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Code Issues Pull Requests Projects Releases Wiki Activity

code refactor see ticket #7065

This commit is contained in:
Sandro La Bruzzo 2021-10-12 08:11:53 +02:00
parent 8f99d2af86
commit 5606014b17
32 changed files with 155 additions and 160 deletions
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9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/BioDBToOAF.scala
View File

@ -1,14 +1,12 @@
package eu.dnetlib.dhp.sx.graph.bio
package eu.dnetllib.dhp.sx.bio
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import scala.collection.JavaConverters._
import collection.JavaConverters._
object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {}
@ -231,7 +229,6 @@ object BioDBToOAF {
}
def generate_unresolved_id(pid: String, pidType: String): String = {
s"unresolved::$pid::$pidType"
}

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/SparkTransformBioDatabaseToOAF.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala
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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.sx.graph.bio
package eu.dnetllib.dhp.sx.bio
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@ -33,7 +33,6 @@ object SparkTransformBioDatabaseToOAF {
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
import spark.implicits._
database.toUpperCase() match {
case "UNIPROT" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath)

14
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.sx.graph.ebi
package eu.dnetllib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
@ -90,10 +90,6 @@ object SparkCreateBaselineDataFrame {
}
def downloadBaseLineUpdate(baselinePath: String, hdfsServerUri: String): Unit = {
@ -153,7 +149,7 @@ object SparkCreateBaselineDataFrame {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val log: Logger = LoggerFactory.getLogger(getClass)
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json")))
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json")))
parser.parseArgument(args)
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
@ -175,9 +171,9 @@ object SparkCreateBaselineDataFrame {
.config(conf)
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
import spark.implicits._
val sc = spark.sparkContext
import spark.implicits._
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
@ -186,7 +182,7 @@ object SparkCreateBaselineDataFrame {
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline_ftp", 2000)
val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => {
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
new PMParser(xml)

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala
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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.sx.graph.ebi
package eu.dnetllib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet
@ -60,6 +60,7 @@ object SparkDownloadEBILinks {
requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
}
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)

15
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala
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@ -1,15 +1,14 @@
package eu.dnetlib.dhp.sx.graph.ebi
package eu.dnetllib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.graph.bio
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
import eu.dnetllib.dhp.sx.bio.BioDBToOAF
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkEBILinksToOaf {
def main(args: Array[String]): Unit = {
@ -24,12 +23,12 @@ object SparkEBILinksToOaf {
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
import spark.implicits._
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
import spark.implicits._
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
val ebLinks: Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links != null)

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMArticle.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMArticle.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
package eu.dnetllib.dhp.sx.bio.pubmed;
import java.io.Serializable;
import java.util.ArrayList;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMAuthor.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMAuthor.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
package eu.dnetllib.dhp.sx.bio.pubmed;
import java.io.Serializable;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMGrant.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMGrant.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
package eu.dnetllib.dhp.sx.bio.pubmed;
public class PMGrant {

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMJournal.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMJournal.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
package eu.dnetllib.dhp.sx.bio.pubmed;
import java.io.Serializable;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMParser.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMParser.scala
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@ -1,4 +1,4 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed
package eu.dnetllib.dhp.sx.bio.pubmed
import scala.xml.MetaData
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMSubject.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMSubject.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
package eu.dnetllib.dhp.sx.bio.pubmed;
public class PMSubject {
private String value;

15
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PubMedToOaf.scala
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@ -1,11 +1,12 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed
package eu.dnetllib.dhp.sx.bio.pubmed
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
import eu.dnetlib.dhp.schema.oaf._
import scala.collection.JavaConverters._
import java.util.regex.Pattern
import scala.collection.JavaConverters._
object PubMedToOaf {
@ -71,7 +72,7 @@ object PubMedToOaf {
if (article.getPublicationTypes == null)
return null
val i = new Instance
var pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
if (pidList == null)
return null
@ -105,7 +106,7 @@ object PubMedToOaf {
if (alternateIdentifier != null)
i.setAlternateIdentifier(List(alternateIdentifier).asJava)
result.setInstance(List(i).asJava)
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection breakOut)
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
val urlLists: List[String] = pidList
.map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
.filter(t => t._1.nonEmpty)
@ -136,7 +137,7 @@ object PubMedToOaf {
}
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection breakOut)
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection.breakOut)
if (subjects != null)
result.setSubject(subjects.asJava)
@ -148,7 +149,7 @@ object PubMedToOaf {
author.setFullname(a.getFullName)
author.setRank(index + 1)
author
}(collection breakOut)
}(collection.breakOut)
if (authors != null && authors.nonEmpty)

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/config-default.xml → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/config-default.xml
View File

13
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
View File

@ -1,13 +1,9 @@
<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="Download_Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>baselineWorkingPath</name>
<description>the Baseline Working Path</description>
</property>
<property>
<name>targetPath</name>
<description>the Target Path</description>
</property>
<property>
<name>isLookupUrl</name>
<description>The IS lookUp service endopoint</description>
@ -24,8 +20,8 @@
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Convert Baseline to Dataset</name>
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkCreateBaselineDataFrame</class>
<name>Convert Baseline to OAF Dataset</name>
<class>eu.dnetllib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
@ -38,9 +34,10 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--targetPath</arg><arg>${baselineWorkingPath}/transformed</arg>
<arg>--master</arg><arg>yarn</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

15
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala → dhp-workflows/dhp-aggregation/src/test/java/eu/dnetllib/dhp/sx/bio/BioScholixTest.scala
View File

@ -1,13 +1,10 @@
package eu.dnetlib.dhp.sx.graph.bio.pubmed
package eu.dnetllib.dhp.sx.bio
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{CleaningFunctions, OafMapperUtils, PidType}
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo
import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
@ -55,7 +52,7 @@ class BioScholixTest extends AbstractVocabularyTest{
@Test
def testEBIData() = {
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")).mkString
val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
}
@ -65,7 +62,7 @@ class BioScholixTest extends AbstractVocabularyTest{
def testPubmedToOaf(): Unit = {
assertNotNull(vocabularies)
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
val records:String =Source.fromInputStream(getClass.getResourceAsStream("pubmed_dump")).mkString
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")).mkString
val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies))
assertEquals(10, r.size)
assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p)))

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ls_result
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed_dump → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved
View File

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump
View File

9
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java
View File

@ -84,7 +84,8 @@ public class PropagationConstant {
return di;
}
public static Qualifier getQualifier(String inference_class_id, String inference_class_name, String qualifierSchema) {
public static Qualifier getQualifier(String inference_class_id, String inference_class_name,
String qualifierSchema) {
Qualifier pa = new Qualifier();
pa.setClassid(inference_class_id);
pa.setClassname(inference_class_name);
@ -108,7 +109,11 @@ public class PropagationConstant {
r.setRelClass(rel_class);
r.setRelType(rel_type);
r.setSubRelType(subrel_type);
r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name, ModelConstants.DNET_PROVENANCE_ACTIONS));
r
.setDataInfo(
getDataInfo(
inference_provenance, inference_class_id, inference_class_name,
ModelConstants.DNET_PROVENANCE_ACTIONS));
return r;
}

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java
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@ -173,7 +173,10 @@ public class SparkOrcidToResultFromSemRelJob {
if (toaddpid) {
StructuredProperty p = new StructuredProperty();
p.setValue(autoritative_author.getOrcid());
p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
p
.setQualifier(
getQualifier(
ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
p
.setDataInfo(
getDataInfo(

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java
View File

@ -10,7 +10,6 @@ import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -22,6 +21,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java
View File

@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala
View File

@ -1,7 +1,6 @@
package eu.dnetlib.dhp.sx.graph.pangaea
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf
import org.apache.spark.rdd.RDD
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}

11
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
View File

@ -84,13 +84,15 @@ public class IndexRecordTransformerTest {
@Test
public void testForEOSCFutureTraining() throws IOException, TransformerException {
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
final String record = IOUtils
.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
testRecordTransformation(record);
}
@Test
public void testForEOSCFutureAirQualityCopernicus() throws IOException, TransformerException {
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml"));
final String record = IOUtils
.toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml"));
testRecordTransformation(record);
}
@ -102,12 +104,11 @@ public class IndexRecordTransformerTest {
@Test
public void testForEOSCFutureB2SharePlotRelatedORP() throws IOException, TransformerException {
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml"));
final String record = IOUtils
.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml"));
testRecordTransformation(record);
}
private void testRecordTransformation(final String record) throws IOException, TransformerException {
final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"));