merge branch with beta

This commit is contained in:
Miriam Baglioni 2021-08-05 15:23:32 +02:00
commit 6bd1eca7e0
72 changed files with 9031 additions and 527 deletions

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@ -67,6 +67,7 @@ public class AuthorMerger {
a -> a a -> a
.getPid() .getPid()
.stream() .stream()
.filter(Objects::nonNull)
.map(p -> new Tuple2<>(pidToComparableString(p), a))) .map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
@ -78,6 +79,7 @@ public class AuthorMerger {
a -> a a -> a
.getPid() .getPid()
.stream() .stream()
.filter(Objects::nonNull)
.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
.map(p -> new Tuple2<>(p, a))) .map(p -> new Tuple2<>(p, a)))
.collect(Collectors.toList()); .collect(Collectors.toList());
@ -150,7 +152,7 @@ public class AuthorMerger {
} }
private static boolean hasPid(Author a) { private static boolean hasPid(Author a) {
if (a == null || a.getPid() == null || a.getPid().size() == 0) if (a == null || a.getPid() == null || a.getPid().isEmpty())
return false; return false;
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
} }
@ -159,7 +161,10 @@ public class AuthorMerger {
if (StringUtils.isNotBlank(author.getSurname())) { if (StringUtils.isNotBlank(author.getSurname())) {
return new Person(author.getSurname() + ", " + author.getName(), false); return new Person(author.getSurname() + ", " + author.getName(), false);
} else { } else {
return new Person(author.getFullname(), false); if (StringUtils.isNotBlank(author.getFullname()))
return new Person(author.getFullname(), false);
else
return new Person("", false);
} }
} }

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@ -1,9 +1,10 @@
package eu.dnetlib.dhp.actionmanager.datacite package eu.dnetlib.dhp.actionmanager.datacite
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest} import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
import org.apache.http.entity.StringEntity import org.apache.http.entity.StringEntity
import org.apache.http.impl.client.HttpClients import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
import java.io.IOException import java.io.IOException
@ -56,31 +57,31 @@ abstract class AbstractRestClient extends Iterator[String]{
private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={ private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
val client = HttpClients.createDefault val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client =HttpClientBuilder.create().setDefaultRequestConfig(config).build()
var tries = 4 var tries = 4
try { while (tries > 0) {
while (tries > 0) {
println(s"requesting ${r.getURI}") println(s"requesting ${r.getURI}")
val response = client.execute(r) try {
println(s"get response with status${response.getStatusLine.getStatusCode}") val response = client.execute(r)
if (response.getStatusLine.getStatusCode > 400) { println(s"get response with status${response.getStatusLine.getStatusCode}")
tries -= 1 if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries-=1
} }
else
return IOUtils.toString(response.getEntity.getContent)
} }
"" ""
} catch { }
case e: Throwable =>
throw new RuntimeException("Error on executing request ", e)
} finally try client.close()
catch {
case e: IOException =>
throw new RuntimeException("Unable to close client ", e)
}
}
getBufferData() getBufferData()
} }

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@ -367,7 +367,7 @@ object DataciteToOAFTransformation {
result.setDateofcollection(ISO8601FORMAT.format(d)) result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(ts)) result.setDateoftransformation(ISO8601FORMAT.format(d))
result.setDataInfo(dataInfo) result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List()) val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())

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@ -140,7 +140,7 @@ object ImportDatacite {
private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = { private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
var from:Long = timestamp * 1000 var from:Long = timestamp * 1000
val delta:Long = 50000000L val delta:Long = 100000000L
var client: DataciteAPIImporter = null var client: DataciteAPIImporter = null
val now :Long =System.currentTimeMillis() val now :Long =System.currentTimeMillis()
var i = 0 var i = 0

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@ -0,0 +1,73 @@
package eu.dnetlib.dhp.actionmanager.scholix
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import org.apache.spark.SparkConf
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkCreateActionset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val workingDirFolder = parser.get("workingDirFolder")
log.info(s"workingDirFolder -> $workingDirFolder")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
log.info("extract source and target Identifier involved in relations")
log.info("save relation filtered")
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
log.info("saving entities")
val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
entities
.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
.map(p => p._1._2)
.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
}
}

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@ -0,0 +1,86 @@
package eu.dnetlib.dhp.actionmanager.scholix
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkSaveActionSet {
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o => toActionSet(o))
.filter(o => o != null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
}
}

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@ -4,10 +4,6 @@
<name>mainPath</name> <name>mainPath</name>
<description>the working path of Datacite stores</description> <description>the working path of Datacite stores</description>
</property> </property>
<property>
<name>oafTargetPath</name>
<description>the target path where the OAF records are stored</description>
</property>
<property> <property>
<name>isLookupUrl</name> <name>isLookupUrl</name>
<description>The IS lookUp service endopoint</description> <description>The IS lookUp service endopoint</description>
@ -17,26 +13,15 @@
<value>100</value> <value>100</value>
<description>The request block size</description> <description>The request block size</description>
</property> </property>
<property>
<name>exportLinks</name>
<value>false</value>
<description>instructs the transformation phase to produce the links or not</description>
</property>
</parameters> </parameters>
<start to="resume_from"/> <start to="ImportDatacite"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<decision name="resume_from">
<switch>
<case to="TransformDatacite">${wf:conf('resumeFrom') eq 'TransformDatacite'}</case>
<default to="ImportDatacite"/>
</switch>
</decision>
<action name="ImportDatacite"> <action name="ImportDatacite">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
@ -60,11 +45,12 @@
<arg>--master</arg><arg>yarn-cluster</arg> <arg>--master</arg><arg>yarn-cluster</arg>
<arg>--blocksize</arg><arg>${blocksize}</arg> <arg>--blocksize</arg><arg>${blocksize}</arg>
</spark> </spark>
<ok to="TransformDatacite"/> <ok to="TransformJob"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="TransformDatacite">
<action name="TransformJob">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
@ -82,9 +68,9 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${mainPath}/datacite_dump</arg> <arg>--sourcePath</arg><arg>${mainPath}/datacite_dump</arg>
<arg>--targetPath</arg><arg>${oafTargetPath}</arg> <arg>--targetPath</arg><arg>${mainPath}/datacite_oaf</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg> <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--exportLinks</arg><arg>${exportLinks}</arg> <arg>--exportLinks</arg><arg>true</arg>
<arg>--master</arg><arg>yarn-cluster</arg> <arg>--master</arg><arg>yarn-cluster</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>

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@ -0,0 +1,6 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingDirFolder","paramDescription": "the working Dir Folder", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
]

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@ -0,0 +1,23 @@
<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>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

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@ -0,0 +1,76 @@
<workflow-app name="Scholexplorer_to_ActionSet_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the path of the consistent graph</description>
</property>
<property>
<name>workingDirFolder</name>
<description>the path of working dir ActionSet</description>
</property>
<property>
<name>outputPath</name>
<description>the path of Scholexplorer ActionSet</description>
</property>
</parameters>
<start to="createActionSet"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="createActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Action Set</name>
<class>eu.dnetlib.dhp.actionmanager.scholix.SparkCreateActionset</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${outputPath}</arg>
<arg>--workingDirFolder</arg><arg>${workingDirFolder}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="SaveActionSet"/>
<error to="Kill"/>
</action>
<action name="SaveActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Save Action Set</name>
<class>eu.dnetlib.dhp.actionmanager.scholix.SparkSaveActionSet</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDirFolder}/actionSetOaf</arg>
<arg>--targetPath</arg><arg>${outputPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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@ -0,0 +1,5 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
]

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@ -3,13 +3,14 @@ package eu.dnetlib.dhp.actionmanager.datacite
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.databind.SerializationFeature import com.fasterxml.jackson.databind.SerializationFeature
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.schema.oaf.Oaf
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{BeforeEach, Test} import org.junit.jupiter.api.{BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import java.text.SimpleDateFormat
import java.util.Locale
import scala.io.Source import scala.io.Source
@ExtendWith(Array(classOf[MockitoExtension])) @ExtendWith(Array(classOf[MockitoExtension]))
@ -22,6 +23,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest{
super.setUpVocabulary() super.setUpVocabulary()
} }
@Test
def testDateMapping:Unit = {
val inputDate = "2021-07-14T11:52:54+0000"
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val dt = ISO8601FORMAT.parse(inputDate)
println(dt.getTime)
}
@Test @Test
def testMapping() :Unit = { def testMapping() :Unit = {
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset { public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset {
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDat
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isReferencedBy"); return relType.equals(ModelConstants.IS_REFERENCED_BY);
} }
} }

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset { public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset {
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDatase
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isRelatedTo"); return relType.equals(ModelConstants.IS_RELATED_TO);
} }
} }

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset { public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset {
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingD
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedBy"); return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY);
} }
} }

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset { public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset {
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingD
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedTo"); return relType.equals(ModelConstants.IS_SUPPLEMENT_TO);
} }
} }

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset { public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset {
@ -11,7 +12,7 @@ public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("references"); return relType.equals(ModelConstants.REFERENCES);
} }
} }

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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication { public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication {
@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissin
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isReferencedBy"); return relType.equals(ModelConstants.IS_REFERENCED_BY);
} }
} }

View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication { public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication {
@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPu
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isRelatedTo"); return relType.equals(ModelConstants.IS_RELATED_TO);
} }
} }

View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication { public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication {
@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMiss
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedBy"); return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY);
} }
} }

View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication { public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication {
@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMiss
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedTo"); return relType.equals(ModelConstants.IS_SUPPLEMENT_TO);
} }
} }

View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication { public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication {
@ -11,7 +12,7 @@ public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPub
@Override @Override
protected boolean filterByType(final String relType) { protected boolean filterByType(final String relType) {
return relType.equals("references"); return relType.equals(ModelConstants.REFERENCES);
} }
} }

View File

@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
public class ClusterUtils { public class ClusterUtils {
@ -52,15 +53,15 @@ public class ClusterUtils {
} }
public static boolean isDedupRoot(final String id) { public static boolean isDedupRoot(final String id) {
return id.contains("dedup_wf_"); return id.contains("dedup");
} }
public static final boolean isValidResultResultClass(final String s) { public static final boolean isValidResultResultClass(final String s) {
return s.equals("isReferencedBy") return s.equals(ModelConstants.IS_REFERENCED_BY)
|| s.equals("isRelatedTo") || s.equals(ModelConstants.IS_RELATED_TO)
|| s.equals("references") || s.equals(ModelConstants.REFERENCES)
|| s.equals("isSupplementedBy") || s.equals(ModelConstants.IS_SUPPLEMENTED_BY)
|| s.equals("isSupplementedTo"); || s.equals(ModelConstants.IS_SUPPLEMENT_TO);
} }
public static <T> T incrementAccumulator(final T o, final LongAccumulator acc) { public static <T> T incrementAccumulator(final T o, final LongAccumulator acc) {

View File

@ -23,6 +23,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
@ -77,48 +78,54 @@ public class SparkUpdateEntity extends AbstractSparkAction {
(type, clazz) -> { (type, clazz) -> {
final String outputPath = dedupGraphPath + "/" + type; final String outputPath = dedupGraphPath + "/" + type;
removeOutputDir(spark, outputPath); removeOutputDir(spark, outputPath);
final String ip = DedupUtility.createEntityPath(graphBasePath, type.toString());
if (HdfsSupport.exists(ip, sc.hadoopConfiguration())) {
JavaRDD<String> sourceEntity = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
JavaRDD<String> sourceEntity = sc if (mergeRelExists(workingPath, type.toString())) {
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
if (mergeRelExists(workingPath, type.toString())) { final String mergeRelPath = DedupUtility
.createMergeRelPath(workingPath, "*", type.toString());
final String dedupRecordPath = DedupUtility
.createDedupRecordPath(workingPath, "*", type.toString());
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", type.toString()); final Dataset<Relation> rel = spark
final String dedupRecordPath = DedupUtility .read()
.createDedupRecordPath(workingPath, "*", type.toString()); .load(mergeRelPath)
.as(Encoders.bean(Relation.class));
final Dataset<Relation> rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); final JavaPairRDD<String, String> mergedIds = rel
.where("relClass == 'merges'")
.where("source != target")
.select(rel.col("target"))
.distinct()
.toJavaRDD()
.mapToPair(
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
final JavaPairRDD<String, String> mergedIds = rel JavaPairRDD<String, String> entitiesWithId = sourceEntity
.where("relClass == 'merges'") .mapToPair(
.where("source != target") (PairFunction<String, String, String>) s -> new Tuple2<>(
.select(rel.col("target")) MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
.distinct() if (type == EntityType.organization) // exclude root records from organizations
.toJavaRDD() entitiesWithId = excludeRootOrgs(entitiesWithId, rel);
.mapToPair(
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
JavaPairRDD<String, String> entitiesWithId = sourceEntity JavaRDD<String> map = entitiesWithId
.mapToPair( .leftOuterJoin(mergedIds)
(PairFunction<String, String, String>) s -> new Tuple2<>( .map(k -> {
MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); if (k._2()._2().isPresent()) {
if (type == EntityType.organization) // exclude root records from organizations return updateDeletedByInference(k._2()._1(), clazz);
entitiesWithId = excludeRootOrgs(entitiesWithId, rel); }
return k._2()._1();
});
JavaRDD<String> map = entitiesWithId sourceEntity = map.union(sc.textFile(dedupRecordPath));
.leftOuterJoin(mergedIds)
.map(k -> {
if (k._2()._2().isPresent()) {
return updateDeletedByInference(k._2()._1(), clazz);
}
return k._2()._1();
});
sourceEntity = map.union(sc.textFile(dedupRecordPath)); }
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
} }
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
}); });
} }

View File

@ -1,12 +1,16 @@
package eu.dnetlib.doiboost package eu.dnetlib.doiboost
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils import org.apache.commons.lang3.StringUtils
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{getClosedAccessQualifier, getEmbargoedAccessQualifier, getUnknownQualifier}
import org.json4s import org.json4s
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
@ -118,14 +122,92 @@ object DoiBoostMappingUtil {
} }
def decideAccessRight(lic : Field[String], date:String) : AccessRight = {
if(lic == null){
//Default value Unknown
return getUnknownQualifier()
}
val license : String = lic.getValue
//CC licenses
if(license.startsWith("cc") ||
license.startsWith("http://creativecommons.org/licenses") ||
license.startsWith("https://creativecommons.org/licenses") ||
//ACS Publications Author choice licenses (considered OPEN also by Unpaywall)
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html") ||
license.equals("http://pubs.acs.org/page/policy/authorchoice_termsofuse.html") ||
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html") ||
//APA (considered OPEN also by Unpaywall)
license.equals("http://www.apa.org/pubs/journals/resources/open-access.aspx")){
val oaq : AccessRight = getOpenAccessQualifier()
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
return oaq
}
//OUP (BUT ONLY AFTER 12 MONTHS FROM THE PUBLICATION DATE, OTHERWISE THEY ARE EMBARGOED)
if(license.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")){
val now = java.time.LocalDate.now
try{
val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd"))
if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){
val oaq : AccessRight = getOpenAccessQualifier()
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
return oaq
}
else{
return getEmbargoedAccessQualifier()
}
}catch {
case e: Exception => {
try{
val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))
if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){
val oaq : AccessRight = getOpenAccessQualifier()
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
return oaq
}
else{
return getEmbargoedAccessQualifier()
}
}catch{
case ex: Exception => return getClosedAccessQualifier()
}
}
}
}
return getClosedAccessQualifier()
}
def getOpenAccessQualifier():AccessRight = { def getOpenAccessQualifier():AccessRight = {
OafMapperUtils.accessRight("OPEN","Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN,"Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
} }
def getRestrictedQualifier():AccessRight = { def getRestrictedQualifier():AccessRight = {
OafMapperUtils.accessRight("RESTRICTED","Restricted",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) OafMapperUtils.accessRight( "RESTRICTED","Restricted",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
}
def getUnknownQualifier():AccessRight = {
OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
}
def getEmbargoedAccessQualifier():AccessRight = {
OafMapperUtils.accessRight("EMBARGO","Embargo",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
}
def getClosedAccessQualifier():AccessRight = {
OafMapperUtils.accessRight("CLOSED","Closed Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
} }
@ -150,10 +232,11 @@ object DoiBoostMappingUtil {
if (item != null) { if (item != null) {
hb.setValue(item.officialname) hb.setValue(item.officialname)
hb.setKey(generateDSId(item.id)) hb.setKey(generateDSId(item.id))
if (item.openAccess) if (item.openAccess) {
i.setAccessright(getOpenAccessQualifier()) i.setAccessright(getOpenAccessQualifier())
val ar = getOpenAccessQualifier() i.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename)) }
} }
else { else {
hb = ModelConstants.UNKNOWN_REPOSITORY hb = ModelConstants.UNKNOWN_REPOSITORY
@ -161,17 +244,8 @@ object DoiBoostMappingUtil {
i.setHostedby(hb) i.setHostedby(hb)
}) })
val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid) publication.setBestaccessright(OafMapperUtils.createBestAccessRights(publication.getInstance()))
if (ar.nonEmpty) {
if(ar.contains(ModelConstants.ACCESS_RIGHT_OPEN)){
val ar = getOpenAccessQualifier()
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename))
}
else {
val ar = getRestrictedQualifier()
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename))
}
}
publication publication
} }

View File

@ -4,7 +4,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._ import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils} import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import eu.dnetlib.doiboost.DoiBoostMappingUtil.{decideAccessRight, _}
import org.apache.commons.lang.StringUtils import org.apache.commons.lang.StringUtils
import org.json4s import org.json4s
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
@ -168,12 +168,22 @@ case object Crossref2Oaf {
// Mapping instance // Mapping instance
val instance = new Instance() val instance = new Instance()
val license = for { val license = for {
JString(lic) <- json \ "license" \ "URL" JObject(license) <- json \ "license"
} yield asField(lic) JField("URL", JString(lic)) <- license
val l = license.filter(d => StringUtils.isNotBlank(d.getValue)) JField("content-version", JString(content_version)) <- license
if (l.nonEmpty) } yield (asField(lic), content_version)
instance.setLicense(l.head) val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue))
if (l.nonEmpty){
if (l exists (d => d._2.equals("vor"))){
for(d <- l){
if (d._2.equals("vor")){
instance.setLicense(d._1)
}
}
}
else{
instance.setLicense(l.head._1)}
}
// Ticket #6281 added pid to Instance // Ticket #6281 added pid to Instance
instance.setPid(result.getPid) instance.setPid(result.getPid)
@ -185,7 +195,7 @@ case object Crossref2Oaf {
OafMapperUtils.qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS, ModelConstants.DNET_REVIEW_LEVELS)) OafMapperUtils.qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS, ModelConstants.DNET_REVIEW_LEVELS))
} }
instance.setAccessright(getRestrictedQualifier()) instance.setAccessright(decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue))
instance.setInstancetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) instance.setInstancetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
result.setResourcetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) result.setResourcetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))

View File

@ -11,6 +11,7 @@ import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color
@ -23,6 +24,21 @@ case class OALocation(evidence:Option[String], host_type:Option[String], is_best
object UnpayWallToOAF { object UnpayWallToOAF {
val logger: Logger = LoggerFactory.getLogger(getClass) val logger: Logger = LoggerFactory.getLogger(getClass)
def get_unpaywall_color(input:String):Option[OpenAccessRoute] = {
if(input == null || input.equalsIgnoreCase("close"))
return None
if(input.equalsIgnoreCase("green"))
return Some(OpenAccessRoute.green)
if(input.equalsIgnoreCase("bronze"))
return Some(OpenAccessRoute.bronze)
if(input.equalsIgnoreCase("hybrid"))
return Some(OpenAccessRoute.hybrid)
else
return Some(OpenAccessRoute.gold)
}
def get_color(is_oa:Boolean, location: OALocation, journal_is_oa:Boolean):Option[OpenAccessRoute] = { def get_color(is_oa:Boolean, location: OALocation, journal_is_oa:Boolean):Option[OpenAccessRoute] = {
if (is_oa) { if (is_oa) {
if (location.host_type.isDefined) { if (location.host_type.isDefined) {
@ -65,7 +81,7 @@ object UnpayWallToOAF {
val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null) val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
val colour = get_color(is_oa, oaLocation, journal_is_oa) val colour = get_unpaywall_color((json \ "oa_status").extractOrElse[String](null))
pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava) pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
pub.setDataInfo(generateDataInfo()) pub.setDataInfo(generateDataInfo())

View File

@ -1,4 +1,4 @@
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Generate DOIBoost ActionSet for BETA - PREPROCESS" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>

View File

@ -1,4 +1,4 @@
<workflow-app name="Generate DOIBoost ActionSet for PROD" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Generate DOIBoost ActionSet for BETA - PROCESS" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
@ -99,7 +99,7 @@
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=7680
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -124,7 +124,7 @@
--executor-memory=${sparkExecutorIntersectionMemory} --executor-memory=${sparkExecutorIntersectionMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=7680
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

View File

@ -492,6 +492,124 @@ class CrossrefMappingTest {
} }
@Test
def testLicenseVorClosed() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
println(mapper.writeValueAsString(item))
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://www.springer.com/vor")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("CLOSED")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
}
@Test
def testLicenseOpen() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid))
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
println(mapper.writeValueAsString(item))
}
@Test
def testLicenseEmbargoOpen() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid))
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
println(mapper.writeValueAsString(item))
}
@Test
def testLicenseEmbargo() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
println(mapper.writeValueAsString(item))
}
@Test
def testLicenseEmbargoDateTime() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO")))
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
println(mapper.writeValueAsString(item))
}
} }

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@ -65,7 +65,6 @@ class MAGMappingTest {
val conf = new SparkConf() val conf = new SparkConf()
conf.setMaster("local[*]") conf.setMaster("local[*]")
conf.set("spark.driver.host", "localhost") conf.set("spark.driver.host", "localhost")
val spark: SparkSession = val spark: SparkSession =
SparkSession SparkSession
.builder() .builder()
@ -93,7 +92,6 @@ class MAGMappingTest {
implicit val formats = DefaultFormats implicit val formats = DefaultFormats
val conf = new SparkConf() val conf = new SparkConf()
conf.setMaster("local[*]") conf.setMaster("local[*]")
conf.set("spark.driver.host", "localhost") conf.set("spark.driver.host", "localhost")
@ -103,7 +101,6 @@ class MAGMappingTest {
.appName(getClass.getSimpleName) .appName(getClass.getSimpleName)
.config(conf) .config(conf)
.getOrCreate() .getOrCreate()
val path = getClass.getResource("duplicatedMagPapers.json").getPath val path = getClass.getResource("duplicatedMagPapers.json").getPath
import org.apache.spark.sql.Encoders import org.apache.spark.sql.Encoders

View File

@ -0,0 +1,42 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertDatasetToJsonRDD {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val resultObject = List("publication","dataset","software", "otherResearchProduct")
val mapper = new ObjectMapper()
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
resultObject.foreach{item =>
spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
}
}
}

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@ -0,0 +1,67 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertRDDtoDataset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val t = parser.get("targetPath")
log.info(s"targetPath -> $t")
val entityPath = s"$t/entities"
val relPath = s"$t/relation"
val mapper = new ObjectMapper()
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
log.info("Converting dataset")
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
log.info("Converting publication")
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
log.info("Converting software")
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
log.info("Converting otherresearchproduct")
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
log.info("Converting Relation")
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation]))
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
}
}

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@ -70,7 +70,7 @@ object SparkCreateInputGraph {
resultObject.foreach { r => resultObject.foreach { r =>
log.info(s"Make ${r._1} unique") log.info(s"Make ${r._1} unique")
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/dedup/${r._1}",spark, r._2) makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/preprocess/${r._1}",spark, r._2)
} }
} }

View File

@ -42,6 +42,7 @@ object SparkCreateScholix {
val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation] val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder)) .map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary] val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]

View File

@ -1,7 +1,7 @@
package eu.dnetlib.dhp.sx.graph package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Result import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
@ -29,11 +29,12 @@ object SparkCreateSummaryObject {
log.info(s"targetPath -> $targetPath") log.info(s"targetPath -> $targetPath")
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result] implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result] val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false)
ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath) ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath)

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@ -1,10 +1,17 @@
package eu.dnetlib.dhp.sx.graph package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Relation, Result} import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql._ 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 org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
@ -25,60 +32,109 @@ object SparkResolveRelation {
val relationPath = parser.get("relationPath") val relationPath = parser.get("relationPath")
log.info(s"sourcePath -> $relationPath") log.info(s"sourcePath -> $relationPath")
val entityPath = parser.get("entityPath") val entityPath = parser.get("entityPath")
log.info(s"targetPath -> $entityPath") log.info(s"entityPath -> $entityPath")
val workingPath = parser.get("workingPath") val workingPath = parser.get("workingPath")
log.info(s"workingPath -> $workingPath") log.info(s"workingPath -> $workingPath")
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
import spark.implicits._ import spark.implicits._
val entities:Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
entities.flatMap(e => e.getPid.asScala
.map(p =>
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
.filter(s => s!= null)
.map(s => (s,e.getId))
).groupByKey(_._1)
.reduceGroups((x,y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
.map(s =>s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedPid")
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/resolvedPid").as[(String,String)] extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath)
val mappper = new ObjectMapper()
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)]
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_1")), "left").map{ relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{
m => m =>
val sourceResolved = m._2 val sourceResolved = m._2
val currentRelation = m._1._2 val currentRelation = m._1._2
if (sourceResolved!=null && sourceResolved._2.nonEmpty) if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty)
currentRelation.setSource(sourceResolved._2) currentRelation.setSource(sourceResolved._1)
currentRelation currentRelation
}.write }.write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedSource") .save(s"$workingPath/relationResolvedSource")
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/resolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_1")), "left").map{ relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{
m => m =>
val targetResolved = m._2 val targetResolved = m._2
val currentRelation = m._1._2 val currentRelation = m._1._2
if (targetResolved!=null && targetResolved._2.nonEmpty) if (targetResolved!=null && targetResolved._1.nonEmpty)
currentRelation.setTarget(targetResolved._2) currentRelation.setTarget(targetResolved._1)
currentRelation currentRelation
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50")) }.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.save(s"$workingPath/resolvedRelation") .save(s"$workingPath/relation_resolved")
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
.map(r => mappper.writeValueAsString(r))
.rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec])
} }
private def extractPidsFromRecord(input:String):(String,List[(String,String)]) = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val id:String = (json \ "id").extract[String]
val result: List[(String,String)] = for {
JObject(pids) <- json \ "pid"
JField("value", JString(pidValue)) <- pids
JField("qualifier", JObject(qualifier)) <- pids
JField("classname", JString(pidType)) <- qualifier
} yield (pidValue, pidType)
(id,result)
}
private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = {
import spark.implicits._
val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*")
.map(i => extractPidsFromRecord(i))
.filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty)
.flatMap{ p =>
p._2.map(pid =>
(p._1, convertPidToDNETIdentifier(pid._1, pid._2))
)
}.filter(r =>r._1 != null || r._2 != null)
spark.createDataset(d)
.groupByKey(_._2)
.reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y)
.map(s => s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/relationResolvedPid")
}
/*
This method should be used once we finally convert everythings in Kryo dataset
instead of using rdd of json
*/
private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = {
import spark.implicits._
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
entities.flatMap(e => e.getPid.asScala
.map(p =>
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
.filter(s => s != null)
.map(s => (s, e.getId))
).groupByKey(_._1)
.reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
.map(s => s._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/relationResolvedPid")
}
def convertPidToDNETIdentifier(pid:String, pidType: String):String = { def convertPidToDNETIdentifier(pid:String, pidType: String):String = {
if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty) if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty)

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@ -199,7 +199,7 @@ object BioDBToOAF {
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
} }
val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version")) val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version"))
.map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO)) .map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
if (relevant_dates != null && relevant_dates.nonEmpty) if (relevant_dates != null && relevant_dates.nonEmpty)
d.setRelevantdate(relevant_dates.asJava) d.setRelevantdate(relevant_dates.asJava)
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
@ -218,12 +218,12 @@ object BioDBToOAF {
if (references_pmid != null && references_pmid.nonEmpty) { if (references_pmid != null && references_pmid.nonEmpty) {
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
rel.getCollectedfrom rel.getCollectedfrom
List(d, rel) List(d, rel)
} }
else if (references_doi != null && references_doi.nonEmpty) { else if (references_doi != null && references_doi.nonEmpty) {
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
List(d, rel) List(d, rel)
} }
else else
@ -243,7 +243,7 @@ object BioDBToOAF {
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
rel.setDataInfo(DATA_INFO) rel.setDataInfo(DATA_INFO)
rel.setRelType("resultResult") rel.setRelType(ModelConstants.RESULT_RESULT)
rel.setSubRelType(subRelType) rel.setSubRelType(subRelType)
rel.setRelClass(relClass) rel.setRelClass(relClass)
@ -263,7 +263,7 @@ object BioDBToOAF {
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = { def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date) createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
} }
@ -392,6 +392,6 @@ object BioDBToOAF {
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date))) List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date)))
} }
} }

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@ -16,7 +16,7 @@ object PubMedToOaf {
) )
def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = { def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
val result_typologies = getVocabularyTerm("dnet:result_typologies", vocabularies, cobjQualifier.getClassid) val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid)
result_typologies.getClassid match { result_typologies.getClassid match {
case "dataset" => new Dataset case "dataset" => new Dataset
case "publication" => new Publication case "publication" => new Publication
@ -68,11 +68,11 @@ object PubMedToOaf {
//else We have to find a terms that match the vocabulary otherwise we discard it //else We have to find a terms that match the vocabulary otherwise we discard it
val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue)) val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
if (ja.isDefined) { if (ja.isDefined) {
val cojbCategory = getVocabularyTerm("dnet:publication_resource", vocabularies, ja.get.getValue) val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue)
i.setInstancetype(cojbCategory) i.setInstancetype(cojbCategory)
} else { } else {
val i_type = article.getPublicationTypes.asScala val i_type = article.getPublicationTypes.asScala
.map(s => getVocabularyTerm("dnet:publication_resource", vocabularies, s.getValue)) .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))
.find(q => q != null) .find(q => q != null)
if (i_type.isDefined) if (i_type.isDefined)
i.setInstancetype(i_type.get) i.setInstancetype(i_type.get)
@ -112,7 +112,7 @@ object PubMedToOaf {
if (article.getLanguage != null) { if (article.getLanguage != null) {
val term = vocabularies.getSynonymAsQualifier("dnet:languages", article.getLanguage) val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage)
if (term != null) if (term != null)
result.setLanguage(term) result.setLanguage(term)
} }

View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.sx.graph.scholix package eu.dnetlib.dhp.sx.graph.scholix
import eu.dnetlib.dhp.schema.oaf.{Dataset, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixCollectedFrom, ScholixEntityId, ScholixIdentifier, ScholixRelationship, ScholixResource} import eu.dnetlib.dhp.schema.sx.scholix._
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology} import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.spark.sql.Encoders.bean
import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Encoder, Encoders} import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s import org.json4s
@ -301,14 +300,14 @@ object ScholixUtils {
if (r.getPid == null || r.getPid.isEmpty) if (r.getPid == null || r.getPid.isEmpty)
return null return null
val pids:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r) val persistentIdentifiers:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
if (pids.isEmpty) if (persistentIdentifiers.isEmpty)
return null return null
s.setLocalIdentifier(pids.asJava) s.setLocalIdentifier(persistentIdentifiers.asJava)
if (r.isInstanceOf[Dataset]) if (r.isInstanceOf[Publication] )
s.setTypology(Typology.dataset)
else
s.setTypology(Typology.publication) s.setTypology(Typology.publication)
else
s.setTypology(Typology.dataset)
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname) s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)

View File

@ -0,0 +1,5 @@
[
{"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}
]

View File

@ -0,0 +1,85 @@
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the graph Raw base path</description>
</property>
</parameters>
<start to="ExtractEntities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extract entities in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--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>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
</spark>
<ok to="DropDedupPath"/>
<error to="Kill"/>
</action>
<action name="DropDedupPath">
<fs>
<delete path='${targetPath}/dedup'/>
<mkdir path='${targetPath}/dedup/'/>
</fs>
<ok to="GenerateInputGraphForDedup"/>
<error to="Kill"/>
</action>
<action name="GenerateInputGraphForDedup">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Generate Input Graph for deduplication</name>
<class>eu.dnetlib.dhp.sx.graph.SparkConvertDatasetToJsonRDD</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=3000
--conf spark.sql.queryExecutionListeners=${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}/preprocess</arg>
<arg>--targetPath</arg><arg>${targetPath}/dedup</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,4 +1,4 @@
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sourcePath</name> <name>sourcePath</name>
@ -6,48 +6,22 @@
</property> </property>
<property> <property>
<name>targetPath</name> <name>targetPath</name>
<description>the graph Raw base path</description> <description>the final graph path</description>
</property> </property>
</parameters> </parameters>
<start to="ExtractEntities"/> <start to="ImportDatasetEntities"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="ExtractEntities"> <action name="ImportDatasetEntities">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Extract entities in raw graph</name> <name>Import JSONRDD to Dataset kryo</name>
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class> <class>eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
</spark>
<ok to="ResolveRelations"/>
<error to="Kill"/>
</action>
<action name="ResolveRelations">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Resolve Relations in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -60,9 +34,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--master</arg><arg>yarn</arg> <arg>--master</arg><arg>yarn</arg>
<arg>--relationPath</arg><arg>${targetPath}/extracted/relation</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--workingPath</arg><arg>${targetPath}/resolved/</arg> <arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--entityPath</arg><arg>${targetPath}/dedup</arg>
</spark> </spark>
<ok to="CreateSummaries"/> <ok to="CreateSummaries"/>
<error to="Kill"/> <error to="Kill"/>
@ -87,7 +60,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--master</arg><arg>yarn</arg> <arg>--master</arg><arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetPath}/dedup</arg> <arg>--sourcePath</arg><arg>${targetPath}/entities</arg>
<arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg> <arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg>
</spark> </spark>
<ok to="CreateScholix"/> <ok to="CreateScholix"/>
@ -114,7 +87,7 @@
<arg>--master</arg><arg>yarn</arg> <arg>--master</arg><arg>yarn</arg>
<arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg> <arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg>
<arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg> <arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg>
<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg> <arg>--relationPath</arg><arg>${targetPath}/relation</arg>
</spark> </spark>
<ok to="DropJSONPath"/> <ok to="DropJSONPath"/>
@ -182,9 +155,5 @@
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<end name="End"/> <end name="End"/>
</workflow-app> </workflow-app>

View File

@ -0,0 +1,62 @@
<workflow-app name="Resolve Relation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>entityPath</name>
<description>the path of deduplicate Entities</description>
</property>
<property>
<name>relationPath</name>
<description>the path of relation unresolved</description>
</property>
<property>
<name>targetPath</name>
<description>the path of relation unresolved</description>
</property>
</parameters>
<start to="DropRelFolder"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DropRelFolder">
<fs>
<delete path='${targetPath}/relation'/>
<delete path='${targetPath}/relation_resolved'/>
<delete path='${targetPath}/resolvedSource'/>
<delete path='${targetPath}/resolvedPid'/>
</fs>
<ok to="ResolveRelations"/>
<error to="Kill"/>
</action>
<action name="ResolveRelations">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Resolve Relations in raw graph</name>
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=3000
--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>--relationPath</arg><arg>${relationPath}</arg>
<arg>--workingPath</arg><arg>${targetPath}</arg>
<arg>--entityPath</arg><arg>${entityPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,120 +0,0 @@
<workflow-app name="Create Raw Graph Step 2: Map XML to OAF Entities" 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>
</parameters>
<start to="ExtractDLIPublication"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractDLIPublication">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Publication)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>publication</arg>
</spark>
<ok to="ExtractDLIDataset"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Dataset)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>dataset</arg>
</spark>
<ok to="ExtractDLIUnknown"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIUnknown">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Unknown)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>unknown</arg>
</spark>
<ok to="ExtractDLIRelation"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIRelation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract DLI Entities (Relation)</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=5000
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>-e</arg><arg>relation</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,61 +0,0 @@
<workflow-app name="Create Raw Graph Final Step: Construct the Scholexplorer Raw Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>targetPath</name>
<description>the source 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>entity</name>
<description>the entity to be merged</description>
</property>
</parameters>
<start to="DeleteTargetPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteTargetPath">
<fs>
<mkdir path="${targetPath}"/>
<delete path='${targetPath}/${entity}'/>
</fs>
<ok to="MergeDLIEntities"/>
<error to="Kill"/>
</action>
<action name="MergeDLIEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Merge ${entity}</name>
<class>eu.dnetlib.dhp.sx.graph.SparkScholexplorerCreateRawGraphJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/${entity}</arg>
<arg>--targetPath</arg><arg>${targetPath}/${entity}</arg>
<arg>--entity</arg><arg>${entity}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -24,6 +24,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -250,7 +251,24 @@ public class MappersTest {
final Relation r1 = (Relation) list.get(1); final Relation r1 = (Relation) list.get(1);
final Relation r2 = (Relation) list.get(2); final Relation r2 = (Relation) list.get(2);
assertEquals(d.getId(), r1.getSource());
assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget());
assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType());
assertEquals(ModelConstants.OUTCOME, r1.getSubRelType());
assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass());
assertTrue(r1.getValidated());
assertEquals("2020-01-01", r1.getValidationDate());
assertEquals(d.getId(), r2.getTarget());
assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource());
assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType());
assertEquals(ModelConstants.OUTCOME, r2.getSubRelType());
assertEquals(ModelConstants.PRODUCES, r2.getRelClass());
assertTrue(r2.getValidated());
assertEquals("2020-01-01", r2.getValidationDate());
assertValidId(d.getId()); assertValidId(d.getId());
assertEquals("50|doi_________::000374d100a9db469bd42b69dbb40b36", d.getId());
assertEquals(2, d.getOriginalId().size()); assertEquals(2, d.getOriginalId().size());
assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
assertValidId(d.getCollectedfrom().get(0).getKey()); assertValidId(d.getCollectedfrom().get(0).getKey());
@ -304,10 +322,12 @@ public class MappersTest {
}); });
assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid()); assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid());
assertNotNull(d.getInstance().get(0).getPid()); assertNotNull(d.getInstance().get(0).getPid());
assertTrue(d.getInstance().get(0).getPid().isEmpty()); assertFalse(d.getInstance().get(0).getPid().isEmpty());
assertEquals("doi", d.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid()); assertEquals("doi", d.getInstance().get(0).getPid().get(0).getQualifier().getClassid());
assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getAlternateIdentifier().get(0).getValue()); assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getPid().get(0).getValue());
assertTrue(d.getInstance().get(0).getAlternateIdentifier().isEmpty());
assertValidId(r1.getSource()); assertValidId(r1.getSource());
assertValidId(r1.getTarget()); assertValidId(r1.getTarget());
@ -561,6 +581,31 @@ public class MappersTest {
assertNotNull(d.getInstance().get(0).getUrl()); assertNotNull(d.getInstance().get(0).getUrl());
} }
@Test
void testEnermaps() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Dataset);
final Dataset d = (Dataset) list.get(0);
assertValidId(d.getId());
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertEquals(1, d.getAuthor().size());
assertEquals(1, d.getInstance().size());
assertNotNull(d.getInstance().get(0).getUrl());
assertNotNull(d.getContext());
assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
}
@Test @Test
void testClaimFromCrossref() throws IOException { void testClaimFromCrossref() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
@ -713,12 +758,11 @@ public class MappersTest {
} }
private void assertValidId(final String id) { private void assertValidId(final String id) {
System.out.println(id); // System.out.println(id);
assertEquals(49, id.length()); assertEquals(49, id.length());
assertEquals('|', id.charAt(2)); assertEquals(IdentifierFactory.ID_PREFIX_SEPARATOR, id.substring(2, 3));
assertEquals(':', id.charAt(15)); assertEquals(IdentifierFactory.ID_SEPARATOR, id.substring(15, 17));
assertEquals(':', id.charAt(16));
} }
private List<String> vocs() throws IOException { private List<String> vocs() throws IOException {

View File

@ -9,6 +9,41 @@
<artifactId>dhp-graph-provision</artifactId> <artifactId>dhp-graph-provision</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>
<args>
<arg>-Xmax-classfile-name</arg>
<arg>200</arg>
</args>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies> <dependencies>
<dependency> <dependency>

View File

@ -71,6 +71,9 @@ public class DropAndCreateESIndex {
log.info(STATUS_CODE_TEXT, response.getStatusLine()); log.info(STATUS_CODE_TEXT, response.getStatusLine());
} }
log.info("Sleeping 60 seconds to avoid to lost the creation of index request");
Thread.sleep(60000);
try (CloseableHttpClient client = HttpClients.createDefault()) { try (CloseableHttpClient client = HttpClients.createDefault()) {
final String summaryConf = IOUtils final String summaryConf = IOUtils

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@ -21,6 +21,7 @@ import com.google.common.collect.Lists;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;

View File

@ -13,7 +13,7 @@ echo "Getting file from " $SCRIPT_PATH
hdfs dfs -copyToLocal $SCRIPT_PATH hdfs dfs -copyToLocal $SCRIPT_PATH
echo "Creating indicators" echo "Creating indicators"
impala-shell -d ${TARGET} -q "invalidate metadata" impala-shell -q "invalidate metadata"
impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f - impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f -
cat step16_7-createIndicatorsTables.sql | impala-shell -d $TARGET -f - cat step16_7-createIndicatorsTables.sql | impala-shell -d $TARGET -f -
echo "Indicators created" echo "Indicators created"

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@ -57,12 +57,14 @@ UNION ALL
SELECT * FROM ${stats_db_name}.software_sources SELECT * FROM ${stats_db_name}.software_sources
UNION ALL UNION ALL
SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
--
-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; create table ${stats_db_name}.result_orcid as
-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS; select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid
-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; from (
-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; SELECT substr(res.id, 4) as id, auth_pid.value as orcid
-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; FROM ${openaire_db_name}.result res
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS; LATERAL VIEW explode(author) a as auth
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS; LATERAL VIEW explode(auth.pid) ap as auth_pid
LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type
WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res

View File

@ -34,12 +34,3 @@ union all
select * from ${stats_db_name}.software_refereed select * from ${stats_db_name}.software_refereed
union all union all
select * from ${stats_db_name}.otherresearchproduct_refereed; select * from ${stats_db_name}.otherresearchproduct_refereed;
--
-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS;

View File

@ -40,3 +40,197 @@ join result_instance ri on ri.id = p.id
join datasource on datasource.id = ri.hostedby join datasource on datasource.id = ri.hostedby
where datasource.id like '%doajarticles%') tmp where datasource.id like '%doajarticles%') tmp
on p.id= tmp.id; on p.id= tmp.id;
create table indi_project_pubs_count stored as parquet as
select pr.id id, count(p.id) total_pubs from project_results pr
join publication p on p.id=pr.result
group by pr.id;
create table indi_project_datasets_count stored as parquet as
select pr.id id, count(d.id) total_datasets from project_results pr
join dataset d on d.id=pr.result
group by pr.id;
create table indi_project_software_count stored as parquet as
select pr.id id, count(s.id) total_software from project_results pr
join software s on s.id=pr.result
group by pr.id;
create table indi_project_otherresearch_count stored as parquet as
select pr.id id, count(o.id) total_other from project_results pr
join otherresearchproduct o on o.id=pr.result
group by pr.id;
create table indi_pub_avg_year_country_oa stored as parquet as
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
from
(SELECT year, country, SUM(CASE
WHEN bestlicence='Open Access' THEN 1
ELSE 0
END) AS OpenAccess, SUM(CASE
WHEN bestlicence<>'Open Access' THEN 1
ELSE 0
END) AS NonOpenAccess
FROM publication p
join result_organization ro on p.id=ro.id
join organization o on o.id=ro.organization
where cast(year as int)>=2003 and cast(year as int)<=2021
group by year, country) tmp;
create table indi_dataset_avg_year_country_oa stored as parquet as
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
from
(SELECT year, country, SUM(CASE
WHEN bestlicence='Open Access' THEN 1
ELSE 0
END) AS OpenAccess, SUM(CASE
WHEN bestlicence<>'Open Access' THEN 1
ELSE 0
END) AS NonOpenAccess
FROM dataset d
join result_organization ro on d.id=ro.id
join organization o on o.id=ro.organization
where cast(year as int)>=2003 and cast(year as int)<=2021
group by year, country) tmp;
create table indi_software_avg_year_country_oa stored as parquet as
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
from
(SELECT year, country, SUM(CASE
WHEN bestlicence='Open Access' THEN 1
ELSE 0
END) AS OpenAccess, SUM(CASE
WHEN bestlicence<>'Open Access' THEN 1
ELSE 0
END) AS NonOpenAccess
FROM software s
join result_organization ro on s.id=ro.id
join SOURCER.organization o on o.id=ro.organization
where cast(year as int)>=2003 and cast(year as int)<=2021
group by year, country) tmp;
create table indi_other_avg_year_country_oa stored as parquet as
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
from
(SELECT year, country, SUM(CASE
WHEN bestlicence='Open Access' THEN 1
ELSE 0
END) AS OpenAccess, SUM(CASE
WHEN bestlicence<>'Open Access' THEN 1
ELSE 0
END) AS NonOpenAccess
FROM otherresearchproduct orp
join result_organization ro on orp.id=ro.id
join organization o on o.id=ro.organization
where cast(year as int)>=2003 and cast(year as int)<=2021
group by year, country) tmp;
create table indi_pub_avg_year_context_oa stored as parquet as
with total as
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc
join context c on pc.concept like concat('%',c.id,'%')
join publication p on p.id=pc.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by c.name, year )
select year, name, round(no_of_pubs/total*100,3) averageofpubs
from total;
create table indi_dataset_avg_year_context_oa stored as parquet as
with total as
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc
join context c on pc.concept like concat('%',c.id,'%')
join dataset p on p.id=pc.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by c.name, year )
select year, name, round(no_of_pubs/total*100,3) averageofdataset
from total;
create table indi_software_avg_year_context_oa stored as parquet as
with total as
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc
join context c on pc.concept like concat('%',c.id,'%')
join software p on p.id=pc.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by c.name, year )
select year, name, round(no_of_pubs/total*100,3) averageofsoftware
from total;
create table indi_other_avg_year_context_oa stored as parquet as
with total as
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc
join context c on pc.concept like concat('%',c.id,'%')
join otherresearchproduct p on p.id=pc.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by c.name, year )
select year, name, round(no_of_pubs/total*100,3) averageofother
from total;
create table indi_other_avg_year_content_oa stored as parquet as
with total as
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
from otherresearchproduct_datasources pd
join datasource d on datasource=d.id
join otherresearchproduct p on p.id=pd.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by d.type, year)
select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct
from total;
create table indi_software_avg_year_content_oa stored as parquet as
with total as
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
from software_datasources pd
join datasource d on datasource=d.id
join software p on p.id=pd.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by d.type, year)
select year, type, round(no_of_pubs/total*100,3) averageOfSoftware
from total;
create table indi_dataset_avg_year_content_oa stored as parquet as
with total as
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
from dataset_datasources pd
join datasource d on datasource=d.id
join dataset p on p.id=pd.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by d.type, year)
select year, type, round(no_of_pubs/total*100,3) averageOfDatasets
from total;
create table indi_pub_avg_year_content_oa stored as parquet as
with total as
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
from publication_datasources pd
join datasource d on datasource=d.id
join publication p on p.id=pd.id
where cast(year as int)>=2003 and cast(year as int)<=2021
group by d.type, year)
select year, type, round(no_of_pubs/total*100,3) averageOfPubs
from total;
create table indi_pub_has_cc_licence stored as parquet as
select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
from publication p
left outer join (select p.id, license.type as lic from publication p
join publication_licenses as license on license.id = p.id
where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
on p.id= tmp.id;
create table indi_pub_has_cc_licence_url stored as parquet as
select distinct p.id, (case when lic_host='' or lic_host is null then 0 else 1 end) as has_cc_license_url
from publication p
left outer join (select p.id, lower(parse_url(license.type, "HOST")) as lic_host
from publication p
join publication_licenses as license on license.id = p.id
WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp
on p.id= tmp.id;
create table indi_pub_has_abstract stored as parquet as
select distinct publication.id, coalesce(abstract, 1) has_abstract
from publication;

View File

@ -90,27 +90,8 @@ FROM ${openaire_db_name}.publication p
where p.datainfo.deletedbyinference = false; where p.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.publication_citations AS CREATE TABLE ${stats_db_name}.publication_citations AS
SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
lateral view explode(p.extrainfo) citations AS citation lateral view explode(p.extrainfo) citations AS citation
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
and p.datainfo.deletedbyinference = false; and p.datainfo.deletedbyinference = false;
-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS;

View File

@ -116,6 +116,13 @@ compute stats TARGET.indi_pub_doi_from_crossref;
create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_gold_oa; compute stats TARGET.indi_pub_gold_oa;
create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig;
create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig;
create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig;
create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig;
create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig;
create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig;
--denorm --denorm
alter table TARGET.result rename to TARGET.res_tmp; alter table TARGET.result rename to TARGET.res_tmp;

View File

@ -41,7 +41,7 @@ FROM ${openaire_db_name}.dataset d
WHERE d.datainfo.deletedbyinference = FALSE; WHERE d.datainfo.deletedbyinference = FALSE;
CREATE TABLE ${stats_db_name}.dataset_citations AS CREATE TABLE ${stats_db_name}.dataset_citations AS
SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.dataset d FROM ${openaire_db_name}.dataset d
LATERAL VIEW explode(d.extrainfo) citations AS citation LATERAL VIEW explode(d.extrainfo) citations AS citation
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
@ -96,20 +96,3 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.subject) subjects AS subject LATERAL VIEW explode(p.subject) subjects AS subject
where p.datainfo.deletedbyinference = false; where p.datainfo.deletedbyinference = false;
--
-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS;

View File

@ -41,7 +41,7 @@ from ${openaire_db_name}.software s
where s.datainfo.deletedbyinference = false; where s.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.software_citations AS CREATE TABLE ${stats_db_name}.software_citations AS
SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.software s FROM ${openaire_db_name}.software s
LATERAL VIEW explode(s.extrainfo) citations as citation LATERAL VIEW explode(s.extrainfo) citations as citation
where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
@ -96,20 +96,3 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.subject) subjects AS subject LATERAL VIEW explode(p.subject) subjects AS subject
where p.datainfo.deletedbyinference = false; where p.datainfo.deletedbyinference = false;
--
-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS;

View File

@ -41,7 +41,7 @@ WHERE o.datainfo.deletedbyinference = FALSE;
-- Otherresearchproduct_citations -- Otherresearchproduct_citations
CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS
SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
and o.datainfo.deletedbyinference = false; and o.datainfo.deletedbyinference = false;
@ -87,20 +87,3 @@ CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS
SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject
where p.datainfo.deletedbyinference = false; where p.datainfo.deletedbyinference = false;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS;

View File

@ -13,11 +13,17 @@ WHERE r.reltype = 'projectOrganization'
and r.datainfo.deletedbyinference = false; and r.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.project_results AS CREATE TABLE ${stats_db_name}.project_results AS
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
FROM ${openaire_db_name}.relation r FROM ${openaire_db_name}.relation r
WHERE r.reltype = 'resultProject' WHERE r.reltype = 'resultProject'
and r.datainfo.deletedbyinference = false; and r.datainfo.deletedbyinference = false;
create table ${stats_db_name}.project_classification as
select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
from ${openaire_db_name}.project p
lateral view explode(p.h2020classification) classifs as class
where p.datainfo.deletedbyinference=false and class.h2020programme is not null;
CREATE TABLE ${stats_db_name}.project_tmp CREATE TABLE ${stats_db_name}.project_tmp
( (
id STRING, id STRING,

View File

@ -130,12 +130,7 @@ WHERE r.reltype = 'resultOrganization'
and r.datainfo.deletedbyinference = false; and r.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.result_projects AS CREATE TABLE ${stats_db_name}.result_projects AS
select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
FROM ${stats_db_name}.result r FROM ${stats_db_name}.result r
JOIN ${stats_db_name}.project_results pr ON r.id = pr.result JOIN ${stats_db_name}.project_results pr ON r.id = pr.result
JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id;
-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS;

View File

@ -17,7 +17,9 @@ CREATE TABLE ${stats_db_name}.datasource_tmp
`latitude` STRING, `latitude` STRING,
`longitude` STRING, `longitude` STRING,
`websiteurl` STRING, `websiteurl` STRING,
`compatibility` STRING `compatibility` STRING,
issn_printed STRING,
issn_online STRING
) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
-- Insert statement that takes into account the piwik_id of the openAIRE graph -- Insert statement that takes into account the piwik_id of the openAIRE graph
@ -32,7 +34,9 @@ SELECT substr(d1.id, 4) AS id,
d1.latitude.value AS latitude, d1.latitude.value AS latitude,
d1.longitude.value AS longitude, d1.longitude.value AS longitude,
d1.websiteurl.value AS websiteurl, d1.websiteurl.value AS websiteurl,
d1.openairecompatibility.classid AS compatibility d1.openairecompatibility.classid AS compatibility,
d1.journal.issnprinted AS issn_printed,
d1.journal.issnonline AS issn_online
FROM ${openaire_db_name}.datasource d1 FROM ${openaire_db_name}.datasource d1
LEFT OUTER JOIN LEFT OUTER JOIN
(SELECT id, split(originalidd, '\\:')[1] as piwik_id (SELECT id, split(originalidd, '\\:')[1] as piwik_id
@ -51,7 +55,7 @@ CREATE TABLE ${stats_db_name}.dual
INSERT INTO ${stats_db_name}.dual INSERT INTO ${stats_db_name}.dual
VALUES ('X'); VALUES ('X');
INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`, INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`,
`piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`) `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`)
SELECT 'other', SELECT 'other',
'Other', 'Other',
'Repository', 'Repository',
@ -62,7 +66,9 @@ SELECT 'other',
NULL, NULL,
NULL, NULL,
NULL, NULL,
'unknown' 'unknown',
null,
null
FROM ${stats_db_name}.dual FROM ${stats_db_name}.dual
WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository');
DROP TABLE ${stats_db_name}.dual; DROP TABLE ${stats_db_name}.dual;
@ -98,12 +104,3 @@ where d.datainfo.deletedbyinference = false;
CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
SELECT datasource AS id, id AS result SELECT datasource AS id, id AS result
FROM ${stats_db_name}.result_datasources; FROM ${stats_db_name}.result_datasources;
-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS;

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@ -741,7 +741,7 @@
<mockito-core.version>3.3.3</mockito-core.version> <mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version> <mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version> <vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.6.14]</dhp-schemas.version> <dhp-schemas.version>[2.7.15]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version> <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version> <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version> <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>