removed all the part related to the crossref dump download since it is done in a separate workflow
This commit is contained in:
parent
a5f82f442b
commit
da20fceaf7
|
|
@ -1,21 +0,0 @@
|
|||
[
|
||||
{
|
||||
"paramName": "s",
|
||||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the source mdstore path",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
||||
{
|
||||
"paramName": "t",
|
||||
"paramLongName": "targetPath",
|
||||
"paramDescription": "the target mdstore path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "m",
|
||||
"paramLongName": "master",
|
||||
"paramDescription": "the master name",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -1,42 +0,0 @@
|
|||
<configuration>
|
||||
<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>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,118 +0,0 @@
|
|||
<workflow-app name="read Crossref dump from HDFS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>crossrefDumpPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>inputPathCrossref</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<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>
|
||||
<value>2</value>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="GenerateCrossrefDataset"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updates</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- <action name="removeFiles">-->
|
||||
<!-- <fs>-->
|
||||
<!-- <delete path="${workingDir}/files"/>-->
|
||||
<!-- </fs>-->
|
||||
<!-- <ok to="renameDataset"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<!-- <action name="renameDataset">-->
|
||||
<!-- <fs>-->
|
||||
<!-- <delete path="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- <move source="${inputPathCrossref}/crossref_ds_updated"-->
|
||||
<!-- target="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- </fs>-->
|
||||
<!-- <ok to="End"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,42 +0,0 @@
|
|||
<configuration>
|
||||
<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>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
#!/bin/bash
|
||||
curl -LSs -H "Crossref-Plus-API-Token: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJodHRwOi8vY3Jvc3NyZWYub3JnLyIsImF1ZCI6Im1kcGx1cyIsImp0aSI6Ijk3YTZkNGVkLTg5MjktNGQ2Yi05NWY1LTY2YmMyNDgzNTRjNCJ9.5DPM4gRibUBYBtrUSpRz3RGHYVB-8f61jQBW_q-r-hs" $1 | hdfs dfs -put - $2/$3
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
#!/bin/bash
|
||||
curl -LSs $1 | hdfs dfs -put - $2/$3
|
||||
|
|
@ -1,121 +0,0 @@
|
|||
<workflow-app name="CROSSREF DUMP - DOWNLOAD" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
|
||||
<!-- Crossref Parameters -->
|
||||
<property>
|
||||
<name>crossrefdumpfilename</name>
|
||||
<description>the Crossref input path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>crossrefDumpPath</name>
|
||||
<description>the Crossref dump path</description>
|
||||
</property>
|
||||
|
||||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${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="removeFiles"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DownloadDump">
|
||||
<shell xmlns="uri:oozie:shell-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<exec>download.sh</exec>
|
||||
<argument>${url}</argument>
|
||||
<argument>${crossrefDumpPath}</argument>
|
||||
<argument>${crossrefdumpfilename}</argument>
|
||||
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
|
||||
<file>download.sh</file>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="ImportCrossRef"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefdumpfilename}</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkUnpackCrossrefEntries</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<delete path="${crossrefDumpPath}/files"/>
|
||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
||||
</fs>
|
||||
<ok to="DownloadDump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
#!/bin/bash
|
||||
curl -LSs $1 | hdfs dfs -put - $2/$3
|
||||
|
|
@ -63,14 +63,10 @@
|
|||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="End">${wf:conf('resumeFrom') eq 'Skip'}</case>
|
||||
<case to="ImportCrossRef">${wf:conf('resumeFrom') eq 'ImportCrossRef'}</case>
|
||||
<case to="UnpackCrossrefEntries">${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'}</case>
|
||||
<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case>
|
||||
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
|
||||
<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
|
||||
<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
|
||||
<default to="removeFiles"/> <!-- first action to be done when downloadDump is to be performed -->
|
||||
<default to="GenerateCrossrefDataset"/> <!-- first action to be done when downloadDump is to be performed -->
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
|
|
@ -79,67 +75,6 @@
|
|||
</kill>
|
||||
|
||||
|
||||
<action name="DownloadDump">
|
||||
<shell xmlns="uri:oozie:shell-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<exec>download.sh</exec>
|
||||
<argument>${url}</argument>
|
||||
<argument>${crossrefDumpPath}</argument>
|
||||
<argument>${crossrefdumpfilename}</argument>
|
||||
<file>download.sh</file>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="ImportCrossRef"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefdumpfilename}</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkUnpackCrossrefEntries</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
|
|
@ -166,14 +101,7 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<delete path="${crossrefDumpPath}/files"/>
|
||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
||||
</fs>
|
||||
<ok to="DownloadDump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<!-- MAG SECTION -->
|
||||
<action name="ResetMagWorkingPath">
|
||||
|
|
|
|||
Loading…
Reference in New Issue