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Fixed workflow generation of delta in datacite

This commit is contained in:
Sandro La Bruzzo 2021-12-21 11:41:49 +01:00
parent b881ee5ef8
commit 3920d68992
15 changed files with 364 additions and 337 deletions
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22
dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala
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@ -12,7 +12,7 @@ import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
import scala.io.Source
object ScholixUtils {
object ScholixUtils extends Serializable {
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
@ -24,7 +24,7 @@ object ScholixUtils {
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
val relations: Map[String, RelationVocabulary] = {
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/relations.json")).mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
@ -62,6 +62,11 @@ object ScholixUtils {
}
def generateScholixResourceFromResult(r:Result) :ScholixResource = {
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
}
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
override def zero: RelatedEntities = null
@ -184,6 +189,19 @@ object ScholixUtils {
}
def generateCompleteScholix(scholix: Scholix, target: ScholixResource): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(scholix.getRelationship)
s.setSource(scholix.getSource)
s.setTarget(target)
s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
s
}
def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
val r = new ScholixResource
r.setIdentifier(summaryObject.getLocalIdentifier)

19
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/datacite/oozie_app/config-default.xml Normal file
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@ -0,0 +1,19 @@
<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>

62
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/datacite/oozie_app/workflow.xml Normal file
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@ -0,0 +1,62 @@
<workflow-app name="Retrieve Scholix Update" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path of scholix graph</description>
</property>
<property>
<name>datacitePath</name>
<description>the datacite native path</description>
</property>
<property>
<name>workingSupportPath</name>
<description>the working Support path</description>
</property>
<property>
<name>isLookupUrl</name>
<description>The IS lookUp service endopoint</description>
</property>
<property>
<name>updateDS</name>
<value>false</value>
<description>The transformation Rule to apply</description>
</property>
</parameters>
<start to="RetrieveDeltaDatacite"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="RetrieveDeltaDatacite">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>New Update from Datacite to Scholix</name>
<class>eu.dnetlib.dhp.sx.graph.SparkRetrieveDataciteDelta</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--datacitePath</arg><arg>${datacitePath}</arg>
<arg>--master</arg><arg>yarn</arg>
<arg>--workingSupportPath</arg><arg>${workingSupportPath}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--updateDS</arg><arg>${updateDS}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

41
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json Normal file
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@ -0,0 +1,41 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source mdstore path",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "datacitePath",
"paramDescription": "the datacite native path",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingSupportPath",
"paramDescription": "the working Support path",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "isLookupUrl",
"paramDescription": "the isLookup URL",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
},
{
"paramName": "u",
"paramLongName": "updateDS",
"paramDescription": "Need to regenerate all support Dataset",
"paramRequired": false
}
]

154
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkRetrieveDataciteDelta.scala
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@ -9,9 +9,10 @@ import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.spark.sql.functions.max
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.Logger
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import java.text.SimpleDateFormat
@ -58,14 +59,15 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
log.info("Retrieve last entities collected From")
implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Result]
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Oaf].filter(o =>o.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
ISO8601toEpochMillis(date)
ISO8601toEpochMillis(date) / 1000
}
@ -73,7 +75,7 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
* The method of update Datacite relationships on Scholexplorer
* needs some utilities data structures
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
* in format (dnetID, ScholixResource )
* in format ScholixResource
* @param summaryPath the path of the summary in Scholix
* @param workingPath the working path
* @param spark the spark session
@ -84,11 +86,37 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
log.info("Convert All summary to ScholixResource")
spark.read.load(summaryPath).as[ScholixSummary]
.map(ScholixUtils.generateScholixResourceFromSummary)
.map(ScholixUtils.generateScholixResourceFromSummary)(scholixResourceEncoder)
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
.write.mode(SaveMode.Overwrite).save(scholixResourcePath(workingPath))
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_native")
}
/**
* This method convert the new Datacite Resource into Scholix Resource
* Needed to fill the source and the type of Scholix Relationships
* @param workingPath the Working Path
* @param spark The spark Session
*/
def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
.filter(_.isInstanceOf[Result])
.map(_.asInstanceOf[Result])
.map(ScholixUtils.generateScholixResourceFromResult)
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_update")
val update = spark.read.load(s"${scholixResourcePath(workingPath)}_update").as[ScholixResource]
val native = spark.read.load(s"${scholixResourcePath(workingPath)}_native").as[ScholixResource]
val graph = update.union(native)
.groupByKey(_.getDnetIdentifier)
.reduceGroups((a,b) => if (a!= null && a.getDnetIdentifier!= null) a else b)
.map(_._2)
graph.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_graph")
}
@ -102,29 +130,20 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
* @param vocabularies Vocabularies needed for transformation
*/
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Unit = {
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Long = {
import spark.implicits._
val ds = spark.read.load(datacitePath).as[DataciteType]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
ds.filter(_.timestamp>=timestamp)
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
.flatMap(i => fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
val total = ds.filter(_.timestamp>=timestamp).count()
if (total >0) {
ds.filter(_.timestamp >= timestamp)
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
.flatMap(i => fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
}
total
}
/**
* This method convert an Instance of OAF Result into
* Scholix Resource
* @param r The input Result
* @return The Scholix Resource
*/
def resultToScholixResource(r:Result):ScholixResource = {
ScholixUtils.generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
}
/**
* After added the new ScholixResource, we need to update the scholix Pid Map
* to intersected with the new Datacite Relations
@ -135,11 +154,11 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
import spark.implicits._
spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource]
.flatMap(r=>
r._2.getIdentifier.asScala
r.getIdentifier.asScala
.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
.map((_, r._1))
.map(t =>(t, r.getDnetIdentifier))
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.groupByKey(_._1)
.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
@ -147,27 +166,6 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
.write.mode(SaveMode.Overwrite).save(pidMapPath(workingPath))
}
/**
* This method convert the new Datacite Resource into Scholix Resource
* Needed to fill the source and the type of Scholix Relationships
* @param workingPath the Working Path
* @param spark The spark Session
*/
def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
.filter(_.isInstanceOf[Result])
.map(_.asInstanceOf[Result])
.map(resultToScholixResource)
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
.write.mode(SaveMode.Append).save(scholixResourcePath(workingPath))
}
/**
* This method resolve the datacite relation and filter the resolved
* relation
@ -222,25 +220,26 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
implicit val intermediateEncoder :Encoder[(String,Scholix)] = Encoders.tuple(Encoders.STRING, scholixEncoder)
val relationss:Dataset[(String, Relation)] = spark.read.load(s"$workingPath/ResolvedRelation").as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
val relations:Dataset[(String, Relation)] = spark.read.load(resolvedRelationPath(workingPath)).as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
relationss.joinWith(id_summary, relationss("_1").equalTo(id_summary("_1")),"inner")
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))(Encoders.tuple(Encoders.STRING, scholixEncoder))
.write.mode(SaveMode.Overwrite)
.save(s"$workingPath/scholix_one_verse")
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource].map(r => (r.getDnetIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
val source_scholix:Dataset[(String,Scholix)] = spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
id_summary.cache()
relations.joinWith(id_summary, relations("_1").equalTo(id_summary("_1")),"inner")
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))
.write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix_one_verse")
val source_scholix:Dataset[(String, Scholix)] =spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
.map(t => {
val target = t._2._2
val scholix = t._1._2
scholix.setTarget(target)
scholix
val target:ScholixResource =t._2._2
val scholix:Scholix = t._1._2
ScholixUtils.generateCompleteScholix(scholix,target)
})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
}
@ -259,7 +258,7 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
val datacitePath = parser.get("datacitePath")
log.info(s"DatacitePath is '$datacitePath'")
val workingPath = parser.get("workingPath")
val workingPath = parser.get("workingSupportPath")
log.info(s"workingPath is '$workingPath'")
val isLookupUrl: String = parser.get("isLookupUrl")
@ -279,13 +278,28 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
log.info("Retrieve last entities collected From starting from scholix Graph")
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
}
else {
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
fs.delete(new Path(s"${scholixResourcePath(workingPath)}_native"), true)
fs.rename(new Path(s"${scholixResourcePath(workingPath)}_graph"), new Path(s"${scholixResourcePath(workingPath)}_native"))
lastCollectionDate = retrieveLastCollectedFrom(spark, dataciteOAFPath(workingPath))
}
getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
addMissingScholixResource(workingPath,spark)
generatePidMap(workingPath, spark)
resolveUpdateRelation(workingPath,spark)
generateScholixUpdate(workingPath, spark)
val numRecords = getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
if (numRecords>0) {
addMissingScholixResource(workingPath,spark)
generatePidMap(workingPath, spark)
resolveUpdateRelation(workingPath,spark)
generateScholixUpdate(workingPath, spark)
}
}
}
object SparkRetrieveDataciteDelta {
val log: Logger = LoggerFactory.getLogger(SparkRetrieveDataciteDelta.getClass)
def main(args: Array[String]): Unit = {
new SparkRetrieveDataciteDelta("/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json", args, log).initialize().run()
}
}

21
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfo.java
View File

@ -33,13 +33,14 @@ public class PrepareInfo implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareInfo.class);
// associate orgs with all their parent
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet " +
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet "
+
"FROM relation " +
"WHERE lower(relclass) = '" + ModelConstants.IS_PARENT_OF.toLowerCase() +
"' and datainfo.deletedbyinference = false " +
"GROUP BY target";
//associates results with all the orgs they are affiliated to
// associates results with all the orgs they are affiliated to
private static final String RESULT_ORGANIZATION_QUERY = "SELECT source key, collect_set(target) as valueSet " +
"FROM relation " +
"WHERE lower(relclass) = '" + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase() +
@ -88,7 +89,7 @@ public class PrepareInfo implements Serializable {
childParentPath,
leavesPath,
resultOrganizationPath,
relationPath));
relationPath));
}
private static void prepareInfo(SparkSession spark, String inputPath, String childParentOrganizationPath,
@ -113,13 +114,13 @@ public class PrepareInfo implements Serializable {
.json(resultOrganizationPath);
relation
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(relationPath);
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(relationPath);
Dataset<String> children = spark
.sql(

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java
View File

@ -2,7 +2,6 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.io.Serializable;
@ -22,13 +21,11 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.KeyValueSet;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class SparkResultToOrganizationFromSemRel implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromSemRel.class);
private static final int MAX_ITERATION = 5;
@ -201,6 +198,4 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
.json(outputPath);
}
}

6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/StepActions.java
View File

@ -75,8 +75,8 @@ public class StepActions implements Serializable {
ret.setValueSet(orgs);
return ret;
}, Encoders.bean(KeyValueSet.class))
.write()
.mode(SaveMode.Overwrite)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
@ -179,7 +179,6 @@ public class StepActions implements Serializable {
"GROUP BY resId")
.as(Encoders.bean(KeyValueSet.class));
// create new relations from result to organization for each result linked to a leaf
return resultParent
.flatMap(
@ -200,7 +199,6 @@ public class StepActions implements Serializable {
.iterator(),
Encoders.bean(Relation.class));
}
}

43
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfoJobTest.java
View File

@ -84,7 +84,7 @@ public class PrepareInfoJobTest {
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
"-relationPath", workingDir.toString() + "/relation"
});
@ -229,7 +229,7 @@ public class PrepareInfoJobTest {
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
"-relationPath", workingDir.toString() + "/relation"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -335,34 +335,35 @@ public class PrepareInfoJobTest {
}
@Test
public void relationTest()throws Exception {
public void relationTest() throws Exception {
PrepareInfo
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
});
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(7, verificationDs.count());
}
@Test
public void resultOrganizationTest1() throws Exception {
@ -378,7 +379,7 @@ public class PrepareInfoJobTest {
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
"-relationPath", workingDir.toString() + "/relation"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -512,7 +513,7 @@ public class PrepareInfoJobTest {
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
"-relationPath", workingDir.toString() + "/relation"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -539,7 +540,7 @@ public class PrepareInfoJobTest {
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
"-relationPath", workingDir.toString() + "/relation"
});

9
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json
View File

@ -1,6 +1,7 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
]

62
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml
View File

@ -90,68 +90,6 @@
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
</spark>
<ok to="DropJSONPath"/>
<error to="Kill"/>
</action>
<action name="DropJSONPath">
<fs>
<delete path='${targetPath}/index'/>
<mkdir path='${targetPath}/index/'/>
</fs>
<ok to="SerializeScholix"/>
<error to="Kill"/>
</action>
<action name="SerializeScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Serialize scholix to JSON</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
<arg>--objectType</arg><arg>scholix</arg>
</spark>
<ok to="SerializeSummary"/>
<error to="Kill"/>
</action>
<action name="SerializeSummary">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Serialize summary to JSON</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
<arg>--objectType</arg><arg>summary</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>

158
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/relations.json
View File

@ -1,158 +0,0 @@
{
"cites":{
"original":"Cites",
"inverse":"IsCitedBy"
},
"compiles":{
"original":"Compiles",
"inverse":"IsCompiledBy"
},
"continues":{
"original":"Continues",
"inverse":"IsContinuedBy"
},
"derives":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"describes":{
"original":"Describes",
"inverse":"IsDescribedBy"
},
"documents":{
"original":"Documents",
"inverse":"IsDocumentedBy"
},
"hasmetadata":{
"original":"HasMetadata",
"inverse":"IsMetadataOf"
},
"hasassociationwith":{
"original":"HasAssociationWith",
"inverse":"HasAssociationWith"
},
"haspart":{
"original":"HasPart",
"inverse":"IsPartOf"
},
"hasversion":{
"original":"HasVersion",
"inverse":"IsVersionOf"
},
"iscitedby":{
"original":"IsCitedBy",
"inverse":"Cites"
},
"iscompiledby":{
"original":"IsCompiledBy",
"inverse":"Compiles"
},
"iscontinuedby":{
"original":"IsContinuedBy",
"inverse":"Continues"
},
"isderivedfrom":{
"original":"IsDerivedFrom",
"inverse":"IsSourceOf"
},
"isdescribedby":{
"original":"IsDescribedBy",
"inverse":"Describes"
},
"isdocumentedby":{
"original":"IsDocumentedBy",
"inverse":"Documents"
},
"isidenticalto":{
"original":"IsIdenticalTo",
"inverse":"IsIdenticalTo"
},
"ismetadatafor":{
"original":"IsMetadataFor",
"inverse":"IsMetadataOf"
},
"ismetadataof":{
"original":"IsMetadataOf",
"inverse":"IsMetadataFor"
},
"isnewversionof":{
"original":"IsNewVersionOf",
"inverse":"IsPreviousVersionOf"
},
"isobsoletedby":{
"original":"IsObsoletedBy",
"inverse":"Obsoletes"
},
"isoriginalformof":{
"original":"IsOriginalFormOf",
"inverse":"IsVariantFormOf"
},
"ispartof":{
"original":"IsPartOf",
"inverse":"HasPart"
},
"ispreviousversionof":{
"original":"IsPreviousVersionOf",
"inverse":"IsNewVersionOf"
},
"isreferencedby":{
"original":"IsReferencedBy",
"inverse":"References"
},
"isrelatedto":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"isrequiredby":{
"original":"IsRequiredBy",
"inverse":"Requires"
},
"isreviewedby":{
"original":"IsReviewedBy",
"inverse":"Reviews"
},
"issourceof":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"issupplementedby":{
"original":"IsSupplementedBy",
"inverse":"IsSupplementTo"
},
"issupplementto":{
"original":"IsSupplementTo",
"inverse":"IsSupplementedBy"
},
"isvariantformof":{
"original":"IsVariantFormOf",
"inverse":"IsOriginalFormOf"
},
"isversionof":{
"original":"IsVersionOf",
"inverse":"HasVersion"
},
"obsoletes":{
"original":"Obsoletes",
"inverse":"IsObsoletedBy"
},
"references":{
"original":"References",
"inverse":"IsReferencedBy"
},
"requires":{
"original":"Requires",
"inverse":"IsRequiredBy"
},
"related":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"reviews":{
"original":"Reviews",
"inverse":"IsReviewedBy"
},
"unknown":{
"original":"Unknown",
"inverse":"Unknown"
}
}

10
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/serializeGraph/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,10 @@
<configuration>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

83
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/serializeGraph/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,83 @@
<workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>scholixUpdatePath</name>
<description>the working dir base path of the scholix updated</description>
</property>
<property>
<name>targetPath</name>
<description>the final graph path</description>
</property>
</parameters>
<start to="DropJSONPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DropJSONPath">
<fs>
<delete path='${targetPath}/index'/>
<mkdir path='${targetPath}/index/'/>
</fs>
<ok to="SerializeScholix"/>
<error to="Kill"/>
</action>
<action name="SerializeScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Serialize scholix to JSON</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
<arg>--scholixUpdatePath</arg><arg>${scholixUpdatePath}</arg>
<arg>--objectType</arg><arg>scholix</arg>
</spark>
<ok to="SerializeSummary"/>
<error to="Kill"/>
</action>
<action name="SerializeSummary">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Serialize summary to JSON</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
<arg>--objectType</arg><arg>summary</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

6
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala
View File

@ -30,6 +30,9 @@ object SparkConvertObjectToJson {
log.info(s"targetPath -> $targetPath")
val objectType = parser.get("objectType")
log.info(s"objectType -> $objectType")
val scholixUpdatePath = parser.get("scholixUpdatePath")
log.info(s"scholixUpdatePath -> $scholixUpdatePath")
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
@ -42,7 +45,8 @@ object SparkConvertObjectToJson {
case "scholix" =>
log.info("Serialize Scholix")
val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
val u :Dataset[Scholix]= spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix]
d.union(u).repartition(8000).map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.saveAsTextFile(targetPath, classOf[GzipCodec])
case "summary" =>
log.info("Serialize Summary")
val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]