Added Action set generation for the MAG organization
This commit is contained in:
Sandro La Bruzzo
parent
41a42dde64
commit
a5ddd8dfbb
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@ -0,0 +1,21 @@
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[
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{
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"paramName": "m",
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"paramLongName": "master",
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"paramDescription": "the master name",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "The as output Path",
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"paramRequired": true
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},
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{
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"paramName": "ma",
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"paramLongName": "magBasePath",
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"paramDescription": "The mag Base path",
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"paramRequired": false
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}
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]
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@ -1,19 +1,11 @@
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package eu.dnetlib.dhp.collection.mag
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
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import eu.dnetlib.dhp.schema.oaf.utils.{OafMapperUtils, PidType}
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import eu.dnetlib.dhp.schema.oaf.{
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Author,
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DataInfo,
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Instance,
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Journal,
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Publication,
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Relation,
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Result,
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Dataset => OafDataset
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}
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Instance, Journal, Organization, Publication, Relation, Result, Dataset => OafDataset}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.spark.sql.types._
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import org.apache.spark.sql.{Dataset, Row, SparkSession}
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@ -121,7 +113,7 @@ object MagUtility extends Serializable {
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"DateTime" -> DateType
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)
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val stream = Map(
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val stream: Map[String, (String, Seq[String])] = Map(
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"Affiliations" -> Tuple2(
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"mag/Affiliations.txt",
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Seq(
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@ -351,7 +343,7 @@ object MagUtility extends Serializable {
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def getSchema(streamName: String): StructType = {
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var schema = new StructType()
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val d: Seq[String] = stream(streamName)._2
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d.foreach { case t =>
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d.foreach { t =>
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val currentType = t.split(":")
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val fieldName: String = currentType.head
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var fieldType: String = currentType.last
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@ -686,6 +678,58 @@ object MagUtility extends Serializable {
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}
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def generateOrganization(r: Row): String = {
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val o = new Organization
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val affId = s"20|mag_________::${DHPUtils.md5(r.getAs[Long]("AffiliationId").toString)}"
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o.setId(affId)
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o.setDataInfo(MAGDataInfo)
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o.setCollectedfrom(List(MAGCollectedFrom).asJava)
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o.setLegalname(field(r.getAs[String]("DisplayName"), null))
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val gid = r.getAs[String]("GridId")
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if (gid != null) {
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o.setPid(List(
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structuredProperty(gid, qualifier(
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PidType.GRID.toString,
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PidType.GRID.toString,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES
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),
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null),
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structuredProperty(r.getAs[Long]("AffiliationId").toString, qualifier(
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PidType.mag_id.toString,
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PidType.mag_id.toString,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES
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),
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null)
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).asJava)
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} else {
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o.setPid(List(
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structuredProperty(r.getAs[Long]("AffiliationId").toString, qualifier(
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PidType.mag_id.toString,
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PidType.mag_id.toString,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES
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),
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null)
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).asJava)
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}
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val c = r.getAs[String]("Iso3166Code")
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if (c != null)
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o.setCountry(qualifier(c, c, "dnet:countries", "dnet:countries"))
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else
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o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
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val ws = r.getAs[String]("OfficialPage")
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if (ws != null)
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o.setWebsiteurl(field(ws, null))
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val a = new AtomicAction[Organization]()
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a.setClazz(classOf[Organization])
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a.setPayload(o)
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mapper.writeValueAsString(a)
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}
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def generateAffiliationRelations(paperAffiliation: Row): List[Relation] = {
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val affId = s"20|mag_________::${DHPUtils.md5(paperAffiliation.getAs[Long]("AffiliationId").toString)}"
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@ -0,0 +1,42 @@
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package eu.dnetlib.dhp.collection.mag
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.Organization
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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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class SparkMagOrganizationAS (propertyPath: String, args: Array[String], log: Logger)
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extends AbstractScalaApplication(propertyPath, args, log: Logger) {
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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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val magBasePath:String = parser.get("magBasePath")
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log.info(s"magBasePath is $magBasePath")
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val outputPath:String = parser.get("outputPath")
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log.info(s"outputPath is $outputPath")
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generateAS(spark,magBasePath, outputPath)
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}
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def generateAS(spark:SparkSession, magBasePath:String,outputPath:String ):Unit = {
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import spark.implicits._
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val organizations = MagUtility.loadMagEntity(spark,"Affiliations", magBasePath)
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organizations.map(r => MagUtility.generateOrganization(r)).write.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(outputPath)
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}
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}
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object SparkMagOrganizationAS{
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val log: Logger = LoggerFactory.getLogger(SparkMagOrganizationAS.getClass)
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def main(args: Array[String]): Unit = {
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new SparkMagOrganizationAS("/eu/dnetlib/dhp/collection/mag/create_organization_AS.json", args, log)
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.initialize()
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.run()
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}
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}
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@ -10,6 +10,7 @@ class MAGMappingTest {
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val mapper = new ObjectMapper()
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def mappingTest(): Unit = {
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val spark = SparkSession
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@ -18,10 +19,9 @@ class MAGMappingTest {
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.master("local[*]")
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.getOrCreate()
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val s = new SparkMAGtoOAF(null, null, null)
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val s = new SparkMagOrganizationAS(null, null, null)
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s.convertMAG(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_oaf")
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s.generateAffiliations(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_oaf")
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s.generateAS(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_AS")
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}
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