Added Action set generation for the MAG organization

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/mag/create_organization_AS.json

@@ -0,0 +1,21 @@
+[
+  {
+    "paramName": "m",
+    "paramLongName": "master",
+    "paramDescription": "the master name",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "The as output Path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ma",
+    "paramLongName": "magBasePath",
+    "paramDescription": "The mag Base path",
+    "paramRequired": false
+  }
+
+]

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/MagUtility.scala

@@ -1,19 +1,11 @@
 package eu.dnetlib.dhp.collection.mag
 
 import com.fasterxml.jackson.databind.ObjectMapper
+import eu.dnetlib.dhp.schema.action.AtomicAction
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
 import eu.dnetlib.dhp.schema.oaf.utils.{OafMapperUtils, PidType}
-import eu.dnetlib.dhp.schema.oaf.{
+import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Instance, Journal, Organization, Publication, Relation, Result, Dataset => OafDataset}
-  Author,
-  DataInfo,
-  Instance,
-  Journal,
-  Publication,
-  Relation,
-  Result,
-  Dataset => OafDataset
-}
 import eu.dnetlib.dhp.utils.DHPUtils
 import org.apache.spark.sql.types._
 import org.apache.spark.sql.{Dataset, Row, SparkSession}
@@ -121,7 +113,7 @@ object MagUtility extends Serializable {
     "DateTime" -> DateType
   )
 
-  val stream = Map(
+  val stream: Map[String, (String, Seq[String])] = Map(
     "Affiliations" -> Tuple2(
       "mag/Affiliations.txt",
       Seq(
@@ -351,7 +343,7 @@ object MagUtility extends Serializable {
   def getSchema(streamName: String): StructType = {
     var schema = new StructType()
     val d: Seq[String] = stream(streamName)._2
-    d.foreach { case t =>
+    d.foreach { t =>
       val currentType = t.split(":")
       val fieldName: String = currentType.head
       var fieldType: String = currentType.last
@@ -686,6 +678,58 @@ object MagUtility extends Serializable {
 
   }
 
+  def generateOrganization(r: Row): String = {
+
+    val o = new Organization
+    val affId = s"20|mag_________::${DHPUtils.md5(r.getAs[Long]("AffiliationId").toString)}"
+    o.setId(affId)
+    o.setDataInfo(MAGDataInfo)
+    o.setCollectedfrom(List(MAGCollectedFrom).asJava)
+    o.setLegalname(field(r.getAs[String]("DisplayName"), null))
+    val gid = r.getAs[String]("GridId")
+    if (gid != null) {
+      o.setPid(List(
+        structuredProperty(gid, qualifier(
+          PidType.GRID.toString,
+          PidType.GRID.toString,
+          ModelConstants.DNET_PID_TYPES,
+          ModelConstants.DNET_PID_TYPES
+        ),
+          null),
+        structuredProperty(r.getAs[Long]("AffiliationId").toString, qualifier(
+          PidType.mag_id.toString,
+          PidType.mag_id.toString,
+          ModelConstants.DNET_PID_TYPES,
+          ModelConstants.DNET_PID_TYPES
+        ),
+          null)
+
+      ).asJava)
+    } else {
+      o.setPid(List(
+        structuredProperty(r.getAs[Long]("AffiliationId").toString, qualifier(
+          PidType.mag_id.toString,
+          PidType.mag_id.toString,
+          ModelConstants.DNET_PID_TYPES,
+          ModelConstants.DNET_PID_TYPES
+        ),
+          null)
+      ).asJava)
+    }
+    val c = r.getAs[String]("Iso3166Code")
+    if (c != null)
+      o.setCountry(qualifier(c, c, "dnet:countries", "dnet:countries"))
+    else
+      o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
+    val ws = r.getAs[String]("OfficialPage")
+    if (ws != null)
+      o.setWebsiteurl(field(ws, null))
+    val a = new AtomicAction[Organization]()
+    a.setClazz(classOf[Organization])
+    a.setPayload(o)
+    mapper.writeValueAsString(a)
+  }
+
   def generateAffiliationRelations(paperAffiliation: Row): List[Relation] = {
 
     val affId = s"20|mag_________::${DHPUtils.md5(paperAffiliation.getAs[Long]("AffiliationId").toString)}"

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/SparkMagOrganizationAS.scala

@@ -0,0 +1,42 @@
+package eu.dnetlib.dhp.collection.mag
+
+import eu.dnetlib.dhp.application.AbstractScalaApplication
+import eu.dnetlib.dhp.schema.action.AtomicAction
+import eu.dnetlib.dhp.schema.oaf.Organization
+import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+class SparkMagOrganizationAS (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 magBasePath:String = parser.get("magBasePath")
+    log.info(s"magBasePath is $magBasePath")
+    val outputPath:String = parser.get("outputPath")
+    log.info(s"outputPath is $outputPath")
+    generateAS(spark,magBasePath, outputPath)
+
+  }
+
+  def generateAS(spark:SparkSession, magBasePath:String,outputPath:String  ):Unit = {
+    import spark.implicits._
+    val organizations = MagUtility.loadMagEntity(spark,"Affiliations", magBasePath)
+    organizations.map(r => MagUtility.generateOrganization(r)).write.mode(SaveMode.Overwrite)
+      .option("compression", "gzip")
+      .text(outputPath)
+  }
+}
+
+object SparkMagOrganizationAS{
+
+  val log: Logger = LoggerFactory.getLogger(SparkMagOrganizationAS.getClass)
+  def main(args: Array[String]): Unit = {
+    new SparkMagOrganizationAS("/eu/dnetlib/dhp/collection/mag/create_organization_AS.json", args, log)
+      .initialize()
+      .run()
+
+  }
+}

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/mag/MAGMappingTest.scala

@@ -10,6 +10,7 @@ class MAGMappingTest {
 
   val mapper = new ObjectMapper()
 
+
   def mappingTest(): Unit = {
 
     val spark = SparkSession
@@ -18,10 +19,9 @@ class MAGMappingTest {
       .master("local[*]")
       .getOrCreate()
 
-    val s = new SparkMAGtoOAF(null, null, null)
+    val s = new SparkMagOrganizationAS(null, null, null)
 
-    s.convertMAG(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_oaf")
+    s.generateAS(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_AS")
-    s.generateAffiliations(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_oaf")
 
   }