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[enrichment single step] refactoring to fix issue in disappeared result type

This commit is contained in:
Miriam Baglioni 2024-01-15 17:49:54 +01:00
parent 2d302e6827
commit 59eaccbd87
8 changed files with 225 additions and 54 deletions
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84
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java Normal file
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@ -0,0 +1,84 @@
package eu.dnetlib.dhp;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
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.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* @author miriam.baglioni
* @Date 15/01/24
*/
public class MoveResult implements Serializable {
private static final Logger log = LoggerFactory.getLogger(MoveResult.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToCommunityFromOrganizationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/wf/subworkflows/input_moveresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
moveResults(spark, inputPath, outputPath);
});
}
public static <R extends Result> void moveResults(SparkSession spark, String inputPath, String outputPath) {
ModelSupport.entityTypes
.keySet()
.parallelStream()
.filter(e -> ModelSupport.isResult(e))
// .parallelStream()
.forEach(e -> {
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
Dataset<R> resultDataset = readPath(spark, inputPath + e.name(), resultClazz);
if (resultDataset.count() > 0) {
resultDataset
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
}
});
}
}

66
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java
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@ -76,29 +76,41 @@ public class SparkResultToCommunityFromOrganizationJob {
ModelSupport.entityTypes
.keySet()
.parallelStream()
.filter(e -> ModelSupport.isResult(e))
// .parallelStream()
.forEach(e -> {
if (ModelSupport.isResult(e)) {
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
removeOutputDir(spark, outputPath + e.name());
Dataset<R> result = readPath(spark, inputPath + e.name(), resultClazz);
// if () {
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
removeOutputDir(spark, outputPath + e.name());
Dataset<R> result = readPath(spark, inputPath + e.name(), resultClazz);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(resultCommunityFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
log.info("executing left join");
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(resultCommunityFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
readPath(spark, outputPath + e.name(), resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + e.name());
}
// log
// .info(
// "reading results from " + outputPath + e.name() + " and copying them to " + inputPath
// + e.name());
// Dataset<R> tmp = readPath(spark, outputPath + e.name(), resultClazz);
// if (tmp.count() > 0){
//
// tmp
// .write()
// .mode(SaveMode.Overwrite)
// .option("compression", "gzip")
// .json(inputPath + e.name());
// }
// }
});
}
@ -115,11 +127,11 @@ public class SparkResultToCommunityFromOrganizationJob {
.map(Context::getId)
.collect(Collectors.toList());
@SuppressWarnings("unchecked")
R res = (R) ret.getClass().newInstance();
// @SuppressWarnings("unchecked")
// R res = (R) ret.getClass().newInstance();
res.setId(ret.getId());
List<Context> propagatedContexts = new ArrayList<>();
// res.setId(ret.getId());
// List<Context> propagatedContexts = new ArrayList<>();
for (String cId : communitySet) {
if (!contextList.contains(cId)) {
Context newContext = new Context();
@ -133,11 +145,11 @@ public class SparkResultToCommunityFromOrganizationJob {
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS)));
propagatedContexts.add(newContext);
ret.getContext().add(newContext);
}
}
res.setContext(propagatedContexts);
ret.mergeFrom(res);
// res.setContext(propagatedContexts);
// ret.mergeFrom(res);
}
return ret;
};

41
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java
View File

@ -86,29 +86,30 @@ public class SparkResultToCommunityFromProject implements Serializable {
ModelSupport.entityTypes
.keySet()
.parallelStream()
.filter(e -> ModelSupport.isResult(e))
.forEach(e -> {
if (ModelSupport.isResult(e)) {
removeOutputDir(spark, outputPath + e.name());
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
Dataset<R> result = readPath(spark, inputPath + e.name(), resultClazz);
// if () {
removeOutputDir(spark, outputPath + e.name());
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
Dataset<R> result = readPath(spark, inputPath + e.name(), resultClazz);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(resultCommunityFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(resultCommunityFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
readPath(spark, outputPath + e.name(), resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + e.name());
}
readPath(spark, outputPath + e.name(), resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + e.name());
// }
});
}

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/job.properties
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@ -1,12 +1,12 @@
sourcePath=/tmp/beta_provision/graph/09_graph_dedup_enriched
resumeFrom=CountryPropagation
sourcePath=/tmp/beta_provision/graph/10_graph_orcid_enriched
resumeFrom=CommunityOrganization
allowedsemrelsorcidprop=isSupplementedBy;isSupplementTo
allowedsemrelsresultproject=isSupplementedBy;isSupplementTo
allowedsemrelscommunitysemrel=isSupplementedBy;isSupplementTo
datasourceWhitelistForCountryPropagation=10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48
#allowedtypes=pubsrepository::institutional
allowedtypes=Institutional
outputPath=/tmp/miriam/enrichment_one_step
outputPath=/tmp/beta_provision/graph/11_graph_orcid
pathMap ={"author":"$['author'][*]['fullname']", \
"title":"$['title'][*]['value']",\
"orcid":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']" ,\

2
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml
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@ -231,7 +231,7 @@
</property>
</configuration>
</sub-workflow>
<ok to="result_project" />
<ok to="End" />
<error to="Kill" />
</action>

22
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/input_moveresult_parameters.json Normal file
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@ -0,0 +1,22 @@
[
{
"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
}
]

29
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromorganization/oozie_app/workflow.xml
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@ -69,7 +69,7 @@
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>community2resultfromorganization-Publication</name>
<name>community2resultfromorganization</name>
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
@ -88,6 +88,33 @@
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/resulttocommunityfromorganization/</arg>
</spark>
<ok to="move-results"/>
<error to="Kill"/>
</action>
<action name="move-results">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>community2resultfromorganization - move results</name>
<class>eu.dnetlib.dhp.MoveResult</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=6
--executor-memory=5G
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--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.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/communityorganization/resulttocommunityfromorganization/</arg>
<arg>--outputPath</arg><arg>${sourcePath}/</arg>
<!-- <arg>&#45;&#45;outputPath</arg><arg>/tmp/miriam/rescomm/</arg>-->
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>

29
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromproject/oozie_app/workflow.xml
View File

@ -86,12 +86,37 @@
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitythroughproject/</arg>
</spark>
<ok to="move-results"/>
<error to="Kill"/>
</action>
<action name="move-results">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>community2resultfromorganization - move results</name>
<class>eu.dnetlib.dhp.MoveResult</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=6
--executor-memory=5G
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/communitythroughproject/</arg>
<arg>--outputPath</arg><arg>${sourcePath}/</arg>
<!-- <arg>outputPath</arg><arg>/tmp/miriam/rescomm/</arg>-->
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>