Hosted By Map - Classes to apply the HBM to results and datasources
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package eu.dnetlib.dhp.oa.graph.hostedbymap
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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.oa.graph.hostedbymap.SparkApplyHostedByMapToResult.{applyHBtoPubs, getClass}
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import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.{Datasource, Publication}
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.json4s.DefaultFormats
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import org.slf4j.{Logger, LoggerFactory}
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object SparkApplyHostedByMapToDatasource {
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def applyHBtoDats(join: Dataset[EntityInfo], dats: Dataset[Datasource]): Dataset[Datasource] = {
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dats.joinWith(join, dats.col("id").equalTo(join.col("hb_id")), "left")
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.map(t2 => {
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val d: Datasource = t2._1
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if (t2._2 != null) {
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if (d.getOpenairecompatibility.getClassid.equals(ModelConstants.UNKNOWN)) {
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d.getOpenairecompatibility.setClassid("hostedBy")
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d.getOpenairecompatibility.setClassname("collected from a compatible aggregator")
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}
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}
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d
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})(Encoders.bean((classOf[Datasource])))
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}
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def main(args: Array[String]): Unit = {
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val logger: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json")))
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val graphPath = parser.get("graphPath")
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val outputPath = parser.get("outputPath")
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val workingPath = parser.get("workingPath")
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implicit val formats = DefaultFormats
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implicit val mapEncoderPubs: Encoder[Datasource] = Encoders.bean(classOf[Datasource])
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implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
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val mapper = new ObjectMapper()
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val dats : Dataset[Datasource] = spark.read.textFile("$graphPath/datasource")
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.map(r => mapper.readValue(r, classOf[Datasource]))
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val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo")
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.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
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//c. dataset join risultato del passo prima di a per datasource id, gruppo per ds id e cambio compatibilita' se necessario
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applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(s"$graphPath/datasource")
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}
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}
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@ -0,0 +1,88 @@
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package eu.dnetlib.dhp.oa.graph.hostedbymap
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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.oa.graph.hostedbymap.model.EntityInfo
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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.{Datasource, Instance, OpenAccessRoute, Publication}
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.json4s.DefaultFormats
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import org.slf4j.{Logger, LoggerFactory}
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import scala.collection.JavaConverters._
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//a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance
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// nel result => salto)con l'hosted by anche access right della instance se openaccess e' true
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object SparkApplyHostedByMapToResult {
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def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = {
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pubs.joinWith(join, pubs.col("id").equalTo(join.col("id")), "left")
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.map(t2 => {
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val p: Publication = t2._1
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if (t2._2 != null) {
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val ei: EntityInfo = t2._2
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val i = p.getInstance().asScala
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if (i.size == 1) {
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val inst: Instance = i(0)
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inst.getHostedby.setKey(ei.getHb_id)
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inst.getHostedby.setValue(ei.getName)
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if (ei.getOpenaccess) {
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inst.setAccessright(OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN, "Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
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inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.hybrid)
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}
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}
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}
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p
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})(Encoders.bean(classOf[Publication]))
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}
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def main(args: Array[String]): Unit = {
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val logger: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json")))
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val graphPath = parser.get("graphPath")
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val outputPath = parser.get("outputPath")
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val workingPath = parser.get("workingPath")
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implicit val formats = DefaultFormats
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implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
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implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
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val mapper = new ObjectMapper()
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val pubs : Dataset[Publication] = spark.read.textFile("$graphPath/publication")
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.map(r => mapper.readValue(r, classOf[Publication]))
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val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo")
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.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
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//a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance
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// nel result => salto)con l'hosted by anche access right della instance se openaccess e' true
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applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json("$graphPath/publication")
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}
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}
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