forked from D-Net/dnet-hadoop
mergin with branch beta
This commit is contained in:
commit
8905a39bf3
|
|
@ -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>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -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()
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,134 @@
|
||||||
|
package eu.dnetlib.dhp.datacite
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||||
|
|
||||||
|
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)
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -2,6 +2,7 @@ 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}
|
||||||
|
|
@ -12,121 +13,30 @@ 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)
|
* @param json
|
||||||
json.extract[Map[String, HostedByMapType]]
|
* @return True if the record should be skipped
|
||||||
}
|
*/
|
||||||
|
def skip_record(json: String): Boolean = {
|
||||||
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)
|
datacite_filter.exists(f => json.contains(f))
|
||||||
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)
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
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()
|
||||||
|
|
||||||
|
|
@ -206,6 +116,8 @@ object DataciteToOAFTransformation {
|
||||||
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 +236,7 @@ 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 +245,7 @@ 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
|
||||||
|
|
@ -516,8 +424,8 @@ 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)
|
||||||
|
|
@ -571,7 +479,7 @@ 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)
|
||||||
|
|
@ -585,18 +493,9 @@ object DataciteToOAFTransformation {
|
||||||
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()
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -7,3 +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
|
||||||
|
|
|
||||||
|
|
@ -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) whose 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 of 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 entities 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/" />
|
||||||
|
|
|
||||||
|
|
@ -4,24 +4,38 @@ package eu.dnetlib.dhp.datacite
|
||||||
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
|
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
|
||||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||||
|
import org.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.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
import org.junit.jupiter.api.{BeforeEach, Test}
|
import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
|
||||||
import org.mockito.junit.jupiter.MockitoExtension
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import java.nio.file.{Files, Path}
|
||||||
import java.text.SimpleDateFormat
|
import java.text.SimpleDateFormat
|
||||||
import java.util.Locale
|
import java.util.Locale
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
|
import org.junit.jupiter.api.Assertions._
|
||||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||||
class DataciteToOAFTest extends AbstractVocabularyTest{
|
class DataciteToOAFTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
|
private var workingDir:Path = null
|
||||||
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
|
||||||
@BeforeEach
|
@BeforeEach
|
||||||
def setUp() :Unit = {
|
def setUp() :Unit = {
|
||||||
|
|
||||||
|
workingDir= Files.createTempDirectory(getClass.getSimpleName)
|
||||||
super.setUpVocabulary()
|
super.setUpVocabulary()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@AfterEach
|
||||||
|
def tearDown() :Unit = {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testDateMapping:Unit = {
|
def testDateMapping:Unit = {
|
||||||
|
|
@ -31,14 +45,57 @@ class DataciteToOAFTest extends AbstractVocabularyTest{
|
||||||
println(dt.getTime)
|
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
|
@Test
|
||||||
def testMapping() :Unit = {
|
def testMapping() :Unit = {
|
||||||
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString
|
val record =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/record.json")).mkString
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
|
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
|
||||||
val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true )
|
val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true )
|
||||||
|
|
|
||||||
Binary file not shown.
|
|
@ -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) {
|
||||||
|
|
|
||||||
|
|
@ -14,6 +14,9 @@ import org.xml.sax.SAXException;
|
||||||
|
|
||||||
import com.google.common.collect.Sets;
|
import com.google.common.collect.Sets;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
|
@ -152,4 +155,25 @@ public class DedupUtility {
|
||||||
return o1.compareTo(o2);
|
return o1.compareTo(o2);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public static Relation createSimRel(String source, String target, String entity) {
|
||||||
|
final Relation r = new Relation();
|
||||||
|
r.setSource(source);
|
||||||
|
r.setTarget(target);
|
||||||
|
r.setSubRelType("dedupSimilarity");
|
||||||
|
r.setRelClass(ModelConstants.IS_SIMILAR_TO);
|
||||||
|
r.setDataInfo(new DataInfo());
|
||||||
|
|
||||||
|
switch (entity) {
|
||||||
|
case "result":
|
||||||
|
r.setRelType(ModelConstants.RESULT_RESULT);
|
||||||
|
break;
|
||||||
|
case "organization":
|
||||||
|
r.setRelType(ModelConstants.ORG_ORG_RELTYPE);
|
||||||
|
break;
|
||||||
|
default:
|
||||||
|
throw new IllegalArgumentException("unmanaged entity type: " + entity);
|
||||||
|
}
|
||||||
|
return r;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -61,9 +61,11 @@ 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));
|
||||||
|
|
||||||
log.info("Number of non-Openorgs relations collected: {}", simRels.count());
|
if (log.isDebugEnabled()) {
|
||||||
|
log.debug("Number of non-Openorgs relations collected: {}", simRels.count());
|
||||||
|
}
|
||||||
|
|
||||||
spark
|
spark
|
||||||
.createDataset(simRels.rdd(), Encoders.bean(Relation.class))
|
.createDataset(simRels.rdd(), Encoders.bean(Relation.class))
|
||||||
|
|
|
||||||
|
|
@ -20,6 +20,7 @@ import org.xml.sax.SAXException;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
|
@ -102,7 +103,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
|
||||||
.createDataset(
|
.createDataset(
|
||||||
Deduper
|
Deduper
|
||||||
.computeRelations(sc, blocks, dedupConf)
|
.computeRelations(sc, blocks, dedupConf)
|
||||||
.map(t -> createSimRel(t._1(), t._2(), entity))
|
.map(t -> DedupUtility.createSimRel(t._1(), t._2(), entity))
|
||||||
.repartition(numPartitions)
|
.repartition(numPartitions)
|
||||||
.rdd(),
|
.rdd(),
|
||||||
Encoders.bean(Relation.class));
|
Encoders.bean(Relation.class));
|
||||||
|
|
@ -111,24 +112,4 @@ public class SparkCreateSimRels extends AbstractSparkAction {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private Relation createSimRel(String source, String target, String entity) {
|
|
||||||
final Relation r = new Relation();
|
|
||||||
r.setSource(source);
|
|
||||||
r.setTarget(target);
|
|
||||||
r.setSubRelType("dedupSimilarity");
|
|
||||||
r.setRelClass("isSimilarTo");
|
|
||||||
r.setDataInfo(new DataInfo());
|
|
||||||
|
|
||||||
switch (entity) {
|
|
||||||
case "result":
|
|
||||||
r.setRelType("resultResult");
|
|
||||||
break;
|
|
||||||
case "organization":
|
|
||||||
r.setRelType("organizationOrganization");
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
throw new IllegalArgumentException("unmanaged entity type: " + entity);
|
|
||||||
}
|
|
||||||
return r;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -124,31 +124,12 @@ public class SparkWhitelistSimRels extends AbstractSparkAction {
|
||||||
|
|
||||||
Dataset<Relation> whiteListSimRels = whiteListRels2
|
Dataset<Relation> whiteListSimRels = whiteListRels2
|
||||||
.map(
|
.map(
|
||||||
(MapFunction<Tuple2<String, String>, Relation>) r -> createSimRel(r._1(), r._2(), entity),
|
(MapFunction<Tuple2<String, String>, Relation>) r -> DedupUtility
|
||||||
|
.createSimRel(r._1(), r._2(), entity),
|
||||||
Encoders.bean(Relation.class));
|
Encoders.bean(Relation.class));
|
||||||
|
|
||||||
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
|
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private Relation createSimRel(String source, String target, String entity) {
|
|
||||||
final Relation r = new Relation();
|
|
||||||
r.setSource(source);
|
|
||||||
r.setTarget(target);
|
|
||||||
r.setSubRelType("dedupSimilarity");
|
|
||||||
r.setRelClass("isSimilarTo");
|
|
||||||
r.setDataInfo(new DataInfo());
|
|
||||||
|
|
||||||
switch (entity) {
|
|
||||||
case "result":
|
|
||||||
r.setRelType("resultResult");
|
|
||||||
break;
|
|
||||||
case "organization":
|
|
||||||
r.setRelType("organizationOrganization");
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
throw new IllegalArgumentException("unmanaged entity type: " + entity);
|
|
||||||
}
|
|
||||||
return r;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -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": []}
|
||||||
|
|
|
||||||
|
|
@ -146,7 +146,7 @@ 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)
|
||||||
|
|
|
||||||
|
|
@ -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>
|
||||||
|
|
@ -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);
|
||||||
|
|
|
||||||
|
|
@ -14,7 +14,7 @@ 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 +36,19 @@ 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 +65,42 @@ 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")
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -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)] = {
|
||||||
|
|
|
||||||
|
|
@ -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}
|
||||||
]
|
]
|
||||||
|
|
@ -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;
|
||||||
|
|
@ -66,6 +68,9 @@ 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());
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -222,4 +227,27 @@ 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);
|
||||||
|
|
||||||
|
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);
|
||||||
|
|
||||||
|
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
|
||||||
|
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.schema.common.EntityType
|
import eu.dnetlib.dhp.schema.common.EntityType
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Result, StructuredProperty}
|
import eu.dnetlib.dhp.schema.oaf.{Publication, Result, StructuredProperty}
|
||||||
import org.apache.commons.io.FileUtils
|
import org.apache.commons.io.FileUtils
|
||||||
import org.apache.spark.SparkConf
|
import org.apache.spark.SparkConf
|
||||||
import org.apache.spark.sql._
|
import org.apache.spark.sql._
|
||||||
|
|
@ -146,27 +146,47 @@ class ResolveEntitiesTest extends Serializable {
|
||||||
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||||
val m = new ObjectMapper()
|
val m = new ObjectMapper()
|
||||||
SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" )
|
SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" )
|
||||||
SparkResolveEntities.generateResolvedEntities(spark,s"$workingDir/work",s"$workingDir/graph" )
|
SparkResolveEntities.generateResolvedEntities(spark,s"$workingDir/work",s"$workingDir/graph", s"$workingDir/target" )
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication))
|
val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/target/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication))
|
||||||
val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
||||||
|
|
||||||
|
|
||||||
|
var ct = pubDS.count()
|
||||||
|
var et = pubDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
|
||||||
|
|
||||||
val datDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/dataset").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.dataset))
|
assertEquals(ct, et)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
val datDS:Dataset[Result] = spark.read.text(s"$workingDir/target/dataset").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.dataset))
|
||||||
val td = datDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
val td = datDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
||||||
|
ct = datDS.count()
|
||||||
|
et = datDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
|
||||||
|
assertEquals(ct, et)
|
||||||
|
|
||||||
|
|
||||||
val softDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/software").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.software))
|
val softDS:Dataset[Result] = spark.read.text(s"$workingDir/target/software").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.software))
|
||||||
val ts = softDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
val ts = softDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
||||||
|
ct = softDS.count()
|
||||||
|
et = softDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
|
||||||
|
assertEquals(ct, et)
|
||||||
|
|
||||||
|
|
||||||
val orpDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/otherresearchproduct").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.otherresearchproduct))
|
val orpDS:Dataset[Result] = spark.read.text(s"$workingDir/target/otherresearchproduct").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.otherresearchproduct))
|
||||||
val to = orpDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
val to = orpDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
|
||||||
|
|
||||||
|
|
||||||
|
ct = orpDS.count()
|
||||||
|
et = orpDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
|
||||||
|
assertEquals(ct, et)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
assertEquals(0, t)
|
assertEquals(0, t)
|
||||||
assertEquals(2, td)
|
assertEquals(2, td)
|
||||||
assertEquals(1, ts)
|
assertEquals(1, ts)
|
||||||
|
|
@ -178,6 +198,32 @@ class ResolveEntitiesTest extends Serializable {
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
@Test
|
||||||
|
def testMerge():Unit = {
|
||||||
|
|
||||||
|
val r = new Result
|
||||||
|
r.setSubject(List(OafMapperUtils.structuredProperty(FAKE_SUBJECT, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava)
|
||||||
|
|
||||||
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
|
val p = mapper.readValue(Source.fromInputStream(this.getClass.getResourceAsStream(s"publication")).mkString.lines.next(), classOf[Publication])
|
||||||
|
|
||||||
|
|
||||||
|
r.mergeFrom(p)
|
||||||
|
|
||||||
|
|
||||||
|
println(mapper.writeValueAsString(r))
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
{"context": [], "dataInfo": {"invisible": false, "trust": "0.9", "provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "inferred": false, "deletedbyinference": false}, "resourcetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}, "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1097/00132586-197308000-00003"}], "contributor": [], "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "created", "classname": "created", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2006-11-06T11:36:37Z"}], "collectedfrom": [{"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}], "id": "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2", "subject": [], "lastupdatetimestamp": 1620353302565, "author": [{"fullname": "N. S. AGRUSS", "surname": "AGRUSS", "name": "N. S.", "rank": 1}, {"fullname": "E. Y. ROSIN", "surname": "ROSIN", "name": "E. Y.", "rank": 2}, {"fullname": "R. J. ADOLPH", "surname": "ADOLPH", "name": "R. J.", "rank": 3}, {"fullname": "N. O. FOWLER", "surname": "FOWLER", "name": "N. O.", "rank": 4}], "instance": [{"hostedby": {"key": "10|issn___print::b8cee613d4f898f8c03956d57ea69be2", "value": "Survey of Anesthesiology"}, "url": ["https://doi.org/10.1097/00132586-197308000-00003"], "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1097/00132586-197308000-00003"}], "dateofacceptance": {"value": "2006-11-06T11:36:37Z"}, "collectedfrom": {"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2021-05-07T02:08:22Z", "fulltext": [], "description": [], "format": [], "journal": {"issnPrinted": "0039-6206", "vol": "17", "sp": "304", "name": "Survey of Anesthesiology"}, "measures": [], "coverage": [], "externalReference": [], "publisher": {"value": "Ovid Technologies (Wolters Kluwer Health)"}, "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["10.1097/00132586-197308000-00003", "50|doiboost____::b0baa0eb88a5788f0b8815560d2a32f2"], "source": [{"value": "Crossref"}], "dateofacceptance": {"value": "2006-11-06T11:36:37Z"}, "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "SIGNIFICANCE OF CHRONIC SINUS BRADYCARDIA IN ELDERLY PEOPLE"}]}
|
||||||
|
|
@ -0,0 +1 @@
|
||||||
|
{"context": [], "dataInfo": {"invisible": false, "trust": "0.9", "provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "inferred": false, "deletedbyinference": false}, "resourcetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}, "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.2143/tvg.62.1.5002364"}], "contributor": [], "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "created", "classname": "created", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2007-08-20T08:35:04Z"}, {"qualifier": {"classid": "published-online", "classname": "published-online", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2006-01-01"}], "collectedfrom": [{"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}], "id": "50|doi_________::4972b0ca81b96b225aed8038bb965656", "subject": [{"qualifier": {"classid": "keywords", "classname": "keywords", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "General Medicine"}], "lastupdatetimestamp": 1620381522840, "author": [{"fullname": "null VERHAMME P", "surname": "VERHAMME P", "rank": 1}], "instance": [{"hostedby": {"key": "10|issn__online::7ec728ad1ac65c60cd563a5137111125", "value": "Tijdschrift voor Geneeskunde"}, "url": ["https://doi.org/10.2143/tvg.62.1.5002364"], "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.2143/tvg.62.1.5002364"}], "dateofacceptance": {"value": "2006-01-01"}, "collectedfrom": {"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2021-05-07T09:58:42Z", "fulltext": [], "description": [], "format": [], "journal": {"vol": "62", "sp": "55", "issnOnline": "0371-683X", "ep": "61", "name": "Tijdschrift voor Geneeskunde"}, "measures": [], "coverage": [], "externalReference": [], "publisher": {"value": "Peeters Publishers"}, "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["10.2143/tvg.62.1.5002364", "50|doiboost____::4972b0ca81b96b225aed8038bb965656"], "source": [{"value": "Crossref"}], "dateofacceptance": {"value": "2006-01-01"}, "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Antitrombotica: nieuwe moleculen"}]}
|
||||||
|
|
@ -1,10 +1,10 @@
|
||||||
{"relType":"resultResult","subRelType":"citation","relClass":"cites","source":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","target":"50|openaire____::007a4870b31056f89b768cf508e1538e"}
|
{"relType":"resultResult","subRelType":"citation","relClass":"cites","source":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","target":"50|openaire____::007a4870b31056f89b768cf508e1538e","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"citation","relClass":"isCitedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"citation","relClass":"isCitedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"part","relClass":"isPartOf","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"part","relClass":"isPartOf","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"part","relClass":"hasPart","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"part","relClass":"hasPart","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"review","relClass":"isReviewedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"review","relClass":"isReviewedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"review","relClass":"reviews","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"review","relClass":"reviews","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"relationship","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"relationship","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
{"relType":"resultResult","subRelType":"publicationDataset","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
|
{"relType":"resultResult","subRelType":"publicationDataset","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","dataInfo": {"provenanceaction": {"classid": "iis", "classname": "erroneous label to be cleaned","schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}}}
|
||||||
|
|
@ -1242,3 +1242,4 @@ dnet:relation_relClass @=@ IsSupplementTo @=@ isSupplementTo
|
||||||
dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy
|
dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy
|
||||||
dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo
|
dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo
|
||||||
dnet:relation_subRelType @=@ relationship @=@ publicationDataset
|
dnet:relation_subRelType @=@ relationship @=@ publicationDataset
|
||||||
|
dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned
|
||||||
|
|
@ -8,7 +8,7 @@ join result_instance ri on ri.id = p.id
|
||||||
join datasource on datasource.id = ri.hostedby
|
join datasource on datasource.id = ri.hostedby
|
||||||
where datasource.type like '%Repository%'
|
where datasource.type like '%Repository%'
|
||||||
and (ri.accessright = 'Open Access'
|
and (ri.accessright = 'Open Access'
|
||||||
or ri.accessright = 'Embargo')) tmp
|
or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp
|
||||||
on p.id= tmp.id;
|
on p.id= tmp.id;
|
||||||
|
|
||||||
create table indi_pub_grey_lit stored as parquet as
|
create table indi_pub_grey_lit stored as parquet as
|
||||||
|
|
@ -41,178 +41,178 @@ join datasource on datasource.id = ri.hostedby
|
||||||
where datasource.id like '%doajarticles%') tmp
|
where datasource.id like '%doajarticles%') tmp
|
||||||
on p.id= tmp.id;
|
on p.id= tmp.id;
|
||||||
|
|
||||||
create table indi_project_pubs_count stored as parquet as
|
--create table indi_project_pubs_count stored as parquet as
|
||||||
select pr.id id, count(p.id) total_pubs from project_results pr
|
--select pr.id id, count(p.id) total_pubs from project_results pr
|
||||||
join publication p on p.id=pr.result
|
--join publication p on p.id=pr.result
|
||||||
group by pr.id;
|
--group by pr.id;
|
||||||
|
|
||||||
create table indi_project_datasets_count stored as parquet as
|
--create table indi_project_datasets_count stored as parquet as
|
||||||
select pr.id id, count(d.id) total_datasets from project_results pr
|
--select pr.id id, count(d.id) total_datasets from project_results pr
|
||||||
join dataset d on d.id=pr.result
|
--join dataset d on d.id=pr.result
|
||||||
group by pr.id;
|
--group by pr.id;
|
||||||
|
|
||||||
create table indi_project_software_count stored as parquet as
|
--create table indi_project_software_count stored as parquet as
|
||||||
select pr.id id, count(s.id) total_software from project_results pr
|
--select pr.id id, count(s.id) total_software from project_results pr
|
||||||
join software s on s.id=pr.result
|
--join software s on s.id=pr.result
|
||||||
group by pr.id;
|
--group by pr.id;
|
||||||
|
|
||||||
create table indi_project_otherresearch_count stored as parquet as
|
--create table indi_project_otherresearch_count stored as parquet as
|
||||||
select pr.id id, count(o.id) total_other from project_results pr
|
--select pr.id id, count(o.id) total_other from project_results pr
|
||||||
join otherresearchproduct o on o.id=pr.result
|
--join otherresearchproduct o on o.id=pr.result
|
||||||
group by pr.id;
|
--group by pr.id;
|
||||||
|
|
||||||
create table indi_pub_avg_year_country_oa stored as parquet as
|
--create table indi_pub_avg_year_country_oa stored as parquet as
|
||||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||||
from
|
--from
|
||||||
(SELECT year, country, SUM(CASE
|
--(SELECT year, country, SUM(CASE
|
||||||
WHEN bestlicence='Open Access' THEN 1
|
--WHEN bestlicence='Open Access' THEN 1
|
||||||
ELSE 0
|
--ELSE 0
|
||||||
END) AS OpenAccess, SUM(CASE
|
--END) AS OpenAccess, SUM(CASE
|
||||||
WHEN bestlicence<>'Open Access' THEN 1
|
--WHEN bestlicence<>'Open Access' THEN 1
|
||||||
ELSE 0
|
--ELSE 0
|
||||||
END) AS NonOpenAccess
|
--END) AS NonOpenAccess
|
||||||
FROM publication p
|
--FROM publication p
|
||||||
join result_organization ro on p.id=ro.id
|
--join result_organization ro on p.id=ro.id
|
||||||
join organization o on o.id=ro.organization
|
--join organization o on o.id=ro.organization
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by year, country) tmp;
|
--group by year, country) tmp;
|
||||||
|
|
||||||
create table indi_dataset_avg_year_country_oa stored as parquet as
|
--create table indi_dataset_avg_year_country_oa stored as parquet as
|
||||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||||
from
|
--from
|
||||||
(SELECT year, country, SUM(CASE
|
--(SELECT year, country, SUM(CASE
|
||||||
WHEN bestlicence='Open Access' THEN 1
|
--WHEN bestlicence='Open Access' THEN 1
|
||||||
ELSE 0
|
--ELSE 0
|
||||||
END) AS OpenAccess, SUM(CASE
|
--END) AS OpenAccess, SUM(CASE
|
||||||
WHEN bestlicence<>'Open Access' THEN 1
|
--WHEN bestlicence<>'Open Access' THEN 1
|
||||||
ELSE 0
|
--ELSE 0
|
||||||
END) AS NonOpenAccess
|
--END) AS NonOpenAccess
|
||||||
FROM dataset d
|
--FROM dataset d
|
||||||
join result_organization ro on d.id=ro.id
|
--join result_organization ro on d.id=ro.id
|
||||||
join organization o on o.id=ro.organization
|
--join organization o on o.id=ro.organization
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by year, country) tmp;
|
--group by year, country) tmp;
|
||||||
|
|
||||||
create table indi_software_avg_year_country_oa stored as parquet as
|
--create table indi_software_avg_year_country_oa stored as parquet as
|
||||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||||
from
|
--from
|
||||||
(SELECT year, country, SUM(CASE
|
-- (SELECT year, country, SUM(CASE
|
||||||
WHEN bestlicence='Open Access' THEN 1
|
--WHEN bestlicence='Open Access' THEN 1
|
||||||
ELSE 0
|
-- ELSE 0
|
||||||
END) AS OpenAccess, SUM(CASE
|
--END) AS OpenAccess, SUM(CASE
|
||||||
WHEN bestlicence<>'Open Access' THEN 1
|
-- WHEN bestlicence<>'Open Access' THEN 1
|
||||||
ELSE 0
|
-- ELSE 0
|
||||||
END) AS NonOpenAccess
|
-- END) AS NonOpenAccess
|
||||||
FROM software s
|
-- FROM software s
|
||||||
join result_organization ro on s.id=ro.id
|
-- join result_organization ro on s.id=ro.id
|
||||||
join organization o on o.id=ro.organization
|
-- join organization o on o.id=ro.organization
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
-- where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by year, country) tmp;
|
-- group by year, country) tmp;
|
||||||
|
|
||||||
|
|
||||||
create table indi_other_avg_year_country_oa stored as parquet as
|
--create table indi_other_avg_year_country_oa stored as parquet as
|
||||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||||
from
|
-- from
|
||||||
(SELECT year, country, SUM(CASE
|
-- (SELECT year, country, SUM(CASE
|
||||||
WHEN bestlicence='Open Access' THEN 1
|
-- WHEN bestlicence='Open Access' THEN 1
|
||||||
ELSE 0
|
-- ELSE 0
|
||||||
END) AS OpenAccess, SUM(CASE
|
-- END) AS OpenAccess, SUM(CASE
|
||||||
WHEN bestlicence<>'Open Access' THEN 1
|
-- WHEN bestlicence<>'Open Access' THEN 1
|
||||||
ELSE 0
|
-- ELSE 0
|
||||||
END) AS NonOpenAccess
|
-- END) AS NonOpenAccess
|
||||||
FROM otherresearchproduct orp
|
-- FROM otherresearchproduct orp
|
||||||
join result_organization ro on orp.id=ro.id
|
-- join result_organization ro on orp.id=ro.id
|
||||||
join organization o on o.id=ro.organization
|
-- join organization o on o.id=ro.organization
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
-- where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by year, country) tmp;
|
-- group by year, country) tmp;
|
||||||
|
|
||||||
create table indi_pub_avg_year_context_oa stored as parquet as
|
--create table indi_pub_avg_year_context_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc
|
--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc
|
||||||
join context c on pc.concept like concat('%',c.id,'%')
|
--join context c on pc.concept like concat('%',c.id,'%')
|
||||||
join publication p on p.id=pc.id
|
--join publication p on p.id=pc.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by c.name, year )
|
--group by c.name, year )
|
||||||
select year, name, round(no_of_pubs/total*100,3) averageofpubs
|
--select year, name, round(no_of_pubs/total*100,3) averageofpubs
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_dataset_avg_year_context_oa stored as parquet as
|
--create table indi_dataset_avg_year_context_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc
|
--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc
|
||||||
join context c on pc.concept like concat('%',c.id,'%')
|
--join context c on pc.concept like concat('%',c.id,'%')
|
||||||
join dataset p on p.id=pc.id
|
--join dataset p on p.id=pc.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by c.name, year )
|
--group by c.name, year )
|
||||||
select year, name, round(no_of_pubs/total*100,3) averageofdataset
|
--select year, name, round(no_of_pubs/total*100,3) averageofdataset
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_software_avg_year_context_oa stored as parquet as
|
--create table indi_software_avg_year_context_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc
|
--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc
|
||||||
join context c on pc.concept like concat('%',c.id,'%')
|
--join context c on pc.concept like concat('%',c.id,'%')
|
||||||
join software p on p.id=pc.id
|
--join software p on p.id=pc.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by c.name, year )
|
--group by c.name, year )
|
||||||
select year, name, round(no_of_pubs/total*100,3) averageofsoftware
|
--select year, name, round(no_of_pubs/total*100,3) averageofsoftware
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_other_avg_year_context_oa stored as parquet as
|
--create table indi_other_avg_year_context_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc
|
--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc
|
||||||
join context c on pc.concept like concat('%',c.id,'%')
|
--join context c on pc.concept like concat('%',c.id,'%')
|
||||||
join otherresearchproduct p on p.id=pc.id
|
--join otherresearchproduct p on p.id=pc.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by c.name, year )
|
--group by c.name, year )
|
||||||
select year, name, round(no_of_pubs/total*100,3) averageofother
|
--select year, name, round(no_of_pubs/total*100,3) averageofother
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_other_avg_year_content_oa stored as parquet as
|
--create table indi_other_avg_year_content_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||||
from otherresearchproduct_datasources pd
|
--from otherresearchproduct_datasources pd
|
||||||
join datasource d on datasource=d.id
|
--join datasource d on datasource=d.id
|
||||||
join otherresearchproduct p on p.id=pd.id
|
--join otherresearchproduct p on p.id=pd.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by d.type, year)
|
--group by d.type, year)
|
||||||
select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct
|
--select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_software_avg_year_content_oa stored as parquet as
|
--create table indi_software_avg_year_content_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||||
from software_datasources pd
|
--from software_datasources pd
|
||||||
join datasource d on datasource=d.id
|
--join datasource d on datasource=d.id
|
||||||
join software p on p.id=pd.id
|
--join software p on p.id=pd.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by d.type, year)
|
--group by d.type, year)
|
||||||
select year, type, round(no_of_pubs/total*100,3) averageOfSoftware
|
--select year, type, round(no_of_pubs/total*100,3) averageOfSoftware
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_dataset_avg_year_content_oa stored as parquet as
|
--create table indi_dataset_avg_year_content_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||||
from dataset_datasources pd
|
--from dataset_datasources pd
|
||||||
join datasource d on datasource=d.id
|
--join datasource d on datasource=d.id
|
||||||
join dataset p on p.id=pd.id
|
--join dataset p on p.id=pd.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by d.type, year)
|
--group by d.type, year)
|
||||||
select year, type, round(no_of_pubs/total*100,3) averageOfDatasets
|
--select year, type, round(no_of_pubs/total*100,3) averageOfDatasets
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_pub_avg_year_content_oa stored as parquet as
|
--create table indi_pub_avg_year_content_oa stored as parquet as
|
||||||
with total as
|
--with total as
|
||||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||||
from publication_datasources pd
|
--from publication_datasources pd
|
||||||
join datasource d on datasource=d.id
|
--join datasource d on datasource=d.id
|
||||||
join publication p on p.id=pd.id
|
--join publication p on p.id=pd.id
|
||||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
--where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||||
group by d.type, year)
|
--group by d.type, year)
|
||||||
select year, type, round(no_of_pubs/total*100,3) averageOfPubs
|
--select year, type, round(no_of_pubs/total*100,3) averageOfPubs
|
||||||
from total;
|
--from total;
|
||||||
|
|
||||||
create table indi_pub_has_cc_licence stored as parquet as
|
create table indi_pub_has_cc_licence stored as parquet as
|
||||||
select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
|
select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
|
||||||
|
|
@ -231,11 +231,40 @@ join publication_licenses as license on license.id = p.id
|
||||||
WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp
|
WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp
|
||||||
on p.id= tmp.id;
|
on p.id= tmp.id;
|
||||||
|
|
||||||
|
-- EOSC-TR1.1-02M:
|
||||||
|
-- ## Indicator: has_cc_license. Creative Commons licensing has become a
|
||||||
|
-- de facto standard in scholarly communication and is promoted by many initiatives
|
||||||
|
-- like Plan S. This indicator might be only useful when applied
|
||||||
|
-- to openly available publications.
|
||||||
|
--create table indi_pub_has_cc_licence_tr stored as parquet as
|
||||||
|
--select distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_tr
|
||||||
|
--from publication p
|
||||||
|
--left outer join (select p.id, license.type as lic from publication p
|
||||||
|
--join publication_licenses as license on license.id = p.id
|
||||||
|
--where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
|
||||||
|
--on p.id= tmp.id
|
||||||
|
|
||||||
|
-- #EOSC-F2-01M_cc Rich metadata for scholarly publications
|
||||||
|
-- ## Indicator: has_cc_license. Creative Commons licensing has become a
|
||||||
|
-- de facto standard in scholarly communication and is promoted by many initiatives
|
||||||
|
-- like Plan S. This indicator might be only useful when applied
|
||||||
|
-- to openly available publications.
|
||||||
|
|
||||||
|
-- Same indicator as EOSC-TR1.1-02M (Najko's instructions)
|
||||||
|
-- create table indi_pub_has_cc_licence_f stored as parquet as
|
||||||
|
-- select
|
||||||
|
-- distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_f
|
||||||
|
-- from publication p
|
||||||
|
-- left outer join (selectp.id,license.type as lic from publication p
|
||||||
|
-- join publication_licenses as license on license.id = p.id
|
||||||
|
-- where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
|
||||||
|
-- on p.id= tmp.id
|
||||||
|
|
||||||
create table indi_pub_has_abstract stored as parquet as
|
create table indi_pub_has_abstract stored as parquet as
|
||||||
select distinct publication.id, coalesce(abstract, 1) has_abstract
|
select distinct publication.id, coalesce(abstract, 1) has_abstract
|
||||||
from publication;
|
from publication;
|
||||||
|
|
||||||
create table indi_with_orcid stored as parquet as
|
create table indi_result_with_orcid stored as parquet as
|
||||||
select distinct r.id, coalesce(has_orcid, 0) as has_orcid
|
select distinct r.id, coalesce(has_orcid, 0) as has_orcid
|
||||||
from result r
|
from result r
|
||||||
left outer join (select id, 1 as has_orcid from result_orcid) tmp
|
left outer join (select id, 1 as has_orcid from result_orcid) tmp
|
||||||
|
|
@ -270,13 +299,64 @@ join tmp as o2 on o1.result=o2.result
|
||||||
where o1.id<>o2.id
|
where o1.id<>o2.id
|
||||||
group by o1.id, o2.id, o1.type
|
group by o1.id, o2.id, o1.type
|
||||||
|
|
||||||
create table indi_result_org_country_collab stored as parquet as
|
create table indi_funder_country_collab stored as parquet as
|
||||||
with tmp as
|
with tmp as (select funder, project, country from organization_projects op
|
||||||
(select o.id as id, o.country , ro.id as result,r.type from organization o
|
join organization o on o.id=op.id
|
||||||
join result_organization ro on o.id=ro.organization
|
join project p on p.id=op.project
|
||||||
join result r on r.id=ro.id where o.country <> 'UNKNOWN')
|
where country <> 'UNKNOWN')
|
||||||
select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations
|
select f1.funder, f1.country, f2.country, count(distinct f1.project) as collaborations
|
||||||
from tmp as o1
|
from tmp as f1
|
||||||
join tmp as o2 on o1.result=o2.result
|
join tmp as f2 on f1.project=f2.project
|
||||||
where o1.id<>o2.id and o1.country<>o2.country
|
where f1.country<>f2.country
|
||||||
group by o1.id, o1.type,o2.country
|
group by f1.funder, f2.country, f1.country
|
||||||
|
|
||||||
|
create table indi_pub_diamond stored as parquet as
|
||||||
|
select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
|
||||||
|
from publication_datasources pd
|
||||||
|
left outer join (
|
||||||
|
select pd.id, 1 as in_diamond_journal from publication_datasources pd
|
||||||
|
join datasource d on d.id=pd.datasource
|
||||||
|
join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||||
|
and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp
|
||||||
|
on pd.id=tmp.id
|
||||||
|
|
||||||
|
create table indi_pub_hybrid stored as parquet as
|
||||||
|
select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid
|
||||||
|
from publication_datasources pd
|
||||||
|
left outer join (
|
||||||
|
select pd.id, 1 as is_hybrid from publication_datasources pd
|
||||||
|
join datasource d on d.id=pd.datasource
|
||||||
|
join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||||
|
and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp
|
||||||
|
on pd.id=tmp.id
|
||||||
|
|
||||||
|
create table indi_is_gold_oa stored as parquet as
|
||||||
|
(select distinct pd.id, coalesce(gold_oa, 0) as gold_oa
|
||||||
|
from publication_datasources pd
|
||||||
|
left outer join (
|
||||||
|
select pd.id, 1 as gold_oa from publication_datasources pd
|
||||||
|
join datasource d on d.id=pd.datasource
|
||||||
|
join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online)
|
||||||
|
where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp
|
||||||
|
on pd.id=tmp.id)
|
||||||
|
|
||||||
|
|
||||||
|
create table indi_pub_in_transformative stored as parquet as
|
||||||
|
select distinct pd.id, coalesce(is_transformative, 0) as is_transformative
|
||||||
|
from publication pd
|
||||||
|
left outer join (
|
||||||
|
select pd.id, 1 as is_transformative from publication_datasources pd
|
||||||
|
join datasource d on d.id=pd.datasource
|
||||||
|
join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||||
|
and ps.is_transformative_journal=true) tmp
|
||||||
|
on pd.id=tmp.id
|
||||||
|
|
||||||
|
create table indi_pub_closed_other_open stored as parquet as
|
||||||
|
select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri
|
||||||
|
left outer join
|
||||||
|
(select ri.id, 1 as pub_closed_other_open from result_instance ri
|
||||||
|
join publication p on p.id=ri.id
|
||||||
|
join datasource d on ri.hostedby=d.id
|
||||||
|
where d.type like '%Journal%' and ri.accessright='Closed Access' and
|
||||||
|
(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp
|
||||||
|
on tmp.id=ri.id
|
||||||
|
|
@ -105,23 +105,6 @@ create table TARGET.project_results stored as parquet as select id as result, pr
|
||||||
compute stats TARGET.project_results;
|
compute stats TARGET.project_results;
|
||||||
|
|
||||||
-- indicators
|
-- indicators
|
||||||
create view TARGET.indi_dataset_avg_year_content_oa as select * from SOURCE.indi_dataset_avg_year_content_oa orig;
|
|
||||||
create view TARGET.indi_dataset_avg_year_context_oa as select * from SOURCE.indi_dataset_avg_year_context_oa orig;
|
|
||||||
create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig;
|
|
||||||
|
|
||||||
create view TARGET.indi_other_avg_year_content_oa as select * from SOURCE.indi_other_avg_year_content_oa orig;
|
|
||||||
create view TARGET.indi_other_avg_year_context_oa as select * from SOURCE.indi_other_avg_year_context_oa orig;
|
|
||||||
create view TARGET.indi_other_avg_year_country_oa as select * from SOURCE.indi_other_avg_year_country_oa orig;
|
|
||||||
|
|
||||||
create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig;
|
|
||||||
create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig;
|
|
||||||
create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig;
|
|
||||||
create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig;
|
|
||||||
|
|
||||||
create view TARGET.indi_pub_avg_year_content_oa as select * from SOURCE.indi_pub_avg_year_content_oa orig;
|
|
||||||
create view TARGET.indi_pub_avg_year_context_oa as select * from SOURCE.indi_pub_avg_year_context_oa orig;
|
|
||||||
create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig;
|
|
||||||
|
|
||||||
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
compute stats TARGET.indi_pub_green_oa;
|
compute stats TARGET.indi_pub_green_oa;
|
||||||
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
|
@ -137,9 +120,20 @@ compute stats TARGET.indi_pub_has_cc_licence;
|
||||||
create table TARGET.indi_pub_has_cc_licence_url stored as parquet as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
create table TARGET.indi_pub_has_cc_licence_url stored as parquet as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
compute stats TARGET.indi_pub_has_cc_licence_url;
|
compute stats TARGET.indi_pub_has_cc_licence_url;
|
||||||
|
|
||||||
create view TARGET.indi_software_avg_year_content_oa as select * from SOURCE.indi_software_avg_year_content_oa orig;
|
create view TARGET.indi_funder_country_collab stored as select * from SOURCE.indi_funder_country_collab;
|
||||||
create view TARGET.indi_software_avg_year_context_oa as select * from SOURCE.indi_software_avg_year_context_oa orig;
|
|
||||||
create view TARGET.indi_software_avg_year_country_oa as select * from SOURCE.indi_software_avg_year_country_oa orig;
|
create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_result_with_orcid;
|
||||||
|
create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_funded_result_with_fundref;
|
||||||
|
create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_pub_diamond;
|
||||||
|
create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_pub_hybrid;
|
||||||
|
create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_pub_in_transformative;
|
||||||
|
create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||||
|
compute stats TARGET.indi_pub_closed_other_open;
|
||||||
|
|
||||||
--denorm
|
--denorm
|
||||||
alter table TARGET.result rename to TARGET.res_tmp;
|
alter table TARGET.result rename to TARGET.res_tmp;
|
||||||
|
|
|
||||||
|
|
@ -15,6 +15,13 @@
|
||||||
|
|
||||||
<description>This module is the container for the oozie workflow definitions in dnet-hadoop project</description>
|
<description>This module is the container for the oozie workflow definitions in dnet-hadoop project</description>
|
||||||
|
|
||||||
|
<distributionManagement>
|
||||||
|
<site>
|
||||||
|
<id>DHPSite</id>
|
||||||
|
<url>${dhp.site.stage.path}/dhp-workflows</url>
|
||||||
|
</site>
|
||||||
|
</distributionManagement>
|
||||||
|
|
||||||
<modules>
|
<modules>
|
||||||
<module>dhp-workflow-profiles</module>
|
<module>dhp-workflow-profiles</module>
|
||||||
<module>dhp-aggregation</module>
|
<module>dhp-aggregation</module>
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,25 @@
|
||||||
|
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||||
|
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
|
||||||
|
name="DHP-Aggregation">
|
||||||
|
<skin>
|
||||||
|
<groupId>org.apache.maven.skins</groupId>
|
||||||
|
<artifactId>maven-fluido-skin</artifactId>
|
||||||
|
<version>1.8</version>
|
||||||
|
</skin>
|
||||||
|
<poweredBy>
|
||||||
|
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
|
||||||
|
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
|
||||||
|
</poweredBy>
|
||||||
|
<body>
|
||||||
|
<links>
|
||||||
|
<item name="Code" href="https://code-repo.d4science.org/" />
|
||||||
|
</links>
|
||||||
|
<menu name="APIDocs">
|
||||||
|
<item name="JavaDoc" href="apidocs/" />
|
||||||
|
<item name="ScalaDoc" href="scaladocs/" />
|
||||||
|
</menu>
|
||||||
|
<menu ref="modules" />
|
||||||
|
<menu ref="reports"/>
|
||||||
|
</body>
|
||||||
|
</project>
|
||||||
5
pom.xml
5
pom.xml
|
|
@ -719,6 +719,10 @@
|
||||||
<id>dnet45-releases</id>
|
<id>dnet45-releases</id>
|
||||||
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
|
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
|
||||||
</repository>
|
</repository>
|
||||||
|
<site>
|
||||||
|
<id>DHPSite</id>
|
||||||
|
<url>${dhp.site.stage.path}/</url>
|
||||||
|
</site>
|
||||||
</distributionManagement>
|
</distributionManagement>
|
||||||
<reporting>
|
<reporting>
|
||||||
<plugins>
|
<plugins>
|
||||||
|
|
@ -734,6 +738,7 @@
|
||||||
</reporting>
|
</reporting>
|
||||||
|
|
||||||
<properties>
|
<properties>
|
||||||
|
<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
|
||||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||||
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
|
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
|
||||||
<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
|
<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
|
||||||
|
|
|
||||||
|
|
@ -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>
|
||||||
Loading…
Reference in New Issue