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grouping graph entities by id turned out to be an easy extension for the already existing cleaning workflow

This commit is contained in:
Claudio Atzori 2020-11-13 15:37:48 +01:00
parent 2bed29eb09
commit 528231a287
6 changed files with 35 additions and 415 deletions

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@ -6,7 +6,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
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.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
@ -69,12 +71,12 @@ public class CleanGraphSparkJob {
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputPath); HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath); cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
}); });
} }
private static <T extends Oaf> void fixGraphTable( private static <T extends Oaf> void cleanGraphTable(
SparkSession spark, SparkSession spark,
VocabularyGroup vocs, VocabularyGroup vocs,
String inputPath, String inputPath,
@ -100,13 +102,15 @@ public class CleanGraphSparkJob {
return spark return spark
.read() .read()
.textFile(inputEntityPath) .textFile(inputEntityPath)
.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
.map( .map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
Encoders.bean(clazz)); Encoders.bean(clazz));
} }
private static void removeOutputDir(SparkSession spark, String path) { private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); return StringUtils.substringBefore(s, "|").equals(clazz.getName());
} }
} }

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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.groupbyid; package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.utils.DHPUtils.toSeq; import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;

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@ -1,97 +0,0 @@
package eu.dnetlib.dhp.oa.graph.groupbyid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import scala.Tuple2;
public class DispatchEntitiesSparkJob {
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
MigrateMongoMdstoresApplication.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dispatch_entities_bytype_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String entitiesPath = parser.get("entitiesPath");
log.info("entitiesPath: {}", entitiesPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
dispatchOaf(spark, entityClazz, entitiesPath, outputPath);
});
}
private static <T extends Oaf> void dispatchOaf(
final SparkSession spark,
final Class<T> clazz,
final String sourcePath,
final String targetPath) {
log.info("Processing entities ({}) in file: {}", clazz.getName(), sourcePath);
spark
.read()
.textFile(sourcePath)
.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.text(targetPath);
}
private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
return StringUtils.substringBefore(s, "|").equals(clazz.getName());
}
}

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@ -50,12 +50,36 @@
</property> </property>
</parameters> </parameters>
<start to="fork_clean_graph"/> <start to="group_entities"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="group_entities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>group graph entities and relations</name>
<class>eu.dnetlib.dhp.oa.graph.clean.GroupEntitiesAndRelationsSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
</spark>
<ok to="fork_clean_graph"/>
<error to="Kill"/>
</action>
<fork name="fork_clean_graph"> <fork name="fork_clean_graph">
<path start="clean_publication"/> <path start="clean_publication"/>
<path start="clean_dataset"/> <path start="clean_dataset"/>

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@ -1,18 +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>
</configuration>

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@ -1,293 +0,0 @@
<workflow-app name="group graph entities and relations" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphInputPath</name>
<description>the graph root input path</description>
</property>
<property>
<name>outputPath</name>
<description>the graph root output 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>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<start to="group_entities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="group_entities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>group graph entities and relations</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.GroupEntitiesAndRelationsSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
</spark>
<ok to="fork_dispatch_entities"/>
<error to="Kill"/>
</action>
<fork name="fork_dispatch_entities">
<path start="dispatch_publication"/>
<path start="dispatch_dataset"/>
<path start="dispatch_software"/>
<path start="dispatch_otherresearchproduct"/>
<path start="dispatch_datasource"/>
<path start="dispatch_organization"/>
<path start="dispatch_project"/>
<path start="dispatch_relation"/>
</fork>
<action name="dispatch_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch publications</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch datasets</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch softwares</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch otherresearchproducts</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_datasource">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch datasources</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/datasource</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_organization">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch organizations</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/organization</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_project">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch project</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/project</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<action name="dispatch_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dispatch relations</name>
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
</spark>
<ok to="wait_dispatch"/>
<error to="Kill"/>
</action>
<join name="wait_dispatch" to="End"/>
<end name="End"/>
</workflow-app>