir=sx/graph/finalGraph
++ whoami
+ user_name=git.dnet
+ export HADOOP_USER_NAME=hdfs
+ HADOOP_USER_NAME=hdfs
+ hdfs_app_source_dir=/user/git.dnet/sx/graph/finalGraph/oozie_app
+ hdfs_target_dir=/lib/dnet/PROD/scholix/sx/graph/finalGraph
+ hdfs dfs -rm -r -f /lib/dnet/PROD/scholix/sx/graph/finalGraph
+ hdfs dfs -mkdir -p /lib/dnet/PROD/scholix/sx/graph/finalGraph
+ hdfs dfs -mv /user/git.dnet/sx/graph/finalGraph/oozie_app /lib/dnet/PROD/scholix/sx/graph/finalGraph
[Pipeline] }
$ ssh-agent -k
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 27939 killed;
[ssh-agent] Stopped.
[Pipeline] // sshagent
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
Deleting 1 temporary files
[Pipeline] // configFileProvider
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Scholexplorer_updateFinalGraphDatacite)
[Pipeline] configFileProvider
provisioning config files...
copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config7251003792509361668tmp
[Pipeline] {
[Pipeline] load
[Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config7251003792509361668tmp)
[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-a8AJG12GE9pU/agent.28214
SSH_AGENT_PID=28216
Running ssh-add (command line suppressed)
Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/private_key_1286902222674025754.key (git.dnet)
[ssh-agent] Started.
[Pipeline] {
[Pipeline] sh
+ cd dnet-hadoop/dhp-workflows/dhp-aggregation
+ mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/graph/datacite -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/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_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf
[INFO] Scalafmt results: 0 of 19 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: 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_scholexplorer@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_scholexplorer/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_scholexplorer/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_scholexplorer/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/scholexplorer_cleaning
[info] git.branch origin/scholexplorer_cleaning
[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]] ]
[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 [ 9c1df1507157c5fcbfa35842c67c8887b137dedc ]
[info] Repo is in dirty state [ false ]
[info] git.commit.id.describe dhp-1.2.4-345-g9c1df15
[info] git.commit.id 9c1df1507157c5fcbfa35842c67c8887b137dedc
[info] git.commit.id.abbrev 9c1df15
[info] git.commit.user.name michele.artini
[info] git.commit.user.email michele.artini@isti.cnr.it
[info] git.commit.message.full null values in date range conditions
[info] git.commit.message.short null values in date range conditions
[info] git.commit.time 2023-02-13T15:05:58+0000
[info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop
[info] git.tags
[info] git.build.time 2023-03-23T15:13:11+0000
[info] git.commit.id.describe-short dhp-1.2.4-345
[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_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala
[INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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 16 Scala sources and 79 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes ...
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java:-1: Some input files use unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.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: 101
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format: 0 file(s)
[INFO] Skipped: 101 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: 101 in 00:01.059
[INFO] Already Sorted: 101
[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 65 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_scholexplorer@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_scholexplorer/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_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/.scalafmt.conf
[INFO] Scalafmt results: 0 of 19 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: 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_scholexplorer@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_scholexplorer/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_scholexplorer/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_scholexplorer/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/scholexplorer_cleaning
[info] git.branch origin/scholexplorer_cleaning
[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]] ]
[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 [ 9c1df1507157c5fcbfa35842c67c8887b137dedc ]
[info] Repo is in dirty state [ false ]
[info] git.commit.id.describe dhp-1.2.4-345-g9c1df15
[info] git.commit.id 9c1df1507157c5fcbfa35842c67c8887b137dedc
[info] git.commit.id.abbrev 9c1df15
[info] git.commit.user.name michele.artini
[info] git.commit.user.email michele.artini@isti.cnr.it
[info] git.commit.message.full null values in date range conditions
[info] git.commit.message.short null values in date range conditions
[info] git.commit.time 2023-02-13T15:05:58+0000
[info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop
[info] git.tags
[info] git.build.time 2023-03-23T15:13:46+0000
[info] git.commit.id.describe-short dhp-1.2.4-345
[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_scholexplorer/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: 101
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format: 0 file(s)
[INFO] Skipped: 101 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: 101 in 00:00.322
[INFO] Already Sorted: 101
[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 149 documentable templates
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-aggregation ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 79 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java: Some input files use unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.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 79 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 22 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes ...
[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] Done compiling.
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-aggregation ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 22 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/test-classes
[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:3.0.0:copy-dependencies (copy dependencies) @ dhp-aggregation ---
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-aggregation ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-aggregation ---
[INFO] Priming eu/dnetlib/dhp/sx/graph/datacite into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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_scholexplorer/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_scholexplorer/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_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts
[WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app
[mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib
[copy] Copying 81 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package/oozie_app/lib
[tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package.tar.gz
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-aggregation/target/oozie-package_shell_scripts
[INFO] Executed tasks
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-aggregation ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-aggregation ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-aggregation ---
+ '[' 0 = 0 ']'
++ pwd
+ target_dir_root=/home/git.dnet/oozie-packages/sx/graph/datacite/2023-03-23_15_13/oozie_app
+ hadoop fs -rm -r /user/git.dnet/sx/graph/datacite
23/03/23 15:14:26 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/graph/datacite' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/graph/datacite
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/datacite
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/datacite/working_dir
+ hadoop fs -put /home/git.dnet/oozie-packages/sx/graph/datacite/2023-03-23_15_13/oozie_app /user/git.dnet/sx/graph/datacite
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:47 min
[INFO] Finished at: 2023-03-23T15:14:47Z
[INFO] ------------------------------------------------------------------------
+ ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl
cd /tmp2/git.dnet/dnet-hadoop/BETA/2023-03-23 &&
sh deploy_release.sh sx/graph/datacite /lib/dnet/PROD/scholix sx/graph/update_graph
+ app_dir=sx/graph/datacite
+ hdfs_target_root_dir=/lib/dnet/PROD/scholix
+ app_target_dir=sx/graph/update_graph
++ whoami
+ user_name=git.dnet
+ export HADOOP_USER_NAME=hdfs
+ HADOOP_USER_NAME=hdfs
+ hdfs_app_source_dir=/user/git.dnet/sx/graph/datacite/oozie_app
+ hdfs_target_dir=/lib/dnet/PROD/scholix/sx/graph/update_graph
+ hdfs dfs -rm -r -f /lib/dnet/PROD/scholix/sx/graph/update_graph
+ hdfs dfs -mkdir -p /lib/dnet/PROD/scholix/sx/graph/update_graph
+ hdfs dfs -mv /user/git.dnet/sx/graph/datacite/oozie_app /lib/dnet/PROD/scholix/sx/graph/update_graph
[Pipeline] }
$ ssh-agent -k
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 28216 killed;
[ssh-agent] Stopped.
[Pipeline] // sshagent
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
Deleting 1 temporary files
[Pipeline] // configFileProvider
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Scholexplorer_serializeGraph)
[Pipeline] configFileProvider
provisioning config files...
copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config5741511770688555876tmp
[Pipeline] {
[Pipeline] load
[Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config5741511770688555876tmp)
[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-TPmT731syNSV/agent.28467
SSH_AGENT_PID=28469
Running ssh-add (command line suppressed)
Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/private_key_3349212986205494265.key (git.dnet)
[ssh-agent] Started.
[Pipeline] {
[Pipeline] sh
+ cd dnet-hadoop/dhp-workflows/dhp-graph-mapper
+ mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/graph/serializeGraph -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/.m2
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------< eu.dnetlib.dhp:dhp-graph-mapper >-------------------
[INFO] Building dhp-graph-mapper 1.2.5-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-graph-mapper ---
[INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target
[INFO]
[INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-graph-mapper ---
[INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
[INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/.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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/.scalafmt.conf
[INFO] Scalafmt results: 0 of 21 were unformatted
Details:
Correctly formatted: SparkApplyHostedByMapToResult.scala
Correctly formatted: Aggregators.scala
Correctly formatted: SparkApplyHostedByMapToDatasource.scala
Correctly formatted: SparkPrepareHostedByInfoToApply.scala
Correctly formatted: SparkProduceHostedByMap.scala
Correctly formatted: CopyHdfsOafSparkApplication.scala
Correctly formatted: SparkResolveEntities.scala
Correctly formatted: SparkResolveRelation.scala
Correctly formatted: SparkDataciteToOAF.scala
Correctly formatted: SparkConvertDatasetToJsonRDD.scala
Correctly formatted: SparkCreateScholix.scala
Correctly formatted: SparkConvertObjectToJson.scala
Correctly formatted: SparkCreateInputGraph.scala
Correctly formatted: SparkCreateSummaryObject.scala
Correctly formatted: SparkConvertRDDtoDataset.scala
Correctly formatted: TestApply.scala
Correctly formatted: TestPreprocess.scala
Correctly formatted: TestPrepare.scala
Correctly formatted: ResolveEntitiesTest.scala
Correctly formatted: RetrieveDataciteDeltaTest.scala
Correctly formatted: ScholixGraphTest.scala
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-graph-mapper ---
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-graph-mapper ---
[INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/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-graph-mapper ---
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-graph-mapper ---
[INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties
[INFO]
[INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-graph-mapper ---
[info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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/scholexplorer_cleaning
[info] git.branch origin/scholexplorer_cleaning
[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]] ]
[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 [ 9c1df1507157c5fcbfa35842c67c8887b137dedc ]
[info] Repo is in dirty state [ false ]
[info] git.commit.id.describe dhp-1.2.4-345-g9c1df15
[info] git.commit.id 9c1df1507157c5fcbfa35842c67c8887b137dedc
[info] git.commit.id.abbrev 9c1df15
[info] git.commit.user.name michele.artini
[info] git.commit.user.email michele.artini@isti.cnr.it
[info] git.commit.message.full null values in date range conditions
[info] git.commit.message.short null values in date range conditions
[info] git.commit.time 2023-02-13T15:05:58+0000
[info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop
[info] git.tags
[info] git.build.time 2023-03-23T15:15:09+0000
[info] git.commit.id.describe-short dhp-1.2.4-345
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/version.properties ] (for module dhp-graph-mapper )...
[info] dhp-graph-mapper ] project dhp-graph-mapper
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-graph-mapper ---
[INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala
[INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/scala
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-graph-mapper ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 15 Scala sources and 53 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes ...
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala:113: abstract type T is unchecked since it is eliminated by erasure
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala:87: match may not be exhaustive.
It would fail on the following inputs: datasource, organization, project
[WARNING] two warnings found
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] : unknown enum constant org.apache.http.annotation.ThreadingBehavior.SAFE
reason: class file for org.apache.http.annotation.ThreadingBehavior not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
reason: class file for javax.persistence.TemporalType not found
[WARNING] [Warn] : unknown enum constant javax.persistence.TemporalType.TIMESTAMP
[WARNING] [Warn] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java:75: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Object for a varargs call
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java:-1: Recompile with -Xlint:deprecation for details.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java:-1: Some input files use unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to format source files.
[INFO] Number of files to be formatted: 69
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format: 0 file(s)
[INFO] Skipped: 69 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-graph-mapper ---
[INFO] Total Files Processed: 69 in 00:00.966
[INFO] Already Sorted: 69
[INFO] Needed Sorting: 0
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 91 resources
[INFO]
[INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-graph-mapper ---
[INFO] Executing tasks
[unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/assembly-resources
[INFO] Executed tasks
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-graph-mapper ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 53 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java uses or overrides a deprecated API.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java: Recompile with -Xlint:deprecation for details.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Some input files use unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-graph-mapper ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 115 resources
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-graph-mapper ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 6 Scala sources and 16 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes ...
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-graph-mapper ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 16 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/test-classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java uses unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-graph-mapper ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-graph-mapper ---
[INFO] Skipping JaCoCo execution due to missing execution data file.
[INFO]
[INFO] --- maven-dependency-plugin:3.0.0:copy-dependencies (copy dependencies) @ dhp-graph-mapper ---
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-graph-mapper ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-graph-mapper ---
[INFO] Priming eu/dnetlib/dhp/sx/graph/serializeGraph into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/primed
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-graph-mapper ---
[INFO] Loading classpath:project-default.properties
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-graph-mapper ---
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-graph-mapper ---
[INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/primed/job.properties'
[INFO] Ignoring non-existent properties file 'job-override.properties'
[INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/job.properties
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-graph-mapper ---
[INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/dhp-graph-mapper-1.2.5-SNAPSHOT.jar
[INFO]
[INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-graph-mapper ---
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package_shell_scripts
[WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/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-graph-mapper ---
[INFO] Executing tasks
[copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app
[mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[copy] Copying 81 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package/oozie_app/lib
[tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package.tar.gz
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-mapper/target/oozie-package_shell_scripts
[INFO] Executed tasks
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-graph-mapper ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-graph-mapper ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-graph-mapper ---
+ '[' 0 = 0 ']'
++ pwd
+ target_dir_root=/home/git.dnet/oozie-packages/sx/graph/serializeGraph/2023-03-23_15_14/oozie_app
+ hadoop fs -rm -r /user/git.dnet/sx/graph/serializeGraph
23/03/23 15:16:02 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/graph/serializeGraph' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/graph/serializeGraph
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/serializeGraph
+ hadoop fs -mkdir -p /user/git.dnet/sx/graph/serializeGraph/working_dir
+ hadoop fs -put /home/git.dnet/oozie-packages/sx/graph/serializeGraph/2023-03-23_15_14/oozie_app /user/git.dnet/sx/graph/serializeGraph
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:29 min
[INFO] Finished at: 2023-03-23T15:16:26Z
[INFO] ------------------------------------------------------------------------
+ ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl
cd /tmp2/git.dnet/dnet-hadoop/BETA/2023-03-23 &&
sh deploy_release.sh sx/graph/serializeGraph /lib/dnet/PROD/scholix sx/graph/serializeGraph
+ app_dir=sx/graph/serializeGraph
+ hdfs_target_root_dir=/lib/dnet/PROD/scholix
+ app_target_dir=sx/graph/serializeGraph
++ whoami
+ user_name=git.dnet
+ export HADOOP_USER_NAME=hdfs
+ HADOOP_USER_NAME=hdfs
+ hdfs_app_source_dir=/user/git.dnet/sx/graph/serializeGraph/oozie_app
+ hdfs_target_dir=/lib/dnet/PROD/scholix/sx/graph/serializeGraph
+ hdfs dfs -rm -r -f /lib/dnet/PROD/scholix/sx/graph/serializeGraph
+ hdfs dfs -mkdir -p /lib/dnet/PROD/scholix/sx/graph/serializeGraph
+ hdfs dfs -mv /user/git.dnet/sx/graph/serializeGraph/oozie_app /lib/dnet/PROD/scholix/sx/graph/serializeGraph
[Pipeline] }
$ ssh-agent -k
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 28469 killed;
[ssh-agent] Stopped.
[Pipeline] // sshagent
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
Deleting 1 temporary files
[Pipeline] // configFileProvider
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (indexScholexplorer)
[Pipeline] configFileProvider
provisioning config files...
copy managed file [dnet-hadoop-build.properties] to file:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config1731763057513744975tmp
[Pipeline] {
[Pipeline] load
[Pipeline] { (/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/config1731763057513744975tmp)
[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-VAlmv53SHWO8/agent.28675
SSH_AGENT_PID=28677
Running ssh-add (command line suppressed)
Identity added: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/private_key_3972551721108052517.key (git.dnet)
[ssh-agent] Started.
[Pipeline] {
[Pipeline] sh
+ cd dnet-hadoop/dhp-workflows/dhp-graph-provision
+ mvn clean package -Poozie-package,deploy -Dworkflow.source.dir=eu/dnetlib/dhp/sx/provision -DdhpConnectionProperties=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties -DskipTests -Dmaven.repo.local=/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@tmp/.m2
[INFO] Scanning for projects...
[INFO]
[INFO] -----------------< eu.dnetlib.dhp:dhp-graph-provision >-----------------
[INFO] Building dhp-graph-provision 1.2.5-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dhp-graph-provision ---
[INFO] Deleting /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target
[INFO]
[INFO] --- mvn-scalafmt_2.11:1.0.1640073709.733712b:format (default) @ dhp-graph-provision ---
[INFO] Reading config from https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
[INFO] Writing remote config to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/.scalafmt.conf
[WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/scala
[WARNING] Could not locate Scala source at /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/scala
[INFO] Scalafmt results: 0 of 0 were unformatted
Details:
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:generate-properties (default) @ dhp-graph-provision ---
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:prepare-agent (default-prepare-agent) @ dhp-graph-provision ---
[INFO] argLine set to -javaagent:/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/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-graph-provision ---
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (reading-dhp-properties) @ dhp-graph-provision ---
[INFO] Loading /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/connection-properties/iis-cdh5-test-gw.properties
[INFO]
[INFO] --- git-commit-id-plugin:2.1.11:revision (default) @ dhp-graph-provision ---
[info] dotGitDirectory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/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/scholexplorer_cleaning
[info] git.branch origin/scholexplorer_cleaning
[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]] ]
[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 [ 9c1df1507157c5fcbfa35842c67c8887b137dedc ]
[info] Repo is in dirty state [ false ]
[info] git.commit.id.describe dhp-1.2.4-345-g9c1df15
[info] git.commit.id 9c1df1507157c5fcbfa35842c67c8887b137dedc
[info] git.commit.id.abbrev 9c1df15
[info] git.commit.user.name michele.artini
[info] git.commit.user.email michele.artini@isti.cnr.it
[info] git.commit.message.full null values in date range conditions
[info] git.commit.message.short null values in date range conditions
[info] git.commit.time 2023-02-13T15:05:58+0000
[info] git.remote.origin.url https://code-repo.d4science.org/D-Net/dnet-hadoop
[info] git.tags
[info] git.build.time 2023-03-23T15:16:42+0000
[info] git.commit.id.describe-short dhp-1.2.4-345
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/oozie_app/version.properties ] (for module dhp-graph-provision )...
[info] dhp-graph-provision ] project dhp-graph-provision
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:add-source (scala-compile-first) @ dhp-graph-provision ---
[INFO] Add Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/scala
[INFO] Add Test Source directory: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/scala
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ dhp-graph-provision ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 31 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/classes ...
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java:-1: Some input files use or override a deprecated API.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java:-1: Recompile with -Xlint:deprecation for details.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java:-1: Some input files use unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- formatter-maven-plugin:2.11.0:format (default) @ dhp-graph-provision ---
[INFO] Using 'UTF-8' encoding to format source files.
[INFO] Number of files to be formatted: 41
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format: 0 file(s)
[INFO] Skipped: 41 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-graph-provision ---
[INFO] Total Files Processed: 41 in 00:00.625
[INFO] Already Sorted: 41
[INFO] Needed Sorting: 0
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ dhp-graph-provision ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 23 resources
[INFO]
[INFO] --- maven-antrun-plugin:1.3:run (installer-copy-custom) @ dhp-graph-provision ---
[INFO] Executing tasks
[unjar] Expanding: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer@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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/assembly-resources
[INFO] Executed tasks
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ dhp-graph-provision ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 31 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java: Some input files use or override a deprecated API.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java: Recompile with -Xlint:deprecation for details.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java: Some input files use unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ dhp-graph-provision ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 111 resources
[INFO]
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile) @ dhp-graph-provision ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 10 Java sources to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/test-classes ...
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java:-1: Some input files use unchecked or unsafe operations.
[INFO] [Info] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java:-1: Recompile with -Xlint:unchecked for details.
[INFO] Done compiling.
[INFO]
[INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ dhp-graph-provision ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 10 source files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/test-classes
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java: Some input files use unchecked or unsafe operations.
[INFO] /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M4:test (default-test) @ dhp-graph-provision ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jacoco-maven-plugin:0.7.9:report (default-report) @ dhp-graph-provision ---
[INFO] Skipping JaCoCo execution due to missing execution data file.
[INFO]
[INFO] --- maven-dependency-plugin:3.0.0:copy-dependencies (copy dependencies) @ dhp-graph-provision ---
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:test-jar (attach-test-resources-package) @ dhp-graph-provision ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- primer-maven-plugin:1.2.0:prime (priming) @ dhp-graph-provision ---
[INFO] Priming eu/dnetlib/dhp/sx/provision into /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/primed
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-default-properties) @ dhp-graph-provision ---
[INFO] Loading classpath:project-default.properties
[INFO]
[INFO] --- properties-maven-plugin:2.0.1:read-project-properties (read-job-properties) @ dhp-graph-provision ---
[INFO]
[INFO] --- dhp-build-properties-maven-plugin:1.2.5-SNAPSHOT:write-project-properties (write-job-properties) @ dhp-graph-provision ---
[INFO] Ignoring non-existent properties file '/var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/primed/job.properties'
[INFO] Ignoring non-existent properties file 'job-override.properties'
[INFO] Creating /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/job.properties
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (default-jar) @ dhp-graph-provision ---
[INFO] Building jar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/dhp-graph-provision-1.2.5-SNAPSHOT.jar
[INFO]
[INFO] --- maven-assembly-plugin:3.0.0:single (assembly-oozie-installer) @ dhp-graph-provision ---
[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_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package_shell_scripts
[WARNING] Assembly file: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/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-graph-provision ---
[INFO] Executing tasks
[copy] Copying 2 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/oozie_app
[mkdir] Created dir: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/oozie_app/lib
[copy] Copying 84 files to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/oozie_app/lib
[copy] Copying 1 file to /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package/oozie_app/lib
[tar] Building tar: /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package.tar.gz
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package
[delete] Deleting directory /var/lib/jenkins/workspace/dnet-hadoop_CD_BETA_scholexplorer/dnet-hadoop/dhp-workflows/dhp-graph-provision/target/oozie-package_shell_scripts
[INFO] Executed tasks
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (create-target-dir) @ dhp-graph-provision ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (upload-oozie-package) @ dhp-graph-provision ---
[INFO]
[INFO] --- exec-maven-plugin:1.5.0:exec (extract-and-upload-to-hdfs) @ dhp-graph-provision ---
+ '[' 0 = 0 ']'
++ pwd
+ target_dir_root=/home/git.dnet/oozie-packages/sx/provision/2023-03-23_15_16/oozie_app
+ hadoop fs -rm -r /user/git.dnet/sx/provision
23/03/23 15:17:08 INFO fs.TrashPolicyDefault: Moved: 'hdfs://nameservice1/user/git.dnet/sx/provision' to trash at: hdfs://nameservice1/user/git.dnet/.Trash/Current/user/git.dnet/sx/provision
+ hadoop fs -mkdir -p /user/git.dnet/sx/provision
+ hadoop fs -mkdir -p /user/git.dnet/sx/provision/working_dir
+ hadoop fs -put /home/git.dnet/oozie-packages/sx/provision/2023-03-23_15_16/oozie_app /user/git.dnet/sx/provision
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 52.936 s
[INFO] Finished at: 2023-03-23T15:17:30Z
[INFO] ------------------------------------------------------------------------
+ ssh git.dnet@iis-cdh5-test-gw.ocean.icm.edu.pl
cd /tmp2/git.dnet/dnet-hadoop/BETA/2023-03-23 &&
sh deploy_release.sh sx/provision /lib/dnet/PROD/scholix sx/provision
+ app_dir=sx/provision
+ hdfs_target_root_dir=/lib/dnet/PROD/scholix
+ app_target_dir=sx/provision
++ whoami
+ user_name=git.dnet
+ export HADOOP_USER_NAME=hdfs
+ HADOOP_USER_NAME=hdfs
+ hdfs_app_source_dir=/user/git.dnet/sx/provision/oozie_app
+ hdfs_target_dir=/lib/dnet/PROD/scholix/sx/provision
+ hdfs dfs -rm -r -f /lib/dnet/PROD/scholix/sx/provision
+ hdfs dfs -mkdir -p /lib/dnet/PROD/scholix/sx/provision
+ hdfs dfs -mv /user/git.dnet/sx/provision/oozie_app /lib/dnet/PROD/scholix/sx/provision
[Pipeline] }
$ ssh-agent -k
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 28677 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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