D-Net
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dnet-hadoop
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Merge branch 'master' into merge_graph

This commit is contained in:
Claudio Atzori 2020-07-20 10:14:55 +02:00
parent 47c7122773 0937c9998f
commit 94ccdb4852
28 changed files with 1312 additions and 201 deletions
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31
dhp-schemas/pom.xml
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@ -14,6 +14,37 @@
<description>This module contains common schema classes meant to be used across the dnet-hadoop submodules</description>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.0.1</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>

90
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/OafUtils.scala Normal file
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@ -0,0 +1,90 @@
package eu.dnetlib.dhp.schema.scholexplorer
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
object OafUtils {
def generateKeyValue(key: String, value: String): KeyValue = {
val kv: KeyValue = new KeyValue()
kv.setKey(key)
kv.setValue(value)
kv.setDataInfo(generateDataInfo("0.9"))
kv
}
def generateDataInfo(trust: String = "0.9", invisibile: Boolean = false): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch, sch)
}
def createQualifier(classId: String, className: String, schemeId: String, schemeName: String): Qualifier = {
val q: Qualifier = new Qualifier
q.setClassid(classId)
q.setClassname(className)
q.setSchemeid(schemeId)
q.setSchemename(schemeName)
q
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)
tmp
}
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
}
def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
}
}

15
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java
View File

@ -34,7 +34,10 @@ public class EventFactory {
final MappedFields map = createMapFromResult(updateInfo);
final String eventId = calculateEventId(
updateInfo.getTopicPath(), updateInfo.getTarget().getOpenaireId(), updateInfo.getHighlightValueAsString());
updateInfo.getTopicPath(), updateInfo.getTargetDs().getOpenaireId(), updateInfo
.getTarget()
.getOpenaireId(),
updateInfo.getHighlightValueAsString());
res.setEventId(eventId);
res.setProducerId(PRODUCER_ID);
@ -93,11 +96,13 @@ public class EventFactory {
return map;
}
private static String calculateEventId(final String topic, final String publicationId, final String value) {
private static String calculateEventId(final String topic, final String dsId, final String publicationId,
final String value) {
return "event-"
+ DigestUtils.md5Hex(topic).substring(0, 6) + "-"
+ DigestUtils.md5Hex(publicationId).substring(0, 8) + "-"
+ DigestUtils.md5Hex(value).substring(0, 8);
+ DigestUtils.md5Hex(topic).substring(0, 4) + "-"
+ DigestUtils.md5Hex(dsId).substring(0, 4) + "-"
+ DigestUtils.md5Hex(publicationId).substring(0, 7) + "-"
+ DigestUtils.md5Hex(value).substring(0, 5);
}
private static long calculateExpiryDate(final long now) {

147
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml
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@ -64,157 +64,12 @@
</configuration>
</global>
<start to="join_entities_step0"/>
<start to="generate_events"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="join_entities_step0">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep0</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep0Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step1"/>
<error to="Kill"/>
</action>
<action name="join_entities_step1">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep1</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep1Job</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step2"/>
<error to="Kill"/>
</action>
<action name="join_entities_step2">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep2</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep2Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step3"/>
<error to="Kill"/>
</action>
<action name="join_entities_step3">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep3</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep3Job</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step4"/>
<error to="Kill"/>
</action>
<action name="join_entities_step4">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep4</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep4Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="prepare_groups"/>
<error to="Kill"/>
</action>
<action name="prepare_groups">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareGroupsJob</name>
<class>eu.dnetlib.dhp.broker.oa.PrepareGroupsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="generate_events"/>
<error to="Kill"/>
</action>
<action name="generate_events">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
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@ -12,8 +12,6 @@ import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Joiner;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;

38
dhp-workflows/dhp-graph-mapper/pom.xml
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@ -9,6 +9,37 @@
<artifactId>dhp-graph-mapper</artifactId>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.0.1</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
@ -61,6 +92,13 @@
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>org.json4s</groupId>
<artifactId>json4s-jackson_2.11</artifactId>
<version>3.5.3</version>
</dependency>
</dependencies>

16
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
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@ -266,7 +266,9 @@ public abstract class AbstractMdRecordToOafMapper {
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setOriginalId(Arrays.asList(findOriginalId(doc)));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(prepareResultPids(doc, info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
@ -429,6 +431,18 @@ public abstract class AbstractMdRecordToOafMapper {
return null;
}
private String findOriginalId(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n != null) {
final String id = n.valueOf("./*[local-name()='identifier']");
if (StringUtils.isNotBlank(id)) {
return id;
}
}
return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']");
}
protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {
return prepareQualifier(node.valueOf(xpath).trim(), schemeId);
}

89
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala Normal file
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@ -0,0 +1,89 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import org.apache.spark.sql.{Encoder, Encoders}
import org.apache.spark.sql.expressions.Aggregator
object EBIAggregator {
def getDatasetAggregator(): Aggregator[(String, OafDataset), OafDataset, OafDataset] = new Aggregator[(String, OafDataset), OafDataset, OafDataset]{
override def zero: OafDataset = new OafDataset()
override def reduce(b: OafDataset, a: (String, OafDataset)): OafDataset = {
b.mergeFrom(a._2)
if (b.getId == null)
b.setId(a._2.getId)
b
}
override def merge(wx: OafDataset, wy: OafDataset): OafDataset = {
wx.mergeFrom(wy)
if(wx.getId == null && wy.getId.nonEmpty)
wx.setId(wy.getId)
wx
}
override def finish(reduction: OafDataset): OafDataset = reduction
override def bufferEncoder: Encoder[OafDataset] =
Encoders.kryo(classOf[OafDataset])
override def outputEncoder: Encoder[OafDataset] =
Encoders.kryo(classOf[OafDataset])
}
def getPublicationAggregator(): Aggregator[(String, Publication), Publication, Publication] = new Aggregator[(String, Publication), Publication, Publication]{
override def zero: Publication = new Publication()
override def reduce(b: Publication, a: (String, Publication)): Publication = {
b.mergeFrom(a._2)
if (b.getId == null)
b.setId(a._2.getId)
b
}
override def merge(wx: Publication, wy: Publication): Publication = {
wx.mergeFrom(wy)
if(wx.getId == null && wy.getId.nonEmpty)
wx.setId(wy.getId)
wx
}
override def finish(reduction: Publication): Publication = reduction
override def bufferEncoder: Encoder[Publication] =
Encoders.kryo(classOf[Publication])
override def outputEncoder: Encoder[Publication] =
Encoders.kryo(classOf[Publication])
}
def getRelationAggregator(): Aggregator[(String, Relation), Relation, Relation] = new Aggregator[(String, Relation), Relation, Relation]{
override def zero: Relation = new Relation()
override def reduce(b: Relation, a: (String, Relation)): Relation = {
a._2
}
override def merge(a: Relation, b: Relation): Relation = {
if(b!= null) b else a
}
override def finish(reduction: Relation): Relation = reduction
override def bufferEncoder: Encoder[Relation] =
Encoders.kryo(classOf[Relation])
override def outputEncoder: Encoder[Relation] =
Encoders.kryo(classOf[Relation])
}
}

138
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala Normal file
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@ -0,0 +1,138 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Instance, KeyValue, Oaf}
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils.createQualifier
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIRelation, OafUtils, ProvenaceInfo}
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.scholexplorer.relation.RelationMapper
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
object SparkAddLinkUpdates {
val relationMapper = RelationMapper.load
case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:String, turl:String, title:String, publisher:String) {}
def generatePubmedDLICollectedFrom(): KeyValue = {
OafUtils.generateKeyValue("dli_________::europe_pmc__", "Europe PMC")
}
def ebiLinksToOaf(input:(String, String)):List[Oaf] = {
val pmid :String = input._1
val input_json :String = input._2
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input_json)
val targets:List[EBILinks] = for {
JObject(link) <- json \\ "Category" \\ "Link"
JField("PublicationDate", JString(pubdate)) <- link
JField("RelationshipType", JObject(relationshipType)) <- link
JField("Name", JString(relname)) <- relationshipType
JField("Target", JObject(target)) <- link
JField("Identifier", JObject(identifier)) <- target
JField("ID", JString(tpid)) <- identifier
JField("IDScheme", JString(tpidtype)) <- identifier
JField("IDURL", JString(turl)) <- identifier
JField("Title", JString(title)) <- target
JField("Publisher", JObject(pub)) <- target
JField("Name", JString(publisher)) <- pub
} yield EBILinks(relname, pubdate, tpid, tpidtype, turl,title, publisher)
val dnetPublicationId = s"50|${DHPUtils.md5(s"$pmid::pmid")}"
targets.flatMap(l => {
val relation = new DLIRelation
val inverseRelation = new DLIRelation
val targetDnetId = s"50|${DHPUtils.md5(s"${l.tpid.toLowerCase.trim}::${l.tpidType.toLowerCase.trim}")}"
val relInfo = relationMapper.get(l.relation.toLowerCase)
val relationSemantic = relInfo.getOriginal
val inverseRelationSemantic = relInfo.getInverse
relation.setSource(dnetPublicationId)
relation.setTarget(targetDnetId)
relation.setRelClass("datacite")
relation.setRelType(relationSemantic)
relation.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava)
inverseRelation.setSource(targetDnetId)
inverseRelation.setTarget(dnetPublicationId)
inverseRelation.setRelClass("datacite")
inverseRelation.setRelType(inverseRelationSemantic)
inverseRelation.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava)
val d = new DLIDataset
d.setId(targetDnetId)
d.setDataInfo(OafUtils.generateDataInfo())
d.setPid(List(OafUtils.createSP(l.tpid.toLowerCase.trim, l.tpidType.toLowerCase.trim, "dnet:pid_types")).asJava)
d.setCompletionStatus("complete")
val pi = new ProvenaceInfo
pi.setId("dli_________::europe_pmc__")
pi.setName( "Europe PMC")
pi.setCompletionStatus("complete")
pi.setCollectionMode("collected")
d.setDlicollectedfrom(List(pi).asJava)
d.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava)
d.setPublisher(OafUtils.asField(l.publisher))
d.setTitle(List(OafUtils.createSP(l.title, "main title", "dnet:dataCite_title")).asJava)
d.setDateofacceptance(OafUtils.asField(l.pubdate))
val i = new Instance
i.setCollectedfrom(generatePubmedDLICollectedFrom())
i.setDateofacceptance(d.getDateofacceptance)
i.setUrl(List(l.turl).asJava)
i.setInstancetype(createQualifier("0021", "Dataset", "dnet:publication_resource", "dnet:publication_resource"))
d.setInstance(List(i).asJava)
List(relation, inverseRelation, d)
})
}
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkCreateEBIDataFrame.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val workingPath = parser.get("workingPath")
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val relEncoder: Encoder[DLIRelation] = Encoders.kryo(classOf[DLIRelation])
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset])
val ds:Dataset[(String,String)] = spark.read.load(s"$workingPath/baseline_links_updates").as[(String,String)](Encoders.tuple(Encoders.STRING, Encoders.STRING))
ds.flatMap(l =>ebiLinksToOaf(l)).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_oaf")
ds.filter(s => s.isInstanceOf)
val oDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/baseline_links_updates_oaf").as[Oaf]
oDataset.filter(p =>p.isInstanceOf[DLIRelation]).map(p => p.asInstanceOf[DLIRelation]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_relation")
oDataset.filter(p =>p.isInstanceOf[DLIDataset]).map(p => p.asInstanceOf[DLIDataset]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_dataset")
}
}

49
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateBaselineDataFrame.scala Normal file
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@ -0,0 +1,49 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal, PMParser}
import scala.io.Source
import scala.xml.pull.XMLEventReader
object SparkCreateBaselineDataFrame {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkCreateEBIDataFrame.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sc = spark.sparkContext
val workingPath = parser.get("workingPath")
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
new PMParser(xml)
} ))
ds.write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
}
}

87
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala Normal file
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@ -0,0 +1,87 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser}
import eu.dnetlib.scholexplorer.relation.RelationMapper
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkCreateEBIDataFrame {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkCreateEBIDataFrame.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkCreateEBIDataFrame.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sc = spark.sparkContext
val workingPath = parser.get("workingPath")
val relationMapper = RelationMapper.load
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val pubEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
logger.info("Extract Publication and relation from publication_xml")
val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s =>
{
new ObjectMapper().readValue(s, classOf[String])
}).flatMap(s => {
val d = new PublicationScholexplorerParser
d.parseObject(s, relationMapper).asScala.iterator})
val mapper = new ObjectMapper()
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf")
logger.info("Extract Publication and relation from dataset_xml")
val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s =>
{
new ObjectMapper().readValue(s, classOf[String])
}).flatMap(s => {
val d = new DatasetScholexplorerParser
d.parseObject(s, relationMapper).asScala.iterator})
spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf")
val dataset: Dataset[OafDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[OafDataset]).map(d => d.asInstanceOf[OafDataset])
val publication: Dataset[Publication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Publication]).map(d => d.asInstanceOf[Publication])
val relations: Dataset[Relation] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Relation]).map(d => d.asInstanceOf[Relation])
publication.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getPublicationAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/publication")
dataset.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datasetEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDatasetAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset")
relations.map(d => (s"${d.getSource}::${d.getRelType}::${d.getTarget}", d))(Encoders.tuple(Encoders.STRING, relEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getRelationAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/relation")
relations.map(r => (r.getSource, r.getTarget))(Encoders.tuple(Encoders.STRING,Encoders.STRING))
}
}

64
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMArticle.java Normal file
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@ -0,0 +1,64 @@
package eu.dnetlib.dhp.sx.ebi.model;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
public class PMArticle implements Serializable {
private String pmid;
private String date;
private PMJournal journal;
private String title;
private String description;
private List<PMAuthor> authors = new ArrayList<>();
public String getPmid() {
return pmid;
}
public void setPmid(String pmid) {
this.pmid = pmid;
}
public String getDate() {
return date;
}
public void setDate(String date) {
this.date = date;
}
public PMJournal getJournal() {
return journal;
}
public void setJournal(PMJournal journal) {
this.journal = journal;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public List<PMAuthor> getAuthors() {
return authors;
}
public void setAuthors(List<PMAuthor> authors) {
this.authors = authors;
}
}

31
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java Normal file
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@ -0,0 +1,31 @@
package eu.dnetlib.dhp.sx.ebi.model;
import java.io.Serializable;
public class PMAuthor implements Serializable {
private String lastName;
private String foreName;
public String getLastName() {
return lastName;
}
public void setLastName(String lastName) {
this.lastName = lastName;
}
public String getForeName() {
return foreName;
}
public void setForeName(String foreName) {
this.foreName = foreName;
}
public String getFullName() {
return String.format("%s, %s", this.foreName, this.lastName);
}
}

53
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMJournal.java Normal file
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@ -0,0 +1,53 @@
package eu.dnetlib.dhp.sx.ebi.model;
import java.io.Serializable;
public class PMJournal implements Serializable {
private String issn;
private String volume;
private String issue;
private String date;
private String title;
public String getIssn() {
return issn;
}
public void setIssn(String issn) {
this.issn = issn;
}
public String getVolume() {
return volume;
}
public void setVolume(String volume) {
this.volume = volume;
}
public String getIssue() {
return issue;
}
public void setIssue(String issue) {
this.issue = issue;
}
public String getDate() {
return date;
}
public void setDate(String date) {
this.date = date;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
}

92
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMParser.scala Normal file
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@ -0,0 +1,92 @@
package eu.dnetlib.dhp.sx.ebi.model
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
var currentArticle:PMArticle = generateNextArticle()
override def hasNext: Boolean = currentArticle!= null
override def next(): PMArticle = {
val tmp = currentArticle
currentArticle = generateNextArticle()
tmp
}
def generateNextArticle():PMArticle = {
var currentAuthor: PMAuthor = null
var currentJournal: PMJournal = null
var currNode: String = null
var currentYear = "0"
var currentMonth = "01"
var currentDay = "01"
while (xml.hasNext) {
xml.next match {
case EvElemStart(_, label, _, _) =>
currNode = label
label match {
case "PubmedArticle" => currentArticle = new PMArticle
case "Author" => currentAuthor = new PMAuthor
case "Journal" => currentJournal = new PMJournal
case _ =>
}
case EvElemEnd(_, label) =>
label match {
case "PubmedArticle" => return currentArticle
case "Author" => currentArticle.getAuthors.add(currentAuthor)
case "Journal" => currentArticle.setJournal(currentJournal)
case "DateCompleted" => currentArticle.setDate(s"$currentYear-$currentMonth-$currentDay")
case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
case _ =>
}
case EvText(text) =>
if (currNode!= null && text.trim.nonEmpty)
currNode match {
case "ArticleTitle" => {
if (currentArticle.getTitle==null)
currentArticle.setTitle(text.trim)
else
currentArticle.setTitle(currentArticle.getTitle + text.trim)
}
case "AbstractText" => {
if (currentArticle.getDescription==null)
currentArticle.setDescription(text.trim)
else
currentArticle.setDescription(currentArticle.getDescription + text.trim)
}
case "PMID" => currentArticle.setPmid(text.trim)
case "ISSN" => currentJournal.setIssn(text.trim)
case "Year" => currentYear = text.trim
case "Month" => currentMonth = text.trim
case "Day" => currentDay = text.trim
case "Volume" => currentJournal.setVolume( text.trim)
case "Issue" => currentJournal.setIssue (text.trim)
case "LastName" => {
if (currentAuthor != null)
currentAuthor.setLastName(text.trim)
}
case "ForeName" => if (currentAuthor != null)
currentAuthor.setForeName(text.trim)
case "Title" =>
if (currentJournal.getTitle==null)
currentJournal.setTitle(text.trim)
else
currentJournal.setTitle(currentJournal.getTitle + text.trim)
case _ =>
}
case _ =>
}
}
null
}
}

11
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java
View File

@ -150,6 +150,17 @@ public abstract class AbstractScholexplorerParser {
return uk;
}
protected Qualifier generateQualifier(final String classId, final String className, final String schemeId,
final String schemeName) {
final Qualifier q = new Qualifier();
q.setClassid(classId);
q.setClassid(className);
q.setSchemeid(schemeId);
q.setSchemename(schemeName);
return q;
}
protected void generateRelations(
RelationMapper relationMapper,
Result parsedObject,

44
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java
View File

@ -64,7 +64,6 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
currentDate.setQualifier(dateQualifier);
parsedObject.setRelevantdate(Collections.singletonList(currentDate));
}
final String completionStatus = VtdUtilityParser
.getSingleValue(ap, vn, "//*[local-name()='completionStatus']");
final String provisionMode = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='provisionMode']");
@ -149,6 +148,37 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
inferPid(currentPid);
parsedObject.setPid(Collections.singletonList(currentPid));
String resolvedURL = null;
switch (currentPid.getQualifier().getClassname().toLowerCase()) {
case "uniprot":
resolvedURL = "https://www.uniprot.org/uniprot/" + currentPid.getValue();
break;
case "ena":
if (StringUtils.isNotBlank(currentPid.getValue()) && currentPid.getValue().length() > 7)
resolvedURL = "https://www.ebi.ac.uk/ena/data/view/" + currentPid.getValue().substring(0, 8);
break;
case "chembl":
resolvedURL = "https://www.ebi.ac.uk/chembl/compound_report_card/" + currentPid.getValue();
break;
case "ncbi-n":
resolvedURL = "https://www.ncbi.nlm.nih.gov/nuccore/" + currentPid.getValue();
break;
case "ncbi-p":
resolvedURL = "https://www.ncbi.nlm.nih.gov/nuccore/" + currentPid.getValue();
break;
case "genbank":
resolvedURL = "https://www.ncbi.nlm.nih.gov/nuccore/" + currentPid.getValue();
break;
case "pdb":
resolvedURL = "https://www.ncbi.nlm.nih.gov/nuccore/" + currentPid.getValue();
break;
case "url":
resolvedURL = currentPid.getValue();
break;
}
final String sourceId = generateId(
currentPid.getValue(), currentPid.getQualifier().getClassid(), "dataset");
parsedObject.setId(sourceId);
@ -251,6 +281,11 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
t -> {
final StructuredProperty st = new StructuredProperty();
st.setValue(t);
st
.setQualifier(
generateQualifier(
"main title", "main title", "dnet:dataCite_title",
"dnet:dataCite_title"));
return st;
})
.collect(Collectors.toList()));
@ -282,6 +317,13 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
.collect(Collectors.toList()));
}
if (StringUtils.isNotBlank(resolvedURL)) {
Instance i = new Instance();
i.setCollectedfrom(parsedObject.getCollectedfrom().get(0));
i.setUrl(Collections.singletonList(resolvedURL));
parsedObject.setInstance(Collections.singletonList(i));
}
result.add(parsedObject);
return result;
} catch (Throwable e) {

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java
View File

@ -202,6 +202,11 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser
t -> {
final StructuredProperty st = new StructuredProperty();
st.setValue(t);
st
.setQualifier(
generateQualifier(
"main title", "main title", "dnet:dataCite_title",
"dnet:dataCite_title"));
return st;
})
.collect(Collectors.toList()));

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json Normal file
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@ -0,0 +1,4 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}
]

68
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml Normal file
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@ -0,0 +1,68 @@
<configuration>
<!-- OCEAN -->
<!--
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
-->
<!-- GARR -->
<property>
<name>jobTracker</name>
<value>yarn</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://hadoop-edge3.garr-pa1.d4science.org:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://hadoop-rm2.garr-pa1.d4science.org:19888</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</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>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

97
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml Normal file
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@ -0,0 +1,97 @@
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the Working Path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="GenerateUpdates"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="GenerateBaselineDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Baselnie DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=1
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="GenerateUpdates">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Baselnie DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkAddLinkUpdates</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=1
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="CreateEBIDataSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create EBI DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=1000
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

6
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -68,6 +68,10 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(p.getId());
assertTrue(p.getOriginalId().size() == 1);
assertEquals("10.3897/oneeco.2.e13718", p.getOriginalId().get(0));
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
assertFalse(p.getDataInfo().getInvisible());
@ -169,6 +173,8 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
assertTrue(d.getOriginalId().size() == 1);
assertEquals("oai:zenodo.org:3234526", d.getOriginalId().get(0));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0);

20
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala Normal file
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@ -0,0 +1,20 @@
package eu.dnetlib.dhp.sx.ebi
import org.junit.jupiter.api.Test
class TestEBI {
@Test
def testEBIData() = {
SparkAddLinkUpdates.main("-mt local[*] -w /home/sandro/Downloads".split(" "))
}
}

55
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/rel1.json Normal file
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@ -0,0 +1,55 @@
{
"Category": [
{
"Section": [
{
"Linklist": {
"Link": [
{
"LinkProvider": {
"Name": "Europe PMC"
},
"Target": {
"Publisher": {
"Name": "Altmetric"
},
"ImageURL": "https://api.altmetric.com/v1/donut/58578459_64.png",
"Identifier": {
"ID": "https://www.altmetric.com/details/58578459",
"IDScheme": "URL",
"IDURL": "https://www.altmetric.com/details/58578459"
},
"Type": {
"Name": "dataset"
},
"Title": "Optical clumped isotope thermometry of carbon dioxide"
},
"Source": {
"Identifier": {
"ID": "30886173",
"IDScheme": "PMID"
},
"Type": {
"Name": "literature"
}
},
"PublicationDate": "06-04-2019",
"RelationshipType": {
"Name": "IsReferencedBy"
},
"ObtainedBy": "ext_links"
}
]
},
"ObtainedBy": "ext_links",
"SectionLinkCount": 1,
"Tags": [
"altmetrics"
]
}
],
"CategoryLinkCount": 1,
"Name": "Altmetric"
}
]
}

191
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/rel_multiple.json Normal file
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@ -0,0 +1,191 @@
{
"version": "6.3",
"hitCount": 4,
"request": {
"id": "28818901",
"source": "MED"
},
"dataLinkList": {
"Category": [
{
"Name": "Nucleotide Sequences",
"CategoryLinkCount": 3,
"Section": [
{
"ObtainedBy": "tm_accession",
"Tags": [
"supporting_data"
],
"SectionLinkCount": 1,
"Linklist": {
"Link": [
{
"ObtainedBy": "tm_accession",
"PublicationDate": "27-02-2020",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "References"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "28818901",
"IDScheme": "MED"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "AP008937",
"IDScheme": "ENA",
"IDURL": "http://identifiers.org/ena.embl/AP008937"
},
"Title": "AP008937",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
}
]
}
},
{
"ObtainedBy": "submission",
"Tags": [
"related_data"
],
"SectionLinkCount": 2,
"CollectionURL": "http://www.ebi.ac.uk/ena/data/search?query=28818901",
"Linklist": {
"Link": [
{
"ObtainedBy": "submission",
"PublicationDate": "25-06-2018",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "IsReferencedBy"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "28818901",
"IDScheme": "PMID"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "NIWV01000000",
"IDScheme": "ENA",
"IDURL": "http://www.ebi.ac.uk/ena/data/view/NIWV01000000"
},
"Title": "Nucleotide sequences",
"Publisher": {
"Name": "ENA"
}
}
},
{
"ObtainedBy": "submission",
"PublicationDate": "25-06-2018",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "IsReferencedBy"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "28818901",
"IDScheme": "PMID"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "PRJNA390617",
"IDScheme": "ENA",
"IDURL": "http://www.ebi.ac.uk/ena/data/view/PRJNA390617"
},
"Title": "Lactobacillus fermentum strain:BFE 6620",
"Publisher": {
"Name": "ENA"
}
}
}
]
}
}
]
},
{
"Name": "BioStudies: supplemental material and supporting data",
"CategoryLinkCount": 1,
"Section": [
{
"ObtainedBy": "ext_links",
"Tags": [
"supporting_data"
],
"SectionLinkCount": 1,
"Linklist": {
"Link": [
{
"ObtainedBy": "ext_links",
"PublicationDate": "24-07-2018",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "IsReferencedBy"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "28818901",
"IDScheme": "PMID"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC5604774?xr=true",
"IDScheme": "URL",
"IDURL": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC5604774?xr=true"
},
"Title": "Draft Genome Sequence of Lactobacillus fermentum BFE 6620, a Potential Starter Culture for African Vegetable Foods, Isolated from Fermented Cassava.",
"Publisher": {
"Name": "BioStudies: supplemental material and supporting data"
}
}
}
]
}
}
]
}
]
}
}

57
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
View File

@ -5,11 +5,12 @@ import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._
import scala.collection.JavaConverters._
@ -99,6 +100,20 @@ object DLIToOAF {
)
def fixInstance(r:Publication) :Publication = {
val collectedFrom = r.getCollectedfrom.asScala.head
r.getInstance().asScala.foreach(i => i.setCollectedfrom(collectedFrom))
r
}
def fixInstanceDataset(r:Dataset) :Dataset = {
val collectedFrom = r.getCollectedfrom.asScala.head
r.getInstance().asScala.foreach(i => i.setCollectedfrom(collectedFrom))
r
}
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
@ -412,46 +427,6 @@ object DLIToOAF {
}
def generateKeyValue(key: String, value: String): KeyValue = {
val kv: KeyValue = new KeyValue()
kv.setKey(key)
kv.setValue(value)
kv.setDataInfo(generateDataInfo("0.9"))
kv
}
def generateDataInfo(trust: String = "0.9", invisibile: Boolean = false): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch, sch)
}
def createQualifier(classId: String, className: String, schemeId: String, schemeName: String): Qualifier = {
val q: Qualifier = new Qualifier
q.setClassid(classId)
q.setClassname(className)
q.setSchemeid(schemeId)
q.setSchemename(schemeName)
q
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)
tmp
}
}

11
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala
View File

@ -1,7 +1,7 @@
package eu.dnetlib.dhp.`export`
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.Text
@ -166,10 +166,13 @@ object SparkExportContentForOpenAire {
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationAS")
val fRels:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationAS").as[Relation].map(DLIToOAF.toActionSet)
val fpubs:Dataset[(String,String)] = spark.read.load(s"$workingPath/publicationAS").as[Publication].map(DLIToOAF.toActionSet)
val fdats:Dataset[(String,String)] = spark.read.load(s"$workingPath/datasetAS").as[OafDataset].map(DLIToOAF.toActionSet)
spark.read.load(s"$workingPath/publicationAS").as[Publication].map(DLIToOAF.fixInstance).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationAS_fixed")
spark.read.load(s"$workingPath/datasetAS").as[OafDataset].map(DLIToOAF.fixInstanceDataset).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetAS_fixed")
val fRels:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationAS").as[Relation].map(DLIToOAF.toActionSet)
val fpubs:Dataset[(String,String)] = spark.read.load(s"$workingPath/publicationAS_fixed").as[Publication].map(DLIToOAF.toActionSet)
val fdats:Dataset[(String,String)] = spark.read.load(s"$workingPath/datasetAS_fixed").as[OafDataset].map(DLIToOAF.toActionSet)
fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}

2
pom.xml
View File

@ -315,7 +315,7 @@
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
<version>4.0.2</version>
<version>4.0.4</version>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>