DispatchEntitiesSparkJob: manage all entity types together, support filtering by dataInfo.invisible flag
This commit is contained in:
parent
c25ac21e5e
commit
fab9920271
|
|
@ -11,25 +11,18 @@ 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.apache.spark.sql.*;
|
||||
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.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
|
||||
public class DispatchEntitiesSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
|
|
@ -54,11 +47,12 @@ public class DispatchEntitiesSparkJob {
|
|||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
boolean filterInvisible = Optional
|
||||
.ofNullable(parser.get("filterInvisible"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.FALSE);
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
|
||||
log.info("filterInvisible: {}", filterInvisible);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
|
|
@ -66,32 +60,43 @@ public class DispatchEntitiesSparkJob {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
||||
dispatchEntities(spark, inputPath, entityClazz, outputPath);
|
||||
dispatchEntities(spark, inputPath, outputPath, filterInvisible);
|
||||
});
|
||||
}
|
||||
|
||||
private static <T extends Oaf> void dispatchEntities(
|
||||
private static void dispatchEntities(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
Class<T> clazz,
|
||||
String outputPath) {
|
||||
String outputPath,
|
||||
boolean filterInvisible) {
|
||||
|
||||
spark
|
||||
Dataset<String> df = spark.read().textFile(inputPath);
|
||||
|
||||
ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
|
||||
String entityType = entry.getKey();
|
||||
Class<?> clazz = entry.getValue();
|
||||
|
||||
if (!entityType.equalsIgnoreCase("relation")) {
|
||||
Dataset<Row> entityDF = spark
|
||||
.read()
|
||||
.textFile(inputPath)
|
||||
.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
|
||||
.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
|
||||
.schema(Encoders.bean(clazz).schema())
|
||||
.json(
|
||||
df
|
||||
.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
|
||||
.map(
|
||||
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
|
||||
Encoders.bean(clazz))
|
||||
(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
|
||||
Encoders.STRING()));
|
||||
|
||||
if (filterInvisible) {
|
||||
entityDF = entityDF.filter("dataInfo.invisible != true");
|
||||
}
|
||||
|
||||
entityDF
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
.json(outputPath + "/" + entityType);
|
||||
}
|
||||
|
||||
private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
|
||||
return StringUtils.substringBefore(s, "|").equals(clazz.getName());
|
||||
});
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -18,9 +18,9 @@
|
|||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "c",
|
||||
"paramLongName": "graphTableClassName",
|
||||
"paramDescription": "the graph entity class name",
|
||||
"paramName": "fi",
|
||||
"paramLongName": "filterInvisible",
|
||||
"paramDescription": "if true filters out invisible entities",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -144,25 +144,15 @@
|
|||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="fork_dispatch_entities"/>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_dispatch_entities">
|
||||
<path start="dispatch_datasource"/>
|
||||
<path start="dispatch_project"/>
|
||||
<path start="dispatch_organization"/>
|
||||
<path start="dispatch_publication"/>
|
||||
<path start="dispatch_dataset"/>
|
||||
<path start="dispatch_software"/>
|
||||
<path start="dispatch_otherresearchproduct"/>
|
||||
</fork>
|
||||
|
||||
<action name="dispatch_datasource">
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publications</name>
|
||||
<name>Dispatch grouped entitities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
@ -176,164 +166,12 @@
|
|||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>true</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<ok to="End"/>
|
||||
<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.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch organization</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/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_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publication</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch dataset</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/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 software</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch otherresearchproduct</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_dispatch" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,15 +1,25 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Sets;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileReader;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
|
|
@ -26,26 +36,19 @@ import org.junit.jupiter.api.extension.ExtendWith;
|
|||
import org.mockito.Mock;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Sets;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileReader;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class SparkDedupTest implements Serializable {
|
||||
|
|
@ -726,7 +729,10 @@ public class SparkDedupTest implements Serializable {
|
|||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
|
||||
// append dangling relations to be cleaned up
|
||||
Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testGraphBasePath + "/relation");
|
||||
Dataset<Row> df_before = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testGraphBasePath + "/relation");
|
||||
Dataset<Row> df_input = df_before
|
||||
.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
|
||||
.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
|
||||
|
|
@ -742,7 +748,10 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
Dataset<Row> df_after = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testDedupGraphBasePath + "/relation");
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_input.count());
|
||||
assertNotEquals(df_input.count(), df_after.count());
|
||||
|
|
@ -772,7 +781,10 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
Dataset<Row> df_after = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testDedupGraphBasePath + "/relation");
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_after.count());
|
||||
assertEquals(0, df_after.count());
|
||||
|
|
|
|||
|
|
@ -94,25 +94,15 @@
|
|||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="fork_dispatch_entities"/>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_dispatch_entities">
|
||||
<path start="dispatch_datasource"/>
|
||||
<path start="dispatch_project"/>
|
||||
<path start="dispatch_organization"/>
|
||||
<path start="dispatch_publication"/>
|
||||
<path start="dispatch_dataset"/>
|
||||
<path start="dispatch_software"/>
|
||||
<path start="dispatch_otherresearchproduct"/>
|
||||
</fork>
|
||||
|
||||
<action name="dispatch_datasource">
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publications</name>
|
||||
<name>Dispatch grouped entities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
@ -126,165 +116,13 @@
|
|||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>false</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<ok to="delete_target_relation"/>
|
||||
<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.merge.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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch organization</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/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_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publication</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch dataset</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/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 software</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch otherresearchproduct</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_dispatch" to="delete_target_relation"/>
|
||||
|
||||
<action name="delete_target_relation">
|
||||
<fs>
|
||||
<delete path="${nameNode}/${graphOutputPath}/relation"/>
|
||||
|
|
|
|||
|
|
@ -1,14 +1,14 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.group;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
|
|
@ -19,17 +19,13 @@ import org.apache.spark.sql.Encoders;
|
|||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Lists;
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class GroupEntitiesSparkJobTest {
|
||||
|
|
@ -101,21 +97,16 @@ public class GroupEntitiesSparkJobTest {
|
|||
@Test
|
||||
@Order(2)
|
||||
void testDispatchEntities() throws Exception {
|
||||
for (String type : Lists
|
||||
.newArrayList(
|
||||
Publication.class.getCanonicalName(), eu.dnetlib.dhp.schema.oaf.Dataset.class.getCanonicalName())) {
|
||||
String directory = StringUtils.substringAfterLast(type, ".").toLowerCase();
|
||||
DispatchEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
groupEntityPath.toString(),
|
||||
"-outputPath",
|
||||
dispatchEntityPath.resolve(directory).toString(),
|
||||
"-graphTableClassName",
|
||||
type
|
||||
dispatchEntityPath.resolve(".").toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.TRUE.toString()
|
||||
});
|
||||
}
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
|
|
@ -140,5 +131,4 @@ public class GroupEntitiesSparkJobTest {
|
|||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue