mergin with branch beta

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java

@@ -4,6 +4,7 @@ package eu.dnetlib.doiboost.orcidnodoi;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -32,10 +33,7 @@ import com.google.gson.JsonParser;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.orcid.AuthorData;
+import eu.dnetlib.dhp.schema.orcid.*;
-import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
-import eu.dnetlib.dhp.schema.orcid.Work;
-import eu.dnetlib.dhp.schema.orcid.WorkDetail;
 import eu.dnetlib.doiboost.orcid.json.JsonHelper;
 import eu.dnetlib.doiboost.orcid.util.HDFSUtil;
 import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
@@ -111,6 +109,10 @@ public class SparkGenEnrichedOrcidWorks {
 						Encoders.bean(WorkDetail.class));
 				logger.info("Works data loaded: " + workDataset.count());
 
+				final LongAccumulator warnNotFoundContributors = spark
+					.sparkContext()
+					.longAccumulator("warnNotFoundContributors");
+
 				JavaRDD<Tuple2<String, String>> enrichedWorksRDD = workDataset
 					.joinWith(
 						authorDataset,
@@ -119,7 +121,21 @@ public class SparkGenEnrichedOrcidWorks {
 						(MapFunction<Tuple2<WorkDetail, AuthorData>, Tuple2<String, String>>) value -> {
 							WorkDetail w = value._1;
 							AuthorData a = value._2;
-							AuthorMatcher.match(a, w.getContributors());
+							if (w.getContributors() == null
+								|| (w.getContributors() != null && w.getContributors().size() == 0)) {
+								Contributor c = new Contributor();
+								c.setName(a.getName());
+								c.setSurname(a.getSurname());
+								c.setCreditName(a.getCreditName());
+								c.setOid(a.getOid());
+								List<Contributor> contributors = Arrays.asList(c);
+								w.setContributors(contributors);
+								if (warnNotFoundContributors != null) {
+									warnNotFoundContributors.add(1);
+								}
+							} else {
+								AuthorMatcher.match(a, w.getContributors());
+							}
 							return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w));
 						},
 						Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
@@ -172,7 +188,7 @@ public class SparkGenEnrichedOrcidWorks {
 							OBJECT_MAPPER.writeValueAsString(new AtomicAction<>(Publication.class, p))))
 					.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
 					.saveAsNewAPIHadoopFile(
-						workingPath.concat(outputEnrichedWorksPath),
+						outputEnrichedWorksPath,
 						Text.class,
 						Text.class,
 						SequenceFileOutputFormat.class,
@@ -180,6 +196,7 @@ public class SparkGenEnrichedOrcidWorks {
 
 				logger.info("parsedPublications: " + parsedPublications.value().toString());
 				logger.info("enrichedPublications: " + enrichedPublications.value().toString());
+				logger.info("warnNotFoundContributors: " + warnNotFoundContributors.value().toString());
 				logger.info("errorsGeneric: " + errorsGeneric.value().toString());
 				logger.info("errorsInvalidTitle: " + errorsInvalidTitle.value().toString());
 				logger.info("errorsNotFoundAuthors: " + errorsNotFoundAuthors.value().toString());

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

@@ -7,9 +7,14 @@
         </property>
         <property>
             <name>outputPath</name>
+            <value>/data/orcid_activities_2020/no_doi_dataset_prod/</value>
             <description>path where to store the action set</description>
         </property>
-
+        <property>
+            <name>processOutputPath</name>
+            <value>/data/orcid_activities_2020/process_no_doi_dataset_prod</value>
+            <description>temporary path where to store the action set</description>
+        </property>
         <property>
             <name>spark2GenNoDoiDatasetMaxExecutors</name>
             <value>40</value>
@@ -66,7 +71,7 @@
     
     <action name="ResetWorkingPath">
         <fs>
-            <delete path='${workingPath}/no_doi_dataset'/>
+            <delete path='${processOutputPath}'/>
         </fs>
         <ok to="GenOrcidNoDoiDataset"/>
         <error to="Kill"/>
@@ -92,7 +97,7 @@
             <arg>--workingPath</arg><arg>${workingPath}/</arg>
             <arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
             <arg>--orcidDataFolder</arg><arg>last_orcid_dataset</arg>
-            <arg>--outputEnrichedWorksPath</arg><arg>no_doi_dataset</arg>
+            <arg>--outputEnrichedWorksPath</arg><arg>${processOutputPath}</arg>
         </spark>
         <ok to="importOrcidNoDoi"/>
         <error to="Kill"/>
@@ -100,7 +105,7 @@
 
     <action name="importOrcidNoDoi">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <arg>${workingPath}/no_doi_dataset/*</arg>
+            <arg>${processOutputPath}/*</arg>
             <arg>${outputPath}</arg>
         </distcp>
         <ok to="End"/>

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala

@@ -1,11 +1,10 @@
 package eu.dnetlib.dhp.sx.graph.scholix
 
 
-import eu.dnetlib.dhp.schema.oaf.{Dataset, Relation, Result, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
-import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixCollectedFrom, ScholixEntityId, ScholixIdentifier, ScholixRelationship, ScholixResource}
+import eu.dnetlib.dhp.schema.sx.scholix._
 import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
 import eu.dnetlib.dhp.utils.DHPUtils
-import org.apache.spark.sql.Encoders.bean
 import org.apache.spark.sql.expressions.Aggregator
 import org.apache.spark.sql.{Encoder, Encoders}
 import org.json4s
@@ -301,14 +300,14 @@ object ScholixUtils {
     if (r.getPid == null || r.getPid.isEmpty)
       return null
 
-    val pids:List[ScholixIdentifier] =  extractTypedIdentifierFromInstance(r)
+    val persistentIdentifiers:List[ScholixIdentifier] =  extractTypedIdentifierFromInstance(r)
-    if (pids.isEmpty)
+    if (persistentIdentifiers.isEmpty)
       return null
-    s.setLocalIdentifier(pids.asJava)
+    s.setLocalIdentifier(persistentIdentifiers.asJava)
-    if (r.isInstanceOf[Dataset])
+    if (r.isInstanceOf[Publication] )
-      s.setTypology(Typology.dataset)
-    else
       s.setTypology(Typology.publication)
+    else
+      s.setTypology(Typology.dataset)
 
     s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)