forked from D-Net/dnet-hadoop
Merge pull request 'mapped oaf:country from results' (#403) from oaf_country_beta into beta
Reviewed-on: D-Net/dnet-hadoop#403
This commit is contained in:
commit
25c2025223
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@ -1,16 +1,50 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.AFFILIATION;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_AUTHOR_INSTITUTION;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_AUTHOR_INSTITUTION_OF;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_ORGANIZATION;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.keyValue;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.oaiIProvenance;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.subject;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.validator.routines.UrlValidator;
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import org.dom4j.*;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentFactory;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -21,7 +55,29 @@ import eu.dnetlib.dhp.common.Constants;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.AccessRight;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.Context;
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import eu.dnetlib.dhp.schema.oaf.Country;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.EoscIfGuidelines;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.GeoLocation;
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import eu.dnetlib.dhp.schema.oaf.Instance;
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import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.Subject;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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@ -42,12 +98,8 @@ public abstract class AbstractMdRecordToOafMapper {
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protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
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protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/";
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protected static final Qualifier ORCID_PID_TYPE = qualifier(
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ModelConstants.ORCID_PENDING,
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ModelConstants.ORCID_CLASSNAME,
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DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier MAG_PID_TYPE = qualifier(
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"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier ORCID_PID_TYPE = qualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999";
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@ -70,14 +122,14 @@ public abstract class AbstractMdRecordToOafMapper {
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static {
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IdentifierFactory.PID_AUTHORITY
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.keySet()
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.stream()
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.forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString()));
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.keySet()
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.stream()
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.forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString()));
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}
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protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible,
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final boolean shouldHashId, final boolean forceOriginalId) {
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final boolean shouldHashId, final boolean forceOriginalId) {
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this.vocs = vocs;
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this.invisible = invisible;
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this.shouldHashId = shouldHashId;
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@ -85,7 +137,7 @@ public abstract class AbstractMdRecordToOafMapper {
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}
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protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible,
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final boolean shouldHashId) {
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final boolean shouldHashId) {
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this.vocs = vocs;
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this.invisible = invisible;
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this.shouldHashId = shouldHashId;
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@ -97,28 +149,22 @@ public abstract class AbstractMdRecordToOafMapper {
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DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
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try {
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final Document doc = DocumentHelper
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.parseText(
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xml
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.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
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.parseText(xml
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.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
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final KeyValue collectedFrom = getProvenanceDatasource(
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doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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if (collectedFrom == null) {
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return Lists.newArrayList();
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}
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if (collectedFrom == null) { return Lists.newArrayList(); }
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final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
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? collectedFrom
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: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
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? collectedFrom
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: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
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if (hostedBy == null) {
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return Lists.newArrayList();
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}
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if (hostedBy == null) { return Lists.newArrayList(); }
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final DataInfo entityInfo = prepareDataInfo(doc, invisible);
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final DataInfo entityInfo = prepareDataInfo(doc, this.invisible);
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final long lastUpdateTimestamp = new Date().getTime();
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final List<Instance> instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
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@ -126,7 +172,7 @@ public abstract class AbstractMdRecordToOafMapper {
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final String type = getResultType(doc, instances);
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return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp);
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} catch (DocumentException e) {
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} catch (final DocumentException e) {
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log.error("Error with record:\n" + xml);
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return Lists.newArrayList();
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}
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@ -135,17 +181,17 @@ public abstract class AbstractMdRecordToOafMapper {
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protected String getResultType(final Document doc, final List<Instance> instances) {
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final String type = doc.valueOf("//dr:CobjCategory/@type");
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if (StringUtils.isBlank(type) && vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
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if (StringUtils.isBlank(type) && this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
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final String instanceType = instances
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.stream()
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.map(i -> i.getInstancetype().getClassid())
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.findFirst()
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.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
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.orElse("0000"); // Unknown
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.stream()
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.map(i -> i.getInstancetype().getClassid())
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.findFirst()
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.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
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.orElse("0000"); // Unknown
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return Optional
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.ofNullable(vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
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.map(Qualifier::getClassid)
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.orElse("0000");
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.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
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.map(Qualifier::getClassid)
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.orElse("0000");
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}
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return type;
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@ -155,30 +201,27 @@ public abstract class AbstractMdRecordToOafMapper {
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final String dsId = doc.valueOf(xpathId);
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final String dsName = doc.valueOf(xpathName);
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if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) {
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return null;
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}
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if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { return null; }
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return keyValue(createOpenaireId(10, dsId, true), dsName);
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}
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protected List<Oaf> createOafs(
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final Document doc,
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final String type,
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final List<Instance> instances,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final Document doc,
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final String type,
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final List<Instance> instances,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final OafEntity entity = createEntity(
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doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
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final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
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final Set<String> originalId = Sets.newHashSet(entity.getOriginalId());
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originalId.add(entity.getId());
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entity.setOriginalId(Lists.newArrayList(originalId));
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if (!forceOriginalId) {
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final String id = IdentifierFactory.createIdentifier(entity, shouldHashId);
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if (!this.forceOriginalId) {
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final String id = IdentifierFactory.createIdentifier(entity, this.shouldHashId);
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if (!id.equals(entity.getId())) {
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entity.setId(id);
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}
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@ -189,7 +232,7 @@ public abstract class AbstractMdRecordToOafMapper {
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final DataInfo relationInfo = prepareDataInfo(doc, false);
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if (!oafs.isEmpty()) {
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Set<Oaf> rels = Sets.newHashSet();
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final Set<Oaf> rels = Sets.newHashSet();
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rels.addAll(addProjectRels(doc, entity, relationInfo));
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rels.addAll(addOtherResultRels(doc, entity, relationInfo));
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@ -203,51 +246,52 @@ public abstract class AbstractMdRecordToOafMapper {
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}
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private OafEntity createEntity(final Document doc,
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final String type,
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final List<Instance> instances,
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final KeyValue collectedFrom,
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final DataInfo info,
|
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final long lastUpdateTimestamp) {
|
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final String type,
|
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final List<Instance> instances,
|
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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switch (type.toLowerCase()) {
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case "publication":
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final Publication p = new Publication();
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populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
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p.setJournal(prepareJournal(doc, info));
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return p;
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case "dataset":
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final Dataset d = new Dataset();
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populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
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d.setStoragedate(prepareDatasetStorageDate(doc, info));
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d.setDevice(prepareDatasetDevice(doc, info));
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d.setSize(prepareDatasetSize(doc, info));
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d.setVersion(prepareDatasetVersion(doc, info));
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d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
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d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
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d.setGeolocation(prepareDatasetGeoLocations(doc, info));
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return d;
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case "software":
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final Software s = new Software();
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populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
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s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
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s.setLicense(prepareSoftwareLicenses(doc, info));
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s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
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s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
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return s;
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case "":
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case "otherresearchproducts":
|
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default:
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final OtherResearchProduct o = new OtherResearchProduct();
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populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
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o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
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o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
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o.setTool(prepareOtherResearchProductTools(doc, info));
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return o;
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case "publication":
|
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final Publication p = new Publication();
|
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populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
|
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p.setJournal(prepareJournal(doc, info));
|
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return p;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
return d;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
return s;
|
||||
case "":
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
return o;
|
||||
}
|
||||
}
|
||||
|
||||
private List<Oaf> addProjectRels(
|
||||
final Document doc,
|
||||
final OafEntity entity, DataInfo info) {
|
||||
final Document doc,
|
||||
final OafEntity entity,
|
||||
final DataInfo info) {
|
||||
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
||||
|
|
@ -263,29 +307,25 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final String projectId = createOpenaireId(40, originalId, true);
|
||||
|
||||
res
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity.getCollectedfrom(),
|
||||
info, entity.getLastupdatetimestamp(), validationdDate, null));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity.getCollectedfrom(), info, entity
|
||||
.getLastupdatetimestamp(), validationdDate, null));
|
||||
res
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationdDate, null));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity.getCollectedfrom(), info, entity
|
||||
.getLastupdatetimestamp(), validationdDate, null));
|
||||
}
|
||||
}
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
private List<Oaf> addRelations(Document doc, OafEntity entity, DataInfo info) {
|
||||
private List<Oaf> addRelations(final Document doc, final OafEntity entity, final DataInfo info) {
|
||||
|
||||
final List<Oaf> rels = Lists.newArrayList();
|
||||
|
||||
for (Object o : doc.selectNodes("//oaf:relation")) {
|
||||
Element element = (Element) o;
|
||||
for (final Object o : doc.selectNodes("//oaf:relation")) {
|
||||
final Element element = (Element) o;
|
||||
|
||||
final String target = StringUtils.trim(element.getText());
|
||||
final String relType = element.attributeValue("relType");
|
||||
|
|
@ -293,11 +333,11 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final String relClass = element.attributeValue("relClass");
|
||||
|
||||
if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType)
|
||||
&& StringUtils.isNotBlank(relClass)) {
|
||||
&& StringUtils.isNotBlank(relClass)) {
|
||||
|
||||
final String relClassInverse = ModelSupport
|
||||
.findInverse(ModelSupport.rel(relType, subRelType, relClass))
|
||||
.getInverseRelClass();
|
||||
.findInverse(ModelSupport.rel(relType, subRelType, relClass))
|
||||
.getInverseRelClass();
|
||||
final String validationDate = ((Node) o).valueOf("@validationDate");
|
||||
|
||||
if (StringUtils.isNotBlank(target)) {
|
||||
|
|
@ -305,19 +345,13 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
if (StringUtils.isNotBlank(targetType)) {
|
||||
final String targetId = createOpenaireId(targetType, target, true);
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
entity.getId(), targetId, relType, subRelType, relClass,
|
||||
entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationDate, null));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(entity.getId(), targetId, relType, subRelType, relClass, entity.getCollectedfrom(), info, entity
|
||||
.getLastupdatetimestamp(), validationDate, null));
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
targetId, entity.getId(), relType, subRelType, relClassInverse,
|
||||
entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationDate, null));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(targetId, entity.getId(), relType, subRelType, relClassInverse, entity.getCollectedfrom(), info, entity
|
||||
.getLastupdatetimestamp(), validationDate, null));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -325,24 +359,24 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
return rels;
|
||||
}
|
||||
|
||||
private List<Oaf> addAffiliations(Document doc, OafEntity entity, DataInfo info) {
|
||||
private List<Oaf> addAffiliations(final Document doc, final OafEntity entity, final DataInfo info) {
|
||||
final List<Oaf> rels = Lists.newArrayList();
|
||||
|
||||
for (Object o : doc.selectNodes("//datacite:affiliation[@affiliationIdentifierScheme='ROR']")) {
|
||||
Element element = (Element) o;
|
||||
for (final Object o : doc.selectNodes("//datacite:affiliation[@affiliationIdentifierScheme='ROR']")) {
|
||||
final Element element = (Element) o;
|
||||
|
||||
String rorId = element.attributeValue("affiliationIdentifier");
|
||||
final String rorId = element.attributeValue("affiliationIdentifier");
|
||||
if (StringUtils.isNotBlank(rorId)) {
|
||||
|
||||
String fullRorId = Constants.ROR_NS_PREFIX + "::" + rorId;
|
||||
final String fullRorId = Constants.ROR_NS_PREFIX + "::" + rorId;
|
||||
|
||||
String resultId = entity.getId();
|
||||
String orgId = createOpenaireId("organization", fullRorId, true);
|
||||
final String resultId = entity.getId();
|
||||
final String orgId = createOpenaireId("organization", fullRorId, true);
|
||||
|
||||
List<KeyValue> properties = Lists.newArrayList();
|
||||
final List<KeyValue> properties = Lists.newArrayList();
|
||||
|
||||
String apcAmount = doc.valueOf("//oaf:processingchargeamount");
|
||||
String apcCurrency = doc.valueOf("//oaf:processingchargeamount/@currency");
|
||||
final String apcAmount = doc.valueOf("//oaf:processingchargeamount");
|
||||
final String apcCurrency = doc.valueOf("//oaf:processingchargeamount/@currency");
|
||||
|
||||
if (StringUtils.isNotBlank(apcAmount) && StringUtils.isNotBlank(apcCurrency)) {
|
||||
properties.add(OafMapperUtils.keyValue("apc_amount", apcAmount));
|
||||
|
|
@ -350,35 +384,30 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
}
|
||||
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
resultId, orgId, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION,
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null,
|
||||
properties));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(resultId, orgId, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION, entity.getCollectedfrom(), info, entity
|
||||
.getLastupdatetimestamp(), null, properties));
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
orgId, resultId, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF,
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null,
|
||||
properties));
|
||||
.add(OafMapperUtils
|
||||
.getRelation(orgId, resultId, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, entity
|
||||
.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null, properties));
|
||||
}
|
||||
}
|
||||
return rels;
|
||||
}
|
||||
|
||||
protected abstract List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final OafEntity entity, DataInfo info);
|
||||
final Document doc,
|
||||
final OafEntity entity,
|
||||
DataInfo info);
|
||||
|
||||
private void populateResultFields(
|
||||
final Result r,
|
||||
final Document doc,
|
||||
final List<Instance> instances,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
final Result r,
|
||||
final Document doc,
|
||||
final List<Instance> instances,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
r.setDataInfo(info);
|
||||
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||
|
|
@ -391,7 +420,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||
r.setAuthor(prepareAuthors(doc, info));
|
||||
r.setLanguage(prepareLanguages(doc));
|
||||
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setCountry(prepareCountries(doc, info));
|
||||
r.setSubject(prepareSubjects(doc, info));
|
||||
r.setTitle(prepareTitles(doc, info));
|
||||
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||
|
|
@ -407,16 +436,31 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
r.setCoverage(prepareCoverages(doc, info));
|
||||
r.setContext(prepareContexts(doc, info));
|
||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r
|
||||
.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
r
|
||||
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
|
||||
r.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
r.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
r.setInstance(instances);
|
||||
r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances));
|
||||
r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info));
|
||||
}
|
||||
|
||||
private List<Country> prepareCountries(final Document doc, final DataInfo info) {
|
||||
final List<Country> list = new ArrayList<>();
|
||||
for (final Object n : doc.selectNodes("//oaf:country")) {
|
||||
final String code = ((Node) n).getText().trim();
|
||||
if (StringUtils.isNotBlank(code)) {
|
||||
final Qualifier q = this.vocs.getTermAsQualifier(ModelConstants.DNET_COUNTRY_TYPE, code);
|
||||
final Country country = new Country();
|
||||
country.setClassid(q.getClassid());
|
||||
country.setClassname(q.getClassname());
|
||||
country.setSchemeid(q.getSchemeid());
|
||||
country.setSchemename(q.getSchemename());
|
||||
country.setDataInfo(info);
|
||||
list.add(country);
|
||||
}
|
||||
}
|
||||
return list;
|
||||
}
|
||||
|
||||
protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
|
||||
|
||||
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
|
||||
|
|
@ -433,7 +477,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
return list;
|
||||
}
|
||||
|
||||
private List<EoscIfGuidelines> prepareEOSCIfGuidelines(Document doc, DataInfo info) {
|
||||
private List<EoscIfGuidelines> prepareEOSCIfGuidelines(final Document doc, final DataInfo info) {
|
||||
final Set<EoscIfGuidelines> set = Sets.newHashSet();
|
||||
for (final Object o : doc.selectNodes("//oaf:eoscifguidelines")) {
|
||||
final String code = ((Node) o).valueOf("@code");
|
||||
|
|
@ -455,10 +499,10 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Instance> prepareInstances(
|
||||
Document doc,
|
||||
DataInfo info,
|
||||
KeyValue collectedfrom,
|
||||
KeyValue hostedby);
|
||||
Document doc,
|
||||
DataInfo info,
|
||||
KeyValue collectedfrom,
|
||||
KeyValue hostedby);
|
||||
|
||||
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||
|
||||
|
|
@ -483,16 +527,16 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||
|
||||
|
|
@ -501,8 +545,8 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||
|
||||
|
|
@ -520,15 +564,15 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
protected abstract String findOriginalType(Document doc);
|
||||
|
||||
protected List<InstanceTypeMapping> prepareInstanceTypeMapping(Document doc) {
|
||||
protected List<InstanceTypeMapping> prepareInstanceTypeMapping(final Document doc) {
|
||||
return Optional
|
||||
.ofNullable(findOriginalType(doc))
|
||||
.map(originalType -> {
|
||||
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
|
||||
mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1));
|
||||
return mappings;
|
||||
})
|
||||
.orElse(new ArrayList<>());
|
||||
.ofNullable(findOriginalType(doc))
|
||||
.map(originalType -> {
|
||||
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
|
||||
mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1));
|
||||
return mappings;
|
||||
})
|
||||
.orElse(new ArrayList<>());
|
||||
}
|
||||
|
||||
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||
|
|
@ -543,9 +587,7 @@ 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;
|
||||
}
|
||||
|
|
@ -554,18 +596,13 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||
if (n != null) {
|
||||
final String id = n.valueOf("./*[local-name()='identifier']");
|
||||
if (StringUtils.isNotBlank(id)) {
|
||||
return Lists.newArrayList(id);
|
||||
}
|
||||
if (StringUtils.isNotBlank(id)) { return Lists.newArrayList(id); }
|
||||
}
|
||||
final List<String> idList = doc
|
||||
.selectNodes(
|
||||
"normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())");
|
||||
.selectNodes("normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())");
|
||||
final Set<String> originalIds = Sets.newHashSet(idList);
|
||||
|
||||
if (originalIds.isEmpty()) {
|
||||
throw new IllegalStateException("missing originalID on " + doc.asXML());
|
||||
}
|
||||
if (originalIds.isEmpty()) { throw new IllegalStateException("missing originalID on " + doc.asXML()); }
|
||||
return Lists.newArrayList(originalIds);
|
||||
}
|
||||
|
||||
|
|
@ -587,32 +624,32 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
}
|
||||
|
||||
protected Qualifier prepareQualifier(final String classId, final String schemeId) {
|
||||
return vocs.getTermAsQualifier(schemeId, classId);
|
||||
return this.vocs.getTermAsQualifier(schemeId, classId);
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String xpathClassId,
|
||||
final String schemeId,
|
||||
final DataInfo info) {
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String xpathClassId,
|
||||
final String schemeId,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
final String classId = n.valueOf(xpathClassId).trim();
|
||||
if (vocs.termExists(schemeId, classId)) {
|
||||
res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info));
|
||||
if (this.vocs.termExists(schemeId, classId)) {
|
||||
res.add(structuredProperty(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info));
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo info) {
|
||||
final Node node,
|
||||
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;
|
||||
|
|
@ -622,33 +659,28 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
final Node node,
|
||||
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));
|
||||
.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n
|
||||
.valueOf("@schemename"), info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<Subject> prepareSubjectList(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
final List<Subject> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res
|
||||
.add(
|
||||
subject(
|
||||
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
|
||||
n.valueOf("@schemename"), info));
|
||||
.add(subject(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
|
@ -656,14 +688,12 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||
final Node n = 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 metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
|
||||
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||
final boolean altered = "true".equalsIgnoreCase(n.valueOf("@altered"));
|
||||
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
|
||||
final String harvestDate = n.valueOf("@harvestDate");
|
||||
|
||||
|
|
@ -673,9 +703,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) {
|
||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||
|
||||
if (n == null) {
|
||||
return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
|
||||
}
|
||||
if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
|
||||
|
||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||
|
|
@ -687,14 +715,11 @@ 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, invisible,
|
||||
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||
return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||
}
|
||||
|
||||
protected List<Field<String>> prepareListURL(final Node node, final String xpath, final DataInfo info) {
|
||||
return listFields(
|
||||
info, prepareListString(node, xpath)
|
||||
return listFields(info, prepareListString(node, xpath)
|
||||
.stream()
|
||||
.filter(URL_VALIDATOR::isValid)
|
||||
.collect(Collectors.toList()));
|
||||
|
|
@ -705,9 +730,9 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
}
|
||||
|
||||
protected List<Field<String>> prepareListFields(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
return listFields(info, prepareListString(node, xpath));
|
||||
}
|
||||
|
||||
|
|
@ -722,15 +747,13 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
return res;
|
||||
}
|
||||
|
||||
protected Set<String> validateUrl(Collection<String> url) {
|
||||
protected Set<String> validateUrl(final Collection<String> url) {
|
||||
|
||||
if (Objects.isNull(url)) {
|
||||
return new HashSet<>();
|
||||
}
|
||||
if (Objects.isNull(url)) { return new HashSet<>(); }
|
||||
return url
|
||||
.stream()
|
||||
.filter(URL_VALIDATOR::isValid)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
.stream()
|
||||
.filter(URL_VALIDATOR::isValid)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -196,6 +196,12 @@ class MappersTest {
|
|||
|
||||
assertEquals(aff1.getSource(), aff2.getTarget());
|
||||
assertEquals(aff2.getSource(), aff1.getTarget());
|
||||
|
||||
// COUNTRIES
|
||||
assertEquals(3, p.getCountry().size());
|
||||
assertEquals("IT", p.getCountry().get(0).getClassid());
|
||||
assertEquals("FR", p.getCountry().get(1).getClassid());
|
||||
assertEquals("DE", p.getCountry().get(2).getClassid());
|
||||
}
|
||||
|
||||
private void verifyRelation(Relation r) {
|
||||
|
|
@ -867,6 +873,12 @@ class MappersTest {
|
|||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
System.out.println(p.getTitle().get(0).getValue());
|
||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||
|
||||
// COUNTRIES
|
||||
assertEquals(3, p.getCountry().size());
|
||||
assertEquals("IT", p.getCountry().get(0).getClassid());
|
||||
assertEquals("FR", p.getCountry().get(1).getClassid());
|
||||
assertEquals("DE", p.getCountry().get(2).getClassid());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -71,6 +71,9 @@
|
|||
subRelType="outcome"
|
||||
targetType="project"
|
||||
validationDate="2020-01-01">corda_______::226852</oaf:relation>
|
||||
<oaf:country>IT</oaf:country>
|
||||
<oaf:country>FR</oaf:country>
|
||||
<oaf:country>DE</oaf:country>
|
||||
</metadata>
|
||||
<about xmlns:oai="http://www.openarchives.org/OAI/2.0/">
|
||||
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
|
||||
|
|
|
|||
|
|
@ -78,6 +78,9 @@
|
|||
<oaf:projectid>corda_______::630786</oaf:projectid>
|
||||
<oaf:hostedBy id="re3data_____::r3d100010386" name="LINDAT/CLARIN repository"/>
|
||||
<oaf:collectedFrom id="re3data_____::r3d100010386" name="LINDAT/CLARIN repository"/>
|
||||
<oaf:country>IT</oaf:country>
|
||||
<oaf:country>FR</oaf:country>
|
||||
<oaf:country>DE</oaf:country>
|
||||
</metadata>
|
||||
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance">
|
||||
|
|
|
|||
Loading…
Reference in New Issue