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Merge remote-tracking branch 'origin/beta_to_master_may2024' into beta_to_master_may2024

This commit is contained in:
Miriam Baglioni 2024-06-11 10:26:24 +02:00
parent 50805e3fc1 d39a1054b8
commit 196fa55774
14 changed files with 145 additions and 19 deletions
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113
dhp-shade-package/dependency-reduced-pom.xml Normal file
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@ -0,0 +1,113 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<parent>
<artifactId>dhp</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-shade-package</artifactId>
<description>This module create a jar of all module dependencies</description>
<build>
<plugins>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer>
<mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
</transformer>
<transformer />
<transformer>
<resource>META-INF/cxf/bus-extensions.txt</resource>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/maven/**</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<relocations>
<relocation>
<pattern>com</pattern>
<shadedPattern>repackaged.com.google.common</shadedPattern>
<includes>
<include>com.google.common.**</include>
</includes>
</relocation>
</relocations>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.28</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>5.6.1</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>junit-jupiter-api</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
<exclusion>
<artifactId>junit-jupiter-params</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
<exclusion>
<artifactId>junit-jupiter-engine</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>3.3.3</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>byte-buddy</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
<exclusion>
<artifactId>byte-buddy-agent</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>3.3.3</version>
<scope>test</scope>
</dependency>
</dependencies>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-common</url>
</site>
</distributionManagement>
</project>

2
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
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@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -156,6 +157,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

1
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml
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@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

1
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
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@ -125,6 +125,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

1
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml
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@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

4
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
View File

@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -155,11 +156,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=2560
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>

1
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml
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@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
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@ -103,11 +103,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@ -156,11 +157,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
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@ -95,11 +95,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=10000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>

4
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
View File

@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -155,11 +156,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=2560
--conf spark.sql.shuffle.partitions=4000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

10
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
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@ -27,10 +27,12 @@ object SparkApplyHostedByMapToResult {
val inst: Instance = i.head
patchInstance(p, ei, inst)
} else if (i.size == 2) {
if (i.map(ii => ii.getCollectedfrom.getValue).contains("UnpayWall")) {
val inst: Instance = i.filter(ii => "Crossref".equals(ii.getCollectedfrom.getValue)).head
patchInstance(p, ei, inst)
} else {
val cf = i.map(ii => ii.getCollectedfrom.getValue)
if (cf.contains("Crossref")) {
i.foreach(ii => {
patchInstance(p, ei, ii)
})
}
}
}

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
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@ -31,7 +31,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
@ -48,7 +47,7 @@ public class IrishOaiExporterJob {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
IrishOaiExporterJob.class
IrishOaiExporterJob.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
parser.parseArgument(args);

14
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
View File

@ -176,13 +176,13 @@ public class XmlSerializationUtils {
StringBuilder sb = new StringBuilder();
for (KeyValue kv : measure.getUnit()) {
sb
.append("<")
.append(name)
.append(" ")
.append(attr("id", measure.getId()))
.append(attr("count", kv.getValue()))
.append(attr("datasource", kv.getKey()))
.append(" />");
.append("<")
.append(name)
.append(" ")
.append(attr("id", measure.getId()))
.append(attr("count", kv.getValue()))
.append(attr("datasource", kv.getKey()))
.append(" />");
}
return sb.toString();
}

1
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -43,7 +43,6 @@ public class XmlRecordFactoryTest {
final Publication p = OBJECT_MAPPER
.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
final String xml = xmlRecordFactory.build(new JoinedEntity(p));
assertNotNull(xml);