Merge branch 'beta' into affiliationPropagation
This commit is contained in:
commit
1790fa2d44
|
|
@ -3,8 +3,6 @@
|
||||||
*.iws
|
*.iws
|
||||||
*.ipr
|
*.ipr
|
||||||
*.iml
|
*.iml
|
||||||
*.ipr
|
|
||||||
*.iws
|
|
||||||
*~
|
*~
|
||||||
.vscode
|
.vscode
|
||||||
.metals
|
.metals
|
||||||
|
|
|
||||||
|
|
@ -22,9 +22,20 @@
|
||||||
<id>dnet45-releases</id>
|
<id>dnet45-releases</id>
|
||||||
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
|
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
|
||||||
</repository>
|
</repository>
|
||||||
|
<site>
|
||||||
|
<id>DHPSite</id>
|
||||||
|
<url>${dhp.site.stage.path}/dhp-build/dhp-code-style</url>
|
||||||
|
</site>
|
||||||
</distributionManagement>
|
</distributionManagement>
|
||||||
|
|
||||||
<build>
|
<build>
|
||||||
|
<extensions>
|
||||||
|
<extension>
|
||||||
|
<groupId>org.apache.maven.wagon</groupId>
|
||||||
|
<artifactId>wagon-ssh</artifactId>
|
||||||
|
<version>2.10</version>
|
||||||
|
</extension>
|
||||||
|
</extensions>
|
||||||
<pluginManagement>
|
<pluginManagement>
|
||||||
<plugins>
|
<plugins>
|
||||||
<plugin>
|
<plugin>
|
||||||
|
|
@ -35,7 +46,7 @@
|
||||||
<plugin>
|
<plugin>
|
||||||
<groupId>org.apache.maven.plugins</groupId>
|
<groupId>org.apache.maven.plugins</groupId>
|
||||||
<artifactId>maven-site-plugin</artifactId>
|
<artifactId>maven-site-plugin</artifactId>
|
||||||
<version>3.7.1</version>
|
<version>3.9.1</version>
|
||||||
</plugin>
|
</plugin>
|
||||||
</plugins>
|
</plugins>
|
||||||
</pluginManagement>
|
</pluginManagement>
|
||||||
|
|
@ -43,6 +54,7 @@
|
||||||
|
|
||||||
<properties>
|
<properties>
|
||||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||||
|
<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
|
||||||
</properties>
|
</properties>
|
||||||
|
|
||||||
</project>
|
</project>
|
||||||
|
|
@ -0,0 +1,21 @@
|
||||||
|
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||||
|
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
|
||||||
|
name="DHP-Aggregation">
|
||||||
|
<skin>
|
||||||
|
<groupId>org.apache.maven.skins</groupId>
|
||||||
|
<artifactId>maven-fluido-skin</artifactId>
|
||||||
|
<version>1.8</version>
|
||||||
|
</skin>
|
||||||
|
<poweredBy>
|
||||||
|
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
|
||||||
|
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
|
||||||
|
</poweredBy>
|
||||||
|
<body>
|
||||||
|
<links>
|
||||||
|
<item name="Code" href="https://code-repo.d4science.org/" />
|
||||||
|
</links>
|
||||||
|
<menu ref="modules" />
|
||||||
|
<menu ref="reports"/>
|
||||||
|
</body>
|
||||||
|
</project>
|
||||||
|
|
@ -10,6 +10,9 @@
|
||||||
<packaging>pom</packaging>
|
<packaging>pom</packaging>
|
||||||
|
|
||||||
<description>This module is a container for the build tools used in dnet-hadoop</description>
|
<description>This module is a container for the build tools used in dnet-hadoop</description>
|
||||||
|
<properties>
|
||||||
|
<maven.javadoc.skip>true</maven.javadoc.skip>
|
||||||
|
</properties>
|
||||||
|
|
||||||
<modules>
|
<modules>
|
||||||
<module>dhp-code-style</module>
|
<module>dhp-code-style</module>
|
||||||
|
|
@ -17,4 +20,12 @@
|
||||||
<module>dhp-build-properties-maven-plugin</module>
|
<module>dhp-build-properties-maven-plugin</module>
|
||||||
</modules>
|
</modules>
|
||||||
|
|
||||||
|
|
||||||
|
<distributionManagement>
|
||||||
|
<site>
|
||||||
|
<id>DHPSite</id>
|
||||||
|
<url>${dhp.site.stage.path}/dhp-build/</url>
|
||||||
|
</site>
|
||||||
|
</distributionManagement>
|
||||||
|
|
||||||
</project>
|
</project>
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,22 @@
|
||||||
|
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||||
|
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
|
||||||
|
name="DHP-Aggregation">
|
||||||
|
<skin>
|
||||||
|
<groupId>org.apache.maven.skins</groupId>
|
||||||
|
<artifactId>maven-fluido-skin</artifactId>
|
||||||
|
<version>1.8</version>
|
||||||
|
</skin>
|
||||||
|
<poweredBy>
|
||||||
|
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
|
||||||
|
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
|
||||||
|
</poweredBy>
|
||||||
|
<body>
|
||||||
|
<links>
|
||||||
|
<item name="Code" href="https://code-repo.d4science.org/" />
|
||||||
|
</links>
|
||||||
|
|
||||||
|
<menu ref="modules" />
|
||||||
|
<menu ref="reports"/>
|
||||||
|
</body>
|
||||||
|
</project>
|
||||||
|
|
@ -13,7 +13,51 @@
|
||||||
<artifactId>dhp-common</artifactId>
|
<artifactId>dhp-common</artifactId>
|
||||||
<packaging>jar</packaging>
|
<packaging>jar</packaging>
|
||||||
|
|
||||||
|
<distributionManagement>
|
||||||
|
<site>
|
||||||
|
<id>DHPSite</id>
|
||||||
|
<url>${dhp.site.stage.path}/dhp-common</url>
|
||||||
|
</site>
|
||||||
|
</distributionManagement>
|
||||||
|
|
||||||
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
|
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
|
||||||
|
<build>
|
||||||
|
<plugins>
|
||||||
|
<plugin>
|
||||||
|
<groupId>net.alchim31.maven</groupId>
|
||||||
|
<artifactId>scala-maven-plugin</artifactId>
|
||||||
|
<version>${net.alchim31.maven.version}</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>
|
||||||
|
<execution>
|
||||||
|
<id>scala-doc</id>
|
||||||
|
<phase>process-resources</phase> <!-- or wherever -->
|
||||||
|
<goals>
|
||||||
|
<goal>doc</goal>
|
||||||
|
</goals>
|
||||||
|
</execution>
|
||||||
|
</executions>
|
||||||
|
<configuration>
|
||||||
|
<scalaVersion>${scala.version}</scalaVersion>
|
||||||
|
</configuration>
|
||||||
|
</plugin>
|
||||||
|
</plugins>
|
||||||
|
|
||||||
|
</build>
|
||||||
|
|
||||||
<dependencies>
|
<dependencies>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
|
||||||
final String syn = arr[2].trim();
|
final String syn = arr[2].trim();
|
||||||
|
|
||||||
vocs.addSynonyms(vocId, termId, syn);
|
vocs.addSynonyms(vocId, termId, syn);
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// add the term names as synonyms
|
||||||
|
vocs.vocs.values().forEach(voc -> {
|
||||||
|
voc.getTerms().values().forEach(term -> {
|
||||||
|
voc.addSynonym(term.getName().toLowerCase(), term.getId());
|
||||||
|
});
|
||||||
|
});
|
||||||
|
|
||||||
return vocs;
|
return vocs;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
|
||||||
import com.google.common.collect.Lists;
|
import com.google.common.collect.Lists;
|
||||||
import com.google.common.collect.Sets;
|
import com.google.common.collect.Sets;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
|
||||||
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
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.*;
|
||||||
|
|
@ -86,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
||||||
}
|
}
|
||||||
|
|
||||||
public static <T extends Oaf> boolean filter(T value) {
|
public static <T extends Oaf> boolean filter(T value) {
|
||||||
|
if (Boolean.TRUE
|
||||||
|
.equals(
|
||||||
|
Optional
|
||||||
|
.ofNullable(value)
|
||||||
|
.map(
|
||||||
|
o -> Optional
|
||||||
|
.ofNullable(o.getDataInfo())
|
||||||
|
.map(
|
||||||
|
d -> Optional
|
||||||
|
.ofNullable(d.getInvisible())
|
||||||
|
.orElse(true))
|
||||||
|
.orElse(true))
|
||||||
|
.orElse(true))) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
if (value instanceof Datasource) {
|
if (value instanceof Datasource) {
|
||||||
// nothing to evaluate here
|
// nothing to evaluate here
|
||||||
} else if (value instanceof Project) {
|
} else if (value instanceof Project) {
|
||||||
|
|
@ -115,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
||||||
return true;
|
return true;
|
||||||
}
|
}
|
||||||
|
|
||||||
public static <T extends Oaf> T cleanup(T value) {
|
public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
|
||||||
if (value instanceof Datasource) {
|
if (value instanceof Datasource) {
|
||||||
// nothing to clean here
|
// nothing to clean here
|
||||||
} else if (value instanceof Project) {
|
} else if (value instanceof Project) {
|
||||||
|
|
@ -212,6 +230,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
||||||
.map(GraphCleaningFunctions::cleanValue)
|
.map(GraphCleaningFunctions::cleanValue)
|
||||||
.collect(Collectors.toList()));
|
.collect(Collectors.toList()));
|
||||||
}
|
}
|
||||||
|
if (Objects.nonNull(r.getFormat())) {
|
||||||
|
r
|
||||||
|
.setFormat(
|
||||||
|
r
|
||||||
|
.getFormat()
|
||||||
|
.stream()
|
||||||
|
.map(GraphCleaningFunctions::cleanValue)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
}
|
||||||
if (Objects.nonNull(r.getDescription())) {
|
if (Objects.nonNull(r.getDescription())) {
|
||||||
r
|
r
|
||||||
.setDescription(
|
.setDescription(
|
||||||
|
|
@ -234,6 +261,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
||||||
if (Objects.nonNull(r.getInstance())) {
|
if (Objects.nonNull(r.getInstance())) {
|
||||||
|
|
||||||
for (Instance i : r.getInstance()) {
|
for (Instance i : r.getInstance()) {
|
||||||
|
if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
|
||||||
|
if (r instanceof Publication) {
|
||||||
|
i
|
||||||
|
.setInstancetype(
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||||
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||||
|
} else if (r instanceof Dataset) {
|
||||||
|
i
|
||||||
|
.setInstancetype(
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||||
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||||
|
} else if (r instanceof Software) {
|
||||||
|
i
|
||||||
|
.setInstancetype(
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||||
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||||
|
} else if (r instanceof OtherResearchProduct) {
|
||||||
|
i
|
||||||
|
.setInstancetype(
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||||
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
if (Objects.nonNull(i.getPid())) {
|
if (Objects.nonNull(i.getPid())) {
|
||||||
i.setPid(processPidCleaning(i.getPid()));
|
i.setPid(processPidCleaning(i.getPid()));
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,72 @@
|
||||||
|
package eu.dnetlib.dhp.application
|
||||||
|
|
||||||
|
import scala.io.Source
|
||||||
|
|
||||||
|
/**
|
||||||
|
* This is the main Interface SparkApplication
|
||||||
|
* where all the Spark Scala class should inherit
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
trait SparkScalaApplication {
|
||||||
|
/**
|
||||||
|
* This is the path in the classpath of the json
|
||||||
|
* describes all the argument needed to run
|
||||||
|
*/
|
||||||
|
val propertyPath: String
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Utility to parse the arguments using the
|
||||||
|
* property json in the classpath identified from
|
||||||
|
* the variable propertyPath
|
||||||
|
*
|
||||||
|
* @param args the list of arguments
|
||||||
|
*/
|
||||||
|
def parseArguments(args: Array[String]): ArgumentApplicationParser = {
|
||||||
|
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString)
|
||||||
|
parser.parseArgument(args)
|
||||||
|
parser
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Here all the spark applications runs this method
|
||||||
|
* where the whole logic of the spark node is defined
|
||||||
|
*/
|
||||||
|
def run(): Unit
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
import org.apache.spark.SparkConf
|
||||||
|
import org.apache.spark.sql.SparkSession
|
||||||
|
import org.slf4j.Logger
|
||||||
|
|
||||||
|
abstract class AbstractScalaApplication (val propertyPath:String, val args:Array[String], log:Logger) extends SparkScalaApplication {
|
||||||
|
|
||||||
|
var parser: ArgumentApplicationParser = null
|
||||||
|
|
||||||
|
var spark:SparkSession = null
|
||||||
|
|
||||||
|
|
||||||
|
def initialize():SparkScalaApplication = {
|
||||||
|
parser = parseArguments(args)
|
||||||
|
spark = createSparkSession()
|
||||||
|
this
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Utility for creating a spark session starting from parser
|
||||||
|
*
|
||||||
|
* @return a spark Session
|
||||||
|
*/
|
||||||
|
private def createSparkSession():SparkSession = {
|
||||||
|
require(parser!= null)
|
||||||
|
|
||||||
|
val conf:SparkConf = new SparkConf()
|
||||||
|
val master = parser.get("master")
|
||||||
|
log.info(s"Creating Spark session: Master: $master")
|
||||||
|
SparkSession.builder().config(conf)
|
||||||
|
.appName(getClass.getSimpleName)
|
||||||
|
.master(master)
|
||||||
|
.getOrCreate()
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -107,7 +107,7 @@ class OafMapperUtilsTest {
|
||||||
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
|
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
|
||||||
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
|
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
|
||||||
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
|
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
|
||||||
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
|
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
|
||||||
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
|
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
|
||||||
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
|
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
|
||||||
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());
|
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());
|
||||||
|
|
|
||||||
|
|
@ -1,69 +0,0 @@
|
||||||
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
|
|
||||||
.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
|
|
||||||
.map(p => p._1._2)
|
|
||||||
.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,86 +0,0 @@
|
||||||
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])
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -7,3 +7,6 @@ log4j.appender.A1=org.apache.log4j.ConsoleAppender
|
||||||
# A1 uses PatternLayout.
|
# A1 uses PatternLayout.
|
||||||
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
|
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
|
||||||
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
|
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
|
||||||
|
|
||||||
|
log4j.logger.org.apache.spark=FATAL
|
||||||
|
log4j.logger.org.spark_project=FATAL
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,134 @@
|
||||||
|
package eu.dnetlib.dhp.datacite
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
|
||||||
|
|
||||||
|
import java.io.InputStream
|
||||||
|
import java.time.format.DateTimeFormatter
|
||||||
|
import java.util.Locale
|
||||||
|
import java.util.regex.Pattern
|
||||||
|
import scala.io.Source
|
||||||
|
|
||||||
|
/**
|
||||||
|
* This class represent the dataModel of the input Dataset of Datacite
|
||||||
|
* @param doi THE DOI
|
||||||
|
* @param timestamp timestamp of last update date
|
||||||
|
* @param isActive the record is active or deleted
|
||||||
|
* @param json the json native records
|
||||||
|
*/
|
||||||
|
case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {}
|
||||||
|
|
||||||
|
/*
|
||||||
|
The following class are utility class used for the mapping from
|
||||||
|
json datacite to OAF Shema
|
||||||
|
*/
|
||||||
|
case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {}
|
||||||
|
|
||||||
|
case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
|
||||||
|
|
||||||
|
case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {}
|
||||||
|
|
||||||
|
case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
|
||||||
|
|
||||||
|
case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
|
||||||
|
|
||||||
|
case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
|
||||||
|
|
||||||
|
case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {}
|
||||||
|
|
||||||
|
case class DateType(date: Option[String], dateType: Option[String]) {}
|
||||||
|
|
||||||
|
case class OAFRelations(relation:String, inverse:String, relType:String)
|
||||||
|
|
||||||
|
|
||||||
|
class DataciteModelConstants extends Serializable {
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
object DataciteModelConstants {
|
||||||
|
|
||||||
|
val REL_TYPE_VALUE:String = "resultResult"
|
||||||
|
val DATE_RELATION_KEY = "RelationDate"
|
||||||
|
val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter"
|
||||||
|
val DOI_CLASS = "doi"
|
||||||
|
val SUBJ_CLASS = "keywords"
|
||||||
|
val DATACITE_NAME = "Datacite"
|
||||||
|
val dataInfo: DataInfo = dataciteDataInfo("0.9")
|
||||||
|
val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME)
|
||||||
|
|
||||||
|
val subRelTypeMapping: Map[String,OAFRelations] = Map(
|
||||||
|
ModelConstants.REFERENCES -> OAFRelations(ModelConstants.REFERENCES, ModelConstants.IS_REFERENCED_BY, ModelConstants.RELATIONSHIP),
|
||||||
|
ModelConstants.IS_REFERENCED_BY -> OAFRelations(ModelConstants.IS_REFERENCED_BY,ModelConstants.REFERENCES, ModelConstants.RELATIONSHIP),
|
||||||
|
|
||||||
|
ModelConstants.IS_SUPPLEMENTED_BY -> OAFRelations(ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.SUPPLEMENT),
|
||||||
|
ModelConstants.IS_SUPPLEMENT_TO -> OAFRelations(ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.SUPPLEMENT),
|
||||||
|
|
||||||
|
ModelConstants.HAS_PART -> OAFRelations(ModelConstants.HAS_PART,ModelConstants.IS_PART_OF, ModelConstants.PART),
|
||||||
|
ModelConstants.IS_PART_OF -> OAFRelations(ModelConstants.IS_PART_OF,ModelConstants.HAS_PART, ModelConstants.PART),
|
||||||
|
|
||||||
|
ModelConstants.IS_VERSION_OF-> OAFRelations(ModelConstants.IS_VERSION_OF,ModelConstants.HAS_VERSION,ModelConstants.VERSION),
|
||||||
|
ModelConstants.HAS_VERSION-> OAFRelations(ModelConstants.HAS_VERSION,ModelConstants.IS_VERSION_OF,ModelConstants.VERSION),
|
||||||
|
|
||||||
|
ModelConstants.IS_IDENTICAL_TO -> OAFRelations(ModelConstants.IS_IDENTICAL_TO,ModelConstants.IS_IDENTICAL_TO, ModelConstants.RELATIONSHIP),
|
||||||
|
|
||||||
|
ModelConstants.IS_CONTINUED_BY -> OAFRelations(ModelConstants.IS_CONTINUED_BY,ModelConstants.CONTINUES, ModelConstants.RELATIONSHIP),
|
||||||
|
ModelConstants.CONTINUES -> OAFRelations(ModelConstants.CONTINUES,ModelConstants.IS_CONTINUED_BY, ModelConstants.RELATIONSHIP),
|
||||||
|
|
||||||
|
ModelConstants.IS_NEW_VERSION_OF-> OAFRelations(ModelConstants.IS_NEW_VERSION_OF,ModelConstants.IS_PREVIOUS_VERSION_OF, ModelConstants.VERSION),
|
||||||
|
ModelConstants.IS_PREVIOUS_VERSION_OF ->OAFRelations(ModelConstants.IS_PREVIOUS_VERSION_OF,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION),
|
||||||
|
|
||||||
|
ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP),
|
||||||
|
ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP),
|
||||||
|
|
||||||
|
ModelConstants.IS_SOURCE_OF -> OAFRelations(ModelConstants.IS_SOURCE_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION),
|
||||||
|
ModelConstants.IS_DERIVED_FROM -> OAFRelations(ModelConstants.IS_DERIVED_FROM,ModelConstants.IS_SOURCE_OF, ModelConstants.VERSION),
|
||||||
|
|
||||||
|
ModelConstants.CITES -> OAFRelations(ModelConstants.CITES,ModelConstants.IS_CITED_BY, ModelConstants.CITATION),
|
||||||
|
ModelConstants.IS_CITED_BY -> OAFRelations(ModelConstants.IS_CITED_BY,ModelConstants.CITES, ModelConstants.CITATION),
|
||||||
|
|
||||||
|
ModelConstants.IS_VARIANT_FORM_OF -> OAFRelations(ModelConstants.IS_VARIANT_FORM_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION),
|
||||||
|
ModelConstants.IS_OBSOLETED_BY -> OAFRelations(ModelConstants.IS_OBSOLETED_BY,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION),
|
||||||
|
|
||||||
|
ModelConstants.REVIEWS -> OAFRelations(ModelConstants.REVIEWS,ModelConstants.IS_REVIEWED_BY, ModelConstants.REVIEW),
|
||||||
|
ModelConstants.IS_REVIEWED_BY -> OAFRelations(ModelConstants.IS_REVIEWED_BY,ModelConstants.REVIEWS, ModelConstants.REVIEW),
|
||||||
|
|
||||||
|
ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP),
|
||||||
|
ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP),
|
||||||
|
|
||||||
|
ModelConstants.COMPILES -> OAFRelations(ModelConstants.COMPILES,ModelConstants.IS_COMPILED_BY, ModelConstants.RELATIONSHIP),
|
||||||
|
ModelConstants.IS_COMPILED_BY -> OAFRelations(ModelConstants.IS_COMPILED_BY,ModelConstants.COMPILES, ModelConstants.RELATIONSHIP)
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
val datacite_filter: List[String] = {
|
||||||
|
val stream: InputStream = getClass.getResourceAsStream(DATACITE_FILTER_PATH)
|
||||||
|
require(stream!= null)
|
||||||
|
Source.fromInputStream(stream).getLines().toList
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def dataciteDataInfo(trust: String): DataInfo = OafMapperUtils.dataInfo(false,null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, trust)
|
||||||
|
|
||||||
|
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH)
|
||||||
|
val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
|
||||||
|
|
||||||
|
val funder_regex: List[(Pattern, String)] = List(
|
||||||
|
(Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"),
|
||||||
|
(Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::")
|
||||||
|
|
||||||
|
)
|
||||||
|
|
||||||
|
val Date_regex: List[Pattern] = List(
|
||||||
|
//Y-M-D
|
||||||
|
Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
|
||||||
|
//M-D-Y
|
||||||
|
Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE),
|
||||||
|
//D-M-Y
|
||||||
|
Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE),
|
||||||
|
//Y
|
||||||
|
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -2,131 +2,42 @@ package eu.dnetlib.dhp.datacite
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
|
import eu.dnetlib.dhp.datacite.DataciteModelConstants._
|
||||||
import eu.dnetlib.dhp.schema.action.AtomicAction
|
import eu.dnetlib.dhp.schema.action.AtomicAction
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
|
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
|
||||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
|
||||||
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 org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||||
import org.json4s.jackson.JsonMethods.parse
|
import org.json4s.jackson.JsonMethods.parse
|
||||||
|
|
||||||
import java.nio.charset.CodingErrorAction
|
|
||||||
import java.text.SimpleDateFormat
|
import java.text.SimpleDateFormat
|
||||||
import java.time.LocalDate
|
import java.time.LocalDate
|
||||||
import java.time.chrono.ThaiBuddhistDate
|
import java.time.chrono.ThaiBuddhistDate
|
||||||
import java.time.format.DateTimeFormatter
|
import java.time.format.DateTimeFormatter
|
||||||
import java.util.regex.Pattern
|
|
||||||
import java.util.{Date, Locale}
|
import java.util.{Date, Locale}
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.io.{Codec, Source}
|
|
||||||
import scala.language.postfixOps
|
|
||||||
|
|
||||||
case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {}
|
|
||||||
|
|
||||||
case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {}
|
|
||||||
|
|
||||||
case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
|
|
||||||
|
|
||||||
case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {}
|
|
||||||
|
|
||||||
case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
|
|
||||||
|
|
||||||
case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
|
|
||||||
|
|
||||||
case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
|
|
||||||
|
|
||||||
case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {}
|
|
||||||
|
|
||||||
case class DateType(date: Option[String], dateType: Option[String]) {}
|
|
||||||
|
|
||||||
case class HostedByMapType(openaire_id: String, datacite_name: String, official_name: String, similarity: Option[Float]) {}
|
|
||||||
|
|
||||||
object DataciteToOAFTransformation {
|
object DataciteToOAFTransformation {
|
||||||
|
|
||||||
val REL_TYPE_VALUE:String = "resultResult"
|
|
||||||
val DATE_RELATION_KEY = "RelationDate"
|
|
||||||
|
|
||||||
val subRelTypeMapping: Map[String,(String,String)] = Map(
|
|
||||||
"References" ->("IsReferencedBy","relationship"),
|
|
||||||
"IsSupplementTo" ->("IsSupplementedBy","supplement"),
|
|
||||||
"IsPartOf" ->("HasPart","part"),
|
|
||||||
"HasPart" ->("IsPartOf","part"),
|
|
||||||
"IsVersionOf" ->("HasVersion","version"),
|
|
||||||
"HasVersion" ->("IsVersionOf","version"),
|
|
||||||
"IsIdenticalTo" ->("IsIdenticalTo","relationship"),
|
|
||||||
"IsPreviousVersionOf" ->("IsNewVersionOf","version"),
|
|
||||||
"IsContinuedBy" ->("Continues","relationship"),
|
|
||||||
"Continues" ->("IsContinuedBy","relationship"),
|
|
||||||
"IsNewVersionOf" ->("IsPreviousVersionOf","version"),
|
|
||||||
"IsSupplementedBy" ->("IsSupplementTo","supplement"),
|
|
||||||
"IsDocumentedBy" ->("Documents","relationship"),
|
|
||||||
"IsSourceOf" ->("IsDerivedFrom","relationship"),
|
|
||||||
"Cites" ->("IsCitedBy","citation"),
|
|
||||||
"IsCitedBy" ->("Cites","citation"),
|
|
||||||
"IsDerivedFrom" ->("IsSourceOf","relationship"),
|
|
||||||
"IsVariantFormOf" ->("IsDerivedFrom","version"),
|
|
||||||
"IsReferencedBy" ->("References","relationship"),
|
|
||||||
"IsObsoletedBy" ->("IsNewVersionOf","version"),
|
|
||||||
"Reviews" ->("IsReviewedBy","review"),
|
|
||||||
"Documents" ->("IsDocumentedBy","relationship"),
|
|
||||||
"IsCompiledBy" ->("Compiles","relationship"),
|
|
||||||
"Compiles" ->("IsCompiledBy","relationship"),
|
|
||||||
"IsReviewedBy" ->("Reviews","review")
|
|
||||||
)
|
|
||||||
|
|
||||||
implicit val codec: Codec = Codec("UTF-8")
|
|
||||||
codec.onMalformedInput(CodingErrorAction.REPLACE)
|
|
||||||
codec.onUnmappableCharacter(CodingErrorAction.REPLACE)
|
|
||||||
|
|
||||||
val DOI_CLASS = "doi"
|
|
||||||
val SUBJ_CLASS = "keywords"
|
|
||||||
|
|
||||||
|
|
||||||
val j_filter: List[String] = {
|
|
||||||
val s = Source.fromInputStream(getClass.getResourceAsStream("datacite_filter")).mkString
|
|
||||||
s.lines.toList
|
|
||||||
}
|
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
val unknown_repository: HostedByMapType = HostedByMapType(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID, ModelConstants.UNKNOWN_REPOSITORY.getValue, ModelConstants.UNKNOWN_REPOSITORY.getValue, Some(1.0F))
|
|
||||||
|
|
||||||
val dataInfo: DataInfo = generateDataInfo("0.9")
|
|
||||||
val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, "Datacite")
|
|
||||||
|
|
||||||
val hostedByMap: Map[String, HostedByMapType] = {
|
/**
|
||||||
val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString
|
* This method should skip record if json contains invalid text
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
* defined in gile datacite_filter
|
||||||
lazy val json: org.json4s.JValue = parse(s)
|
*
|
||||||
json.extract[Map[String, HostedByMapType]]
|
* @param json
|
||||||
}
|
* @return True if the record should be skipped
|
||||||
|
*/
|
||||||
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH)
|
def skip_record(json: String): Boolean = {
|
||||||
val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
|
datacite_filter.exists(f => json.contains(f))
|
||||||
|
|
||||||
val funder_regex: List[(Pattern, String)] = List(
|
|
||||||
(Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"),
|
|
||||||
(Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::")
|
|
||||||
|
|
||||||
)
|
|
||||||
|
|
||||||
val Date_regex: List[Pattern] = List(
|
|
||||||
//Y-M-D
|
|
||||||
Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
|
|
||||||
//M-D-Y
|
|
||||||
Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE),
|
|
||||||
//D-M-Y
|
|
||||||
Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE),
|
|
||||||
//Y
|
|
||||||
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def filter_json(json: String): Boolean = {
|
|
||||||
j_filter.exists(f => json.contains(f))
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@deprecated("this method will be removed", "dhp")
|
||||||
def toActionSet(item: Oaf): (String, String) = {
|
def toActionSet(item: Oaf): (String, String) = {
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
|
|
@ -197,15 +108,17 @@ object DataciteToOAFTransformation {
|
||||||
d
|
d
|
||||||
}
|
}
|
||||||
|
|
||||||
def fix_thai_date(input:String, format:String) :String = {
|
def fix_thai_date(input: String, format: String): String = {
|
||||||
try {
|
try {
|
||||||
val a_date = LocalDate.parse(input,DateTimeFormatter.ofPattern(format))
|
val a_date = LocalDate.parse(input, DateTimeFormatter.ofPattern(format))
|
||||||
val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
|
val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
|
||||||
LocalDate.from(d).toString
|
LocalDate.from(d).toString
|
||||||
} catch {
|
} catch {
|
||||||
case _: Throwable => ""
|
case _: Throwable => ""
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = {
|
def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = {
|
||||||
if (resourceType != null && resourceType.nonEmpty) {
|
if (resourceType != null && resourceType.nonEmpty) {
|
||||||
val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType)
|
val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType)
|
||||||
|
|
@ -324,11 +237,7 @@ object DataciteToOAFTransformation {
|
||||||
val p = match_pattern.get._2
|
val p = match_pattern.get._2
|
||||||
val grantId = m.matcher(awardUri).replaceAll("$2")
|
val grantId = m.matcher(awardUri).replaceAll("$2")
|
||||||
val targetId = s"$p${DHPUtils.md5(grantId)}"
|
val targetId = s"$p${DHPUtils.md5(grantId)}"
|
||||||
List(
|
List(generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo))
|
||||||
generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo)
|
|
||||||
// REMOVED INVERSE RELATION since there is a specific method that should generate later
|
|
||||||
// generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo)
|
|
||||||
)
|
|
||||||
}
|
}
|
||||||
else
|
else
|
||||||
List()
|
List()
|
||||||
|
|
@ -337,7 +246,7 @@ object DataciteToOAFTransformation {
|
||||||
|
|
||||||
|
|
||||||
def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup, exportLinks: Boolean): List[Oaf] = {
|
def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup, exportLinks: Boolean): List[Oaf] = {
|
||||||
if (filter_json(input))
|
if (skip_record(input))
|
||||||
return List()
|
return List()
|
||||||
|
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
@ -427,15 +336,15 @@ object DataciteToOAFTransformation {
|
||||||
.map(d => d.get)
|
.map(d => d.get)
|
||||||
|
|
||||||
if (a_date.isDefined) {
|
if (a_date.isDefined) {
|
||||||
if(doi.startsWith("10.14457"))
|
if (doi.startsWith("10.14457"))
|
||||||
result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get,"[yyyy-MM-dd]"), null))
|
result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get, "[yyyy-MM-dd]"), null))
|
||||||
else
|
else
|
||||||
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
|
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
|
||||||
}
|
}
|
||||||
if (i_date.isDefined && i_date.get.isDefined) {
|
if (i_date.isDefined && i_date.get.isDefined) {
|
||||||
if(doi.startsWith("10.14457")) {
|
if (doi.startsWith("10.14457")) {
|
||||||
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
|
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null))
|
||||||
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
|
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null))
|
||||||
}
|
}
|
||||||
else {
|
else {
|
||||||
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
|
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
|
||||||
|
|
@ -443,9 +352,9 @@ object DataciteToOAFTransformation {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
else if (publication_year != null) {
|
else if (publication_year != null) {
|
||||||
if(doi.startsWith("10.14457")) {
|
if (doi.startsWith("10.14457")) {
|
||||||
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
|
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null))
|
||||||
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
|
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null))
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
|
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
|
||||||
|
|
@ -516,8 +425,8 @@ object DataciteToOAFTransformation {
|
||||||
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||||
|
|
||||||
if (client.isDefined) {
|
if (client.isDefined) {
|
||||||
val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository)
|
|
||||||
instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name))
|
instance.setHostedby(OafMapperUtils.keyValue(generateDSId(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID), ModelConstants.UNKNOWN_REPOSITORY.getValue))
|
||||||
instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
|
instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
|
||||||
instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
|
instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
|
||||||
instance.setAccessright(access_rights_qualifier)
|
instance.setAccessright(access_rights_qualifier)
|
||||||
|
|
@ -549,7 +458,7 @@ object DataciteToOAFTransformation {
|
||||||
JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
|
JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
|
||||||
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
|
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
|
||||||
|
|
||||||
relations = relations ::: generateRelations(rels,result.getId, if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null)
|
relations = relations ::: generateRelations(rels, result.getId, if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null)
|
||||||
}
|
}
|
||||||
if (relations != null && relations.nonEmpty) {
|
if (relations != null && relations.nonEmpty) {
|
||||||
List(result) ::: relations
|
List(result) ::: relations
|
||||||
|
|
@ -558,7 +467,7 @@ object DataciteToOAFTransformation {
|
||||||
List(result)
|
List(result)
|
||||||
}
|
}
|
||||||
|
|
||||||
private def generateRelations(rels: List[RelatedIdentifierType], id:String, date:String):List[Relation] = {
|
private def generateRelations(rels: List[RelatedIdentifierType], id: String, date: String): List[Relation] = {
|
||||||
rels
|
rels
|
||||||
.filter(r =>
|
.filter(r =>
|
||||||
subRelTypeMapping.contains(r.relationType) && (
|
subRelTypeMapping.contains(r.relationType) && (
|
||||||
|
|
@ -571,32 +480,23 @@ object DataciteToOAFTransformation {
|
||||||
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
||||||
rel.setDataInfo(dataInfo)
|
rel.setDataInfo(dataInfo)
|
||||||
|
|
||||||
val subRelType = subRelTypeMapping(r.relationType)._2
|
val subRelType = subRelTypeMapping(r.relationType).relType
|
||||||
rel.setRelType(REL_TYPE_VALUE)
|
rel.setRelType(REL_TYPE_VALUE)
|
||||||
rel.setSubRelType(subRelType)
|
rel.setSubRelType(subRelType)
|
||||||
rel.setRelClass(r.relationType)
|
rel.setRelClass(r.relationType)
|
||||||
|
|
||||||
val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
|
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
|
||||||
|
|
||||||
rel.setProperties(List(dateProps).asJava)
|
rel.setProperties(List(dateProps).asJava)
|
||||||
|
|
||||||
rel.setSource(id)
|
rel.setSource(id)
|
||||||
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType))
|
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType))
|
||||||
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
||||||
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
|
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
|
||||||
rel
|
rel
|
||||||
}).toList
|
})
|
||||||
}
|
}
|
||||||
|
|
||||||
def generateDataInfo(trust: String): DataInfo = {
|
|
||||||
val di = new DataInfo
|
|
||||||
di.setDeletedbyinference(false)
|
|
||||||
di.setInferred(false)
|
|
||||||
di.setInvisible(false)
|
|
||||||
di.setTrust(trust)
|
|
||||||
di.setProvenanceaction(ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER)
|
|
||||||
di
|
|
||||||
}
|
|
||||||
|
|
||||||
def generateDSId(input: String): String = {
|
def generateDSId(input: String): String = {
|
||||||
val b = StringUtils.substringBefore(input, "::")
|
val b = StringUtils.substringBefore(input, "::")
|
||||||
|
|
@ -1,64 +1,94 @@
|
||||||
package eu.dnetlib.dhp.datacite
|
package eu.dnetlib.dhp.datacite
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||||||
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
|
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
|
||||||
import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
|
import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
|
||||||
import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH
|
|
||||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
|
import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
|
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||||
import org.apache.spark.SparkConf
|
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.io.Source
|
|
||||||
|
|
||||||
object GenerateDataciteDatasetSpark {
|
class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
|
||||||
|
/**
|
||||||
|
* Here all the spark applications runs this method
|
||||||
|
* where the whole logic of the spark node is defined
|
||||||
|
*/
|
||||||
|
override def run(): Unit = {
|
||||||
|
|
||||||
val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
|
||||||
val conf = new SparkConf
|
|
||||||
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
|
|
||||||
parser.parseArgument(args)
|
|
||||||
val master = parser.get("master")
|
|
||||||
val sourcePath = parser.get("sourcePath")
|
val sourcePath = parser.get("sourcePath")
|
||||||
|
log.info(s"SourcePath is '$sourcePath'")
|
||||||
val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
|
val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
|
||||||
|
log.info(s"exportLinks is '$exportLinks'")
|
||||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||||
log.info("isLookupUrl: {}", isLookupUrl)
|
log.info("isLookupUrl: {}", isLookupUrl)
|
||||||
|
|
||||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||||
val spark: SparkSession = SparkSession.builder().config(conf)
|
require(vocabularies != null)
|
||||||
.appName(GenerateDataciteDatasetSpark.getClass.getSimpleName)
|
|
||||||
.master(master)
|
|
||||||
.getOrCreate()
|
|
||||||
|
|
||||||
|
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
|
||||||
|
log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
|
||||||
|
|
||||||
|
val mapper = new ObjectMapper()
|
||||||
|
val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
|
||||||
|
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
|
||||||
|
log.info(s"outputBasePath is '$outputBasePath'")
|
||||||
|
val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
|
||||||
|
log.info(s"targetPath is '$targetPath'")
|
||||||
|
|
||||||
|
generateDataciteDataset(sourcePath, exportLinks, vocabularies, targetPath, spark)
|
||||||
|
|
||||||
|
reportTotalSize(targetPath, outputBasePath)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* For working with MDStore we need to store in a file on hdfs the size of
|
||||||
|
* the current dataset
|
||||||
|
* @param targetPath
|
||||||
|
* @param outputBasePath
|
||||||
|
*/
|
||||||
|
def reportTotalSize( targetPath: String, outputBasePath: String ):Unit = {
|
||||||
|
val total_items = spark.read.load(targetPath).count()
|
||||||
|
writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generate the transformed and cleaned OAF Dataset from the native one
|
||||||
|
|
||||||
|
* @param sourcePath sourcePath of the native Dataset in format JSON/Datacite
|
||||||
|
* @param exportLinks If true it generates unresolved links
|
||||||
|
* @param vocabularies vocabularies for cleaning
|
||||||
|
* @param targetPath the targetPath of the result Dataset
|
||||||
|
*/
|
||||||
|
def generateDataciteDataset(sourcePath: String, exportLinks: Boolean, vocabularies: VocabularyGroup, targetPath: String, spark:SparkSession):Unit = {
|
||||||
|
require(spark!= null)
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
|
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
|
||||||
|
|
||||||
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
|
||||||
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
|
|
||||||
val mapper = new ObjectMapper()
|
|
||||||
val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
|
|
||||||
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
|
|
||||||
|
|
||||||
log.info("outputBasePath: {}", outputBasePath)
|
|
||||||
val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
|
|
||||||
|
|
||||||
spark.read.load(sourcePath).as[DataciteType]
|
spark.read.load(sourcePath).as[DataciteType]
|
||||||
.filter(d => d.isActive)
|
.filter(d => d.isActive)
|
||||||
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
|
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
|
||||||
.filter(d => d != null)
|
.filter(d => d != null)
|
||||||
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
||||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
|
}
|
||||||
|
|
||||||
val total_items = spark.read.load(targetPath).as[Oaf].count()
|
}
|
||||||
writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
|
|
||||||
|
|
||||||
|
object GenerateDataciteDatasetSpark {
|
||||||
|
|
||||||
|
val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
|
||||||
|
|
||||||
|
def main(args: Array[String]): Unit = {
|
||||||
|
new GenerateDataciteDatasetSpark("/eu/dnetlib/dhp/datacite/generate_dataset_params.json", args, log).initialize().run()
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -7,6 +7,7 @@ import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||||
import org.json4s.jackson.JsonMethods.{compact, parse, render}
|
import org.json4s.jackson.JsonMethods.{compact, parse, render}
|
||||||
import collection.JavaConverters._
|
import collection.JavaConverters._
|
||||||
|
|
||||||
object BioDBToOAF {
|
object BioDBToOAF {
|
||||||
|
|
||||||
case class EBILinkItem(id: Long, links: String) {}
|
case class EBILinkItem(id: Long, links: String) {}
|
||||||
|
|
@ -1,9 +1,9 @@
|
||||||
package eu.dnetlib.dhp.sx.bio
|
package eu.dnetlib.dhp.sx.bio
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
|
||||||
import BioDBToOAF.ScholixResolved
|
|
||||||
import eu.dnetlib.dhp.collection.CollectionUtils
|
import eu.dnetlib.dhp.collection.CollectionUtils
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
|
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
|
|
@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
database.toUpperCase() match {
|
database.toUpperCase() match {
|
||||||
case "UNIPROT" =>
|
case "UNIPROT" =>
|
||||||
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
case "PDB" =>
|
case "PDB" =>
|
||||||
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
case "SCHOLIX" =>
|
case "SCHOLIX" =>
|
||||||
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
case "CROSSREF_LINKS" =>
|
case "CROSSREF_LINKS" =>
|
||||||
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -3,7 +3,7 @@ package eu.dnetlib.dhp.sx.bio.ebi
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result
|
import eu.dnetlib.dhp.schema.oaf.Result
|
||||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
|
import eu.dnetlib.dhp.sx.bio.pubmed._
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.hadoop.conf.Configuration
|
import org.apache.hadoop.conf.Configuration
|
||||||
|
|
@ -1,9 +1,8 @@
|
||||||
package eu.dnetlib.dhp.sx.bio.ebi
|
package eu.dnetlib.dhp.sx.bio.ebi
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
|
||||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||||
import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
|
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.http.client.config.RequestConfig
|
import org.apache.http.client.config.RequestConfig
|
||||||
import org.apache.http.client.methods.HttpGet
|
import org.apache.http.client.methods.HttpGet
|
||||||
|
|
@ -1,11 +1,10 @@
|
||||||
package eu.dnetlib.dhp.sx.bio.ebi
|
package eu.dnetlib.dhp.sx.bio.ebi
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
|
import eu.dnetlib.dhp.collection.CollectionUtils
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
|
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
|
||||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||||
import BioDBToOAF.EBILinkItem
|
|
||||||
import eu.dnetlib.dhp.collection.CollectionUtils
|
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql._
|
import org.apache.spark.sql._
|
||||||
|
|
@ -38,7 +37,7 @@ object SparkEBILinksToOaf {
|
||||||
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
|
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
|
||||||
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
|
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
|
||||||
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
|
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
|
||||||
.flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null)
|
.flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null)
|
||||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -4,7 +4,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
||||||
import eu.dnetlib.dhp.schema.oaf._
|
import eu.dnetlib.dhp.schema.oaf._
|
||||||
import scala.collection.JavaConverters._
|
import collection.JavaConverters._
|
||||||
|
|
||||||
import java.util.regex.Pattern
|
import java.util.regex.Pattern
|
||||||
|
|
||||||
|
|
@ -22,10 +22,10 @@ object PubMedToOaf {
|
||||||
val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
|
val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Cleaning the DOI Applying regex in order to
|
* Cleaning the DOI Applying regex in order to
|
||||||
* remove doi starting with URL
|
* remove doi starting with URL
|
||||||
|
*
|
||||||
* @param doi input DOI
|
* @param doi input DOI
|
||||||
* @return cleaned DOI
|
* @return cleaned DOI
|
||||||
*/
|
*/
|
||||||
|
|
@ -93,7 +93,6 @@ object PubMedToOaf {
|
||||||
* @param vocabularyName the input vocabulary name
|
* @param vocabularyName the input vocabulary name
|
||||||
* @param vocabularies all the vocabularies
|
* @param vocabularies all the vocabularies
|
||||||
* @param term the term to find
|
* @param term the term to find
|
||||||
*
|
|
||||||
* @return the cleaned term value
|
* @return the cleaned term value
|
||||||
*/
|
*/
|
||||||
def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
|
def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
|
||||||
|
|
@ -106,7 +105,6 @@ object PubMedToOaf {
|
||||||
/**
|
/**
|
||||||
* Map the Pubmed Article into the OAF instance
|
* Map the Pubmed Article into the OAF instance
|
||||||
*
|
*
|
||||||
*
|
|
||||||
* @param article the pubmed articles
|
* @param article the pubmed articles
|
||||||
* @param vocabularies the vocabularies
|
* @param vocabularies the vocabularies
|
||||||
* @return The OAF instance if the mapping did not fail
|
* @return The OAF instance if the mapping did not fail
|
||||||
|
|
@ -185,7 +183,6 @@ object PubMedToOaf {
|
||||||
//--------------------------------------------------------------------------------------
|
//--------------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
// RESULT MAPPING
|
// RESULT MAPPING
|
||||||
//--------------------------------------------------------------------------------------
|
//--------------------------------------------------------------------------------------
|
||||||
result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
|
result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
|
||||||
|
|
@ -1,9 +1,20 @@
|
||||||
##DHP-Aggregation
|
##DHP-Aggregation
|
||||||
|
|
||||||
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
|
This module defines a set of oozie workflows for
|
||||||
|
|
||||||
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
|
1. the **collection** and **transformation** of metadata records.
|
||||||
|
2. the **integration** of new external information in the result
|
||||||
|
|
||||||
|
|
||||||
|
### Collection and Transformation
|
||||||
|
|
||||||
|
The workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
|
||||||
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
|
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
|
||||||
of each MDStore.
|
of each MDStore.
|
||||||
|
|
||||||
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
|
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
|
||||||
|
|
||||||
|
### Integration of external information in the result
|
||||||
|
|
||||||
|
The workflows create new entity in the OpenAIRE format (OAF) which aim is to enrich the result already contained in the graph.
|
||||||
|
See integration section for more insight
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,36 @@
|
||||||
|
DHP Aggregation - Integration method
|
||||||
|
=====================================
|
||||||
|
|
||||||
|
The integration method can be applied every time new information, which is not aggregated from the repositories
|
||||||
|
nor computed directly by OpenAIRE, should be added to the results of the graph.
|
||||||
|
|
||||||
|
The information integrated so far is:
|
||||||
|
|
||||||
|
1. Article impact measures
|
||||||
|
1. [Bip!Finder](https://dl.acm.org/doi/10.1145/3357384.3357850) scores
|
||||||
|
2. Result Subjects
|
||||||
|
1. Integration of Fields od Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in
|
||||||
|
results subjects.
|
||||||
|
|
||||||
|
|
||||||
|
The method always consists in the creation of a new entity in the OpenAIRE format (OAF entity) containing only the id
|
||||||
|
and the element in the OAF model that should be used to map the information we want to integrate.
|
||||||
|
|
||||||
|
The id is set by using a particular encoding of the given PID
|
||||||
|
|
||||||
|
*unresolved:[pid]:[pidtype]*
|
||||||
|
|
||||||
|
where
|
||||||
|
|
||||||
|
1. *unresolved* is a constant value
|
||||||
|
2. *pid* is the persistent id value, e.g. 10.5281/zenodo.4707307
|
||||||
|
3. *pidtype* is the persistent id type, e.g. doi
|
||||||
|
|
||||||
|
Such entities are matched against those available in the graph using the result.instance.pid values.
|
||||||
|
|
||||||
|
This mechanism can be used to integrate enrichments produced as associated by a given PID.
|
||||||
|
If a match will be found with one of the results already in the graph that said result will be enriched with the information
|
||||||
|
present in the new OAF.
|
||||||
|
All the objects for which a match is not found are discarded.
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -4,13 +4,13 @@ This section describes the mapping implemented for [MEDLINE/PubMed](https://pubm
|
||||||
Collection
|
Collection
|
||||||
---------
|
---------
|
||||||
The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with
|
The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with
|
||||||
the following [shcema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
|
the following [schema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
|
||||||
|
|
||||||
|
|
||||||
Parsing
|
Parsing
|
||||||
-------
|
-------
|
||||||
The resposible class of parsing is [PMParser](./scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
|
The resposible class of parsing is [PMParser](/dnet-hadoop/scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
|
||||||
an intermediate mapping of PubMed Article defined [here](/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
|
an intermediate mapping of PubMed Article defined [here](/dnet-hadoop/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
|
||||||
|
|
||||||
|
|
||||||
Mapping
|
Mapping
|
||||||
|
|
@ -50,6 +50,10 @@ The table below describes the mapping from the XML Native to the OAF mapping
|
||||||
|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
|
|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
|
||||||
|FOR ALL AUTHOR | author.rank| sequential number starting from 1|
|
|FOR ALL AUTHOR | author.rank| sequential number starting from 1|
|
||||||
|
|
||||||
|
#TODO
|
||||||
|
|
||||||
|
Missing item mapped
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -20,7 +20,9 @@
|
||||||
<item name="Pubmed" href="pubmed.html"/>
|
<item name="Pubmed" href="pubmed.html"/>
|
||||||
<item name="Datacite" href="datacite.html"/>
|
<item name="Datacite" href="datacite.html"/>
|
||||||
</item>
|
</item>
|
||||||
<item name="Release Notes" href="release-notes.html" />
|
<item name="Integration" href="integration.html" collapse="true">
|
||||||
|
|
||||||
|
</item>
|
||||||
<item name="General Information" href="about.html"/>
|
<item name="General Information" href="about.html"/>
|
||||||
|
|
||||||
<item name="JavaDoc" href="apidocs/" />
|
<item name="JavaDoc" href="apidocs/" />
|
||||||
|
|
|
||||||
|
|
@ -89,13 +89,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet1"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -121,13 +121,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet2"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -153,13 +153,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet3"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -186,13 +186,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet4"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -226,13 +226,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet5"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -261,13 +261,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet6"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
@ -306,13 +306,13 @@ public class CreateOpenCitationsASTest {
|
||||||
"-inputPath",
|
"-inputPath",
|
||||||
inputPath,
|
inputPath,
|
||||||
"-outputPath",
|
"-outputPath",
|
||||||
workingDir.toString() + "/actionSet"
|
workingDir.toString() + "/actionSet7"
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<Relation> tmp = sc
|
JavaRDD<Relation> tmp = sc
|
||||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
|
||||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||||
.map(aa -> ((Relation) aa.getPayload()));
|
.map(aa -> ((Relation) aa.getPayload()));
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,56 +0,0 @@
|
||||||
package eu.dnetlib.dhp.datacite
|
|
||||||
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
|
|
||||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
|
||||||
import org.junit.jupiter.api.extension.ExtendWith
|
|
||||||
import org.junit.jupiter.api.{BeforeEach, Test}
|
|
||||||
import org.mockito.junit.jupiter.MockitoExtension
|
|
||||||
|
|
||||||
import java.text.SimpleDateFormat
|
|
||||||
import java.util.Locale
|
|
||||||
import scala.io.Source
|
|
||||||
|
|
||||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
|
||||||
class DataciteToOAFTest extends AbstractVocabularyTest{
|
|
||||||
|
|
||||||
|
|
||||||
@BeforeEach
|
|
||||||
def setUp() :Unit = {
|
|
||||||
|
|
||||||
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
|
|
||||||
def testMapping() :Unit = {
|
|
||||||
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
|
|
||||||
val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true )
|
|
||||||
|
|
||||||
res.foreach(r => {
|
|
||||||
println (mapper.writeValueAsString(r))
|
|
||||||
println("----------------------------")
|
|
||||||
|
|
||||||
})
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
Binary file not shown.
|
|
@ -0,0 +1,114 @@
|
||||||
|
package eu.dnetlib.dhp.datacite
|
||||||
|
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
|
||||||
|
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
|
import org.apache.commons.io.FileUtils
|
||||||
|
import org.apache.spark.SparkConf
|
||||||
|
import org.apache.spark.sql.functions.{col, count}
|
||||||
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||||
|
import org.junit.jupiter.api.Assertions._
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import java.nio.file.{Files, Path}
|
||||||
|
import java.text.SimpleDateFormat
|
||||||
|
import java.util.Locale
|
||||||
|
import scala.io.Source
|
||||||
|
|
||||||
|
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||||
|
class DataciteToOAFTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
|
private var workingDir:Path = null
|
||||||
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
def setUp() :Unit = {
|
||||||
|
|
||||||
|
workingDir= Files.createTempDirectory(getClass.getSimpleName)
|
||||||
|
super.setUpVocabulary()
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterEach
|
||||||
|
def tearDown() :Unit = {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@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
|
||||||
|
def testConvert(): Unit = {
|
||||||
|
|
||||||
|
|
||||||
|
val path = getClass.getResource("/eu/dnetlib/dhp/actionmanager/datacite/dataset").getPath
|
||||||
|
|
||||||
|
val conf = new SparkConf()
|
||||||
|
val spark:SparkSession = SparkSession.builder().config(conf)
|
||||||
|
.appName(getClass.getSimpleName)
|
||||||
|
.master("local[*]")
|
||||||
|
.getOrCreate()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
val instance = new GenerateDataciteDatasetSpark(null, null, log)
|
||||||
|
val targetPath = s"$workingDir/result"
|
||||||
|
|
||||||
|
instance.generateDataciteDataset(path, exportLinks = true, vocabularies,targetPath, spark)
|
||||||
|
|
||||||
|
import spark.implicits._
|
||||||
|
|
||||||
|
val nativeSize =spark.read.load(path).count()
|
||||||
|
|
||||||
|
|
||||||
|
assertEquals(100, nativeSize)
|
||||||
|
|
||||||
|
val result:Dataset[Oaf] = spark.read.load(targetPath).as[Oaf]
|
||||||
|
|
||||||
|
|
||||||
|
result.map(s => s.getClass.getSimpleName).groupBy(col("value").alias("class")).agg(count("value").alias("Total")).show(false)
|
||||||
|
|
||||||
|
val t = spark.read.load(targetPath).count()
|
||||||
|
|
||||||
|
assertTrue(t >0)
|
||||||
|
|
||||||
|
|
||||||
|
spark.stop()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@Test
|
||||||
|
def testMapping() :Unit = {
|
||||||
|
val record =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/record.json")).mkString
|
||||||
|
|
||||||
|
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
|
||||||
|
val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true )
|
||||||
|
|
||||||
|
res.foreach(r => {
|
||||||
|
println (mapper.writeValueAsString(r))
|
||||||
|
println("----------------------------")
|
||||||
|
|
||||||
|
})
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -90,7 +90,7 @@ public class ReadBlacklistFromDB implements Closeable {
|
||||||
inverse.setSource(target_direct);
|
inverse.setSource(target_direct);
|
||||||
|
|
||||||
String encoding = rs.getString("relationship");
|
String encoding = rs.getString("relationship");
|
||||||
RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
|
RelationInverse ri = ModelSupport.findInverse(encoding);
|
||||||
direct.setRelClass(ri.getRelClass());
|
direct.setRelClass(ri.getRelClass());
|
||||||
inverse.setRelClass(ri.getInverseRelClass());
|
inverse.setRelClass(ri.getInverseRelClass());
|
||||||
direct.setRelType(ri.getRelType());
|
direct.setRelType(ri.getRelType());
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.blacklist;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.common.RelationInverse;
|
||||||
|
|
||||||
|
public class BlacklistRelationTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testRelationInverseLookup() {
|
||||||
|
|
||||||
|
final List<String> rels = Arrays
|
||||||
|
.asList(
|
||||||
|
"resultResult_relationship_IsRelatedTo",
|
||||||
|
"resultOrganization_affiliation_isAuthorInstitutionOf",
|
||||||
|
"resultOrganization_affiliation_hasAuthorInstitution",
|
||||||
|
"datasourceOrganization_provision_isProvidedBy",
|
||||||
|
"projectOrganization_participation_hasParticipant",
|
||||||
|
"resultProject_outcome_produces",
|
||||||
|
"resultProject_outcome_isProducedBy");
|
||||||
|
|
||||||
|
rels.forEach(r -> {
|
||||||
|
RelationInverse inverse = ModelSupport.relationInverseMap.get(r);
|
||||||
|
Assertions.assertNotNull(inverse);
|
||||||
|
Assertions.assertNotNull(inverse.getRelType());
|
||||||
|
Assertions.assertNotNull(inverse.getSubReltype());
|
||||||
|
Assertions.assertNotNull(inverse.getRelClass());
|
||||||
|
});
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -19,7 +19,7 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
|
||||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
|
|
||||||
@ExtendWith(MockitoExtension.class)
|
@ExtendWith(MockitoExtension.class)
|
||||||
class UpdateMatcherTest {
|
public class UpdateMatcherTest {
|
||||||
|
|
||||||
UpdateMatcher<String> matcher = new EnrichMissingPublicationDate();
|
UpdateMatcher<String> matcher = new EnrichMissingPublicationDate();
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||||
|
|
||||||
class EnrichMissingPublicationDateTest {
|
public class EnrichMissingPublicationDateTest {
|
||||||
|
|
||||||
final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate();
|
final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate();
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -8,7 +8,7 @@ import java.util.Arrays;
|
||||||
|
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
class SubscriptionUtilsTest {
|
public class SubscriptionUtilsTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void testVerifyListSimilar() {
|
void testVerifyListSimilar() {
|
||||||
|
|
|
||||||
|
|
@ -9,7 +9,7 @@ import eu.dnetlib.broker.objects.OaBrokerAuthor;
|
||||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||||
import eu.dnetlib.broker.objects.OaBrokerTypedValue;
|
import eu.dnetlib.broker.objects.OaBrokerTypedValue;
|
||||||
|
|
||||||
class TrustUtilsTest {
|
public class TrustUtilsTest {
|
||||||
|
|
||||||
private static final double THRESHOLD = 0.95;
|
private static final double THRESHOLD = 0.95;
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -139,12 +139,26 @@ abstract class AbstractSparkAction implements Serializable {
|
||||||
protected boolean isOpenorgs(Relation rel) {
|
protected boolean isOpenorgs(Relation rel) {
|
||||||
return Optional
|
return Optional
|
||||||
.ofNullable(rel.getCollectedfrom())
|
.ofNullable(rel.getCollectedfrom())
|
||||||
.map(
|
.map(c -> isCollectedFromOpenOrgs(c))
|
||||||
c -> c
|
.orElse(false);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected boolean isOpenorgsDedupRel(Relation rel) {
|
||||||
|
return isOpenorgs(rel) && isOpenOrgsDedupMergeRelation(rel);
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean isCollectedFromOpenOrgs(List<KeyValue> c) {
|
||||||
|
return c
|
||||||
.stream()
|
.stream()
|
||||||
.filter(Objects::nonNull)
|
.filter(Objects::nonNull)
|
||||||
.anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue())))
|
.anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue()));
|
||||||
.orElse(false);
|
}
|
||||||
|
|
||||||
|
private boolean isOpenOrgsDedupMergeRelation(Relation rel) {
|
||||||
|
return ModelConstants.ORG_ORG_RELTYPE.equals(rel.getRelType()) &&
|
||||||
|
ModelConstants.DEDUP.equals(rel.getSubRelType())
|
||||||
|
&& (ModelConstants.IS_MERGED_IN.equals(rel.getRelClass()) ||
|
||||||
|
ModelConstants.MERGES.equals(rel.getRelClass()));
|
||||||
}
|
}
|
||||||
|
|
||||||
protected static Boolean parseECField(Field<String> field) {
|
protected static Boolean parseECField(Field<String> field) {
|
||||||
|
|
|
||||||
|
|
@ -61,7 +61,7 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
|
||||||
.textFile(relationPath)
|
.textFile(relationPath)
|
||||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||||
.toJavaRDD()
|
.toJavaRDD()
|
||||||
.filter(x -> !isOpenorgs(x));
|
.filter(x -> !isOpenorgsDedupRel(x));
|
||||||
|
|
||||||
if (log.isDebugEnabled()) {
|
if (log.isDebugEnabled()) {
|
||||||
log.debug("Number of non-Openorgs relations collected: {}", simRels.count());
|
log.debug("Number of non-Openorgs relations collected: {}", simRels.count());
|
||||||
|
|
|
||||||
|
|
@ -11,6 +11,8 @@ import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.net.URISyntaxException;
|
import java.net.URISyntaxException;
|
||||||
import java.nio.file.Paths;
|
import java.nio.file.Paths;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
|
|
@ -29,6 +31,8 @@ import org.mockito.Mock;
|
||||||
import org.mockito.Mockito;
|
import org.mockito.Mockito;
|
||||||
import org.mockito.junit.jupiter.MockitoExtension;
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
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;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
|
@ -226,9 +230,10 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
||||||
|
|
||||||
new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
|
new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
|
||||||
|
|
||||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
final JavaRDD<String> rels = jsc.textFile(testDedupGraphBasePath + "/relation");
|
||||||
|
|
||||||
|
assertEquals(2382, rels.count());
|
||||||
|
|
||||||
assertEquals(2380, relations);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
|
|
@ -250,7 +255,7 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
||||||
|
|
||||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||||
|
|
||||||
assertEquals(4894, relations);
|
assertEquals(4896, relations);
|
||||||
|
|
||||||
// check deletedbyinference
|
// check deletedbyinference
|
||||||
final Dataset<Relation> mergeRels = spark
|
final Dataset<Relation> mergeRels = spark
|
||||||
|
|
|
||||||
|
|
@ -2518,3 +2518,5 @@
|
||||||
{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::5c351d85f02db01ca291acd119f0bd78", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|opendoar____::37248e2f6987b18670dd2b8a51d6ef55", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::5c351d85f02db01ca291acd119f0bd78", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|opendoar____::37248e2f6987b18670dd2b8a51d6ef55", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
||||||
{"subRelType": "dedup", "relClass": "merges", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
{"subRelType": "dedup", "relClass": "merges", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
||||||
{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
||||||
|
{"subRelType": "relationship", "relClass": "IsParentOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
||||||
|
{"subRelType": "relationship", "relClass": "IsChildOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
|
||||||
|
|
|
||||||
|
|
@ -1,21 +1,19 @@
|
||||||
package eu.dnetlib.doiboost
|
package eu.dnetlib.doiboost
|
||||||
|
|
||||||
import java.time.LocalDate
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
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, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
|
import eu.dnetlib.dhp.schema.oaf._
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||||
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 eu.dnetlib.dhp.schema.common.ModelConstants
|
|
||||||
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
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import java.time.LocalDate
|
||||||
|
import java.time.format.DateTimeFormatter
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -8,11 +8,12 @@ import org.apache.hadoop.io.Text
|
||||||
import org.apache.hadoop.io.compress.GzipCodec
|
import org.apache.hadoop.io.compress.GzipCodec
|
||||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat
|
import org.apache.hadoop.mapred.SequenceFileOutputFormat
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkGenerateDOIBoostActionSet {
|
object SparkGenerateDOIBoostActionSet {
|
||||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
||||||
val conf: SparkConf = new SparkConf()
|
val conf: SparkConf = new SparkConf()
|
||||||
|
|
@ -42,44 +43,32 @@ object SparkGenerateDOIBoostActionSet {
|
||||||
|
|
||||||
val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
|
val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
|
||||||
.filter(p => p != null || p.getId != null)
|
.filter(p => p != null || p.getId != null)
|
||||||
.map(d =>DoiBoostMappingUtil.fixResult(d))
|
.map(d => DoiBoostMappingUtil.fixResult(d))
|
||||||
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
|
|
||||||
|
|
||||||
val asPublication =spark.read.load(dbPublicationPath).as[Publication]
|
val asPublication = spark.read.load(dbPublicationPath).as[Publication]
|
||||||
.filter(p => p != null || p.getId != null)
|
.filter(p => p != null || p.getId != null)
|
||||||
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
|
|
||||||
|
|
||||||
val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
|
val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
|
||||||
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
|
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
|
||||||
.filter(r => r!= null && r.getSource != null && r.getTarget != null)
|
.filter(r => r != null && r.getSource != null && r.getTarget != null)
|
||||||
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
|
|
||||||
|
|
||||||
val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
|
val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
|
||||||
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
|
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
|
||||||
|
|
||||||
|
|
||||||
|
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
|
||||||
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -9,28 +9,26 @@ import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.expressions.Aggregator
|
import org.apache.spark.sql.expressions.Aggregator
|
||||||
import org.apache.spark.sql.functions.col
|
import org.apache.spark.sql.functions.col
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST.{JField, JObject, JString,JArray}
|
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||||
import org.json4s.jackson.JsonMethods.parse
|
import org.json4s.jackson.JsonMethods.parse
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
import scala.collection.JavaConverters._
|
||||||
object SparkGenerateDoiBoost {
|
object SparkGenerateDoiBoost {
|
||||||
|
|
||||||
|
|
||||||
def extractIdGRID(input:String):List[(String,String)] = {
|
def extractIdGRID(input: String): List[(String, String)] = {
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: org.json4s.JValue = parse(input)
|
lazy val json: org.json4s.JValue = parse(input)
|
||||||
|
|
||||||
val id:String = (json \ "id").extract[String]
|
val id: String = (json \ "id").extract[String]
|
||||||
|
|
||||||
val grids:List[String] = for {
|
val grids: List[String] = for {
|
||||||
|
|
||||||
JObject(pid) <- json \ "pid"
|
JObject(pid) <- json \ "pid"
|
||||||
JField("qualifier", JObject(qualifier)) <- pid
|
JField("qualifier", JObject(qualifier)) <- pid
|
||||||
JField("classid", JString(classid)) <-qualifier
|
JField("classid", JString(classid)) <- qualifier
|
||||||
JField("value", JString(vl)) <- pid
|
JField("value", JString(vl)) <- pid
|
||||||
if classid == "GRID"
|
if classid == "GRID"
|
||||||
} yield vl
|
} yield vl
|
||||||
|
|
@ -38,7 +36,6 @@ object SparkGenerateDoiBoost {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
||||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
@ -73,7 +70,7 @@ object SparkGenerateDoiBoost {
|
||||||
if (a != null && a._2 != null) {
|
if (a != null && a._2 != null) {
|
||||||
b.mergeFrom(a._2)
|
b.mergeFrom(a._2)
|
||||||
b.setId(a._1)
|
b.setId(a._1)
|
||||||
val authors =AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
|
val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
|
||||||
b.setAuthor(authors)
|
b.setAuthor(authors)
|
||||||
return b
|
return b
|
||||||
}
|
}
|
||||||
|
|
@ -87,11 +84,11 @@ object SparkGenerateDoiBoost {
|
||||||
return b2
|
return b2
|
||||||
}
|
}
|
||||||
else {
|
else {
|
||||||
if (b2 != null ) {
|
if (b2 != null) {
|
||||||
b1.mergeFrom(b2)
|
b1.mergeFrom(b2)
|
||||||
val authors =AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
|
val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
|
||||||
b1.setAuthor(authors)
|
b1.setAuthor(authors)
|
||||||
if (b2.getId!= null && b2.getId.nonEmpty)
|
if (b2.getId != null && b2.getId.nonEmpty)
|
||||||
b1.setId(b2.getId)
|
b1.setId(b2.getId)
|
||||||
return b1
|
return b1
|
||||||
}
|
}
|
||||||
|
|
@ -118,10 +115,9 @@ object SparkGenerateDoiBoost {
|
||||||
val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p))
|
val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p))
|
||||||
val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p))
|
val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p))
|
||||||
|
|
||||||
def applyMerge(item:((String, Publication), (String, Publication))) : Publication =
|
def applyMerge(item: ((String, Publication), (String, Publication))): Publication = {
|
||||||
{
|
|
||||||
val crossrefPub = item._1._2
|
val crossrefPub = item._1._2
|
||||||
if (item._2!= null) {
|
if (item._2 != null) {
|
||||||
val otherPub = item._2._2
|
val otherPub = item._2._2
|
||||||
if (otherPub != null) {
|
if (otherPub != null) {
|
||||||
crossrefPub.mergeFrom(otherPub)
|
crossrefPub.mergeFrom(otherPub)
|
||||||
|
|
@ -130,6 +126,7 @@ object SparkGenerateDoiBoost {
|
||||||
}
|
}
|
||||||
crossrefPub
|
crossrefPub
|
||||||
}
|
}
|
||||||
|
|
||||||
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin")
|
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin")
|
||||||
logger.info("Phase 3) Join Result with ORCID")
|
logger.info("Phase 3) Join Result with ORCID")
|
||||||
val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p))
|
val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p))
|
||||||
|
|
@ -143,9 +140,9 @@ object SparkGenerateDoiBoost {
|
||||||
sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
|
sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
|
||||||
|
|
||||||
|
|
||||||
val doiBoostPublication: Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
|
val doiBoostPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p => DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
|
||||||
|
|
||||||
val hostedByDataset : Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
|
val hostedByDataset: Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
|
||||||
|
|
||||||
|
|
||||||
doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left")
|
doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left")
|
||||||
|
|
@ -164,21 +161,20 @@ object SparkGenerateDoiBoost {
|
||||||
val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId"))
|
val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId"))
|
||||||
|
|
||||||
|
|
||||||
val a:Dataset[DoiBoostAffiliation] = paperAffiliation
|
val a: Dataset[DoiBoostAffiliation] = paperAffiliation
|
||||||
.joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId")))
|
.joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId")))
|
||||||
.select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
|
.select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
|
||||||
|
|
||||||
|
|
||||||
|
val magPubs: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
|
||||||
val magPubs:Dataset[(String,Publication)]= spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
|
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s => s._1 != null)
|
||||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s =>s._1!= null )
|
|
||||||
|
|
||||||
|
|
||||||
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
|
magPubs.joinWith(a, magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
|
||||||
val pub:Publication = item._1._2
|
val pub: Publication = item._1._2
|
||||||
val affiliation = item._2
|
val affiliation = item._2
|
||||||
val affId:String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
|
val affId: String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
|
||||||
val r:Relation = new Relation
|
val r: Relation = new Relation
|
||||||
r.setSource(pub.getId)
|
r.setSource(pub.getId)
|
||||||
r.setTarget(affId)
|
r.setTarget(affId)
|
||||||
r.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
r.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
||||||
|
|
@ -186,7 +182,7 @@ object SparkGenerateDoiBoost {
|
||||||
r.setSubRelType(ModelConstants.AFFILIATION)
|
r.setSubRelType(ModelConstants.AFFILIATION)
|
||||||
r.setDataInfo(pub.getDataInfo)
|
r.setDataInfo(pub.getDataInfo)
|
||||||
r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
|
r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
|
||||||
val r1:Relation = new Relation
|
val r1: Relation = new Relation
|
||||||
r1.setTarget(pub.getId)
|
r1.setTarget(pub.getId)
|
||||||
r1.setSource(affId)
|
r1.setSource(affId)
|
||||||
r1.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
r1.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
||||||
|
|
@ -198,33 +194,31 @@ object SparkGenerateDoiBoost {
|
||||||
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
|
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
|
||||||
|
|
||||||
|
|
||||||
|
val unresolvedRels: Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
|
||||||
|
|
||||||
val unresolvedRels:Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
|
|
||||||
|
|
||||||
if (r.getSource.startsWith("unresolved"))
|
if (r.getSource.startsWith("unresolved"))
|
||||||
(r.getSource, r)
|
(r.getSource, r)
|
||||||
else if (r.getTarget.startsWith("unresolved"))
|
else if (r.getTarget.startsWith("unresolved"))
|
||||||
(r.getTarget,r)
|
(r.getTarget, r)
|
||||||
else
|
else
|
||||||
("resolved", r)
|
("resolved", r)
|
||||||
})(Encoders.tuple(Encoders.STRING, mapEncoderRel))
|
})(Encoders.tuple(Encoders.STRING, mapEncoderRel))
|
||||||
|
|
||||||
val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
|
val openaireOrganization: Dataset[(String, String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x, y) => if (x != null) x else y).map(_._2)
|
||||||
|
|
||||||
unresolvedRels.joinWith(openaireOrganization,unresolvedRels("_1").equalTo(openaireOrganization("_2")))
|
unresolvedRels.joinWith(openaireOrganization, unresolvedRels("_1").equalTo(openaireOrganization("_2")))
|
||||||
.map { x =>
|
.map { x =>
|
||||||
val currentRels = x._1._2
|
val currentRels = x._1._2
|
||||||
val currentOrgs = x._2
|
val currentOrgs = x._2
|
||||||
if (currentOrgs!= null)
|
if (currentOrgs != null)
|
||||||
if(currentRels.getSource.startsWith("unresolved"))
|
if (currentRels.getSource.startsWith("unresolved"))
|
||||||
currentRels.setSource(currentOrgs._1)
|
currentRels.setSource(currentOrgs._1)
|
||||||
else
|
else
|
||||||
currentRels.setTarget(currentOrgs._1)
|
currentRels.setTarget(currentOrgs._1)
|
||||||
currentRels
|
currentRels
|
||||||
}.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
}.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
||||||
|
|
||||||
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
|
magPubs.joinWith(a, magPubs("_1").equalTo(a("PaperId"))).map(item => {
|
||||||
val affiliation = item._2
|
val affiliation = item._2
|
||||||
if (affiliation.GridId.isEmpty) {
|
if (affiliation.GridId.isEmpty) {
|
||||||
val o = new Organization
|
val o = new Organization
|
||||||
|
|
@ -241,7 +235,7 @@ object SparkGenerateDoiBoost {
|
||||||
}
|
}
|
||||||
else
|
else
|
||||||
null
|
null
|
||||||
}).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
|
}).filter(o => o != null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -4,20 +4,19 @@ 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.{decideAccessRight, _}
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||||
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
|
||||||
import org.json4s.JsonAST.{JValue, _}
|
import org.json4s.JsonAST._
|
||||||
import org.json4s.jackson.JsonMethods._
|
import org.json4s.jackson.JsonMethods._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import java.util
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.collection.mutable
|
import scala.collection.mutable
|
||||||
import scala.util.matching.Regex
|
import scala.util.matching.Regex
|
||||||
import java.util
|
|
||||||
|
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
|
||||||
|
|
||||||
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}
|
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}
|
||||||
|
|
||||||
|
|
@ -6,7 +6,7 @@ import org.apache.commons.io.IOUtils
|
||||||
import org.apache.hadoop.io.{IntWritable, Text}
|
import org.apache.hadoop.io.{IntWritable, Text}
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.expressions.Aggregator
|
import org.apache.spark.sql.expressions.Aggregator
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
|
||||||
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
|
||||||
|
|
@ -17,12 +17,12 @@ object CrossrefDataset {
|
||||||
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
|
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
|
||||||
|
|
||||||
|
|
||||||
def to_item(input:String):CrossrefDT = {
|
def to_item(input: String): CrossrefDT = {
|
||||||
|
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
val ts:Long = (json \ "indexed" \ "timestamp").extract[Long]
|
val ts: Long = (json \ "indexed" \ "timestamp").extract[Long]
|
||||||
val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
||||||
CrossrefDT(doi, input, ts)
|
CrossrefDT(doi, input, ts)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -30,7 +30,6 @@ object CrossrefDataset {
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val conf: SparkConf = new SparkConf()
|
val conf: SparkConf = new SparkConf()
|
||||||
val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
|
val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
|
||||||
parser.parseArgument(args)
|
parser.parseArgument(args)
|
||||||
|
|
@ -54,7 +53,7 @@ object CrossrefDataset {
|
||||||
return b
|
return b
|
||||||
|
|
||||||
|
|
||||||
if(a.timestamp >b.timestamp) {
|
if (a.timestamp > b.timestamp) {
|
||||||
return a
|
return a
|
||||||
}
|
}
|
||||||
b
|
b
|
||||||
|
|
@ -66,7 +65,7 @@ object CrossrefDataset {
|
||||||
if (a == null)
|
if (a == null)
|
||||||
return b
|
return b
|
||||||
|
|
||||||
if(a.timestamp >b.timestamp) {
|
if (a.timestamp > b.timestamp) {
|
||||||
return a
|
return a
|
||||||
}
|
}
|
||||||
b
|
b
|
||||||
|
|
@ -79,20 +78,20 @@ object CrossrefDataset {
|
||||||
override def finish(reduction: CrossrefDT): CrossrefDT = reduction
|
override def finish(reduction: CrossrefDT): CrossrefDT = reduction
|
||||||
}
|
}
|
||||||
|
|
||||||
val workingPath:String = parser.get("workingPath")
|
val workingPath: String = parser.get("workingPath")
|
||||||
|
|
||||||
|
|
||||||
val main_ds:Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
|
val main_ds: Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
|
||||||
|
|
||||||
|
|
||||||
val update =
|
val update =
|
||||||
spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
|
spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
|
||||||
.map(i =>CrossrefImporter.decompressBlob(i._2.toString))
|
.map(i => CrossrefImporter.decompressBlob(i._2.toString))
|
||||||
.map(i =>to_item(i)))
|
.map(i => to_item(i)))
|
||||||
|
|
||||||
main_ds.union(update).groupByKey(_.doi)
|
main_ds.union(update).groupByKey(_.doi)
|
||||||
.agg(crossrefAggregator.toColumn)
|
.agg(crossrefAggregator.toColumn)
|
||||||
.map(s=>s._2)
|
.map(s => s._2)
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated")
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated")
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -2,17 +2,12 @@ package eu.dnetlib.doiboost.crossref
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item
|
|
||||||
import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass
|
|
||||||
import org.apache.hadoop.io.{IntWritable, Text}
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec
|
|
||||||
import org.apache.spark.rdd.RDD
|
import org.apache.spark.rdd.RDD
|
||||||
import org.apache.spark.{SparkConf, SparkContext}
|
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
|
import org.apache.spark.{SparkConf, SparkContext}
|
||||||
import org.json4s
|
import org.json4s
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST.JArray
|
import org.json4s.jackson.JsonMethods.parse
|
||||||
import org.json4s.jackson.JsonMethods.{compact, parse, render}
|
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
|
|
@ -24,11 +19,10 @@ object GenerateCrossrefDataset {
|
||||||
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
|
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def crossrefElement(meta: String): CrossrefDT = {
|
def crossrefElement(meta: String): CrossrefDT = {
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: json4s.JValue = parse(meta)
|
lazy val json: json4s.JValue = parse(meta)
|
||||||
val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
||||||
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
|
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
|
||||||
CrossrefDT(doi, meta, timestamp)
|
CrossrefDT(doi, meta, timestamp)
|
||||||
|
|
||||||
|
|
@ -51,14 +45,14 @@ object GenerateCrossrefDataset {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
|
|
||||||
val tmp : RDD[String] = sc.textFile(sourcePath,6000)
|
val tmp: RDD[String] = sc.textFile(sourcePath, 6000)
|
||||||
|
|
||||||
spark.createDataset(tmp)
|
spark.createDataset(tmp)
|
||||||
.map(entry => crossrefElement(entry))
|
.map(entry => crossrefElement(entry))
|
||||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
// .map(meta => crossrefElement(meta))
|
// .map(meta => crossrefElement(meta))
|
||||||
// .toDS.as[CrossrefDT]
|
// .toDS.as[CrossrefDT]
|
||||||
// .write.mode(SaveMode.Overwrite).save(targetPath)
|
// .write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -4,10 +4,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.schema.oaf
|
import eu.dnetlib.dhp.schema.oaf
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
|
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
|
import org.apache.spark.sql._
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -2,8 +2,8 @@ package eu.dnetlib.doiboost.crossref
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import org.apache.hadoop.io.compress.GzipCodec
|
import org.apache.hadoop.io.compress.GzipCodec
|
||||||
|
import org.apache.spark.sql.SparkSession
|
||||||
import org.apache.spark.{SparkConf, SparkContext}
|
import org.apache.spark.{SparkConf, SparkContext}
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
|
||||||
import org.json4s
|
import org.json4s
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST.JArray
|
import org.json4s.JsonAST.JArray
|
||||||
|
|
@ -17,9 +17,7 @@ object UnpackCrtossrefEntries {
|
||||||
val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
|
val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
|
||||||
|
|
||||||
|
|
||||||
|
def extractDump(input: String): List[String] = {
|
||||||
|
|
||||||
def extractDump(input:String):List[String] = {
|
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
|
|
||||||
|
|
@ -30,7 +28,6 @@ object UnpackCrtossrefEntries {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
val conf = new SparkConf
|
val conf = new SparkConf
|
||||||
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
|
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
|
||||||
|
|
@ -45,7 +42,7 @@ object UnpackCrtossrefEntries {
|
||||||
.getOrCreate()
|
.getOrCreate()
|
||||||
val sc: SparkContext = spark.sparkContext
|
val sc: SparkContext = spark.sparkContext
|
||||||
|
|
||||||
sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
|
sc.wholeTextFiles(sourcePath, 6000).flatMap(d => extractDump(d._2))
|
||||||
.saveAsTextFile(targetPath, classOf[GzipCodec])
|
.saveAsTextFile(targetPath, classOf[GzipCodec])
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -5,10 +5,10 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
|
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||||
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
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.collection.mutable
|
import scala.collection.mutable
|
||||||
|
|
@ -3,8 +3,8 @@ package eu.dnetlib.doiboost.mag
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{SaveMode, SparkSession}
|
|
||||||
import org.apache.spark.sql.types._
|
import org.apache.spark.sql.types._
|
||||||
|
import org.apache.spark.sql.{SaveMode, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkImportMagIntoDataset {
|
object SparkImportMagIntoDataset {
|
||||||
|
|
@ -24,13 +24,13 @@ object SparkImportMagIntoDataset {
|
||||||
"Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
|
"Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
|
||||||
"AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")),
|
"AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")),
|
||||||
"Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
"Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
||||||
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
|
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
|
||||||
"ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
"ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
||||||
"EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")),
|
"EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")),
|
||||||
"FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
|
"FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
|
||||||
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")),
|
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")),
|
||||||
"FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
"FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
||||||
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "CreatedDate:DateTime")),
|
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
|
||||||
"PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")),
|
"PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")),
|
||||||
"PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")),
|
"PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")),
|
||||||
"PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
|
"PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
|
||||||
|
|
@ -75,7 +75,6 @@ object SparkImportMagIntoDataset {
|
||||||
.master(parser.get("master")).getOrCreate()
|
.master(parser.get("master")).getOrCreate()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
stream.foreach { case (k, v) =>
|
stream.foreach { case (k, v) =>
|
||||||
val s: StructType = getSchema(k)
|
val s: StructType = getSchema(k)
|
||||||
val df = spark.read
|
val df = spark.read
|
||||||
|
|
@ -5,22 +5,19 @@ import eu.dnetlib.dhp.schema.oaf.Publication
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.rdd.RDD
|
import org.apache.spark.sql.functions.{col, collect_list, struct}
|
||||||
import org.apache.spark.sql.functions._
|
|
||||||
import org.apache.spark.sql._
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
|
|
||||||
object SparkProcessMAG {
|
object SparkProcessMAG {
|
||||||
|
|
||||||
def getDistinctResults (d:Dataset[MagPapers]):Dataset[MagPapers]={
|
def getDistinctResults(d: Dataset[MagPapers]): Dataset[MagPapers] = {
|
||||||
d.where(col("Doi").isNotNull)
|
d.where(col("Doi").isNotNull)
|
||||||
.groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING)
|
.groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING)
|
||||||
.reduceGroups((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2))
|
.reduceGroups((p1: MagPapers, p2: MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1, p2))
|
||||||
.map(_._2)(Encoders.product[MagPapers])
|
.map(_._2)(Encoders.product[MagPapers])
|
||||||
.map(mp => {
|
.map(mp => {
|
||||||
new MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
|
MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
|
||||||
mp.DocType, mp.PaperTitle, mp.OriginalTitle,
|
mp.DocType, mp.PaperTitle, mp.OriginalTitle,
|
||||||
mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String,
|
mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String,
|
||||||
mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId,
|
mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId,
|
||||||
|
|
@ -102,9 +99,9 @@ object SparkProcessMAG {
|
||||||
|
|
||||||
|
|
||||||
val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
|
val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
|
||||||
.select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
|
.select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate", $"EndDate")
|
||||||
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci")))
|
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci")))
|
||||||
.select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
|
.select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate", $"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
|
||||||
|
|
||||||
|
|
||||||
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
|
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
|
||||||
|
|
@ -146,13 +143,12 @@ object SparkProcessMAG {
|
||||||
.save(s"$workingPath/mag_publication")
|
.save(s"$workingPath/mag_publication")
|
||||||
|
|
||||||
spark.read.load(s"$workingPath/mag_publication").as[Publication]
|
spark.read.load(s"$workingPath/mag_publication").as[Publication]
|
||||||
.filter(p => p.getId == null)
|
.filter(p => p.getId != null)
|
||||||
.groupByKey(p => p.getId)
|
.groupByKey(p => p.getId)
|
||||||
.reduceGroups((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
|
.reduceGroups((a: Publication, b: Publication) => ConversionUtil.mergePublication(a, b))
|
||||||
.map(_._2)
|
.map(_._2)
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
|
.write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -4,17 +4,16 @@ 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.IdentifierFactory
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
|
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
|
||||||
import eu.dnetlib.dhp.schema.orcid.{AuthorData, OrcidDOI}
|
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
|
||||||
import org.apache.commons.lang.StringUtils
|
import org.apache.commons.lang.StringUtils
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
|
||||||
import org.json4s
|
import org.json4s
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.json4s.JsonAST._
|
import org.json4s.JsonAST._
|
||||||
import org.json4s.jackson.JsonMethods._
|
import org.json4s.jackson.JsonMethods._
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import scala.collection.JavaConverters._
|
||||||
|
|
||||||
|
|
||||||
case class ORCIDItem(doi:String, authors:List[OrcidAuthor]){}
|
case class ORCIDItem(doi:String, authors:List[OrcidAuthor]){}
|
||||||
|
|
@ -11,10 +11,10 @@ object SparkConvertORCIDToOAF {
|
||||||
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
|
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
|
||||||
|
|
||||||
|
|
||||||
def run(spark:SparkSession, workingPath:String, targetPath:String) :Unit = {
|
def run(spark: SparkSession, workingPath: String, targetPath: String): Unit = {
|
||||||
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
|
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
|
val dataset: Dataset[ORCIDItem] = spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
|
||||||
|
|
||||||
logger.info("Converting ORCID to OAF")
|
logger.info("Converting ORCID to OAF")
|
||||||
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
|
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
|
|
@ -35,7 +35,7 @@ object SparkConvertORCIDToOAF {
|
||||||
val workingPath = parser.get("workingPath")
|
val workingPath = parser.get("workingPath")
|
||||||
val targetPath = parser.get("targetPath")
|
val targetPath = parser.get("targetPath")
|
||||||
|
|
||||||
run(spark,workingPath, targetPath)
|
run(spark, workingPath, targetPath)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -1,44 +1,41 @@
|
||||||
package eu.dnetlib.doiboost.orcid
|
package eu.dnetlib.doiboost.orcid
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.oa.merge.AuthorMerger
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||||
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
|
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.rdd.RDD
|
import org.apache.spark.rdd.RDD
|
||||||
import org.apache.spark.sql.functions._
|
import org.apache.spark.sql.functions.{col, collect_list}
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkPreprocessORCID {
|
object SparkPreprocessORCID {
|
||||||
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
|
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
|
||||||
|
|
||||||
def fixORCIDItem(item :ORCIDItem):ORCIDItem = {
|
def fixORCIDItem(item: ORCIDItem): ORCIDItem = {
|
||||||
ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList)
|
ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def run(spark:SparkSession,sourcePath:String,workingPath:String):Unit = {
|
def run(spark: SparkSession, sourcePath: String, workingPath: String): Unit = {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
|
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
|
||||||
|
|
||||||
val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))
|
val inputRDD: RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s != null).filter(s => ORCIDToOAF.authorValid(s))
|
||||||
|
|
||||||
spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
|
spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
|
||||||
|
|
||||||
val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)
|
val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s != null)
|
||||||
|
|
||||||
spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
|
spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
|
||||||
|
|
||||||
val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
|
val authors: Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
|
||||||
|
|
||||||
val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
|
val works: Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
|
||||||
|
|
||||||
works.joinWith(authors, authors("oid").equalTo(works("oid")))
|
works.joinWith(authors, authors("oid").equalTo(works("oid")))
|
||||||
.map(i =>{
|
.map(i => {
|
||||||
val doi = i._1.doi
|
val doi = i._1.doi
|
||||||
val author = i._2
|
val author = i._2
|
||||||
(doi, author)
|
(doi, author)
|
||||||
|
|
@ -1,16 +1,14 @@
|
||||||
package eu.dnetlib.doiboost.uw
|
package eu.dnetlib.doiboost.uw
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||||
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
|
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.rdd.RDD
|
import org.apache.spark.rdd.RDD
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
|
||||||
object SparkMapUnpayWallToOAF {
|
object SparkMapUnpayWallToOAF {
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
@ -32,11 +30,11 @@ object SparkMapUnpayWallToOAF {
|
||||||
|
|
||||||
val sourcePath = parser.get("sourcePath")
|
val sourcePath = parser.get("sourcePath")
|
||||||
val targetPath = parser.get("targetPath")
|
val targetPath = parser.get("targetPath")
|
||||||
val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
|
val inputRDD: RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
|
||||||
|
|
||||||
logger.info("Converting UnpayWall to OAF")
|
logger.info("Converting UnpayWall to OAF")
|
||||||
|
|
||||||
val d:Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
|
val d: Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p => p != null)).as[Publication]
|
||||||
d.write.mode(SaveMode.Overwrite).save(targetPath)
|
d.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Instance, OpenAccessRoute, Publication}
|
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Instance, OpenAccessRoute, Publication}
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||||
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
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
|
||||||
import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -1,70 +0,0 @@
|
||||||
package eu.dnetlib.dhp.doiboost
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
|
|
||||||
import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType}
|
|
||||||
import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass
|
|
||||||
import eu.dnetlib.doiboost.mag.ConversionUtil
|
|
||||||
import eu.dnetlib.doiboost.orcid.ORCIDElement
|
|
||||||
import org.apache.spark.SparkConf
|
|
||||||
import org.apache.spark.rdd.RDD
|
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
||||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
|
||||||
import org.junit.jupiter.api.Test
|
|
||||||
|
|
||||||
import scala.io.Source
|
|
||||||
|
|
||||||
class DoiBoostHostedByMapTest {
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
// @Test
|
|
||||||
// def testMerge():Unit = {
|
|
||||||
// val conf: SparkConf = new SparkConf()
|
|
||||||
// val spark: SparkSession =
|
|
||||||
// SparkSession
|
|
||||||
// .builder()
|
|
||||||
// .config(conf)
|
|
||||||
// .appName(getClass.getSimpleName)
|
|
||||||
// .master("local[*]").getOrCreate()
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
|
|
||||||
// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
|
|
||||||
// implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// import spark.implicits._
|
|
||||||
// val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz")
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem))
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// hbMap.show()
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// }
|
|
||||||
|
|
||||||
|
|
||||||
@Test
|
|
||||||
def idDSGeneration():Unit = {
|
|
||||||
val s ="doajarticles::0066-782X"
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
println(DoiBoostMappingUtil.generateDSId(s))
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,20 @@
|
||||||
|
package eu.dnetlib.dhp.doiboost
|
||||||
|
|
||||||
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
|
||||||
|
class DoiBoostHostedByMapTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
def idDSGeneration():Unit = {
|
||||||
|
val s ="doajarticles::0066-782X"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
println(DoiBoostMappingUtil.generateDSId(s))
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,7 +1,8 @@
|
||||||
package eu.dnetlib.doiboost.crossref
|
package eu.dnetlib.dhp.doiboost.crossref
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf._
|
import eu.dnetlib.dhp.schema.oaf._
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils
|
import eu.dnetlib.dhp.utils.DHPUtils
|
||||||
|
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
|
||||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
||||||
import org.junit.jupiter.api.Assertions._
|
import org.junit.jupiter.api.Assertions._
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
|
|
@ -21,9 +22,9 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testFunderRelationshipsMapping(): Unit = {
|
def testFunderRelationshipsMapping(): Unit = {
|
||||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
|
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
|
||||||
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
|
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
|
||||||
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
|
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
|
||||||
|
|
||||||
|
|
||||||
for (line <- funder_doi.lines) {
|
for (line <- funder_doi.lines) {
|
||||||
|
|
@ -72,7 +73,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testOrcidID() :Unit = {
|
def testOrcidID() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("orcid_data.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/orcid_data.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -93,7 +94,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testEmptyTitle() :Unit = {
|
def testEmptyTitle() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/empty_title.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -115,7 +116,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testPeerReviewed(): Unit = {
|
def testPeerReviewed(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/prwTest.json")).mkString
|
||||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -156,7 +157,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testJournalRelation(): Unit = {
|
def testJournalRelation(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("awardTest.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/awardTest.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty)
|
assertFalse(json.isEmpty)
|
||||||
|
|
@ -177,7 +178,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testConvertBookFromCrossRef2Oaf(): Unit = {
|
def testConvertBookFromCrossRef2Oaf(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("book.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/book.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty);
|
assertFalse(json.isEmpty);
|
||||||
|
|
@ -233,7 +234,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testConvertPreprintFromCrossRef2Oaf(): Unit = {
|
def testConvertPreprintFromCrossRef2Oaf(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("preprint.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/preprint.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty);
|
assertFalse(json.isEmpty);
|
||||||
|
|
@ -291,7 +292,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testConvertDatasetFromCrossRef2Oaf(): Unit = {
|
def testConvertDatasetFromCrossRef2Oaf(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dataset.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty);
|
assertFalse(json.isEmpty);
|
||||||
|
|
@ -332,7 +333,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testConvertArticleFromCrossRef2Oaf(): Unit = {
|
def testConvertArticleFromCrossRef2Oaf(): Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty);
|
assertFalse(json.isEmpty);
|
||||||
|
|
@ -400,7 +401,7 @@ class CrossrefMappingTest {
|
||||||
@Test
|
@Test
|
||||||
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
|
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
|
||||||
|
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dump_file.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dump_file.json")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
||||||
assertFalse(json.isEmpty);
|
assertFalse(json.isEmpty);
|
||||||
|
|
@ -415,55 +416,12 @@ class CrossrefMappingTest {
|
||||||
assert(items.size == 1)
|
assert(items.size == 1)
|
||||||
val result: Result = items.head.asInstanceOf[Publication]
|
val result: Result = items.head.asInstanceOf[Publication]
|
||||||
assertNotNull(result)
|
assertNotNull(result)
|
||||||
|
|
||||||
logger.info(mapper.writeValueAsString(result));
|
logger.info(mapper.writeValueAsString(result));
|
||||||
|
|
||||||
// assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
|
|
||||||
// assertNotNull(
|
|
||||||
// result.getDataInfo.getProvenanceaction,
|
|
||||||
// "DataInfo/Provenance test not null Failed");
|
|
||||||
// assertFalse(
|
|
||||||
// result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
|
|
||||||
// "DataInfo/Provenance/classId test not null Failed");
|
|
||||||
// assertFalse(
|
|
||||||
// result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
|
|
||||||
// "DataInfo/Provenance/className test not null Failed");
|
|
||||||
// assertFalse(
|
|
||||||
// result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
|
|
||||||
// "DataInfo/Provenance/SchemeId test not null Failed");
|
|
||||||
// assertFalse(
|
|
||||||
// result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
|
|
||||||
// "DataInfo/Provenance/SchemeName test not null Failed");
|
|
||||||
//
|
|
||||||
// assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
|
|
||||||
// assertFalse(result.getCollectedfrom.isEmpty);
|
|
||||||
//
|
|
||||||
// val collectedFromList = result.getCollectedfrom.asScala
|
|
||||||
// assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
|
|
||||||
//
|
|
||||||
// assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// val relevantDates = result.getRelevantdate.asScala
|
|
||||||
//
|
|
||||||
// assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
|
|
||||||
//
|
|
||||||
// val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
|
|
||||||
// assertFalse(rels.isEmpty)
|
|
||||||
// rels.foreach(relation => {
|
|
||||||
// assertNotNull(relation)
|
|
||||||
// assertFalse(relation.getSource.isEmpty)
|
|
||||||
// assertFalse(relation.getTarget.isEmpty)
|
|
||||||
// assertFalse(relation.getRelClass.isEmpty)
|
|
||||||
// assertFalse(relation.getRelType.isEmpty)
|
|
||||||
// assertFalse(relation.getSubRelType.isEmpty)
|
|
||||||
//
|
|
||||||
// })
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testNormalizeDOI(): Unit = {
|
def testNormalizeDOI(): Unit = {
|
||||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
|
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
|
||||||
val line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
|
val line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
|
||||||
val json = template.replace("%s", line)
|
val json = template.replace("%s", line)
|
||||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||||
|
|
@ -479,7 +437,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testNormalizeDOI2(): Unit = {
|
def testNormalizeDOI2(): Unit = {
|
||||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
|
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
|
||||||
|
|
||||||
val resultList: List[Oaf] = Crossref2Oaf.convert(template)
|
val resultList: List[Oaf] = Crossref2Oaf.convert(template)
|
||||||
assertTrue(resultList.nonEmpty)
|
assertTrue(resultList.nonEmpty)
|
||||||
|
|
@ -494,7 +452,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testLicenseVorClosed() :Unit = {
|
def testLicenseVorClosed() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_vor.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -521,7 +479,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testLicenseOpen() :Unit = {
|
def testLicenseOpen() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_open.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -544,7 +502,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testLicenseEmbargoOpen() :Unit = {
|
def testLicenseEmbargoOpen() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_open.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -567,7 +525,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testLicenseEmbargo() :Unit = {
|
def testLicenseEmbargo() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -591,7 +549,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testLicenseEmbargoDateTime() :Unit = {
|
def testLicenseEmbargoDateTime() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -614,7 +572,7 @@ class CrossrefMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testMultipleURLs() :Unit = {
|
def testMultipleURLs() :Unit = {
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("multiple_urls.json")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/multiple_urls.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
|
|
@ -1,11 +1,12 @@
|
||||||
package eu.dnetlib.doiboost.mag
|
package eu.dnetlib.dhp.doiboost.mag
|
||||||
|
|
||||||
|
import eu.dnetlib.doiboost.mag.{ConversionUtil, MagPapers, SparkProcessMAG}
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, SparkSession}
|
import org.apache.spark.sql.{Dataset, SparkSession}
|
||||||
import org.codehaus.jackson.map.ObjectMapper
|
import org.codehaus.jackson.map.ObjectMapper
|
||||||
|
import org.json4s.DefaultFormats
|
||||||
import org.junit.jupiter.api.Assertions._
|
import org.junit.jupiter.api.Assertions._
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
import org.json4s.DefaultFormats
|
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import java.sql.Timestamp
|
import java.sql.Timestamp
|
||||||
|
|
@ -47,7 +48,7 @@ class MAGMappingTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def buildInvertedIndexTest(): Unit = {
|
def buildInvertedIndexTest(): Unit = {
|
||||||
val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString
|
val json_input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/mag/invertedIndex.json")).mkString
|
||||||
val description = ConversionUtil.convertInvertedIndexString(json_input)
|
val description = ConversionUtil.convertInvertedIndexString(json_input)
|
||||||
assertNotNull(description)
|
assertNotNull(description)
|
||||||
assertTrue(description.nonEmpty)
|
assertTrue(description.nonEmpty)
|
||||||
|
|
@ -71,7 +72,7 @@ class MAGMappingTest {
|
||||||
.appName(getClass.getSimpleName)
|
.appName(getClass.getSimpleName)
|
||||||
.config(conf)
|
.config(conf)
|
||||||
.getOrCreate()
|
.getOrCreate()
|
||||||
val path = getClass.getResource("magPapers.json").getPath
|
val path = getClass.getResource("/eu/dnetlib/doiboost/mag/magPapers.json").getPath
|
||||||
|
|
||||||
import org.apache.spark.sql.Encoders
|
import org.apache.spark.sql.Encoders
|
||||||
val schema = Encoders.product[MagPapers].schema
|
val schema = Encoders.product[MagPapers].schema
|
||||||
|
|
@ -101,7 +102,7 @@ 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("/eu/dnetlib/doiboost/mag/duplicatedMagPapers.json").getPath
|
||||||
|
|
||||||
import org.apache.spark.sql.Encoders
|
import org.apache.spark.sql.Encoders
|
||||||
val schema = Encoders.product[MagPapers].schema
|
val schema = Encoders.product[MagPapers].schema
|
||||||
|
|
@ -1,7 +1,8 @@
|
||||||
package eu.dnetlib.doiboost.orcid
|
package eu.dnetlib.dhp.doiboost.orcid
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||||
|
import eu.dnetlib.doiboost.orcid._
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||||
import org.junit.jupiter.api.Assertions._
|
import org.junit.jupiter.api.Assertions._
|
||||||
|
|
@ -10,9 +11,8 @@ import org.junit.jupiter.api.io.TempDir
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import java.nio.file.Path
|
import java.nio.file.Path
|
||||||
import scala.io.Source
|
|
||||||
|
|
||||||
import scala.collection.JavaConversions._
|
import scala.collection.JavaConversions._
|
||||||
|
import scala.io.Source
|
||||||
|
|
||||||
class MappingORCIDToOAFTest {
|
class MappingORCIDToOAFTest {
|
||||||
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
|
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
|
||||||
|
|
@ -20,7 +20,7 @@ class MappingORCIDToOAFTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testExtractData():Unit ={
|
def testExtractData():Unit ={
|
||||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
|
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/orcid/dataOutput")).mkString
|
||||||
assertNotNull(json)
|
assertNotNull(json)
|
||||||
assertFalse(json.isEmpty)
|
assertFalse(json.isEmpty)
|
||||||
json.lines.foreach(s => {
|
json.lines.foreach(s => {
|
||||||
|
|
@ -1,13 +1,13 @@
|
||||||
package eu.dnetlib.doiboost.uw
|
package eu.dnetlib.dhp.doiboost.uw
|
||||||
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.schema.oaf.OpenAccessRoute
|
import eu.dnetlib.dhp.schema.oaf.OpenAccessRoute
|
||||||
|
import eu.dnetlib.doiboost.uw.UnpayWallToOAF
|
||||||
|
import org.junit.jupiter.api.Assertions._
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
import org.junit.jupiter.api.Assertions._
|
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
|
||||||
|
|
||||||
class UnpayWallMappingTest {
|
class UnpayWallMappingTest {
|
||||||
|
|
||||||
|
|
@ -18,7 +18,7 @@ class UnpayWallMappingTest {
|
||||||
@Test
|
@Test
|
||||||
def testMappingToOAF():Unit ={
|
def testMappingToOAF():Unit ={
|
||||||
|
|
||||||
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
|
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/uw/input.json")).mkString
|
||||||
|
|
||||||
var i:Int = 0
|
var i:Int = 0
|
||||||
for (line <-Ilist.lines) {
|
for (line <-Ilist.lines) {
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
#DHP Enrichment
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||||
|
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
|
||||||
|
name="DHP-Aggregation">
|
||||||
|
<skin>
|
||||||
|
<groupId>org.apache.maven.skins</groupId>
|
||||||
|
<artifactId>maven-fluido-skin</artifactId>
|
||||||
|
<version>1.8</version>
|
||||||
|
</skin>
|
||||||
|
<poweredBy>
|
||||||
|
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
|
||||||
|
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
|
||||||
|
</poweredBy>
|
||||||
|
<body>
|
||||||
|
<links>
|
||||||
|
<item name="Code" href="https://code-repo.d4science.org/" />
|
||||||
|
</links>
|
||||||
|
<menu name="Documentation">
|
||||||
|
<item name="Link1 Collapsable" href="about.html" collapse="true">
|
||||||
|
<item name="item1" href="pubmed.html"/>
|
||||||
|
<item name="item2" href="datacite.html"/>
|
||||||
|
</item>
|
||||||
|
</menu>
|
||||||
|
<menu ref="reports"/>
|
||||||
|
</body>
|
||||||
|
</project>
|
||||||
|
|
@ -88,7 +88,7 @@ public class CleanGraphSparkJob {
|
||||||
readTableFromPath(spark, inputPath, clazz)
|
readTableFromPath(spark, inputPath, clazz)
|
||||||
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
|
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
|
||||||
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
|
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
|
||||||
.map((MapFunction<T, T>) GraphCleaningFunctions::cleanup, Encoders.bean(clazz))
|
.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
|
||||||
.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
|
.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
|
||||||
.write()
|
.write()
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
|
|
|
||||||
|
|
@ -30,6 +30,11 @@ public class OafCleaner implements Serializable {
|
||||||
}
|
}
|
||||||
} else if (hasMapping(o, mapping)) {
|
} else if (hasMapping(o, mapping)) {
|
||||||
mapping.get(o.getClass()).accept(o);
|
mapping.get(o.getClass()).accept(o);
|
||||||
|
for (final Field f : getAllFields(o.getClass())) {
|
||||||
|
f.setAccessible(true);
|
||||||
|
final Object val = f.get(o);
|
||||||
|
navigate(val, mapping);
|
||||||
|
}
|
||||||
} else {
|
} else {
|
||||||
for (final Field f : getAllFields(o.getClass())) {
|
for (final Field f : getAllFields(o.getClass())) {
|
||||||
f.setAccessible(true);
|
f.setAccessible(true);
|
||||||
|
|
|
||||||
|
|
@ -8,3 +8,12 @@ CREATE VIEW IF NOT EXISTS ${hiveDbName}.result as
|
||||||
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.software s
|
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.software s
|
||||||
union all
|
union all
|
||||||
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.otherresearchproduct o;
|
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.otherresearchproduct o;
|
||||||
|
|
||||||
|
ANALYZE TABLE ${hiveDbName}.datasource COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.organization COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.project COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.publication COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.dataset COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.otherresearchproduct COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.software COMPUTE STATISTICS;
|
||||||
|
ANALYZE TABLE ${hiveDbName}.relation COMPUTE STATISTICS;
|
||||||
|
|
@ -292,7 +292,7 @@
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
<master>yarn</master>
|
<master>yarn</master>
|
||||||
<mode>cluster</mode>
|
<mode>cluster</mode>
|
||||||
<name>Import table project</name>
|
<name>Import table relation</name>
|
||||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
<spark-opts>
|
<spark-opts>
|
||||||
|
|
|
||||||
|
|
@ -8,6 +8,15 @@
|
||||||
<name>unresolvedPath</name>
|
<name>unresolvedPath</name>
|
||||||
<description>the path of the unresolved Entities</description>
|
<description>the path of the unresolved Entities</description>
|
||||||
</property>
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>targetPath</name>
|
||||||
|
<description>the target path after resolution</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shouldResolveEntities</name>
|
||||||
|
<value>true</value>
|
||||||
|
<description>allows to activate/deactivate the resolution process over the entities</description>
|
||||||
|
</property>
|
||||||
</parameters>
|
</parameters>
|
||||||
|
|
||||||
<start to="ResolveRelations"/>
|
<start to="ResolveRelations"/>
|
||||||
|
|
@ -36,11 +45,20 @@
|
||||||
<arg>--master</arg><arg>yarn</arg>
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||||
<arg>--workingPath</arg><arg>${workingDir}</arg>
|
<arg>--workingPath</arg><arg>${workingDir}</arg>
|
||||||
|
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="ResolveEntities"/>
|
<ok to="decision_resolveEntities"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
|
<decision name="decision_resolveEntities">
|
||||||
|
<switch>
|
||||||
|
<case to="copy_result">${wf:conf('shouldResolveEntities') eq false}</case>
|
||||||
|
<case to="ResolveEntities">${wf:conf('shouldResolveEntities') eq true}</case>
|
||||||
|
<default to="ResolveEntities"/>
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
<action name="ResolveEntities">
|
<action name="ResolveEntities">
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
<master>yarn</master>
|
<master>yarn</master>
|
||||||
|
|
@ -62,11 +80,91 @@
|
||||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||||
<arg>--unresolvedPath</arg><arg>${unresolvedPath}</arg>
|
<arg>--unresolvedPath</arg><arg>${unresolvedPath}</arg>
|
||||||
<arg>--workingPath</arg><arg>${workingDir}</arg>
|
<arg>--workingPath</arg><arg>${workingDir}</arg>
|
||||||
|
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="End"/>
|
<ok to="copy_entities"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
<end name="End"/>
|
<fork name="copy_result">
|
||||||
|
<path start="copy_publication"/>
|
||||||
|
<path start="copy_dataset"/>
|
||||||
|
<path start="copy_otherresearchproduct"/>
|
||||||
|
<path start="copy_software"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="copy_publication">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/publication</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/publication</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait_result"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_dataset">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/dataset</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/dataset</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait_result"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_otherresearchproduct">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/otherresearchproduct</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/otherresearchproduct</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait_result"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_software">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/software</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/software</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait_result"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="copy_wait_result" to="copy_entities"/>
|
||||||
|
|
||||||
|
<fork name="copy_entities">
|
||||||
|
<path start="copy_organization"/>
|
||||||
|
<path start="copy_projects"/>
|
||||||
|
<path start="copy_datasource"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="copy_organization">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/organization</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/organization</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_projects">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/project</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/project</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_datasource">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<arg>${nameNode}/${graphBasePath}/datasource</arg>
|
||||||
|
<arg>${nameNode}/${targetPath}/datasource</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="copy_wait" to="End"/>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
</workflow-app>
|
</workflow-app>
|
||||||
|
|
@ -2,5 +2,6 @@
|
||||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
{"paramName":"u", "paramLongName":"unresolvedPath", "paramDescription": "the source Path", "paramRequired": true},
|
{"paramName":"u", "paramLongName":"unresolvedPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
||||||
|
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true}
|
||||||
]
|
]
|
||||||
|
|
@ -1,5 +1,6 @@
|
||||||
[
|
[
|
||||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
||||||
|
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true}
|
||||||
]
|
]
|
||||||
|
|
@ -1,8 +1,8 @@
|
||||||
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||||
|
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
|
|
||||||
import org.apache.spark.sql.expressions.Aggregator
|
import org.apache.spark.sql.expressions.Aggregator
|
||||||
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
|
||||||
|
|
||||||
|
|
||||||
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
|
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
|
||||||
|
|
@ -2,13 +2,12 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult.{applyHBtoPubs, getClass}
|
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Datasource, Publication}
|
import eu.dnetlib.dhp.schema.oaf.Datasource
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
|
@ -52,18 +51,18 @@ object SparkApplyHostedByMapToDatasource {
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
val dats : Dataset[Datasource] = spark.read.textFile(graphPath + "/datasource")
|
val dats: Dataset[Datasource] = spark.read.textFile(graphPath + "/datasource")
|
||||||
.map(r => mapper.readValue(r, classOf[Datasource]))
|
.map(r => mapper.readValue(r, classOf[Datasource]))
|
||||||
|
|
||||||
val pinfo : Dataset[EntityInfo] = Aggregators.datasourceToSingleId( spark.read.textFile(preparedInfoPath)
|
val pinfo: Dataset[EntityInfo] = Aggregators.datasourceToSingleId(spark.read.textFile(preparedInfoPath)
|
||||||
.map(ei => mapper.readValue(ei, classOf[EntityInfo])))
|
.map(ei => mapper.readValue(ei, classOf[EntityInfo])))
|
||||||
|
|
||||||
applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath)
|
applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath)
|
||||||
|
|
||||||
spark.read.textFile(outputPath)
|
spark.read.textFile(outputPath)
|
||||||
.write
|
.write
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
.option("compression","gzip")
|
.option("compression", "gzip")
|
||||||
.text(graphPath + "/datasource")
|
.text(graphPath + "/datasource")
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -5,16 +5,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||||
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.dhp.schema.oaf.{Datasource, Instance, OpenAccessRoute, Publication}
|
import eu.dnetlib.dhp.schema.oaf.{Instance, OpenAccessRoute, Publication}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
|
|
||||||
|
|
||||||
object SparkApplyHostedByMapToResult {
|
object SparkApplyHostedByMapToResult {
|
||||||
|
|
||||||
def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = {
|
def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = {
|
||||||
|
|
@ -25,7 +23,7 @@ object SparkApplyHostedByMapToResult {
|
||||||
val ei: EntityInfo = t2._2
|
val ei: EntityInfo = t2._2
|
||||||
val i = p.getInstance().asScala
|
val i = p.getInstance().asScala
|
||||||
if (i.size == 1) {
|
if (i.size == 1) {
|
||||||
val inst: Instance = i(0)
|
val inst: Instance = i.head
|
||||||
inst.getHostedby.setKey(ei.getHostedById)
|
inst.getHostedby.setKey(ei.getHostedById)
|
||||||
inst.getHostedby.setValue(ei.getName)
|
inst.getHostedby.setValue(ei.getName)
|
||||||
if (ei.getOpenAccess) {
|
if (ei.getOpenAccess) {
|
||||||
|
|
@ -39,6 +37,7 @@ object SparkApplyHostedByMapToResult {
|
||||||
p
|
p
|
||||||
})(Encoders.bean(classOf[Publication]))
|
})(Encoders.bean(classOf[Publication]))
|
||||||
}
|
}
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -67,18 +66,18 @@ object SparkApplyHostedByMapToResult {
|
||||||
implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
|
implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
val pubs : Dataset[Publication] = spark.read.textFile(graphPath + "/publication")
|
val pubs: Dataset[Publication] = spark.read.textFile(graphPath + "/publication")
|
||||||
.map(r => mapper.readValue(r, classOf[Publication]))
|
.map(r => mapper.readValue(r, classOf[Publication]))
|
||||||
|
|
||||||
val pinfo : Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath)
|
val pinfo: Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath)
|
||||||
.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
|
.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
|
||||||
|
|
||||||
applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath)
|
applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath)
|
||||||
|
|
||||||
spark.read.textFile(outputPath)
|
spark.read.textFile(outputPath)
|
||||||
.write
|
.write
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
.option("compression","gzip")
|
.option("compression", "gzip")
|
||||||
.text(graphPath + "/publication")
|
.text(graphPath + "/publication")
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -3,61 +3,58 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication}
|
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
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
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
object SparkPrepareHostedByInfoToApply {
|
object SparkPrepareHostedByInfoToApply {
|
||||||
|
|
||||||
implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
|
implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
|
||||||
|
|
||||||
def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = {
|
def getList(id: String, j: Journal, name: String): List[EntityInfo] = {
|
||||||
var lst:List[EntityInfo] = List()
|
var lst: List[EntityInfo] = List()
|
||||||
|
|
||||||
|
|
||||||
if (j.getIssnLinking != null && !j.getIssnLinking.equals("")){
|
if (j.getIssnLinking != null && !j.getIssnLinking.equals("")) {
|
||||||
lst = EntityInfo.newInstance(id, j.getIssnLinking, name) :: lst
|
lst = EntityInfo.newInstance(id, j.getIssnLinking, name) :: lst
|
||||||
}
|
}
|
||||||
if (j.getIssnOnline != null && !j.getIssnOnline.equals("")){
|
if (j.getIssnOnline != null && !j.getIssnOnline.equals("")) {
|
||||||
lst = EntityInfo.newInstance(id, j.getIssnOnline, name) :: lst
|
lst = EntityInfo.newInstance(id, j.getIssnOnline, name) :: lst
|
||||||
}
|
}
|
||||||
if (j.getIssnPrinted != null && !j.getIssnPrinted.equals("")){
|
if (j.getIssnPrinted != null && !j.getIssnPrinted.equals("")) {
|
||||||
lst = EntityInfo.newInstance(id, j.getIssnPrinted, name) :: lst
|
lst = EntityInfo.newInstance(id, j.getIssnPrinted, name) :: lst
|
||||||
}
|
}
|
||||||
lst
|
lst
|
||||||
}
|
}
|
||||||
|
|
||||||
def prepareResultInfo(spark:SparkSession, publicationPath:String) : Dataset[EntityInfo] = {
|
def prepareResultInfo(spark: SparkSession, publicationPath: String): Dataset[EntityInfo] = {
|
||||||
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
|
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
val dd : Dataset[Publication] = spark.read.textFile(publicationPath)
|
val dd: Dataset[Publication] = spark.read.textFile(publicationPath)
|
||||||
.map(r => mapper.readValue(r, classOf[Publication]))
|
.map(r => mapper.readValue(r, classOf[Publication]))
|
||||||
|
|
||||||
dd.filter(p => p.getJournal != null ).flatMap(p => getList(p.getId, p.getJournal, ""))
|
dd.filter(p => p.getJournal != null).flatMap(p => getList(p.getId, p.getJournal, ""))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def toEntityInfo(input:String): EntityInfo = {
|
def toEntityInfo(input: String): EntityInfo = {
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]]
|
val c: Map[String, HostedByItemType] = json.extract[Map[String, HostedByItemType]]
|
||||||
toEntityItem(c.keys.head, c.values.head)
|
toEntityItem(c.keys.head, c.values.head)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def toEntityItem(journal_id: String , hbi: HostedByItemType): EntityInfo = {
|
def toEntityItem(journal_id: String, hbi: HostedByItemType): EntityInfo = {
|
||||||
|
|
||||||
EntityInfo.newInstance(hbi.id, journal_id, hbi.officialname, hbi.openAccess)
|
EntityInfo.newInstance(hbi.id, journal_id, hbi.officialname, hbi.openAccess)
|
||||||
|
|
||||||
|
|
@ -67,7 +64,7 @@ object SparkPrepareHostedByInfoToApply {
|
||||||
Aggregators.resultToSingleId(res.joinWith(hbm, res.col("journalId").equalTo(hbm.col("journalId")), "left")
|
Aggregators.resultToSingleId(res.joinWith(hbm, res.col("journalId").equalTo(hbm.col("journalId")), "left")
|
||||||
.map(t2 => {
|
.map(t2 => {
|
||||||
val res: EntityInfo = t2._1
|
val res: EntityInfo = t2._1
|
||||||
if(t2._2 != null ){
|
if (t2._2 != null) {
|
||||||
val ds = t2._2
|
val ds = t2._2
|
||||||
res.setHostedById(ds.getId)
|
res.setHostedById(ds.getId)
|
||||||
res.setOpenAccess(ds.getOpenAccess)
|
res.setOpenAccess(ds.getOpenAccess)
|
||||||
|
|
@ -107,10 +104,10 @@ object SparkPrepareHostedByInfoToApply {
|
||||||
|
|
||||||
|
|
||||||
//STEP1: read the hostedbymap and transform it in EntityInfo
|
//STEP1: read the hostedbymap and transform it in EntityInfo
|
||||||
val hostedByInfo:Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo)
|
val hostedByInfo: Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo)
|
||||||
|
|
||||||
//STEP2: create association (publication, issn), (publication, eissn), (publication, lissn)
|
//STEP2: create association (publication, issn), (publication, eissn), (publication, lissn)
|
||||||
val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication")
|
val resultInfoDataset: Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication")
|
||||||
|
|
||||||
//STEP3: left join resultInfo with hostedByInfo on journal_id. Reduction of all the results with the same id in just
|
//STEP3: left join resultInfo with hostedByInfo on journal_id. Reduction of all the results with the same id in just
|
||||||
//one entry (one result could be associated to issn and eissn and so possivly matching more than once against the map)
|
//one entry (one result could be associated to issn and eissn and so possivly matching more than once against the map)
|
||||||
|
|
@ -1,29 +1,27 @@
|
||||||
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel}
|
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel}
|
||||||
import eu.dnetlib.dhp.schema.oaf.Datasource
|
import eu.dnetlib.dhp.schema.oaf.Datasource
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
|
import org.apache.hadoop.conf.Configuration
|
||||||
|
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||||
|
import org.apache.hadoop.io.compress.GzipCodec
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||||
import org.json4s.DefaultFormats
|
import org.json4s.DefaultFormats
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
|
||||||
import org.apache.hadoop.conf.Configuration
|
|
||||||
import org.apache.hadoop.fs.FileSystem
|
|
||||||
import org.apache.hadoop.fs.Path
|
|
||||||
import java.io.PrintWriter
|
import java.io.PrintWriter
|
||||||
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec
|
|
||||||
|
|
||||||
|
|
||||||
object SparkProduceHostedByMap {
|
object SparkProduceHostedByMap {
|
||||||
|
|
||||||
|
|
||||||
implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])
|
implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])
|
||||||
|
|
||||||
|
|
||||||
def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)) : HostedByItemType = {
|
def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)): HostedByItemType = {
|
||||||
val openaire: HostedByInfo = input._1._1
|
val openaire: HostedByInfo = input._1._1
|
||||||
val doaj: HostedByInfo = input._1._2
|
val doaj: HostedByInfo = input._1._2
|
||||||
val gold: HostedByInfo = input._2
|
val gold: HostedByInfo = input._2
|
||||||
|
|
@ -44,7 +42,7 @@ object SparkProduceHostedByMap {
|
||||||
|
|
||||||
implicit val formats = org.json4s.DefaultFormats
|
implicit val formats = org.json4s.DefaultFormats
|
||||||
|
|
||||||
val map: Map [String, HostedByItemType] = Map (input._1 -> input._2 )
|
val map: Map[String, HostedByItemType] = Map(input._1 -> input._2)
|
||||||
|
|
||||||
Serialization.write(map)
|
Serialization.write(map)
|
||||||
|
|
||||||
|
|
@ -52,34 +50,33 @@ object SparkProduceHostedByMap {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def getHostedByItemType(id: String, officialname: String, issn: String, eissn: String, issnl: String, oa: Boolean): HostedByItemType = {
|
||||||
def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = {
|
if (issn != null) {
|
||||||
if(issn != null){
|
if (eissn != null) {
|
||||||
if(eissn != null){
|
if (issnl != null) {
|
||||||
if(issnl != null){
|
HostedByItemType(id, officialname, issn, eissn, issnl, oa)
|
||||||
HostedByItemType(id, officialname, issn, eissn, issnl , oa)
|
} else {
|
||||||
}else{
|
HostedByItemType(id, officialname, issn, eissn, "", oa)
|
||||||
HostedByItemType(id, officialname, issn, eissn, "" , oa)
|
|
||||||
}
|
}
|
||||||
}else{
|
} else {
|
||||||
if(issnl != null){
|
if (issnl != null) {
|
||||||
HostedByItemType(id, officialname, issn, "", issnl , oa)
|
HostedByItemType(id, officialname, issn, "", issnl, oa)
|
||||||
}else{
|
} else {
|
||||||
HostedByItemType(id, officialname, issn, "", "" , oa)
|
HostedByItemType(id, officialname, issn, "", "", oa)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}else{
|
} else {
|
||||||
if(eissn != null){
|
if (eissn != null) {
|
||||||
if(issnl != null){
|
if (issnl != null) {
|
||||||
HostedByItemType(id, officialname, "", eissn, issnl , oa)
|
HostedByItemType(id, officialname, "", eissn, issnl, oa)
|
||||||
}else{
|
} else {
|
||||||
HostedByItemType(id, officialname, "", eissn, "" , oa)
|
HostedByItemType(id, officialname, "", eissn, "", oa)
|
||||||
}
|
}
|
||||||
}else{
|
} else {
|
||||||
if(issnl != null){
|
if (issnl != null) {
|
||||||
HostedByItemType(id, officialname, "", "", issnl , oa)
|
HostedByItemType(id, officialname, "", "", issnl, oa)
|
||||||
}else{
|
} else {
|
||||||
HostedByItemType("", "", "", "", "" , oa)
|
HostedByItemType("", "", "", "", "", oa)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -90,10 +87,10 @@ object SparkProduceHostedByMap {
|
||||||
|
|
||||||
return getHostedByItemType(dats.getId, dats.getOfficialname.getValue, dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, false)
|
return getHostedByItemType(dats.getId, dats.getOfficialname.getValue, dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, false)
|
||||||
}
|
}
|
||||||
HostedByItemType("","","","","",false)
|
HostedByItemType("", "", "", "", "", false)
|
||||||
}
|
}
|
||||||
|
|
||||||
def oaHostedByDataset(spark:SparkSession, datasourcePath : String) : Dataset[HostedByItemType] = {
|
def oaHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
|
||||||
|
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
|
|
@ -102,10 +99,10 @@ object SparkProduceHostedByMap {
|
||||||
|
|
||||||
implicit var encoderD = Encoders.kryo[Datasource]
|
implicit var encoderD = Encoders.kryo[Datasource]
|
||||||
|
|
||||||
val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath)
|
val dd: Dataset[Datasource] = spark.read.textFile(datasourcePath)
|
||||||
.map(r => mapper.readValue(r, classOf[Datasource]))
|
.map(r => mapper.readValue(r, classOf[Datasource]))
|
||||||
|
|
||||||
dd.map{ddt => oaToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
|
dd.map { ddt => oaToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -115,17 +112,17 @@ object SparkProduceHostedByMap {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def goldHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
|
def goldHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
|
implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
val dd : Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath)
|
val dd: Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath)
|
||||||
.map(r => mapper.readValue(r, classOf[UnibiGoldModel]))
|
.map(r => mapper.readValue(r, classOf[UnibiGoldModel]))
|
||||||
|
|
||||||
dd.map{ddt => goldToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
|
dd.map { ddt => goldToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -134,41 +131,40 @@ object SparkProduceHostedByMap {
|
||||||
return getHostedByItemType(Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", true)
|
return getHostedByItemType(Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", true)
|
||||||
}
|
}
|
||||||
|
|
||||||
def doajHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
|
def doajHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
|
implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
val dd : Dataset[DOAJModel] = spark.read.textFile(datasourcePath)
|
val dd: Dataset[DOAJModel] = spark.read.textFile(datasourcePath)
|
||||||
.map(r => mapper.readValue(r, classOf[DOAJModel]))
|
.map(r => mapper.readValue(r, classOf[DOAJModel]))
|
||||||
|
|
||||||
dd.map{ddt => doajToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
|
dd.map { ddt => doajToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
def toList(input: HostedByItemType): List[(String, HostedByItemType)] = {
|
def toList(input: HostedByItemType): List[(String, HostedByItemType)] = {
|
||||||
var lst : List[(String, HostedByItemType)] = List()
|
var lst: List[(String, HostedByItemType)] = List()
|
||||||
if(!input.issn.equals("")){
|
if (!input.issn.equals("")) {
|
||||||
lst = (input.issn, input) :: lst
|
lst = (input.issn, input) :: lst
|
||||||
}
|
}
|
||||||
if(!input.eissn.equals("")){
|
if (!input.eissn.equals("")) {
|
||||||
lst = (input.eissn, input) :: lst
|
lst = (input.eissn, input) :: lst
|
||||||
}
|
}
|
||||||
if(!input.lissn.equals("")){
|
if (!input.lissn.equals("")) {
|
||||||
lst = (input.lissn, input) :: lst
|
lst = (input.lissn, input) :: lst
|
||||||
}
|
}
|
||||||
lst
|
lst
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode: String): Unit = {
|
||||||
def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode : String):Unit = {
|
|
||||||
val conf = new Configuration()
|
val conf = new Configuration()
|
||||||
|
|
||||||
conf.set("fs.defaultFS", hdfsNameNode)
|
conf.set("fs.defaultFS", hdfsNameNode)
|
||||||
val fs= FileSystem.get(conf)
|
val fs = FileSystem.get(conf)
|
||||||
val output = fs.create(new Path(outputPath))
|
val output = fs.create(new Path(outputPath))
|
||||||
val writer = new PrintWriter(output)
|
val writer = new PrintWriter(output)
|
||||||
try {
|
try {
|
||||||
|
|
@ -182,7 +178,6 @@ object SparkProduceHostedByMap {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
||||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
@ -213,7 +208,7 @@ object SparkProduceHostedByMap {
|
||||||
.union(doajHostedByDataset(spark, workingDirPath + "/doaj.json"))
|
.union(doajHostedByDataset(spark, workingDirPath + "/doaj.json"))
|
||||||
.flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|"))
|
.flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|"))
|
||||||
.map(hbi => toHostedByMap(hbi))(Encoders.STRING)
|
.map(hbi => toHostedByMap(hbi))(Encoders.STRING)
|
||||||
.rdd.saveAsTextFile(outputPath , classOf[GzipCodec])
|
.rdd.saveAsTextFile(outputPath, classOf[GzipCodec])
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -4,17 +4,11 @@ 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.ModelSupport
|
import eu.dnetlib.dhp.schema.common.ModelSupport
|
||||||
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils
|
import eu.dnetlib.dhp.utils.DHPUtils
|
||||||
import org.apache.commons.io.IOUtils
|
|
||||||
import org.apache.commons.lang3.StringUtils
|
|
||||||
import org.apache.http.client.methods.HttpGet
|
|
||||||
import org.apache.http.impl.client.HttpClients
|
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
import org.apache.spark.{SparkConf, SparkContext}
|
import org.apache.spark.{SparkConf, SparkContext}
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
|
|
||||||
|
|
@ -59,7 +53,7 @@ object CopyHdfsOafSparkApplication {
|
||||||
if (validPaths.nonEmpty) {
|
if (validPaths.nonEmpty) {
|
||||||
val oaf = spark.read.load(validPaths: _*).as[Oaf]
|
val oaf = spark.read.load(validPaths: _*).as[Oaf]
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
|
val l = ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
|
||||||
l.foreach(
|
l.foreach(
|
||||||
e =>
|
e =>
|
||||||
oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))
|
oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))
|
||||||
|
|
@ -2,9 +2,8 @@ package eu.dnetlib.dhp.oa.graph.resolution
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
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.schema.common.EntityType
|
import eu.dnetlib.dhp.schema.common.EntityType
|
||||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
|
|
@ -14,7 +13,7 @@ import org.slf4j.{Logger, LoggerFactory}
|
||||||
object SparkResolveEntities {
|
object SparkResolveEntities {
|
||||||
|
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
val entities = List(EntityType.dataset,EntityType.publication, EntityType.software, EntityType.otherresearchproduct)
|
val entities = List(EntityType.dataset, EntityType.publication, EntityType.software, EntityType.otherresearchproduct)
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
@ -36,25 +35,19 @@ object SparkResolveEntities {
|
||||||
val unresolvedPath = parser.get("unresolvedPath")
|
val unresolvedPath = parser.get("unresolvedPath")
|
||||||
log.info(s"unresolvedPath -> $unresolvedPath")
|
log.info(s"unresolvedPath -> $unresolvedPath")
|
||||||
|
|
||||||
|
val targetPath = parser.get("targetPath")
|
||||||
|
log.info(s"targetPath -> $targetPath")
|
||||||
|
|
||||||
|
|
||||||
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
|
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
|
||||||
fs.mkdirs(new Path(workingPath))
|
fs.mkdirs(new Path(workingPath))
|
||||||
|
|
||||||
resolveEntities(spark, workingPath, unresolvedPath)
|
resolveEntities(spark, workingPath, unresolvedPath)
|
||||||
generateResolvedEntities(spark, workingPath, graphBasePath)
|
generateResolvedEntities(spark, workingPath, graphBasePath, targetPath)
|
||||||
|
|
||||||
// TO BE conservative we keep the original entities in the working dir
|
|
||||||
// and save the resolved entities on the graphBasePath
|
|
||||||
//In future these lines of code should be removed
|
|
||||||
entities.foreach {
|
|
||||||
e =>
|
|
||||||
fs.rename(new Path(s"$graphBasePath/$e"), new Path(s"$workingPath/${e}_old"))
|
|
||||||
fs.rename(new Path(s"$workingPath/resolvedGraph/$e"), new Path(s"$graphBasePath/$e"))
|
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = {
|
||||||
def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = {
|
|
||||||
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
|
|
@ -71,37 +64,42 @@ def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: St
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def deserializeObject(input:String, entity:EntityType ) :Result = {
|
def deserializeObject(input: String, entity: EntityType): Result = {
|
||||||
|
|
||||||
entity match {
|
entity match {
|
||||||
case EntityType.publication => mapper.readValue(input, classOf[Publication])
|
case EntityType.publication => mapper.readValue(input, classOf[Publication])
|
||||||
case EntityType.dataset => mapper.readValue(input, classOf[OafDataset])
|
case EntityType.dataset => mapper.readValue(input, classOf[OafDataset])
|
||||||
case EntityType.software=> mapper.readValue(input, classOf[Software])
|
case EntityType.software => mapper.readValue(input, classOf[Software])
|
||||||
case EntityType.otherresearchproduct=> mapper.readValue(input, classOf[OtherResearchProduct])
|
case EntityType.otherresearchproduct => mapper.readValue(input, classOf[OtherResearchProduct])
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
def generateResolvedEntities(spark:SparkSession, workingPath: String, graphBasePath:String) = {
|
def generateResolvedEntities(spark: SparkSession, workingPath: String, graphBasePath: String, targetPath: String) = {
|
||||||
|
|
||||||
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
val re:Dataset[Result] = spark.read.load(s"$workingPath/resolvedEntities").as[Result]
|
val re: Dataset[(String, Result)] = spark.read.load(s"$workingPath/resolvedEntities").as[Result].map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder))
|
||||||
entities.foreach {
|
entities.foreach {
|
||||||
e =>
|
e => {
|
||||||
|
|
||||||
|
val currentEntityDataset: Dataset[(String, Result)] = spark.read.text(s"$graphBasePath/$e").as[String].map(s => deserializeObject(s, e)).map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder))
|
||||||
|
|
||||||
|
currentEntityDataset.joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left").map(k => {
|
||||||
|
|
||||||
|
val a = k._1
|
||||||
|
val b = k._2
|
||||||
|
if (b == null)
|
||||||
|
a._2
|
||||||
|
else {
|
||||||
|
a._2.mergeFrom(b._2)
|
||||||
|
a._2
|
||||||
|
}
|
||||||
|
}).map(r => mapper.writeValueAsString(r))(Encoders.STRING)
|
||||||
|
.write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$targetPath/$e")
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
spark.read.text(s"$graphBasePath/$e").as[String]
|
|
||||||
.map(s => deserializeObject(s, e))
|
|
||||||
.union(re)
|
|
||||||
.groupByKey(_.getId)
|
|
||||||
.reduceGroups {
|
|
||||||
(x, y) =>
|
|
||||||
x.mergeFrom(y)
|
|
||||||
x
|
|
||||||
}.map(_._2)
|
|
||||||
.filter(r => r.getClass.getSimpleName.toLowerCase != "result")
|
|
||||||
.map(r => mapper.writeValueAsString(r))(Encoders.STRING)
|
|
||||||
.write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$workingPath/resolvedGraph/$e")
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -3,7 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
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.oaf.{Relation, Result}
|
import eu.dnetlib.dhp.schema.oaf.Relation
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils
|
import eu.dnetlib.dhp.utils.DHPUtils
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||||
|
|
@ -35,6 +35,9 @@ object SparkResolveRelation {
|
||||||
val workingPath = parser.get("workingPath")
|
val workingPath = parser.get("workingPath")
|
||||||
log.info(s"workingPath -> $workingPath")
|
log.info(s"workingPath -> $workingPath")
|
||||||
|
|
||||||
|
val targetPath = parser.get("targetPath")
|
||||||
|
log.info(s"targetPath -> $targetPath")
|
||||||
|
|
||||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
|
|
@ -80,20 +83,13 @@ object SparkResolveRelation {
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
.save(s"$workingPath/relation_resolved")
|
.save(s"$workingPath/relation_resolved")
|
||||||
|
|
||||||
|
|
||||||
// TO BE conservative we keep the original relation in the working dir
|
|
||||||
// and save the relation resolved on the graphBasePath
|
|
||||||
//In future this two line of code should be removed
|
|
||||||
|
|
||||||
fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation"))
|
|
||||||
|
|
||||||
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
|
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
|
||||||
.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
|
.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
|
||||||
.map(r => mapper.writeValueAsString(r))
|
.map(r => mapper.writeValueAsString(r))
|
||||||
.write
|
.write
|
||||||
.option("compression", "gzip")
|
.option("compression", "gzip")
|
||||||
.mode(SaveMode.Overwrite)
|
.mode(SaveMode.Overwrite)
|
||||||
.text(s"$graphBasePath/relation")
|
.text(s"$targetPath/relation")
|
||||||
}
|
}
|
||||||
|
|
||||||
def extractInstanceCF(input: String): List[(String, String)] = {
|
def extractInstanceCF(input: String): List[(String, String)] = {
|
||||||
|
|
@ -18,7 +18,6 @@ object SparkDataciteToOAF {
|
||||||
.config(conf)
|
.config(conf)
|
||||||
.appName(getClass.getSimpleName)
|
.appName(getClass.getSimpleName)
|
||||||
.master(parser.get("master")).getOrCreate()
|
.master(parser.get("master")).getOrCreate()
|
||||||
import spark.implicits._
|
|
||||||
|
|
||||||
|
|
||||||
val sc = spark.sparkContext
|
val sc = spark.sparkContext
|
||||||
|
|
@ -2,7 +2,7 @@ package eu.dnetlib.dhp.sx.graph
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.Result
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.hadoop.io.compress.GzipCodec
|
import org.apache.hadoop.io.compress.GzipCodec
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
|
|
@ -29,13 +29,13 @@ object SparkConvertDatasetToJsonRDD {
|
||||||
val targetPath = parser.get("targetPath")
|
val targetPath = parser.get("targetPath")
|
||||||
log.info(s"targetPath -> $targetPath")
|
log.info(s"targetPath -> $targetPath")
|
||||||
|
|
||||||
val resultObject = List("publication","dataset","software", "otherResearchProduct")
|
val resultObject = List("publication", "dataset", "software", "otherResearchProduct")
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||||
|
|
||||||
|
|
||||||
resultObject.foreach{item =>
|
resultObject.foreach { item =>
|
||||||
spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
|
spark.read.load(s"$sourcePath/$item").as[Result].map(r => mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -5,10 +5,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.schema.sx.scholix.Scholix
|
import eu.dnetlib.dhp.schema.sx.scholix.Scholix
|
||||||
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
||||||
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.sql.{Dataset, Encoder, Encoders, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
import org.apache.hadoop.io.compress._
|
|
||||||
|
|
||||||
object SparkConvertObjectToJson {
|
object SparkConvertObjectToJson {
|
||||||
|
|
||||||
|
|
@ -32,8 +32,8 @@ object SparkConvertObjectToJson {
|
||||||
log.info(s"objectType -> $objectType")
|
log.info(s"objectType -> $objectType")
|
||||||
|
|
||||||
|
|
||||||
implicit val scholixEncoder :Encoder[Scholix]= Encoders.kryo[Scholix]
|
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
|
||||||
implicit val summaryEncoder :Encoder[ScholixSummary]= Encoders.kryo[ScholixSummary]
|
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
||||||
|
|
||||||
|
|
||||||
val mapper = new ObjectMapper
|
val mapper = new ObjectMapper
|
||||||
|
|
@ -2,11 +2,12 @@ package eu.dnetlib.dhp.sx.graph
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Software,Dataset => OafDataset}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkConvertRDDtoDataset {
|
object SparkConvertRDDtoDataset {
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
@ -39,31 +40,31 @@ object SparkConvertRDDtoDataset {
|
||||||
|
|
||||||
|
|
||||||
log.info("Converting dataset")
|
log.info("Converting dataset")
|
||||||
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
|
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")
|
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
|
||||||
|
|
||||||
|
|
||||||
log.info("Converting publication")
|
log.info("Converting publication")
|
||||||
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[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")
|
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
|
||||||
|
|
||||||
log.info("Converting software")
|
log.info("Converting software")
|
||||||
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[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")
|
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
|
||||||
|
|
||||||
log.info("Converting otherresearchproduct")
|
log.info("Converting otherresearchproduct")
|
||||||
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[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")
|
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
|
||||||
|
|
||||||
|
|
||||||
log.info("Converting Relation")
|
log.info("Converting Relation")
|
||||||
|
|
||||||
|
|
||||||
val relationSemanticFilter = List("cites", "iscitedby","merges", "ismergedin")
|
val relationSemanticFilter = List("cites", "iscitedby", "merges", "ismergedin")
|
||||||
|
|
||||||
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation")
|
val rddRelation = spark.sparkContext.textFile(s"$sourcePath/relation")
|
||||||
.map(s => mapper.readValue(s, classOf[Relation]))
|
.map(s => mapper.readValue(s, classOf[Relation]))
|
||||||
.filter(r=> r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
|
.filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
|
||||||
.filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)))
|
.filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)))
|
||||||
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
|
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
|
||||||
|
|
||||||
|
|
@ -1,14 +1,12 @@
|
||||||
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.{Oaf, OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
object SparkCreateInputGraph {
|
object SparkCreateInputGraph {
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
|
|
@ -41,16 +39,13 @@ object SparkCreateInputGraph {
|
||||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val sourcePath = parser.get("sourcePath")
|
val sourcePath = parser.get("sourcePath")
|
||||||
log.info(s"sourcePath -> $sourcePath")
|
log.info(s"sourcePath -> $sourcePath")
|
||||||
val targetPath = parser.get("targetPath")
|
val targetPath = parser.get("targetPath")
|
||||||
log.info(s"targetPath -> $targetPath")
|
log.info(s"targetPath -> $targetPath")
|
||||||
|
|
||||||
|
|
||||||
val oafDs:Dataset[Oaf] = spark.read.load(s"$sourcePath/*").as[Oaf]
|
val oafDs: Dataset[Oaf] = spark.read.load(s"$sourcePath/*").as[Oaf]
|
||||||
|
|
||||||
|
|
||||||
log.info("Extract Publication")
|
log.info("Extract Publication")
|
||||||
|
|
@ -70,12 +65,12 @@ 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/preprocess/${r._1}",spark, r._2)
|
makeDatasetUnique(s"$targetPath/extracted/${r._1}", s"$targetPath/preprocess/${r._1}", spark, r._2)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def extractEntities[T <: Oaf ](oafDs:Dataset[Oaf], targetPath:String, clazz:Class[T], log:Logger) :Unit = {
|
def extractEntities[T <: Oaf](oafDs: Dataset[Oaf], targetPath: String, clazz: Class[T], log: Logger): Unit = {
|
||||||
|
|
||||||
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
|
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
|
||||||
log.info(s"Extract ${clazz.getSimpleName}")
|
log.info(s"Extract ${clazz.getSimpleName}")
|
||||||
|
|
@ -83,14 +78,14 @@ object SparkCreateInputGraph {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def makeDatasetUnique[T <: Result ](sourcePath:String, targetPath:String, spark:SparkSession, clazz:Class[T]) :Unit = {
|
def makeDatasetUnique[T <: Result](sourcePath: String, targetPath: String, spark: SparkSession, clazz: Class[T]): Unit = {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
|
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
|
||||||
|
|
||||||
val ds:Dataset[T] = spark.read.load(sourcePath).as[T]
|
val ds: Dataset[T] = spark.read.load(sourcePath).as[T]
|
||||||
|
|
||||||
ds.groupByKey(_.getId).reduceGroups{(x,y) =>
|
ds.groupByKey(_.getId).reduceGroups { (x, y) =>
|
||||||
x.mergeFrom(y)
|
x.mergeFrom(y)
|
||||||
x
|
x
|
||||||
}.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath)
|
}.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||||
|
|
@ -9,7 +9,7 @@ import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils.RelatedEntities
|
||||||
import org.apache.commons.io.IOUtils
|
import org.apache.commons.io.IOUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.functions.count
|
import org.apache.spark.sql.functions.count
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkCreateScholix {
|
object SparkCreateScholix {
|
||||||
|
|
@ -42,7 +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"))
|
.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]
|
||||||
|
|
@ -51,54 +51,54 @@ object SparkCreateScholix {
|
||||||
|
|
||||||
relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
|
relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
|
||||||
.map { input: ((String, Relation), (String, ScholixSummary)) =>
|
.map { input: ((String, Relation), (String, ScholixSummary)) =>
|
||||||
if (input._1!= null && input._2!= null) {
|
if (input._1 != null && input._2 != null) {
|
||||||
val rel: Relation = input._1._2
|
val rel: Relation = input._1._2
|
||||||
val source: ScholixSummary = input._2._2
|
val source: ScholixSummary = input._2._2
|
||||||
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
|
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
|
||||||
}
|
}
|
||||||
else null
|
else null
|
||||||
}(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
}(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
||||||
.filter(r => r!= null)
|
.filter(r => r != null)
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
|
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
|
||||||
|
|
||||||
val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))
|
val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))
|
||||||
|
|
||||||
scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left")
|
scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left")
|
||||||
.map { input: ((String, Scholix), (String, ScholixSummary)) =>
|
.map { input: ((String, Scholix), (String, ScholixSummary)) =>
|
||||||
if (input._2== null) {
|
if (input._2 == null) {
|
||||||
null
|
null
|
||||||
} else {
|
} else {
|
||||||
val s: Scholix = input._1._2
|
val s: Scholix = input._1._2
|
||||||
val target: ScholixSummary = input._2._2
|
val target: ScholixSummary = input._2._2
|
||||||
ScholixUtils.generateCompleteScholix(s, target)
|
ScholixUtils.generateCompleteScholix(s, target)
|
||||||
}
|
}
|
||||||
}.filter(s => s!= null).write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse")
|
}.filter(s => s != null).write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse")
|
||||||
|
|
||||||
|
|
||||||
val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix]
|
val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix]
|
||||||
|
|
||||||
scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).as[Scholix]
|
scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).as[Scholix]
|
||||||
.map(s=> (s.getIdentifier,s))(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
.map(s => (s.getIdentifier, s))(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
||||||
.groupByKey(_._1)
|
.groupByKey(_._1)
|
||||||
.agg(ScholixUtils.scholixAggregator.toColumn)
|
.agg(ScholixUtils.scholixAggregator.toColumn)
|
||||||
.map(s => s._2)
|
.map(s => s._2)
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix")
|
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix")
|
||||||
|
|
||||||
val scholix_final:Dataset[Scholix] = spark.read.load(s"$targetPath/scholix").as[Scholix]
|
val scholix_final: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix").as[Scholix]
|
||||||
|
|
||||||
val stats:Dataset[(String,String,Long)]= scholix_final.map(s => (s.getSource.getDnetIdentifier, s.getTarget.getObjectType)).groupBy("_1", "_2").agg(count("_1")).as[(String,String,Long)]
|
val stats: Dataset[(String, String, Long)] = scholix_final.map(s => (s.getSource.getDnetIdentifier, s.getTarget.getObjectType)).groupBy("_1", "_2").agg(count("_1")).as[(String, String, Long)]
|
||||||
|
|
||||||
|
|
||||||
stats
|
stats
|
||||||
.map(s => RelatedEntities(s._1, if ("dataset".equalsIgnoreCase(s._2)) s._3 else 0, if ("publication".equalsIgnoreCase(s._2)) s._3 else 0 ))
|
.map(s => RelatedEntities(s._1, if ("dataset".equalsIgnoreCase(s._2)) s._3 else 0, if ("publication".equalsIgnoreCase(s._2)) s._3 else 0))
|
||||||
.groupByKey(_.id)
|
.groupByKey(_.id)
|
||||||
.reduceGroups((a, b) => RelatedEntities(a.id, a.relatedDataset+b.relatedDataset, a.relatedPublication+b.relatedPublication))
|
.reduceGroups((a, b) => RelatedEntities(a.id, a.relatedDataset + b.relatedDataset, a.relatedPublication + b.relatedPublication))
|
||||||
.map(_._2)
|
.map(_._2)
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$targetPath/related_entities")
|
.write.mode(SaveMode.Overwrite).save(s"$targetPath/related_entities")
|
||||||
|
|
||||||
val relatedEntitiesDS:Dataset[RelatedEntities] = spark.read.load(s"$targetPath/related_entities").as[RelatedEntities].filter(r => r.relatedPublication>0 || r.relatedDataset > 0)
|
val relatedEntitiesDS: Dataset[RelatedEntities] = spark.read.load(s"$targetPath/related_entities").as[RelatedEntities].filter(r => r.relatedPublication > 0 || r.relatedDataset > 0)
|
||||||
|
|
||||||
relatedEntitiesDS.joinWith(summaryDS, relatedEntitiesDS("id").equalTo(summaryDS("_1")), "inner").map{i =>
|
relatedEntitiesDS.joinWith(summaryDS, relatedEntitiesDS("id").equalTo(summaryDS("_1")), "inner").map { i =>
|
||||||
val re = i._1
|
val re = i._1
|
||||||
val sum = i._2._2
|
val sum = i._2._2
|
||||||
|
|
||||||
|
|
@ -6,7 +6,7 @@ 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
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql._
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
object SparkCreateSummaryObject {
|
object SparkCreateSummaryObject {
|
||||||
|
|
@ -28,15 +28,15 @@ object SparkCreateSummaryObject {
|
||||||
val targetPath = parser.get("targetPath")
|
val targetPath = parser.get("targetPath")
|
||||||
log.info(s"targetPath -> $targetPath")
|
log.info(s"targetPath -> $targetPath")
|
||||||
|
|
||||||
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
implicit val resultEncoder: Encoder[Result] = Encoders.kryo[Result]
|
||||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
|
||||||
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
||||||
|
|
||||||
|
|
||||||
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false)
|
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)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -5,6 +5,7 @@ import org.apache.spark.sql.{Encoder, Encoders}
|
||||||
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
|
||||||
|
|
||||||
import java.util.regex.Pattern
|
import java.util.regex.Pattern
|
||||||
import scala.language.postfixOps
|
import scala.language.postfixOps
|
||||||
import scala.xml.{Elem, Node, XML}
|
import scala.xml.{Elem, Node, XML}
|
||||||
|
|
@ -2,11 +2,11 @@ package eu.dnetlib.dhp.sx.graph.pangaea
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
import org.apache.spark.rdd.RDD
|
import org.apache.spark.rdd.RDD
|
||||||
import org.apache.spark.{SparkConf, SparkContext}
|
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||||
|
import org.apache.spark.{SparkConf, SparkContext}
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
|
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
|
|
||||||
object SparkGeneratePanagaeaDataset {
|
object SparkGeneratePanagaeaDataset {
|
||||||
|
|
@ -28,16 +28,16 @@ object SparkGeneratePanagaeaDataset {
|
||||||
|
|
||||||
parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}"))
|
parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}"))
|
||||||
logger.info("Converting sequential file into Dataset")
|
logger.info("Converting sequential file into Dataset")
|
||||||
val sc:SparkContext = spark.sparkContext
|
val sc: SparkContext = spark.sparkContext
|
||||||
|
|
||||||
val workingPath:String = parser.get("workingPath")
|
val workingPath: String = parser.get("workingPath")
|
||||||
|
|
||||||
implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
|
implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
|
||||||
|
|
||||||
val inputRDD:RDD[PangaeaDataModel] = sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s))
|
val inputRDD: RDD[PangaeaDataModel] = sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s))
|
||||||
|
|
||||||
spark.createDataset(inputRDD).as[PangaeaDataModel]
|
spark.createDataset(inputRDD).as[PangaeaDataModel]
|
||||||
.map(s => (s.identifier,s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders))
|
.map(s => (s.identifier, s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders))
|
||||||
.groupByKey(_._1)(Encoders.STRING)
|
.groupByKey(_._1)(Encoders.STRING)
|
||||||
.agg(PangaeaUtils.getDatasetAggregator().toColumn)
|
.agg(PangaeaUtils.getDatasetAggregator().toColumn)
|
||||||
.map(s => s._2)
|
.map(s => s._2)
|
||||||
|
|
@ -46,7 +46,4 @@ object SparkGeneratePanagaeaDataset {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -1,6 +1,5 @@
|
||||||
package eu.dnetlib.dhp.sx.graph.scholix
|
package eu.dnetlib.dhp.sx.graph.scholix
|
||||||
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
|
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
|
||||||
import eu.dnetlib.dhp.schema.sx.scholix._
|
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}
|
||||||
|
|
@ -10,23 +9,22 @@ import org.apache.spark.sql.{Encoder, Encoders}
|
||||||
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
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
import scala.language.postfixOps
|
|
||||||
|
|
||||||
object ScholixUtils {
|
object ScholixUtils {
|
||||||
|
|
||||||
|
|
||||||
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
|
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
|
||||||
|
|
||||||
val DATE_RELATION_KEY:String = "RelationDate"
|
val DATE_RELATION_KEY: String = "RelationDate"
|
||||||
case class RelationVocabulary(original:String, inverse:String){}
|
|
||||||
|
|
||||||
case class RelatedEntities(id:String, relatedDataset:Long, relatedPublication:Long){}
|
case class RelationVocabulary(original: String, inverse: String) {}
|
||||||
|
|
||||||
val relations:Map[String, RelationVocabulary] = {
|
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
|
||||||
val input =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
|
|
||||||
|
val relations: Map[String, RelationVocabulary] = {
|
||||||
|
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
|
|
@ -35,12 +33,12 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def extractRelationDate(relation: Relation):String = {
|
def extractRelationDate(relation: Relation): String = {
|
||||||
|
|
||||||
if (relation.getProperties== null || !relation.getProperties.isEmpty)
|
if (relation.getProperties == null || !relation.getProperties.isEmpty)
|
||||||
null
|
null
|
||||||
else {
|
else {
|
||||||
val date =relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue)
|
val date = relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue)
|
||||||
if (date.isDefined)
|
if (date.isDefined)
|
||||||
date.get
|
date.get
|
||||||
else
|
else
|
||||||
|
|
@ -48,9 +46,9 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
def extractRelationDate(summary: ScholixSummary):String = {
|
def extractRelationDate(summary: ScholixSummary): String = {
|
||||||
|
|
||||||
if(summary.getDate== null || summary.getDate.isEmpty)
|
if (summary.getDate == null || summary.getDate.isEmpty)
|
||||||
null
|
null
|
||||||
else {
|
else {
|
||||||
summary.getDate.get(0)
|
summary.getDate.get(0)
|
||||||
|
|
@ -59,15 +57,14 @@ object ScholixUtils {
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
def inverseRelationShip(rel:ScholixRelationship):ScholixRelationship = {
|
def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
|
||||||
new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
|
new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
|
||||||
val statsAggregator:Aggregator[(String,String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String,String, Long), RelatedEntities, RelatedEntities] with Serializable {
|
|
||||||
override def zero: RelatedEntities = null
|
override def zero: RelatedEntities = null
|
||||||
|
|
||||||
override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
|
override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
|
||||||
|
|
@ -78,15 +75,14 @@ object ScholixUtils {
|
||||||
if (b == null)
|
if (b == null)
|
||||||
RelatedEntities(a._1, relatedDataset, relatedPublication)
|
RelatedEntities(a._1, relatedDataset, relatedPublication)
|
||||||
else
|
else
|
||||||
RelatedEntities(a._1,b.relatedDataset+ relatedDataset, b.relatedPublication+ relatedPublication )
|
RelatedEntities(a._1, b.relatedDataset + relatedDataset, b.relatedPublication + relatedPublication)
|
||||||
}
|
}
|
||||||
|
|
||||||
override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
|
override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
|
||||||
if (b1!= null && b2!= null)
|
if (b1 != null && b2 != null)
|
||||||
RelatedEntities(b1.id, b1.relatedDataset+ b2.relatedDataset, b1.relatedPublication+ b2.relatedPublication)
|
RelatedEntities(b1.id, b1.relatedDataset + b2.relatedDataset, b1.relatedPublication + b2.relatedPublication)
|
||||||
|
|
||||||
else
|
else if (b1 != null)
|
||||||
if (b1!= null)
|
|
||||||
b1
|
b1
|
||||||
else
|
else
|
||||||
b2
|
b2
|
||||||
|
|
@ -104,8 +100,8 @@ object ScholixUtils {
|
||||||
override def zero: Scholix = null
|
override def zero: Scholix = null
|
||||||
|
|
||||||
|
|
||||||
def scholix_complete(s:Scholix):Boolean ={
|
def scholix_complete(s: Scholix): Boolean = {
|
||||||
if (s== null || s.getIdentifier==null) {
|
if (s == null || s.getIdentifier == null) {
|
||||||
false
|
false
|
||||||
} else if (s.getSource == null || s.getTarget == null) {
|
} else if (s.getSource == null || s.getTarget == null) {
|
||||||
false
|
false
|
||||||
|
|
@ -132,7 +128,7 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def createInverseScholixRelation(scholix: Scholix):Scholix = {
|
def createInverseScholixRelation(scholix: Scholix): Scholix = {
|
||||||
val s = new Scholix
|
val s = new Scholix
|
||||||
s.setPublicationDate(scholix.getPublicationDate)
|
s.setPublicationDate(scholix.getPublicationDate)
|
||||||
s.setPublisher(scholix.getPublisher)
|
s.setPublisher(scholix.getPublisher)
|
||||||
|
|
@ -144,34 +140,33 @@ object ScholixUtils {
|
||||||
s
|
s
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def extractCollectedFrom(summary:ScholixSummary): List[ScholixEntityId] = {
|
def extractCollectedFrom(summary: ScholixSummary): List[ScholixEntityId] = {
|
||||||
if (summary.getDatasources!= null && !summary.getDatasources.isEmpty) {
|
if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
|
||||||
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map{
|
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map {
|
||||||
d => new ScholixEntityId(d.getDatasourceName, List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava)
|
d => new ScholixEntityId(d.getDatasourceName, List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava)
|
||||||
}(collection.breakOut)
|
}(collection.breakOut)
|
||||||
l
|
l
|
||||||
} else List()
|
} else List()
|
||||||
}
|
}
|
||||||
|
|
||||||
def extractCollectedFrom(relation: Relation) : List[ScholixEntityId] = {
|
def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
|
||||||
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
|
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
|
||||||
|
|
||||||
|
|
||||||
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map {
|
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map {
|
||||||
c =>
|
c =>
|
||||||
|
|
||||||
new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA,null)).asJava)
|
new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava)
|
||||||
}(collection breakOut)
|
}(collection breakOut)
|
||||||
l
|
l
|
||||||
} else List()
|
} else List()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def generateCompleteScholix(scholix: Scholix, target:ScholixSummary): Scholix = {
|
def generateCompleteScholix(scholix: Scholix, target: ScholixSummary): Scholix = {
|
||||||
val s = new Scholix
|
val s = new Scholix
|
||||||
s.setPublicationDate(scholix.getPublicationDate)
|
s.setPublicationDate(scholix.getPublicationDate)
|
||||||
s.setPublisher(scholix.getPublisher)
|
s.setPublisher(scholix.getPublisher)
|
||||||
|
|
@ -192,29 +187,28 @@ object ScholixUtils {
|
||||||
r.setObjectType(summaryObject.getTypology.toString)
|
r.setObjectType(summaryObject.getTypology.toString)
|
||||||
r.setObjectSubType(summaryObject.getSubType)
|
r.setObjectSubType(summaryObject.getSubType)
|
||||||
|
|
||||||
if (summaryObject.getTitle!= null && !summaryObject.getTitle.isEmpty)
|
if (summaryObject.getTitle != null && !summaryObject.getTitle.isEmpty)
|
||||||
r.setTitle(summaryObject.getTitle.get(0))
|
r.setTitle(summaryObject.getTitle.get(0))
|
||||||
|
|
||||||
if (summaryObject.getAuthor!= null && !summaryObject.getAuthor.isEmpty){
|
if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
|
||||||
val l:List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a,null)).toList
|
val l: List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
|
||||||
if (l.nonEmpty)
|
if (l.nonEmpty)
|
||||||
r.setCreator(l.asJava)
|
r.setCreator(l.asJava)
|
||||||
}
|
}
|
||||||
|
|
||||||
if (summaryObject.getDate!= null && !summaryObject.getDate.isEmpty)
|
if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
|
||||||
r.setPublicationDate(summaryObject.getDate.get(0))
|
r.setPublicationDate(summaryObject.getDate.get(0))
|
||||||
if (summaryObject.getPublisher!= null && !summaryObject.getPublisher.isEmpty)
|
if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
|
||||||
{
|
val plist: List[ScholixEntityId] = summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
|
||||||
val plist:List[ScholixEntityId] =summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
|
|
||||||
|
|
||||||
if (plist.nonEmpty)
|
if (plist.nonEmpty)
|
||||||
r.setPublisher(plist.asJava)
|
r.setPublisher(plist.asJava)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
if (summaryObject.getDatasources!= null && !summaryObject.getDatasources.isEmpty) {
|
if (summaryObject.getDatasources != null && !summaryObject.getDatasources.isEmpty) {
|
||||||
|
|
||||||
val l:List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom(
|
val l: List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom(
|
||||||
new ScholixEntityId(c.getDatasourceName, List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava)
|
new ScholixEntityId(c.getDatasourceName, List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava)
|
||||||
, "collected", "complete"
|
, "collected", "complete"
|
||||||
|
|
||||||
|
|
@ -228,12 +222,9 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
|
||||||
|
|
||||||
|
if (relation == null || source == null)
|
||||||
|
|
||||||
def scholixFromSource(relation:Relation, source:ScholixSummary):Scholix = {
|
|
||||||
|
|
||||||
if (relation== null || source== null)
|
|
||||||
return null
|
return null
|
||||||
|
|
||||||
val s = new Scholix
|
val s = new Scholix
|
||||||
|
|
@ -253,9 +244,9 @@ object ScholixUtils {
|
||||||
s.setPublicationDate(d)
|
s.setPublicationDate(d)
|
||||||
|
|
||||||
|
|
||||||
if (source.getPublisher!= null && !source.getPublisher.isEmpty) {
|
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
|
||||||
val l: List[ScholixEntityId] = source.getPublisher.asScala
|
val l: List[ScholixEntityId] = source.getPublisher.asScala
|
||||||
.map{
|
.map {
|
||||||
p =>
|
p =>
|
||||||
new ScholixEntityId(p, null)
|
new ScholixEntityId(p, null)
|
||||||
}(collection.breakOut)
|
}(collection.breakOut)
|
||||||
|
|
@ -265,7 +256,7 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
|
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
|
||||||
if (semanticRelation== null)
|
if (semanticRelation == null)
|
||||||
return null
|
return null
|
||||||
s.setRelationship(new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse))
|
s.setRelationship(new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse))
|
||||||
s.setSource(generateScholixResourceFromSummary(source))
|
s.setSource(generateScholixResourceFromSummary(source))
|
||||||
|
|
@ -274,8 +265,8 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def findURLForPID(pidValue:List[StructuredProperty], urls:List[String]):List[(StructuredProperty, String)] = {
|
def findURLForPID(pidValue: List[StructuredProperty], urls: List[String]): List[(StructuredProperty, String)] = {
|
||||||
pidValue.map{
|
pidValue.map {
|
||||||
p =>
|
p =>
|
||||||
val pv = p.getValue
|
val pv = p.getValue
|
||||||
|
|
||||||
|
|
@ -285,67 +276,67 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
def extractTypedIdentifierFromInstance(r:Result):List[ScholixIdentifier] = {
|
def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
|
||||||
if (r.getInstance() == null || r.getInstance().isEmpty)
|
if (r.getInstance() == null || r.getInstance().isEmpty)
|
||||||
return List()
|
return List()
|
||||||
r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty)
|
r.getInstance().asScala.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
|
||||||
.filter(i => i.getPid!= null && i.getUrl != null)
|
.filter(i => i.getPid != null && i.getUrl != null)
|
||||||
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
|
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
|
||||||
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
|
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
|
||||||
}
|
}
|
||||||
|
|
||||||
def resultToSummary(r:Result):ScholixSummary = {
|
def resultToSummary(r: Result): ScholixSummary = {
|
||||||
val s = new ScholixSummary
|
val s = new ScholixSummary
|
||||||
s.setId(r.getId)
|
s.setId(r.getId)
|
||||||
if (r.getPid == null || r.getPid.isEmpty)
|
if (r.getPid == null || r.getPid.isEmpty)
|
||||||
return null
|
return null
|
||||||
|
|
||||||
val persistentIdentifiers:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
|
val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
|
||||||
if (persistentIdentifiers.isEmpty)
|
if (persistentIdentifiers.isEmpty)
|
||||||
return null
|
return null
|
||||||
s.setLocalIdentifier(persistentIdentifiers.asJava)
|
s.setLocalIdentifier(persistentIdentifiers.asJava)
|
||||||
if (r.isInstanceOf[Publication] )
|
if (r.isInstanceOf[Publication])
|
||||||
s.setTypology(Typology.publication)
|
s.setTypology(Typology.publication)
|
||||||
else
|
else
|
||||||
s.setTypology(Typology.dataset)
|
s.setTypology(Typology.dataset)
|
||||||
|
|
||||||
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
|
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
|
||||||
|
|
||||||
if (r.getTitle!= null && r.getTitle.asScala.nonEmpty) {
|
if (r.getTitle != null && r.getTitle.asScala.nonEmpty) {
|
||||||
val titles:List[String] =r.getTitle.asScala.map(t => t.getValue)(collection breakOut)
|
val titles: List[String] = r.getTitle.asScala.map(t => t.getValue)(collection breakOut)
|
||||||
if (titles.nonEmpty)
|
if (titles.nonEmpty)
|
||||||
s.setTitle(titles.asJava)
|
s.setTitle(titles.asJava)
|
||||||
else
|
else
|
||||||
return null
|
return null
|
||||||
}
|
}
|
||||||
|
|
||||||
if(r.getAuthor!= null && !r.getAuthor.isEmpty) {
|
if (r.getAuthor != null && !r.getAuthor.isEmpty) {
|
||||||
val authors:List[String] = r.getAuthor.asScala.map(a=> a.getFullname)(collection breakOut)
|
val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname)(collection breakOut)
|
||||||
if (authors nonEmpty)
|
if (authors nonEmpty)
|
||||||
s.setAuthor(authors.asJava)
|
s.setAuthor(authors.asJava)
|
||||||
}
|
}
|
||||||
if (r.getInstance() != null) {
|
if (r.getInstance() != null) {
|
||||||
val dt:List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut)
|
val dt: List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut)
|
||||||
if (dt.nonEmpty)
|
if (dt.nonEmpty)
|
||||||
s.setDate(dt.distinct.asJava)
|
s.setDate(dt.distinct.asJava)
|
||||||
}
|
}
|
||||||
if (r.getDescription!= null && !r.getDescription.isEmpty) {
|
if (r.getDescription != null && !r.getDescription.isEmpty) {
|
||||||
val d = r.getDescription.asScala.find(f => f!= null && f.getValue!=null)
|
val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
|
||||||
if (d.isDefined)
|
if (d.isDefined)
|
||||||
s.setDescription(d.get.getValue)
|
s.setDescription(d.get.getValue)
|
||||||
}
|
}
|
||||||
|
|
||||||
if (r.getSubject!= null && !r.getSubject.isEmpty) {
|
if (r.getSubject != null && !r.getSubject.isEmpty) {
|
||||||
val subjects:List[SchemeValue] =r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))(collection breakOut)
|
val subjects: List[SchemeValue] = r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))(collection breakOut)
|
||||||
if (subjects.nonEmpty)
|
if (subjects.nonEmpty)
|
||||||
s.setSubject(subjects.asJava)
|
s.setSubject(subjects.asJava)
|
||||||
}
|
}
|
||||||
|
|
||||||
if (r.getPublisher!= null)
|
if (r.getPublisher != null)
|
||||||
s.setPublisher(List(r.getPublisher.getValue).asJava)
|
s.setPublisher(List(r.getPublisher.getValue).asJava)
|
||||||
|
|
||||||
if (r.getCollectedfrom!= null && !r.getCollectedfrom.isEmpty) {
|
if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
|
||||||
val cf:List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut)
|
val cf: List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut)
|
||||||
if (cf.nonEmpty)
|
if (cf.nonEmpty)
|
||||||
s.setDatasources(cf.distinct.asJava)
|
s.setDatasources(cf.distinct.asJava)
|
||||||
}
|
}
|
||||||
|
|
@ -12,6 +12,8 @@ import java.util.stream.Collectors;
|
||||||
import java.util.stream.Stream;
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.hadoop.hdfs.server.datanode.fsdataset.impl.MappableBlock;
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
import org.junit.jupiter.api.BeforeEach;
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
import org.junit.jupiter.api.extension.ExtendWith;
|
import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
|
|
@ -66,9 +68,59 @@ public class GraphCleaningFunctionsTest {
|
||||||
Relation r_out = OafCleaner.apply(r_in, mapping);
|
Relation r_out = OafCleaner.apply(r_in, mapping);
|
||||||
assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_out.getRelClass()));
|
assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_out.getRelClass()));
|
||||||
assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r_out.getSubRelType()));
|
assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r_out.getSubRelType()));
|
||||||
|
|
||||||
|
assertEquals("iis", r_out.getDataInfo().getProvenanceaction().getClassid());
|
||||||
|
assertEquals("Inferred by OpenAIRE", r_out.getDataInfo().getProvenanceaction().getClassname());
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testFilter_false() throws Exception {
|
||||||
|
|
||||||
|
assertNotNull(vocabularies);
|
||||||
|
assertNotNull(mapping);
|
||||||
|
|
||||||
|
String json = IOUtils
|
||||||
|
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
|
||||||
|
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||||
|
|
||||||
|
assertTrue(p_in instanceof Result);
|
||||||
|
assertTrue(p_in instanceof Publication);
|
||||||
|
|
||||||
|
assertEquals(false, GraphCleaningFunctions.filter(p_in));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testFilter_true() throws Exception {
|
||||||
|
|
||||||
|
assertNotNull(vocabularies);
|
||||||
|
assertNotNull(mapping);
|
||||||
|
|
||||||
|
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
|
||||||
|
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||||
|
|
||||||
|
assertTrue(p_in instanceof Result);
|
||||||
|
assertTrue(p_in instanceof Publication);
|
||||||
|
|
||||||
|
assertEquals(true, GraphCleaningFunctions.filter(p_in));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testFilter_missing_invisible() throws Exception {
|
||||||
|
|
||||||
|
assertNotNull(vocabularies);
|
||||||
|
assertNotNull(mapping);
|
||||||
|
|
||||||
|
String json = IOUtils
|
||||||
|
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
|
||||||
|
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||||
|
|
||||||
|
assertTrue(p_in instanceof Result);
|
||||||
|
assertTrue(p_in instanceof Publication);
|
||||||
|
|
||||||
|
assertEquals(true, GraphCleaningFunctions.filter(p_in));
|
||||||
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void testCleaning() throws Exception {
|
void testCleaning() throws Exception {
|
||||||
|
|
||||||
|
|
@ -99,6 +151,12 @@ public class GraphCleaningFunctionsTest {
|
||||||
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
|
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
|
||||||
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
|
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
|
||||||
|
|
||||||
|
assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
|
||||||
|
assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
|
||||||
|
|
||||||
|
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
|
||||||
|
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
|
||||||
|
|
||||||
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
|
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
|
||||||
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
|
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
|
||||||
|
|
||||||
|
|
@ -112,7 +170,7 @@ public class GraphCleaningFunctionsTest {
|
||||||
|
|
||||||
List<Instance> poi = p_out.getInstance();
|
List<Instance> poi = p_out.getInstance();
|
||||||
assertNotNull(poi);
|
assertNotNull(poi);
|
||||||
assertEquals(1, poi.size());
|
assertEquals(3, poi.size());
|
||||||
|
|
||||||
final Instance poii = poi.get(0);
|
final Instance poii = poi.get(0);
|
||||||
assertNotNull(poii);
|
assertNotNull(poii);
|
||||||
|
|
@ -140,7 +198,7 @@ public class GraphCleaningFunctionsTest {
|
||||||
|
|
||||||
assertEquals(5, p_out.getTitle().size());
|
assertEquals(5, p_out.getTitle().size());
|
||||||
|
|
||||||
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
|
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||||
|
|
||||||
assertEquals(3, p_cleaned.getTitle().size());
|
assertEquals(3, p_cleaned.getTitle().size());
|
||||||
|
|
||||||
|
|
@ -159,9 +217,12 @@ public class GraphCleaningFunctionsTest {
|
||||||
|
|
||||||
assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
|
assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
|
||||||
|
|
||||||
|
assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
|
||||||
|
assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
|
||||||
|
|
||||||
final List<Instance> pci = p_cleaned.getInstance();
|
final List<Instance> pci = p_cleaned.getInstance();
|
||||||
assertNotNull(pci);
|
assertNotNull(pci);
|
||||||
assertEquals(1, pci.size());
|
assertEquals(3, pci.size());
|
||||||
|
|
||||||
final Instance pcii = pci.get(0);
|
final Instance pcii = pci.get(0);
|
||||||
assertNotNull(pcii);
|
assertNotNull(pcii);
|
||||||
|
|
@ -222,4 +283,27 @@ public class GraphCleaningFunctionsTest {
|
||||||
.readLines(
|
.readLines(
|
||||||
GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
|
GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testCleanDoiBoost() throws IOException {
|
||||||
|
String json = IOUtils
|
||||||
|
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
|
||||||
|
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||||
|
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
|
||||||
|
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||||
|
|
||||||
|
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testCleanDoiBoost2() throws IOException {
|
||||||
|
String json = IOUtils
|
||||||
|
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
|
||||||
|
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||||
|
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
|
||||||
|
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||||
|
|
||||||
|
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
|
||||||
|
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -171,24 +171,6 @@ public class DumpJobTest {
|
||||||
|
|
||||||
GraphResult gr = verificationDataset.first();
|
GraphResult gr = verificationDataset.first();
|
||||||
|
|
||||||
Assertions.assertEquals(2, gr.getMeasures().size());
|
|
||||||
Assertions
|
|
||||||
.assertTrue(
|
|
||||||
gr
|
|
||||||
.getMeasures()
|
|
||||||
.stream()
|
|
||||||
.anyMatch(
|
|
||||||
m -> m.getKey().equals("influence")
|
|
||||||
&& m.getValue().equals("1.62759106106e-08")));
|
|
||||||
Assertions
|
|
||||||
.assertTrue(
|
|
||||||
gr
|
|
||||||
.getMeasures()
|
|
||||||
.stream()
|
|
||||||
.anyMatch(
|
|
||||||
m -> m.getKey().equals("popularity")
|
|
||||||
&& m.getValue().equals("0.22519296")));
|
|
||||||
|
|
||||||
Assertions.assertEquals(6, gr.getAuthor().size());
|
Assertions.assertEquals(6, gr.getAuthor().size());
|
||||||
Assertions
|
Assertions
|
||||||
.assertTrue(
|
.assertTrue(
|
||||||
|
|
|
||||||
|
|
@ -708,7 +708,7 @@ class MappersTest {
|
||||||
assertEquals(1, p.getTitle().size());
|
assertEquals(1, p.getTitle().size());
|
||||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||||
|
|
||||||
final Publication p_cleaned = cleanup(fixVocabularyNames(p));
|
final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
|
||||||
|
|
||||||
assertNotNull(p_cleaned.getTitle());
|
assertNotNull(p_cleaned.getTitle());
|
||||||
assertFalse(p_cleaned.getTitle().isEmpty());
|
assertFalse(p_cleaned.getTitle().isEmpty());
|
||||||
|
|
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue