integrated changes from master

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java

@@ -1,4 +1,3 @@
-
 package eu.dnetlib.dhp.oa.graph.raw;
 
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
@@ -46,9 +45,8 @@ public abstract class AbstractMdRecordToOafMapper {
 
   protected final Map<String, String> code2name;
 
-	protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
+  protected static final Qualifier MAIN_TITLE_QUALIFIER =
-		"main title", "main title",
+      qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
-		"dnet:dataCite_title", "dnet:dataCite_title");
 
   protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
     this.code2name = code2name;
@@ -66,17 +64,18 @@ public abstract class AbstractMdRecordToOafMapper {
       nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
       DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
 
-			final Document doc = DocumentHelper
+      final Document doc =
-				.parseText(
+          DocumentHelper.parseText(
-					xml
+              xml.replaceAll(
-						.replaceAll(
                   "http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
 
       final String type = doc.valueOf("//dr:CobjCategory/@type");
-			final KeyValue collectedFrom = keyValue(
+      final KeyValue collectedFrom =
+          keyValue(
               createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
               doc.valueOf("//oaf:collectedFrom/@name"));
-			final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
+      final KeyValue hostedBy =
+          StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
               ? collectedFrom
               : keyValue(
                   createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
@@ -164,7 +163,11 @@ public abstract class AbstractMdRecordToOafMapper {
     final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
 
     for (final Object o : doc.selectNodes("//oaf:projectid")) {
-			final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
+
+      final String originalId = ((Node) o).getText();
+
+      if (StringUtils.isNotBlank(originalId)) {
+        final String projectId = createOpenaireId(40, originalId, true);
 
         final Relation r1 = new Relation();
         r1.setRelType("resultProject");
@@ -188,6 +191,7 @@ public abstract class AbstractMdRecordToOafMapper {
         r2.setLastupdatetimestamp(lastUpdateTimestamp);
         res.add(r2);
       }
+    }
 
     return res;
   }
@@ -210,8 +214,7 @@ public abstract class AbstractMdRecordToOafMapper {
     r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
     r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
     r.setCollectedfrom(Arrays.asList(collectedFrom));
-		r
+    r.setPid(
-			.setPid(
         prepareListStructProps(
             doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
     r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
@@ -382,8 +385,7 @@ public abstract class AbstractMdRecordToOafMapper {
     final List<StructuredProperty> res = new ArrayList<>();
     for (final Object o : node.selectNodes(xpath)) {
       final Node n = (Node) o;
-			res
+      res.add(
-				.add(
           structuredProperty(
               n.getText(),
               n.valueOf("@classid"),
@@ -396,7 +398,8 @@ public abstract class AbstractMdRecordToOafMapper {
   }
 
   protected OAIProvenance prepareOAIprovenance(final Document doc) {
-		final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
+    final Node n =
+        doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
 
     if (n == null) {
       return null;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java

@@ -1,15 +1,24 @@
-
 package eu.dnetlib.dhp.oa.graph.raw;
 
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
 
 import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.Author;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Field;
+import eu.dnetlib.dhp.schema.oaf.GeoLocation;
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
+import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.Node;
 
@@ -90,8 +99,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
       if (url.startsWith("http")) {
         final Instance instance = new Instance();
         instance.setUrl(Arrays.asList(url));
-				instance
+        instance.setInstancetype(
-					.setInstancetype(
             prepareQualifier(
                 doc,
                 "//dr:CobjCategory",
@@ -101,16 +109,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
         instance.setHostedby(hostedby);
         instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
         instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
-				instance
+        instance.setAccessright(
-					.setAccessright(
             prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
         instance.setLicense(field(doc.valueOf("//oaf:license"), info));
         instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
-				instance
+        instance.setProcessingchargeamount(
-					.setProcessingchargeamount(
             field(doc.valueOf("//oaf:processingchargeamount"), info));
-				instance
+        instance.setProcessingchargecurrency(
-					.setProcessingchargecurrency(
             field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
         res.add(instance);
       }
@@ -222,7 +227,12 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
     final List<Oaf> res = new ArrayList<>();
 
     for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) {
-			final String otherId = createOpenaireId(50, ((Node) o).getText(), false);
+
+      final String originalId = ((Node) o).getText();
+
+      if (StringUtils.isNotBlank(originalId)) {
+
+        final String otherId = createOpenaireId(50, originalId, false);
 
         final Relation r1 = new Relation();
         r1.setRelType("resultResult");
@@ -246,6 +256,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
         r2.setLastupdatetimestamp(lastUpdateTimestamp);
         res.add(r2);
       }
+    }
     return res;
   }
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java

@@ -1,4 +1,3 @@
-
 package eu.dnetlib.dhp.oa.graph.raw;
 
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
@@ -55,8 +54,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
   private List<StructuredProperty> preparePids(final Document doc, final DataInfo info) {
     final List<StructuredProperty> res = new ArrayList<>();
     for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) {
-			res
+      res.add(
-				.add(
           structuredProperty(
               ((Node) o).getText(),
               prepareQualifier(
@@ -75,31 +73,30 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
     final Instance instance = new Instance();
     instance.setUrl(new ArrayList<>());
-		instance
+    instance.setInstancetype(
-			.setInstancetype(
         prepareQualifier(
             doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
     instance.setCollectedfrom(collectedfrom);
     instance.setHostedby(hostedby);
     instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
     instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
-		instance
+    instance.setAccessright(
-			.setAccessright(
         prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
     instance.setLicense(field(doc.valueOf("//oaf:license"), info));
     instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
     instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
-		instance
+    instance.setProcessingchargecurrency(
-			.setProcessingchargecurrency(
         field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
 
-		for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
+    for (final Object o :
+        doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
       instance.getUrl().add(((Node) o).getText().trim());
     }
     for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) {
       instance.getUrl().add(((Node) o).getText().trim());
     }
-		for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
+    for (final Object o :
+        doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
       instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
     }
     for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
@@ -123,8 +120,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
           && !dateType.equalsIgnoreCase("Issued")
           && !dateType.equalsIgnoreCase("Updated")
           && !dateType.equalsIgnoreCase("Available")) {
-				res
+        res.add(
-					.add(
             structuredProperty(
                 ((Node) o).getText(),
                 "UNKNOWN",
@@ -282,13 +278,17 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
     final List<Oaf> res = new ArrayList<>();
 
-		for (final Object o : doc.selectNodes("//datacite:relatedIdentifier[@relatedIdentifierType='OPENAIRE']")) {
+    for (final Object o :
-			final String otherId = createOpenaireId(50, ((Node) o).getText(), false);
+        doc.selectNodes("//datacite:relatedIdentifier[@relatedIdentifierType='OPENAIRE']")) {
+
+      final String originalId = ((Node) o).getText();
+
+      if (StringUtils.isNotBlank(originalId)) {
+        final String otherId = createOpenaireId(50, originalId, false);
         final String type = ((Node) o).valueOf("@relationType");
 
         if (type.equals("IsSupplementTo")) {
-				res
+          res.add(
-					.add(
               prepareOtherResultRel(
                   collectedFrom,
                   info,
@@ -297,8 +297,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
                   otherId,
                   "supplement",
                   "isSupplementTo"));
-				res
+          res.add(
-					.add(
               prepareOtherResultRel(
                   collectedFrom,
                   info,
@@ -308,17 +307,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
                   "supplement",
                   "isSupplementedBy"));
         } else if (type.equals("IsPartOf")) {
-				res
+          res.add(
-					.add(
               prepareOtherResultRel(
                   collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf"));
-				res
+          res.add(
-					.add(
               prepareOtherResultRel(
                   collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts"));
         } else {
         }
       }
+    }
     return res;
   }