integrated changes from master

2020-04-28 08:55:28 +02:00 · 2020-04-28 08:55:28 +02:00 · ac25f2d8d1
parent a0bdbacdae 1260d03eba
commit ac25f2d8d1
3 changed files with 925 additions and 913 deletions
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/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(
-		"main title", "main title",
-		"dnet:dataCite_title", "dnet:dataCite_title");
+  protected static final Qualifier MAIN_TITLE_QUALIFIER =
+      qualifier("main title", "main 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
-				.parseText(
-					xml
-						.replaceAll(
+      final Document doc =
+          DocumentHelper.parseText(
+              xml.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
-			.setPid(
+    r.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
-				.add(
+      res.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;
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
+++ b/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
-					.setInstancetype(
+        instance.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
-					.setAccessright(
+        instance.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(
+        instance.setProcessingchargeamount(
            field(doc.valueOf("//oaf:processingchargeamount"), info));
-				instance
-					.setProcessingchargecurrency(
+        instance.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;
  }

--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
+++ b/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
-				.add(
+      res.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
-			.setInstancetype(
+    instance.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
-			.setAccessright(
+    instance.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
-			.setProcessingchargecurrency(
+    instance.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
-					.add(
+        res.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']")) {
-			final String otherId = createOpenaireId(50, ((Node) o).getText(), false);
+    for (final Object o :
+        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
-					.add(
+          res.add(
              prepareOtherResultRel(
                  collectedFrom,
                  info,
@ -297,8 +297,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
                  otherId,
                  "supplement",
                  "isSupplementTo"));
-				res
-					.add(
+          res.add(
              prepareOtherResultRel(
                  collectedFrom,
                  info,
@ -308,17 +307,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
                  "supplement",
                  "isSupplementedBy"));
        } else if (type.equals("IsPartOf")) {
-				res
-					.add(
+          res.add(
              prepareOtherResultRel(
                  collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf"));
-				res
-					.add(
+          res.add(
              prepareOtherResultRel(
                  collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts"));
        } else {
        }
      }
+    }
    return res;
  }