forked from D-Net/dnet-hadoop
added workflow and last step of collection and save
This commit is contained in:
parent
45d06c45c7
commit
62ff4999e3
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@ -16,17 +16,5 @@
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"paramLongName": "outputPath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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},
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{
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"paramName": "rtn",
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"paramLongName": "resultTableName",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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},
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{
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"paramName": "bsp",
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"paramLongName": "bipScorePath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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}
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}
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]
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@ -1,22 +1,17 @@
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<workflow-app name="H2020Programme" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>projectFileURL</name>
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<description>the url where to get the projects file</description>
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<name>inputPath</name>
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<description>the input path of the resources to be extended</description>
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</property>
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<property>
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<name>programmeFileURL</name>
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<description>the url where to get the programme file</description>
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</property>
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<property>
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<name>topicFileURL</name>
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<description>the url where to get the topic file</description>
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<name>bipScorePath</name>
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<description>the path where to find the bipFinder scores</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>path where to store the action set</description>
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<description>the path where to store the actionset</description>
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</property>
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</parameters>
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@ -31,128 +26,141 @@
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<delete path='${workingDir}'/>
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<mkdir path='${workingDir}'/>
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</fs>
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<ok to="get_project_file"/>
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<ok to="atomicactions"/>
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<error to="Kill"/>
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</action>
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<action name="get_project_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${projectFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/projects</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.CSVProject</arg>
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</java>
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<ok to="get_programme_file"/>
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<error to="Kill"/>
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</action>
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<fork name="atomicactions">
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<path start="atomicactions_publication"/>
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<path start="atomicactions_dataset"/>
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<path start="atomicactions_orp"/>
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<path start="atomicactions_software"/>
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</fork>
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<action name="get_programme_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${programmeFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/programme</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme</arg>
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</java>
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<ok to="get_topic_file"/>
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<error to="Kill"/>
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</action>
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<action name="get_topic_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadExcel</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${topicFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/topic</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic</arg>
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</java>
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<ok to="read_projects"/>
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<error to="Kill"/>
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</action>
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<action name="read_projects">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/dbProjects</arg>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--postgresUrl</arg><arg>${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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</java>
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<ok to="prepare_programme"/>
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<error to="Kill"/>
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</action>
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<action name="prepare_programme">
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<action name="atomicactions_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>PrepareProgramme</name>
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<class>eu.dnetlib.dhp.actionmanager.project.PrepareProgramme</class>
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<name>Produces the atomic action with the bip finder scores for publications</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--programmePath</arg><arg>${workingDir}/programme</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedProgramme</arg>
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<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="prepare_project"/>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="prepare_project">
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<action name="atomicactions_dataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>PrepareProjects</name>
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<class>eu.dnetlib.dhp.actionmanager.project.PrepareProjects</class>
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<name>Produces the atomic action with the bip finder scores for datasets</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--projectPath</arg><arg>${workingDir}/projects</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedProjects</arg>
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<arg>--dbProjectPath</arg><arg>${workingDir}/dbProjects</arg>
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<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="create_updates"/>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="create_updates">
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<action name="atomicactions_orp">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ProjectProgrammeAS</name>
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<class>eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob</class>
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<name>Produces the atomic action with the bip finder scores for orp</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--projectPath</arg><arg>${workingDir}/preparedProjects</arg>
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<arg>--programmePath</arg><arg>${workingDir}/preparedProgramme</arg>
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<arg>--topicPath</arg><arg>${workingDir}/topic</arg>
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<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="atomicactions_software">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the bip finder scores for software</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}/software</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${workingDir}/software</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<join name="join_aa" to="collectandsave"/>
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<action name="collectandsave">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>saves all the aa produced for the several types of results in the as output path</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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