forked from D-Net/dnet-hadoop
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
This commit is contained in:
commit
edf6c6c4dc
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@ -37,7 +37,7 @@ public class Deduper implements Serializable {
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public static JavaPairRDD<String, Block> createSortedBlocks(
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JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
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final String of = config.getWf().getOrderField();
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final int maxQueueSize = config.getWf().getGroupMaxSize();
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final int maxQueueSize = config.getWf().getQueueMaxSize();
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return mapDocs
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// the reduce is just to be sure that we haven't document with same id
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@ -0,0 +1,157 @@
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<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>reuseContent</name>
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<value>false</value>
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<description>should import content from the aggregator or reuse a previous version</description>
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</property>
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<property>
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<name>contentPath</name>
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<description>path location to store (or reuse) content from the aggregator</description>
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</property>
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<property>
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<name>postgresURL</name>
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<description>the postgres URL to access to the database</description>
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</property>
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<property>
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<name>postgresUser</name>
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<description>the user postgres</description>
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</property>
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<property>
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<name>postgresPassword</name>
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<description>the password postgres</description>
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</property>
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<property>
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<name>dbSchema</name>
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<value>beta</value>
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<description>the database schema according to the D-Net infrastructure (beta or production)</description>
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</property>
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<property>
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<name>mongoURL</name>
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<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
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</property>
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<property>
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<name>mongoDb</name>
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<description>mongo database</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>the address of the lookUp service</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="ImportDB_claims"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportDB_claims">
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<java>
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<prepare>
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<delete path="${contentPath}/db_claims"/>
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</prepare>
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<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
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<arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
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<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--action</arg><arg>claims</arg>
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<arg>--dbschema</arg><arg>${dbSchema}</arg>
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</java>
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<ok to="ImportODF_claims"/>
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<error to="Kill"/>
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</action>
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<action name="ImportODF_claims">
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<java>
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<prepare>
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<delete path="${contentPath}/odf_claims"/>
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</prepare>
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<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
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<arg>-p</arg><arg>${contentPath}/odf_claims</arg>
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<arg>-mongourl</arg><arg>${mongoURL}</arg>
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<arg>-mongodb</arg><arg>${mongoDb}</arg>
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<arg>-f</arg><arg>ODF</arg>
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<arg>-l</arg><arg>store</arg>
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<arg>-i</arg><arg>claim</arg>
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</java>
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<ok to="ImportOAF_claims"/>
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<error to="Kill"/>
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</action>
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<action name="ImportOAF_claims">
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<java>
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<prepare>
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<delete path="${contentPath}/oaf_claims"/>
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</prepare>
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<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
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<arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
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<arg>-mongourl</arg><arg>${mongoURL}</arg>
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<arg>-mongodb</arg><arg>${mongoDb}</arg>
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<arg>-f</arg><arg>OAF</arg>
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<arg>-l</arg><arg>store</arg>
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<arg>-i</arg><arg>claim</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -1,169 +0,0 @@
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<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>migrationClaimsPathStep1</name>
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<description>the base path to store hdfs file</description>
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</property>
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<property>
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<name>migrationClaimsPathStep2</name>
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<description>the temporary path to store entities before dispatching</description>
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</property>
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<property>
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<name>migrationClaimsPathStep3</name>
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<description>the graph Raw base path</description>
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</property>
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<property>
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<name>postgresURL</name>
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<description>the postgres URL to access to the database</description>
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</property>
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<property>
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<name>postgresUser</name>
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<description>the user postgres</description>
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</property>
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<property>
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<name>postgresPassword</name>
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<description>the password postgres</description>
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</property>
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<property>
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<name>mongoURL</name>
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<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
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</property>
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<property>
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<name>mongoDb</name>
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<description>mongo database</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${migrationClaimsPathStep1}'/>
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<mkdir path='${migrationClaimsPathStep1}'/>
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</fs>
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<ok to="ImportDBClaims"/>
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<error to="Kill"/>
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</action>
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<action name="ImportDBClaims">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
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<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
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<arg>-pgurl</arg><arg>${postgresURL}</arg>
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<arg>-pguser</arg><arg>${postgresUser}</arg>
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<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
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<arg>-a</arg><arg>claims</arg>
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</java>
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<ok to="ImportODFClaims"/>
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<error to="Kill"/>
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</action>
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<action name="ImportODFClaims">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
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<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
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<arg>-mongourl</arg><arg>${mongoURL}</arg>
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<arg>-mongodb</arg><arg>${mongoDb}</arg>
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<arg>-f</arg><arg>ODF</arg>
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<arg>-l</arg><arg>store</arg>
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<arg>-i</arg><arg>claim</arg>
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</java>
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<ok to="ImportOAFClaims"/>
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<error to="Kill"/>
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</action>
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<action name="ImportOAFClaims">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
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<arg>-p</arg><arg>${migrationClaimsPathStep1}/oaf_claims</arg>
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<arg>-mongourl</arg><arg>${mongoURL}</arg>
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<arg>-mongodb</arg><arg>${mongoDb}</arg>
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<arg>-f</arg><arg>OAF</arg>
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<arg>-l</arg><arg>store</arg>
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<arg>-i</arg><arg>claim</arg>
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</java>
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<ok to="ResetClaimEntities"/>
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<error to="Kill"/>
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</action>
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<action name="ResetClaimEntities">
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<fs>
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<delete path='${migrationClaimsPathStep2}'/>
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<mkdir path='${migrationClaimsPathStep2}'/>
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</fs>
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<ok to="GenerateClaimEntities"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateClaimEntities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>GenerateClaimEntities</name>
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<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>-s</arg><arg>${migrationClaimsPathStep1}/db_claims,${migrationClaimsPathStep1}/oaf_claims,${migrationClaimsPathStep1}/odf_claims</arg>
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<arg>-t</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
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<arg>-pgurl</arg><arg>${postgresURL}</arg>
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<arg>-pguser</arg><arg>${postgresUser}</arg>
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<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
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</spark>
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<ok to="ResetClaimGraph"/>
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<error to="Kill"/>
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</action>
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<action name="ResetClaimGraph">
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<fs>
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<delete path='${migrationClaimsPathStep3}'/>
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<mkdir path='${migrationClaimsPathStep3}'/>
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</fs>
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<ok to="GenerateClaimGraph"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateClaimGraph">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>GenerateClaimGraph</name>
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<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>-s</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
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<arg>-g</arg><arg>${migrationClaimsPathStep3}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -1,9 +1,10 @@
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package eu.dnetlib.dhp.oa.provision;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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@ -19,9 +20,10 @@ import org.junit.jupiter.api.io.TempDir;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class PrepareRelationsJobTest {
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@ -74,14 +76,19 @@ public class PrepareRelationsJobTest {
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"-maxRelations", String.valueOf(maxRelations)
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});
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Dataset<Relation> out = spark.read()
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Dataset<Relation> out = spark
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.read()
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.parquet(testPath.toString())
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.as(Encoders.bean(Relation.class))
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.cache();
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Assertions.assertEquals(10, out.count());
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Dataset<Row> freq = out.toDF().cube(SUBRELTYPE).count().filter((FilterFunction<Row>) value -> !value.isNullAt(0));
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Dataset<Row> freq = out
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.toDF()
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.cube(SUBRELTYPE)
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.count()
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.filter((FilterFunction<Row>) value -> !value.isNullAt(0));
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long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
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long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");
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||||
|
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