fixed a problem with missing instances

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

@@ -10,19 +10,6 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.StringUtils;
-import org.dom4j.Document;
-import org.dom4j.DocumentFactory;
-import org.dom4j.DocumentHelper;
-import org.dom4j.Node;
-
 import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
 import eu.dnetlib.dhp.schema.oaf.Author;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
@@ -41,6 +28,17 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.Software;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.lang3.StringUtils;
+import org.dom4j.Document;
+import org.dom4j.DocumentFactory;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Node;
 
 public abstract class AbstractMdRecordToOafMapper {
 
@@ -66,15 +64,22 @@ public abstract class AbstractMdRecordToOafMapper {
             DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
 
             final Document doc =
-					DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
+                    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(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name"));
+                    keyValue(
+                            createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
+                            doc.valueOf("//oaf:collectedFrom/@name"));
             final KeyValue hostedBy =
                     StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
                             ? collectedFrom
-							: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name"));
+                            : keyValue(
+                                    createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
+                                    doc.valueOf("//oaf:hostedBy/@name"));
 
             final DataInfo info = prepareDataInfo(doc);
             final long lastUpdateTimestamp = new Date().getTime();
@@ -204,7 +209,14 @@ 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(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
+        r.setPid(
+                prepareListStructProps(
+                        doc,
+                        "//oaf:identifier",
+                        "@identifierType",
+                        "dnet:pid_types",
+                        "dnet:pid_types",
+                        info));
         r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
         r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
         r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@@ -233,10 +245,7 @@ public abstract class AbstractMdRecordToOafMapper {
     protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
 
     protected abstract List<Instance> prepareInstances(
-			Document doc,
+            Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
-			DataInfo info,
-			KeyValue collectedfrom,
-			KeyValue hostedby);
 
     protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
 
@@ -261,34 +270,28 @@ public abstract class AbstractMdRecordToOafMapper {
     protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
 
     protected abstract List<Field<String>> prepareOtherResearchProductTools(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
 
     protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
 
     protected abstract List<StructuredProperty> prepareSoftwareLicenses(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
 
     protected abstract Field<String> prepareDatasetMetadataVersionNumber(
-			Document doc,
+            Document doc, DataInfo info);
-			DataInfo info);
 
     protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
 
@@ -312,16 +315,27 @@ public abstract class AbstractMdRecordToOafMapper {
             final String sp = n.valueOf("@sp");
             final String vol = n.valueOf("@vol");
             final String edition = n.valueOf("@edition");
-			if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
+            if (StringUtils.isNotBlank(name)) {
+                return journal(
+                        name,
+                        issnPrinted,
+                        issnOnline,
+                        issnLinking,
+                        ep,
+                        iss,
+                        sp,
+                        vol,
+                        edition,
+                        null,
+                        null,
+                        info);
+            }
         }
         return null;
     }
 
     protected Qualifier prepareQualifier(
-			final Node node,
+            final Node node, final String xpath, final String schemeId, final String schemeName) {
-			final String xpath,
-			final String schemeId,
-			final String schemeName) {
         final String classId = node.valueOf(xpath);
         final String className = code2name.get(classId);
         return qualifier(classId, className, schemeId, schemeName);
@@ -339,16 +353,15 @@ public abstract class AbstractMdRecordToOafMapper {
             final Node n = (Node) o;
             final String classId = n.valueOf(xpathClassId);
             final String className = code2name.get(classId);
-			res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
+            res.add(
+                    structuredProperty(
+                            n.getText(), classId, className, schemeId, schemeName, info));
         }
         return res;
     }
 
     protected List<StructuredProperty> prepareListStructProps(
-			final Node node,
+            final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
-			final String xpath,
-			final Qualifier qualifier,
-			final DataInfo info) {
         final List<StructuredProperty> res = new ArrayList<>();
         for (final Object o : node.selectNodes(xpath)) {
             final Node n = (Node) o;
@@ -358,37 +371,58 @@ public abstract class AbstractMdRecordToOafMapper {
     }
 
     protected List<StructuredProperty> prepareListStructProps(
-			final Node node,
+            final Node node, final String xpath, final DataInfo info) {
-			final String xpath,
-			final DataInfo info) {
         final List<StructuredProperty> res = new ArrayList<>();
         for (final Object o : node.selectNodes(xpath)) {
             final Node n = (Node) o;
-			res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
+            res.add(
+                    structuredProperty(
+                            n.getText(),
+                            n.valueOf("@classid"),
+                            n.valueOf("@classname"),
+                            n.valueOf("@schemeid"),
+                            n.valueOf("@schemename"),
+                            info));
         }
         return res;
     }
 
     protected OAIProvenance prepareOAIprovenance(final Document doc) {
         final Node n =
-				doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
+                doc.selectSingleNode(
+                        "//*[local-name()='provenance']/*[local-name()='originDescription']");
 
-		if (n == null) { return null; }
+        if (n == null) {
+            return null;
+        }
 
         final String identifier = n.valueOf("./*[local-name()='identifier']");
-		final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
+        final String baseURL = n.valueOf("./*[local-name()='baseURL']");
-		final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
+        ;
+        final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
+        ;
         final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
-		final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
+        final String datestamp = n.valueOf("./*[local-name()='datestamp']");
-		final String harvestDate = n.valueOf("@harvestDate");;
+        ;
+        final String harvestDate = n.valueOf("@harvestDate");
+        ;
 
-		return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
+        return oaiIProvenance(
+                identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
     }
 
     protected DataInfo prepareDataInfo(final Document doc) {
         final Node n = doc.selectSingleNode("//oaf:datainfo");
 
-		if (n == null) { return dataInfo(false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
+        if (n == null) {
+            return dataInfo(
+                    false,
+                    null,
+                    false,
+                    false,
+                    MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS,
+                    "0.9");
+        }
 
         final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
         final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@@ -401,7 +435,13 @@ public abstract class AbstractMdRecordToOafMapper {
         final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
         final String trust = n.valueOf("./oaf:trust");
 
-		return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
+        return dataInfo(
+                deletedbyinference,
+                inferenceprovenance,
+                inferred,
+                false,
+                qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
+                trust);
     }
 
     protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
@@ -409,9 +449,7 @@ public abstract class AbstractMdRecordToOafMapper {
     }
 
     protected List<Field<String>> prepareListFields(
-			final Node node,
+            final Node node, final String xpath, final DataInfo info) {
-			final String xpath,
-			final DataInfo info) {
         return listFields(info, prepareListString(node, xpath));
     }
 

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

@@ -10,23 +10,6 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
 
-import java.io.Closeable;
-import java.io.IOException;
-import java.sql.Array;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-import java.util.function.Consumer;
-import java.util.function.Function;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
 import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
@@ -48,6 +31,21 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.Software;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import java.io.Closeable;
+import java.io.IOException;
+import java.sql.Array;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+import java.util.function.Consumer;
+import java.util.function.Function;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
         implements Closeable {
@@ -61,8 +59,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
     public static void main(final String[] args) throws Exception {
         final ArgumentApplicationParser parser =
                 new ArgumentApplicationParser(
-						IOUtils.toString(MigrateDbEntitiesApplication.class
+                        IOUtils.toString(
-								.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
+                                MigrateDbEntitiesApplication.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
 
         parser.parseArgument(args);
 
@@ -91,7 +90,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
                 smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
 
                 log.info("Processing relations ds <-> orgs ...");
-				smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
+                smdbe.execute(
+                        "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
 
                 log.info("Processing projects <-> orgs ...");
                 smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
@@ -117,7 +117,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
     public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
             throws Exception {
         final String sql =
-				IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
+                IOUtils.toString(
+                        getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
 
         final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
 
@@ -134,14 +135,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
 
             ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true));
             ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
-			ds.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
+            ds.setCollectedfrom(
+                    listKeyValues(
+                            createOpenaireId(10, rs.getString("collectedfromid"), true),
+                            rs.getString("collectedfromname")));
             ds.setPid(new ArrayList<>());
             ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
             ds.setDateoftransformation(null); // Value not returned by the SQL query
             ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
             ds.setOaiprovenance(null); // Values not present in the DB
             ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
-			ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
+            ds.setOpenairecompatibility(
+                    prepareQualifierSplitting(rs.getString("openairecompatibility")));
             ds.setOfficialname(field(rs.getString("officialname"), info));
             ds.setEnglishname(field(rs.getString("englishname"), info));
             ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
@@ -174,7 +179,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             ds.setPidsystems(field(rs.getString("pidsystems"), info));
             ds.setCertificates(field(rs.getString("certificates"), info));
             ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
-			ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
+            ds.setJournal(
+                    prepareJournal(
+                            rs.getString("officialname"),
+                            rs.getString("journal"),
+                            info)); // Journal
             ds.setDataInfo(info);
             ds.setLastupdatetimestamp(lastUpdateTimestamp);
 
@@ -193,7 +202,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
 
             p.setId(createOpenaireId(40, rs.getString("projectid"), true));
             p.setOriginalId(Arrays.asList(rs.getString("projectid")));
-			p.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
+            p.setCollectedfrom(
+                    listKeyValues(
+                            createOpenaireId(10, rs.getString("collectedfromid"), true),
+                            rs.getString("collectedfromname")));
             p.setPid(new ArrayList<>());
             p.setDateofcollection(asString(rs.getDate("dateofcollection")));
             p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
@@ -209,7 +221,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             p.setKeywords(field(rs.getString("keywords"), info));
             p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
             p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
-			p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
+            p.setOamandatepublications(
+                    field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
             p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
             p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
             p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info));
@@ -245,7 +258,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
 
             o.setId(createOpenaireId(20, rs.getString("organizationid"), true));
             o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
-			o.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
+            o.setCollectedfrom(
+                    listKeyValues(
+                            createOpenaireId(10, rs.getString("collectedfromid"), true),
+                            rs.getString("collectedfromname")));
             o.setPid(new ArrayList<>());
             o.setDateofcollection(asString(rs.getDate("dateofcollection")));
             o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
@@ -259,10 +275,17 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
             o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
             o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
-			o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
+            o.setEcresearchorganization(
-			o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info));
+                    field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
-			o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
+            o.setEchighereducation(
-			o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
+                    field(Boolean.toString(rs.getBoolean("echighereducation")), info));
+            o.setEcinternationalorganizationeurinterests(
+                    field(
+                            Boolean.toString(
+                                    rs.getBoolean("ecinternationalorganizationeurinterests")),
+                            info));
+            o.setEcinternationalorganization(
+                    field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
             o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
             o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
             o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
@@ -282,7 +305,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             final String orgId = createOpenaireId(20, rs.getString("organization"), true);
             final String dsId = createOpenaireId(10, rs.getString("datasource"), true);
             final List<KeyValue> collectedFrom =
-					listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
+                    listKeyValues(
+                            createOpenaireId(10, rs.getString("collectedfromid"), true),
+                            rs.getString("collectedfromname"));
 
             final Relation r1 = new Relation();
             r1.setRelType("datasourceOrganization");
@@ -316,7 +341,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             final String orgId = createOpenaireId(20, rs.getString("resporganization"), true);
             final String projectId = createOpenaireId(40, rs.getString("project"), true);
             final List<KeyValue> collectedFrom =
-					listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
+                    listKeyValues(
+                            createOpenaireId(10, rs.getString("collectedfromid"), true),
+                            rs.getString("collectedfromname"));
 
             final Relation r1 = new Relation();
             r1.setRelType("projectOrganization");
@@ -347,7 +374,17 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
     public List<Oaf> processClaims(final ResultSet rs) {
 
         final DataInfo info =
-				dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
+                dataInfo(
+                        false,
+                        null,
+                        false,
+                        false,
+                        qualifier(
+                                "user:claim",
+                                "user:claim",
+                                "dnet:provenanceActions",
+                                "dnet:provenanceActions"),
+                        "0.9");
 
         final List<KeyValue> collectedFrom =
                 listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
@@ -379,9 +416,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
                 return Arrays.asList(r);
             } else {
                 final String sourceId =
-						createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false);
+                        createOpenaireId(
+                                rs.getString("source_type"), rs.getString("source_id"), false);
                 final String targetId =
-						createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false);
+                        createOpenaireId(
+                                rs.getString("target_type"), rs.getString("target_id"), false);
 
                 final Relation r1 = new Relation();
                 final Relation r2 = new Relation();
@@ -438,11 +477,19 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
         final String inferenceprovenance = rs.getString("inferenceprovenance");
         final Boolean inferred = rs.getBoolean("inferred");
         final String trust = rs.getString("trust");
-		return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION, trust);
+        return dataInfo(
+                deletedbyinference,
+                inferenceprovenance,
+                inferred,
+                false,
+                MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION,
+                trust);
     }
 
     private Qualifier prepareQualifierSplitting(final String s) {
-		if (StringUtils.isBlank(s)) { return null; }
+        if (StringUtils.isBlank(s)) {
+            return null;
+        }
         final String[] arr = s.split("@@@");
         return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
     }
@@ -458,19 +505,22 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
     }
 
     private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
-		if (StringUtils.isBlank(s)) { return null; }
+        if (StringUtils.isBlank(s)) {
+            return null;
+        }
         final String[] parts = s.split("###");
         if (parts.length == 2) {
             final String value = parts[0];
             final String[] arr = parts[1].split("@@@");
-			if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); }
+            if (arr.length == 4) {
+                return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo);
+            }
         }
         return null;
     }
 
     private List<StructuredProperty> prepareListOfStructProps(
-			final Array array,
+            final Array array, final DataInfo dataInfo) throws SQLException {
-			final DataInfo dataInfo) throws SQLException {
         final List<StructuredProperty> res = new ArrayList<>();
         if (array != null) {
             for (final String s : (String[]) array.getArray()) {
@@ -489,10 +539,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
             final String[] arr = sj.split("@@@");
             if (arr.length == 3) {
                 final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
-				final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;;
+                final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;
-				final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;;
+                ;
+                final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;
+                ;
                 if (issn != null || eissn != null || lissn != null) {
-					return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
+                    return journal(
+                            name, issn, eissn, eissn, null, null, null, null, null, null, null,
+                            info);
                 }
             }
         }

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

@@ -1,8 +1,19 @@
 package eu.dnetlib.dhp.oa.graph.raw;
 
-import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
 
-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;
@@ -62,11 +73,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
             final DataInfo info,
             final KeyValue collectedfrom,
             final KeyValue hostedby) {
-        final List<Instance> res = new ArrayList<>();
+
-        for (final Object o :
-                doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
         final Instance instance = new Instance();
-            instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
+        instance.setUrl(new ArrayList<>());
         instance.setInstancetype(
                 prepareQualifier(
                         doc,
@@ -86,9 +95,22 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
                 field(doc.valueOf("//oaf:processingchargeamount"), info));
         instance.setProcessingchargecurrency(
                 field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
-            res.add(instance);
+
+        for (final Object o :
+                doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
+            instance.getUrl().add(((Node) o).getText().trim());
         }
-        return res;
+        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']")) {
+            instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
+        }
+        for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
+            instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
+        }
+        return Arrays.asList(instance);
     }
 
     @Override

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

@@ -7,7 +7,11 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
 public class MigrationConstants {
 
     public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
-			qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
+            qualifier(
+                    "publication",
+                    "publication",
+                    "dnet:result_typologies",
+                    "dnet:result_typologies");
     public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
             qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
     public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
@@ -15,8 +19,15 @@ public class MigrationConstants {
     public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
             qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
     public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
-			qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions");
+            qualifier(
+                    "sysimport:crosswalk:repository",
+                    "sysimport:crosswalk:repository",
+                    "dnet:provenanceActions",
+                    "dnet:provenanceActions");
     public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
-			qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenanceActions", "dnet:provenanceActions");
+            qualifier(
-
+                    "sysimport:crosswalk:entityregistry",
+                    "sysimport:crosswalk:entityregistry",
+                    "dnet:provenanceActions",
+                    "dnet:provenanceActions");
 }

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -54,6 +54,7 @@ public class MappersTest {
         assertTrue(p.getSubject().size() > 0);
         assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
         assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
+        assertTrue(p.getInstance().size() > 0);
 
         assertValidId(r1.getSource());
         assertValidId(r1.getTarget());
@@ -96,6 +97,7 @@ public class MappersTest {
         assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
         assertTrue(d.getAuthor().size() > 0);
         assertTrue(d.getSubject().size() > 0);
+        assertTrue(d.getInstance().size() > 0);
 
         assertValidId(r1.getSource());
         assertValidId(r1.getTarget());
@@ -129,6 +131,7 @@ public class MappersTest {
         assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
         assertTrue(s.getAuthor().size() > 0);
         assertTrue(s.getSubject().size() > 0);
+        assertTrue(s.getInstance().size() > 0);
     }
 
     private void assertValidId(final String id) {