Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala

@@ -1,6 +1,11 @@
 package eu.dnetlib.doiboost.crossref
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item
+import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass
+import org.apache.hadoop.io.{IntWritable, Text}
+import org.apache.hadoop.io.compress.GzipCodec
+import org.apache.spark.rdd.RDD
 import org.apache.spark.{SparkConf, SparkContext}
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
 import org.json4s
@@ -17,13 +22,6 @@ object GenerateCrossrefDataset {
 
   implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
 
-  def extractDump(input:String):List[String] = {
-    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
-    lazy val json: json4s.JValue = parse(input)
-
-    val a = (json \ "items").extract[JArray]
-    a.arr.map(s => compact(render(s)))
-  }
 
 
   def crossrefElement(meta: String): CrossrefDT = {
@@ -44,7 +42,7 @@ object GenerateCrossrefDataset {
     val targetPath = parser.get("targetPath")
 
     val spark: SparkSession = SparkSession.builder().config(conf)
-      .appName(GenerateCrossrefDataset.getClass.getSimpleName)
+      .appName(UnpackCrtossrefEntries.getClass.getSimpleName)
       .master(master)
       .getOrCreate()
     val sc: SparkContext = spark.sparkContext
@@ -52,19 +50,14 @@ object GenerateCrossrefDataset {
     import spark.implicits._
 
 
-    def extractDump(input:String):List[String] = {
+    val tmp : RDD[String] = sc.textFile(sourcePath,6000)
-      implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
-      lazy val json: json4s.JValue = parse(input)
 
-      val a = (json \ "items").extract[JArray]
+    spark.createDataset(tmp)
-      a.arr.map(s => compact(render(s)))
+      .map(entry => crossrefElement(entry))
-    }
-
-
-    sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
-          .map(meta => crossrefElement(meta))
-          .toDS()//.as[CrossrefDT]
       .write.mode(SaveMode.Overwrite).save(targetPath)
+//               .map(meta => crossrefElement(meta))
+//               .toDS.as[CrossrefDT]
+//              .write.mode(SaveMode.Overwrite).save(targetPath)
 
   }
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala

@@ -4,9 +4,9 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.oaf
 import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
 import org.apache.commons.io.IOUtils
-import org.apache.hadoop.io.{IntWritable, Text}
+
 import org.apache.spark.SparkConf
-import org.apache.spark.rdd.RDD
+
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
 
@@ -17,6 +17,7 @@ object SparkMapDumpIntoOAF {
 
   def main(args: Array[String]): Unit = {
 
+    implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
 
     val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
     val conf: SparkConf = new SparkConf()
@@ -35,7 +36,6 @@ object SparkMapDumpIntoOAF {
     implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
 
     val targetPath = parser.get("targetPath")
-    import spark.implicits._
 
     spark.read.load(parser.get("sourcePath")).as[CrossrefDT]
       .flatMap(k => Crossref2Oaf.convert(k.json))

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/UnpackCrtossrefEntries.scala

@@ -0,0 +1,54 @@
+package eu.dnetlib.doiboost.crossref
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import org.apache.hadoop.io.compress.GzipCodec
+import org.apache.spark.{SparkConf, SparkContext}
+import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.JsonAST.JArray
+import org.json4s.jackson.JsonMethods.{compact, parse, render}
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.io.Source
+
+object UnpackCrtossrefEntries {
+
+  val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
+
+
+
+
+  def extractDump(input:String):List[String] = {
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+    lazy val json: json4s.JValue = parse(input)
+
+    val a = (json \ "items").extract[JArray]
+    a.arr.map(s => compact(render(s)))
+
+
+  }
+
+
+
+  def main(args: Array[String]): Unit = {
+    val conf = new SparkConf
+    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
+    parser.parseArgument(args)
+    val master = parser.get("master")
+    val sourcePath = parser.get("sourcePath")
+    val targetPath = parser.get("targetPath")
+
+    val spark: SparkSession = SparkSession.builder().config(conf)
+      .appName(UnpackCrtossrefEntries.getClass.getSimpleName)
+      .master(master)
+      .getOrCreate()
+    val sc: SparkContext = spark.sparkContext
+
+    sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
+      .saveAsTextFile(targetPath, classOf[GzipCodec])
+
+
+  }
+
+}

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/workflow.xml

@@ -24,7 +24,7 @@
 
     </parameters>
 
-    <start to="ImportCrossRef"/>
+    <start to="GenerateCrossrefDataset"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -40,11 +40,37 @@
             <arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/files/</arg>
         </java>
-        <ok to="generateCrossrefDataset"/>
+        <ok to="UnpackCrossrefEntries"/>
         <error to="Kill"/>
     </action>
 
-    <action name="generateCrossrefDataset">
+    <action name="UnpackCrossrefEntries">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>SparkGenerateCrossrefDataset</name>
+            <class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
+            <arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
+
+        </spark>
+        <ok to="GenerateCrossrefDataset"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="GenerateCrossrefDataset">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
@@ -62,31 +88,31 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--master</arg><arg>yarn-cluster</arg>
-            <arg>--sourcePath</arg><arg>${workingDir}/files</arg>
+            <arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
-            <arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updated</arg>
+            <arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updates</arg>
 
         </spark>
-        <ok to="removeFiles"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="removeFiles">
-        <fs>
-        <delete path="${workingDir}/files"/>
-        </fs>
-        <ok to="renameDataset"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="renameDataset">
-        <fs>
-            <delete path="${inputPathCrossref}/crossref_ds"/>
-            <move source="${inputPathCrossref}/crossref_ds_updated"
-                  target="${inputPathCrossref}/crossref_ds"/>
-        </fs>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
 
+<!--    <action name="removeFiles">-->
+<!--        <fs>-->
+<!--        <delete path="${workingDir}/files"/>-->
+<!--        </fs>-->
+<!--        <ok to="renameDataset"/>-->
+<!--        <error to="Kill"/>-->
+<!--    </action>-->
+
+<!--    <action name="renameDataset">-->
+<!--        <fs>-->
+<!--            <delete path="${inputPathCrossref}/crossref_ds"/>-->
+<!--            <move source="${inputPathCrossref}/crossref_ds_updated"-->
+<!--                  target="${inputPathCrossref}/crossref_ds"/>-->
+<!--        </fs>-->
+<!--        <ok to="End"/>-->
+<!--        <error to="Kill"/>-->
+<!--    </action>-->
+
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml

@@ -142,6 +142,32 @@
             <arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
             <arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
         </java>
+        <ok to="UnpackCrossrefEntries"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="UnpackCrossrefEntries">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>SparkUnpackCrossrefEntries</name>
+            <class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
+            <arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
+
+        </spark>
         <ok to="GenerateCrossrefDataset"/>
         <error to="Kill"/>
     </action>
@@ -154,9 +180,9 @@
             <class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
             <jar>dhp-doiboost-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                --executor-memory=7G
                 --executor-cores=2
-                --driver-memory=${sparkDriverMemory}
+                --driver-memory=7G
                 --conf spark.sql.shuffle.partitions=3840
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -164,7 +190,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--master</arg><arg>yarn-cluster</arg>
-            <arg>--sourcePath</arg><arg>${crossrefDumpPath}/files/</arg>
+            <arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
             <arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
 
         </spark>
@@ -174,7 +200,8 @@
 
         <action name="removeFiles">
             <fs>
-                <delete path="${crossrefDumpPath}/files"/>
+<!--                <delete path="${crossrefDumpPath}/files"/>-->
+                    <delete path="${crossrefDumpPath}/crossref_unpack/"/>
             </fs>
             <ok to="ResetMagWorkingPath"/>
             <error to="Kill"/>

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala

@@ -395,4 +395,71 @@ class CrossrefMappingTest {
 
   }
 
+
+
+  @Test
+  def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
+
+    val json = Source.fromInputStream(getClass.getResourceAsStream("dump_file.json")).mkString
+    assertNotNull(json)
+
+    assertFalse(json.isEmpty);
+
+    val resultList: List[Oaf] = Crossref2Oaf.convert(json)
+
+    assertTrue(resultList.nonEmpty)
+
+    val items = resultList.filter(p => p.isInstanceOf[Publication])
+
+    assert(items.nonEmpty)
+    assert(items.size == 1)
+    val result: Result = items.head.asInstanceOf[Publication]
+    assertNotNull(result)
+
+    logger.info(mapper.writeValueAsString(result));
+
+//    assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
+//    assertNotNull(
+//      result.getDataInfo.getProvenanceaction,
+//      "DataInfo/Provenance test not null Failed");
+//    assertFalse(
+//      result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
+//      "DataInfo/Provenance/classId test not null Failed");
+//    assertFalse(
+//      result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
+//      "DataInfo/Provenance/className test not null Failed");
+//    assertFalse(
+//      result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
+//      "DataInfo/Provenance/SchemeId test not null Failed");
+//    assertFalse(
+//      result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
+//      "DataInfo/Provenance/SchemeName test not null Failed");
+//
+//    assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
+//    assertFalse(result.getCollectedfrom.isEmpty);
+//
+//    val collectedFromList = result.getCollectedfrom.asScala
+//    assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
+//
+//    assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
+//
+//
+//    val relevantDates = result.getRelevantdate.asScala
+//
+//    assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
+//
+//    val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
+//    assertFalse(rels.isEmpty)
+//    rels.foreach(relation => {
+//      assertNotNull(relation)
+//      assertFalse(relation.getSource.isEmpty)
+//      assertFalse(relation.getTarget.isEmpty)
+//      assertFalse(relation.getRelClass.isEmpty)
+//      assertFalse(relation.getRelType.isEmpty)
+//      assertFalse(relation.getSubRelType.isEmpty)
+//
+//    })
+  }
+
+
 }

dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/dump_file.json

@@ -0,0 +1 @@
+{"indexed":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T00:38:19Z","timestamp":1586479099385},"reference-count":0,"publisher":"American Medical Association (AMA)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Archives of Internal Medicine"],"published-print":{"date-parts":[[2006,2,27]]},"DOI":"10.1001/.389","type":"journal-article","created":{"date-parts":[[2006,2,27]],"date-time":"2006-02-27T21:28:23Z","timestamp":1141075703000},"page":"389-390","source":"Crossref","is-referenced-by-count":0,"title":["Decision Making at the Fringe of Evidence: Take What You Can Get"],"prefix":"10.1001","volume":"166","author":[{"given":"N. F.","family":"Col","affiliation":[]}],"member":"10","container-title":["Archives of Internal Medicine"],"original-title":[],"deposited":{"date-parts":[[2007,2,13]],"date-time":"2007-02-13T20:56:13Z","timestamp":1171400173000},"score":null,"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,2,27]]},"references-count":0,"URL":"http://dx.doi.org/10.1001/.389","relation":{},"ISSN":["0003-9926"],"issn-type":[{"value":"0003-9926","type":"print"}],"subject":["Internal Medicine"]}