migrate configuration to ocean, fix publication dataset creation
This commit is contained in:
parent
a6acb37689
commit
c82b15b5f4
|
|
@ -91,19 +91,18 @@ public class SparkGenEnrichedOrcidWorks {
|
|||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
|
||||
.filter(Objects::nonNull)
|
||||
.toJavaRDD();
|
||||
logger.info("Works enriched data created: " + enrichedWorksRDD.count());
|
||||
enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath);
|
||||
logger.info("Works enriched data saved");
|
||||
JavaRDD<Tuple2<String, Publication>> oafPublicationRDD = enrichedWorksRDD.map(e -> {
|
||||
JavaRDD<Publication> oafPublicationRDD = enrichedWorksRDD.map(e -> {
|
||||
JsonElement j = new JsonParser().parse(e._2());
|
||||
return new Tuple2<>(e._1(), (Publication) PublicationToOaf
|
||||
.generatePublicationActionsFromDump(j.getAsJsonObject()));
|
||||
});
|
||||
return (Publication) PublicationToOaf
|
||||
.generatePublicationActionsFromDump(j.getAsJsonObject());
|
||||
}).filter(p -> p != null);
|
||||
|
||||
Dataset<Tuple2<String, Publication>> publicationDataset = spark
|
||||
Dataset<Publication> publicationDataset = spark
|
||||
.createDataset(
|
||||
oafPublicationRDD.repartition(1).rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.bean(Publication.class)));
|
||||
Encoders.bean(Publication.class));
|
||||
publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output");
|
||||
});
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,31 +0,0 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.java</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||
<value>-Xmx4g</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,11 +1,56 @@
|
|||
<workflow-app name="Gen Enriched Orcid Works" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="gen_orcid_no_doi_dataset" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
|
@ -16,20 +61,25 @@
|
|||
<fs>
|
||||
<delete path='${workingPath}/no_doi_enriched_works/output'/>
|
||||
</fs>
|
||||
<ok to="Gen_Enriched_Orcid_Works"/>
|
||||
<ok to="GenOrcidNoDoiDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Enriched_Orcid_Works">
|
||||
<action name="GenOrcidNoDoiDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn</master>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Gen_Enriched_Orcid_Works</name>
|
||||
<name>GenOrcidNoDoiDataset</name>
|
||||
<class>eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks</class>
|
||||
<jar>dhp-doiboost-1.2.4-SNAPSHOT.jar</jar>
|
||||
<spark-opts>--num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ import eu.dnetlib.doiboost.orcid.model.WorkData;
|
|||
public class XMLRecordParserTest {
|
||||
|
||||
@Test
|
||||
public void testOrcidAuthorDataXMLParser() throws Exception {
|
||||
private void testOrcidAuthorDataXMLParser() throws Exception {
|
||||
|
||||
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
|
||||
|
||||
|
|
@ -27,7 +27,7 @@ public class XMLRecordParserTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testOrcidXMLErrorRecordParser() throws Exception {
|
||||
private void testOrcidXMLErrorRecordParser() throws Exception {
|
||||
|
||||
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml"));
|
||||
|
||||
|
|
@ -40,7 +40,7 @@ public class XMLRecordParserTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testOrcidWorkDataXMLParser() throws Exception {
|
||||
private void testOrcidWorkDataXMLParser() throws Exception {
|
||||
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
|
|
|
|||
Loading…
Reference in New Issue