Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta
commit
ac07ed8251
@ -0,0 +1,37 @@
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package eu.dnetlib.dhp.application
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.SparkSession
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import org.slf4j.Logger
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abstract class AbstractScalaApplication (val propertyPath:String, val args:Array[String], log:Logger) extends SparkScalaApplication {
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var parser: ArgumentApplicationParser = null
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var spark:SparkSession = null
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def initialize():SparkScalaApplication = {
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parser = parseArguments(args)
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spark = createSparkSession()
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this
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}
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/**
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* Utility for creating a spark session starting from parser
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*
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* @return a spark Session
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*/
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private def createSparkSession():SparkSession = {
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require(parser!= null)
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val conf:SparkConf = new SparkConf()
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val master = parser.get("master")
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log.info(s"Creating Spark session: Master: $master")
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SparkSession.builder().config(conf)
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.appName(getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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}
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}
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@ -0,0 +1,35 @@
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package eu.dnetlib.dhp.application
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import scala.io.Source
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/**
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* This is the main Interface SparkApplication
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* where all the Spark Scala class should inherit
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*
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*/
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trait SparkScalaApplication {
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/**
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* This is the path in the classpath of the json
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* describes all the argument needed to run
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*/
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val propertyPath: String
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/**
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* Utility to parse the arguments using the
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* property json in the classpath identified from
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* the variable propertyPath
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*
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* @param args the list of arguments
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*/
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def parseArguments(args: Array[String]): ArgumentApplicationParser = {
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString)
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parser.parseArgument(args)
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parser
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}
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/**
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* Here all the spark applications runs this method
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* where the whole logic of the spark node is defined
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*/
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def run(): Unit
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}
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@ -0,0 +1,134 @@
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package eu.dnetlib.dhp.datacite
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
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import java.io.InputStream
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import java.time.format.DateTimeFormatter
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import java.util.Locale
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import java.util.regex.Pattern
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import scala.io.Source
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/**
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* This class represent the dataModel of the input Dataset of Datacite
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* @param doi THE DOI
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* @param timestamp timestamp of last update date
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* @param isActive the record is active or deleted
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* @param json the json native records
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*/
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case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {}
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/*
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The following class are utility class used for the mapping from
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json datacite to OAF Shema
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*/
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case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {}
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case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
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case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {}
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case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
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case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
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case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
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case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {}
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case class DateType(date: Option[String], dateType: Option[String]) {}
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case class OAFRelations(relation:String, inverse:String, relType:String)
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class DataciteModelConstants extends Serializable {
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}
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object DataciteModelConstants {
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val REL_TYPE_VALUE:String = "resultResult"
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val DATE_RELATION_KEY = "RelationDate"
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val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter"
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val DOI_CLASS = "doi"
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val SUBJ_CLASS = "keywords"
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val DATACITE_NAME = "Datacite"
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val dataInfo: DataInfo = dataciteDataInfo("0.9")
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val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME)
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val subRelTypeMapping: Map[String,OAFRelations] = Map(
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ModelConstants.REFERENCES -> OAFRelations(ModelConstants.REFERENCES, ModelConstants.IS_REFERENCED_BY, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_REFERENCED_BY -> OAFRelations(ModelConstants.IS_REFERENCED_BY,ModelConstants.REFERENCES, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_SUPPLEMENTED_BY -> OAFRelations(ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.SUPPLEMENT),
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ModelConstants.IS_SUPPLEMENT_TO -> OAFRelations(ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.SUPPLEMENT),
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ModelConstants.HAS_PART -> OAFRelations(ModelConstants.HAS_PART,ModelConstants.IS_PART_OF, ModelConstants.PART),
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ModelConstants.IS_PART_OF -> OAFRelations(ModelConstants.IS_PART_OF,ModelConstants.HAS_PART, ModelConstants.PART),
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ModelConstants.IS_VERSION_OF-> OAFRelations(ModelConstants.IS_VERSION_OF,ModelConstants.HAS_VERSION,ModelConstants.VERSION),
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ModelConstants.HAS_VERSION-> OAFRelations(ModelConstants.HAS_VERSION,ModelConstants.IS_VERSION_OF,ModelConstants.VERSION),
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ModelConstants.IS_IDENTICAL_TO -> OAFRelations(ModelConstants.IS_IDENTICAL_TO,ModelConstants.IS_IDENTICAL_TO, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_CONTINUED_BY -> OAFRelations(ModelConstants.IS_CONTINUED_BY,ModelConstants.CONTINUES, ModelConstants.RELATIONSHIP),
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ModelConstants.CONTINUES -> OAFRelations(ModelConstants.CONTINUES,ModelConstants.IS_CONTINUED_BY, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_NEW_VERSION_OF-> OAFRelations(ModelConstants.IS_NEW_VERSION_OF,ModelConstants.IS_PREVIOUS_VERSION_OF, ModelConstants.VERSION),
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ModelConstants.IS_PREVIOUS_VERSION_OF ->OAFRelations(ModelConstants.IS_PREVIOUS_VERSION_OF,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION),
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ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP),
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ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_SOURCE_OF -> OAFRelations(ModelConstants.IS_SOURCE_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION),
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ModelConstants.IS_DERIVED_FROM -> OAFRelations(ModelConstants.IS_DERIVED_FROM,ModelConstants.IS_SOURCE_OF, ModelConstants.VERSION),
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ModelConstants.CITES -> OAFRelations(ModelConstants.CITES,ModelConstants.IS_CITED_BY, ModelConstants.CITATION),
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ModelConstants.IS_CITED_BY -> OAFRelations(ModelConstants.IS_CITED_BY,ModelConstants.CITES, ModelConstants.CITATION),
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ModelConstants.IS_VARIANT_FORM_OF -> OAFRelations(ModelConstants.IS_VARIANT_FORM_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION),
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ModelConstants.IS_OBSOLETED_BY -> OAFRelations(ModelConstants.IS_OBSOLETED_BY,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION),
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ModelConstants.REVIEWS -> OAFRelations(ModelConstants.REVIEWS,ModelConstants.IS_REVIEWED_BY, ModelConstants.REVIEW),
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ModelConstants.IS_REVIEWED_BY -> OAFRelations(ModelConstants.IS_REVIEWED_BY,ModelConstants.REVIEWS, ModelConstants.REVIEW),
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ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP),
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ModelConstants.COMPILES -> OAFRelations(ModelConstants.COMPILES,ModelConstants.IS_COMPILED_BY, ModelConstants.RELATIONSHIP),
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ModelConstants.IS_COMPILED_BY -> OAFRelations(ModelConstants.IS_COMPILED_BY,ModelConstants.COMPILES, ModelConstants.RELATIONSHIP)
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)
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val datacite_filter: List[String] = {
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val stream: InputStream = getClass.getResourceAsStream(DATACITE_FILTER_PATH)
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require(stream!= null)
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Source.fromInputStream(stream).getLines().toList
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}
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def dataciteDataInfo(trust: String): DataInfo = OafMapperUtils.dataInfo(false,null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, trust)
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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)
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val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
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val funder_regex: List[(Pattern, String)] = List(
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(Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"),
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(Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::")
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)
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val Date_regex: List[Pattern] = List(
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//Y-M-D
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Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
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//M-D-Y
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Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE),
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//D-M-Y
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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),
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//Y
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Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
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)
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}
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@ -1,64 +1,94 @@
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package eu.dnetlib.dhp.datacite
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
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import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
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import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH
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import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object GenerateDataciteDatasetSpark {
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val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
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class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
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/**
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* Here all the spark applications runs this method
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* where the whole logic of the spark node is defined
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*/
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override def run(): Unit = {
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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log.info(s"SourcePath is '$sourcePath'")
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val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
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log.info(s"exportLinks is '$exportLinks'")
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val isLookupUrl: String = parser.get("isLookupUrl")
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log.info("isLookupUrl: {}", isLookupUrl)
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val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
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val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(GenerateDataciteDatasetSpark.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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import spark.implicits._
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implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
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implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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require(vocabularies != null)
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val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
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log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
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val mapper = new ObjectMapper()
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val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
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val outputBasePath = cleanedMdStoreVersion.getHdfsPath
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log.info("outputBasePath: {}", outputBasePath)
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log.info(s"outputBasePath is '$outputBasePath'")
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val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
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log.info(s"targetPath is '$targetPath'")
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generateDataciteDataset(sourcePath, exportLinks, vocabularies, targetPath, spark)
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reportTotalSize(targetPath, outputBasePath)
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}
|
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|
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|
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/**
|
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* For working with MDStore we need to store in a file on hdfs the size of
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* the current dataset
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* @param targetPath
|
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* @param outputBasePath
|
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*/
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def reportTotalSize( targetPath: String, outputBasePath: String ):Unit = {
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val total_items = spark.read.load(targetPath).count()
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writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
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}
|
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|
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/**
|
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* Generate the transformed and cleaned OAF Dataset from the native one
|
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|
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* @param sourcePath sourcePath of the native Dataset in format JSON/Datacite
|
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* @param exportLinks If true it generates unresolved links
|
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* @param vocabularies vocabularies for cleaning
|
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* @param targetPath the targetPath of the result Dataset
|
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*/
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def generateDataciteDataset(sourcePath: String, exportLinks: Boolean, vocabularies: VocabularyGroup, targetPath: String, spark:SparkSession):Unit = {
|
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require(spark!= null)
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import spark.implicits._
|
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|
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implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
|
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|
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implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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spark.read.load(sourcePath).as[DataciteType]
|
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.filter(d => d.isActive)
|
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.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
|
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.filter(d => d != null)
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.flatMap(i => fixRelations(i)).filter(i => i != null)
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.write.mode(SaveMode.Overwrite).save(targetPath)
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}
|
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|
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val total_items = spark.read.load(targetPath).as[Oaf].count()
|
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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 = {
|
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new GenerateDataciteDatasetSpark("/eu/dnetlib/dhp/datacite/generate_dataset_params.json", args, log).initialize().run()
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue