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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public static JavaPairRDD<String, Block> createSortedBlocks(
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JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
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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 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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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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// 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>${mongoDb}</arg>
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||||||
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<arg>-f</arg><arg>ODF</arg>
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||||||
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<arg>-l</arg><arg>store</arg>
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||||||
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<arg>-i</arg><arg>claim</arg>
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||||||
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</java>
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||||||
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<ok to="ImportOAF_claims"/>
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<error to="Kill"/>
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</action>
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||||||
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||||||
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<action name="ImportOAF_claims">
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||||||
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<java>
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||||||
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<prepare>
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||||||
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<delete path="${contentPath}/oaf_claims"/>
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||||||
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</prepare>
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||||||
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<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
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||||||
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<arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
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||||||
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<arg>-mongourl</arg><arg>${mongoURL}</arg>
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||||||
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<arg>-mongodb</arg><arg>${mongoDb}</arg>
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||||||
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<arg>-f</arg><arg>OAF</arg>
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||||||
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<arg>-l</arg><arg>store</arg>
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||||||
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<arg>-i</arg><arg>claim</arg>
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||||||
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</java>
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||||||
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<ok to="End"/>
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||||||
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<error to="Kill"/>
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||||||
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</action>
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||||||
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||||||
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||||||
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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>
|
|
||||||
<name>sparkExecutorMemory</name>
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|
||||||
<description>memory for individual executor</description>
|
|
||||||
</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>
|
|
||||||
</parameters>
|
|
||||||
|
|
||||||
<start to="ResetWorkingPath"/>
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|
||||||
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|
||||||
<kill name="Kill">
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|
||||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
|
||||||
</kill>
|
|
||||||
|
|
||||||
<action name="ResetWorkingPath">
|
|
||||||
<fs>
|
|
||||||
<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>
|
|
||||||
|
|
||||||
<action name="ImportDBClaims">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
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|
||||||
<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
|
|
||||||
<arg>-pgurl</arg><arg>${postgresURL}</arg>
|
|
||||||
<arg>-pguser</arg><arg>${postgresUser}</arg>
|
|
||||||
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
|
|
||||||
<arg>-a</arg><arg>claims</arg>
|
|
||||||
</java>
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|
||||||
<ok to="ImportODFClaims"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ImportODFClaims">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
|
|
||||||
<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
|
|
||||||
<arg>-mongourl</arg><arg>${mongoURL}</arg>
|
|
||||||
<arg>-mongodb</arg><arg>${mongoDb}</arg>
|
|
||||||
<arg>-f</arg><arg>ODF</arg>
|
|
||||||
<arg>-l</arg><arg>store</arg>
|
|
||||||
<arg>-i</arg><arg>claim</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="ImportOAFClaims"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ImportOAFClaims">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
|
|
||||||
<arg>-p</arg><arg>${migrationClaimsPathStep1}/oaf_claims</arg>
|
|
||||||
<arg>-mongourl</arg><arg>${mongoURL}</arg>
|
|
||||||
<arg>-mongodb</arg><arg>${mongoDb}</arg>
|
|
||||||
<arg>-f</arg><arg>OAF</arg>
|
|
||||||
<arg>-l</arg><arg>store</arg>
|
|
||||||
<arg>-i</arg><arg>claim</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="ResetClaimEntities"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ResetClaimEntities">
|
|
||||||
<fs>
|
|
||||||
<delete path='${migrationClaimsPathStep2}'/>
|
|
||||||
<mkdir path='${migrationClaimsPathStep2}'/>
|
|
||||||
</fs>
|
|
||||||
<ok to="GenerateClaimEntities"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenerateClaimEntities">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<master>yarn-cluster</master>
|
|
||||||
<mode>cluster</mode>
|
|
||||||
<name>GenerateClaimEntities</name>
|
|
||||||
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
|
|
||||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
|
||||||
<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>
|
|
||||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
|
||||||
<arg>-s</arg><arg>${migrationClaimsPathStep1}/db_claims,${migrationClaimsPathStep1}/oaf_claims,${migrationClaimsPathStep1}/odf_claims</arg>
|
|
||||||
<arg>-t</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
|
|
||||||
<arg>-pgurl</arg><arg>${postgresURL}</arg>
|
|
||||||
<arg>-pguser</arg><arg>${postgresUser}</arg>
|
|
||||||
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
|
|
||||||
</spark>
|
|
||||||
<ok to="ResetClaimGraph"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ResetClaimGraph">
|
|
||||||
<fs>
|
|
||||||
<delete path='${migrationClaimsPathStep3}'/>
|
|
||||||
<mkdir path='${migrationClaimsPathStep3}'/>
|
|
||||||
</fs>
|
|
||||||
<ok to="GenerateClaimGraph"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenerateClaimGraph">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<master>yarn-cluster</master>
|
|
||||||
<mode>cluster</mode>
|
|
||||||
<name>GenerateClaimGraph</name>
|
|
||||||
<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
|
|
||||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
|
||||||
<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>
|
|
||||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
|
||||||
<arg>-s</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
|
|
||||||
<arg>-g</arg><arg>${migrationClaimsPathStep3}</arg>
|
|
||||||
</spark>
|
|
||||||
<ok to="End"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<end name="End"/>
|
|
||||||
</workflow-app>
|
|
||||||
|
|
@ -1,9 +1,10 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.provision;
|
package eu.dnetlib.dhp.oa.provision;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import java.io.IOException;
|
||||||
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
|
import java.nio.file.Files;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import java.nio.file.Path;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
|
|
@ -19,9 +20,10 @@ import org.junit.jupiter.api.io.TempDir;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import java.io.IOException;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
import java.nio.file.Files;
|
|
||||||
import java.nio.file.Path;
|
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
|
||||||
public class PrepareRelationsJobTest {
|
public class PrepareRelationsJobTest {
|
||||||
|
|
||||||
|
|
@ -74,14 +76,19 @@ public class PrepareRelationsJobTest {
|
||||||
"-maxRelations", String.valueOf(maxRelations)
|
"-maxRelations", String.valueOf(maxRelations)
|
||||||
});
|
});
|
||||||
|
|
||||||
Dataset<Relation> out = spark.read()
|
Dataset<Relation> out = spark
|
||||||
|
.read()
|
||||||
.parquet(testPath.toString())
|
.parquet(testPath.toString())
|
||||||
.as(Encoders.bean(Relation.class))
|
.as(Encoders.bean(Relation.class))
|
||||||
.cache();
|
.cache();
|
||||||
|
|
||||||
Assertions.assertEquals(10, out.count());
|
Assertions.assertEquals(10, out.count());
|
||||||
|
|
||||||
Dataset<Row> freq = out.toDF().cube(SUBRELTYPE).count().filter((FilterFunction<Row>) value -> !value.isNullAt(0));
|
Dataset<Row> freq = out
|
||||||
|
.toDF()
|
||||||
|
.cube(SUBRELTYPE)
|
||||||
|
.count()
|
||||||
|
.filter((FilterFunction<Row>) value -> !value.isNullAt(0));
|
||||||
long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
|
long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
|
||||||
long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");
|
long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue