forked from D-Net/dnet-hadoop
new logic and workflow for dump of results with link to projects. In this implementation the result match the model of the communityresult.
This commit is contained in:
parent
fafb688887
commit
24c56fa7a3
|
@ -3,9 +3,9 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults;
|
||||||
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||||
|
|
||||||
public class FunderResults extends Result implements Serializable {
|
public class FunderResults extends CommunityResult implements Serializable {
|
||||||
private String funder_id;
|
private String funder_id;
|
||||||
|
|
||||||
public String getFunder_id() {
|
public String getFunder_id() {
|
||||||
|
|
|
@ -17,9 +17,11 @@ import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.common.api.zenodo.Community;
|
||||||
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
|
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
|
||||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||||
|
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
@ -53,8 +55,8 @@ public class SparkDumpFunderResults implements Serializable {
|
||||||
final String outputPath = parser.get("outputPath");
|
final String outputPath = parser.get("outputPath");
|
||||||
log.info("outputPath: {}", outputPath);
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
final String communityMapPath = parser.get("communityMapPath");
|
final String relationPath = parser.get("relationPath");
|
||||||
log.info("communityMapPath: {}", communityMapPath);
|
log.info("relationPath: {}", relationPath);
|
||||||
|
|
||||||
SparkConf conf = new SparkConf();
|
SparkConf conf = new SparkConf();
|
||||||
|
|
||||||
|
@ -63,36 +65,33 @@ public class SparkDumpFunderResults implements Serializable {
|
||||||
isSparkSessionManaged,
|
isSparkSessionManaged,
|
||||||
spark -> {
|
spark -> {
|
||||||
Utils.removeOutputDir(spark, outputPath);
|
Utils.removeOutputDir(spark, outputPath);
|
||||||
writeResultProjectList(spark, inputPath, outputPath, communityMapPath);
|
writeResultProjectList(spark, inputPath, outputPath);
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
||||||
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath,
|
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) {
|
||||||
String communityMapPath) {
|
|
||||||
|
|
||||||
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
|
|
||||||
|
|
||||||
Dataset<Relation> relation = Utils
|
Dataset<Relation> relation = Utils
|
||||||
.readPath(spark, inputPath + "/relation", Relation.class)
|
.readPath(spark, inputPath + "/relation", Relation.class)
|
||||||
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
|
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
|
||||||
|
|
||||||
Dataset<eu.dnetlib.dhp.schema.oaf.Result> result = Utils
|
Dataset<CommunityResult> result = Utils
|
||||||
.readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class)
|
.readPath(spark, inputPath + "/publication", CommunityResult.class)
|
||||||
.union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class))
|
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
|
||||||
.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class))
|
.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class))
|
||||||
.union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class));
|
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
|
||||||
|
|
||||||
result
|
result
|
||||||
.joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner")
|
.joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner")
|
||||||
.map((MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, FunderResults>) value ->{
|
.map((MapFunction<Tuple2<CommunityResult, Relation>, FunderResults>) value -> {
|
||||||
FunderResults res = (FunderResults) ResultMapper.map(value._1(), communityMap, false);
|
FunderResults res = (FunderResults) value._1();
|
||||||
res.setFunder_id(value._2().getSource().substring(3,15));
|
res.setFunder_id(value._2().getSource().substring(3, 15));
|
||||||
return res;
|
return res;
|
||||||
}, Encoders.bean(FunderResults.class))
|
}, Encoders.bean(FunderResults.class))
|
||||||
.write()
|
.write()
|
||||||
.partitionBy("funder_id")
|
.partitionBy("funder_id")
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
.json(outputPath);
|
.json(outputPath);
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -0,0 +1,82 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.oa.graph.dump.funderresults;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
|
public class SparkResultLinkedToProject implements Serializable {
|
||||||
|
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class);
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
String jsonConfiguration = IOUtils
|
||||||
|
.toString(
|
||||||
|
SparkResultLinkedToProject.class
|
||||||
|
.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json"));
|
||||||
|
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
Boolean isSparkSessionManaged = Optional
|
||||||
|
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||||
|
.map(Boolean::valueOf)
|
||||||
|
.orElse(Boolean.TRUE);
|
||||||
|
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||||
|
|
||||||
|
final String inputPath = parser.get("sourcePath");
|
||||||
|
log.info("inputPath: {}", inputPath);
|
||||||
|
|
||||||
|
final String outputPath = parser.get("outputPath");
|
||||||
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
|
final String resultClassName = parser.get("resultTableName");
|
||||||
|
log.info("resultTableName: {}", resultClassName);
|
||||||
|
|
||||||
|
final String relationPath = parser.get("relationPath");
|
||||||
|
log.info("relationPath: {}", relationPath);
|
||||||
|
|
||||||
|
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
|
||||||
|
runWithSparkSession(
|
||||||
|
conf,
|
||||||
|
isSparkSessionManaged,
|
||||||
|
spark -> {
|
||||||
|
Utils.removeOutputDir(spark, outputPath);
|
||||||
|
writeResultsLikedToProjects(spark, inputClazz, inputPath, outputPath, relationPath);
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <R extends Result> void writeResultsLikedToProjects(SparkSession spark, Class<R> inputClazz,
|
||||||
|
String inputPath, String outputPath, String relationPath) {
|
||||||
|
|
||||||
|
Dataset<R> results = Utils.readPath(spark, inputPath, inputClazz);
|
||||||
|
Dataset<Relation> relations = Utils
|
||||||
|
.readPath(spark, relationPath, Relation.class)
|
||||||
|
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
|
||||||
|
relations
|
||||||
|
.joinWith(
|
||||||
|
results, relations.col("target").equalTo(results.col("id")),
|
||||||
|
"inner")
|
||||||
|
.write()
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.option("compression", "gzip")
|
||||||
|
.json(outputPath);
|
||||||
|
}
|
||||||
|
}
|
|
@ -127,10 +127,367 @@
|
||||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
</java>
|
</java>
|
||||||
<ok to="dump_funder_results"/>
|
<ok to="fork_result_linked_to_projects"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
|
<fork name="fork_result_linked_to_projects">
|
||||||
|
<path start="select_publication_linked_to_projects"/>
|
||||||
|
<path start="select_dataset_linked_to_projects"/>
|
||||||
|
<path start="select_orp_linked_to_project"/>
|
||||||
|
<path start="select_software_linked_to_projects"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="select_publication_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
|
||||||
|
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_dataset_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
|
||||||
|
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_orp_linked_to_project">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||||
|
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_software_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
|
||||||
|
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_link" to="fork_dump"/>
|
||||||
|
|
||||||
|
<fork name="fork_dump">
|
||||||
|
<path start="dump_publication"/>
|
||||||
|
<path start="dump_dataset"/>
|
||||||
|
<path start="dump_orp"/>
|
||||||
|
<path start="dump_software"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="dump_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table publication for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/result/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/publication</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table dataset for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/result/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table ORP for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table software for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/result/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/software</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_dump" to="prepareResultProject"/>
|
||||||
|
|
||||||
|
<action name="prepareResultProject">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Prepare association result subset of project info</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="fork_extendWithProject"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<fork name="fork_extendWithProject">
|
||||||
|
<path start="extend_publication"/>
|
||||||
|
<path start="extend_dataset"/>
|
||||||
|
<path start="extend_orp"/>
|
||||||
|
<path start="extend_software"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="extend_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped publications with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/ext/publication</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped dataset with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/ext/dataset</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped ORP with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/ext/orp</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped software with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--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.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/ext/software</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<join name="join_extend" to="dump_funder_results"/>
|
||||||
|
|
||||||
<action name="dump_funder_results">
|
<action name="dump_funder_results">
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
@ -149,9 +506,9 @@
|
||||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
</spark-opts>
|
</spark-opts>
|
||||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
<arg>--sourcePath</arg><arg>${workingDir}/ext</arg>
|
||||||
<arg>--outputPath</arg><arg>${workingDir}/result</arg>
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="End"/>
|
<ok to="End"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
|
|
|
@ -0,0 +1,36 @@
|
||||||
|
[
|
||||||
|
|
||||||
|
{
|
||||||
|
"paramName":"cmp",
|
||||||
|
"paramLongName":"communityMapPath",
|
||||||
|
"paramDescription": "the path to the serialization of the community map",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"s",
|
||||||
|
"paramLongName":"sourcePath",
|
||||||
|
"paramDescription": "the path of the sequencial file to read",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "out",
|
||||||
|
"paramLongName": "outputPath",
|
||||||
|
"paramDescription": "the path used to store temporary output files",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "ssm",
|
||||||
|
"paramLongName": "isSparkSessionManaged",
|
||||||
|
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"tn",
|
||||||
|
"paramLongName":"resultTableName",
|
||||||
|
"paramDescription": "the name of the result table we are currently working on",
|
||||||
|
"paramRequired": true
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
|
Loading…
Reference in New Issue