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fixed a problem with missing instances

This commit is contained in:
Michele Artini 2020-04-23 16:18:40 +02:00
parent 9e4d58f505
commit d920ce501e
5 changed files with 1032 additions and 904 deletions

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@ -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.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; 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.oa.graph.raw.common.MigrationConstants;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
@ -41,388 +28,439 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; 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 { public abstract class AbstractMdRecordToOafMapper {
protected final Map<String, String> code2name; protected final Map<String, String> code2name;
protected static final Qualifier MAIN_TITLE_QUALIFIER = protected static final Qualifier MAIN_TITLE_QUALIFIER =
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) { protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name; this.code2name = code2name;
} }
public List<Oaf> processMdRecord(final String xml) { public List<Oaf> processMdRecord(final String xml) {
try { try {
final Map<String, String> nsContext = new HashMap<>(); final Map<String, String> nsContext = new HashMap<>();
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final Document doc = final Document doc =
DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); DocumentHelper.parseText(
xml.replaceAll(
final String type = doc.valueOf("//dr:CobjCategory/@type"); "http://datacite.org/schema/kernel-4",
final KeyValue collectedFrom = "http://datacite.org/schema/kernel-3"));
keyValue(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy = final String type = doc.valueOf("//dr:CobjCategory/@type");
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) final KeyValue collectedFrom =
? collectedFrom keyValue(
: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
doc.valueOf("//oaf:collectedFrom/@name"));
final DataInfo info = prepareDataInfo(doc); final KeyValue hostedBy =
final long lastUpdateTimestamp = new Date().getTime(); StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); : keyValue(
} catch (final Exception e) { createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
throw new RuntimeException(e); doc.valueOf("//oaf:hostedBy/@name"));
}
} final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
protected List<Oaf> createOafs(
final Document doc, return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
final String type, } catch (final Exception e) {
final KeyValue collectedFrom, throw new RuntimeException(e);
final KeyValue hostedBy, }
final DataInfo info, }
final long lastUpdateTimestamp) {
protected List<Oaf> createOafs(
final List<Oaf> oafs = new ArrayList<>(); final Document doc,
final String type,
switch (type.toLowerCase()) { final KeyValue collectedFrom,
case "": final KeyValue hostedBy,
case "publication": final DataInfo info,
final Publication p = new Publication(); final long lastUpdateTimestamp) {
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER); final List<Oaf> oafs = new ArrayList<>();
p.setJournal(prepareJournal(doc, info));
oafs.add(p); switch (type.toLowerCase()) {
break; case "":
case "dataset": case "publication":
final Dataset d = new Dataset(); final Publication p = new Publication();
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER); p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
d.setStoragedate(prepareDatasetStorageDate(doc, info)); p.setJournal(prepareJournal(doc, info));
d.setDevice(prepareDatasetDevice(doc, info)); oafs.add(p);
d.setSize(prepareDatasetSize(doc, info)); break;
d.setVersion(prepareDatasetVersion(doc, info)); case "dataset":
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); final Dataset d = new Dataset();
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setGeolocation(prepareDatasetGeoLocations(doc, info)); d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
oafs.add(d); d.setStoragedate(prepareDatasetStorageDate(doc, info));
break; d.setDevice(prepareDatasetDevice(doc, info));
case "software": d.setSize(prepareDatasetSize(doc, info));
final Software s = new Software(); d.setVersion(prepareDatasetVersion(doc, info));
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER); d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); d.setGeolocation(prepareDatasetGeoLocations(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info)); oafs.add(d);
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); break;
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); case "software":
oafs.add(s); final Software s = new Software();
break; populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
case "otherresearchproducts": s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
default: s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
final OtherResearchProduct o = new OtherResearchProduct(); s.setLicense(prepareSoftwareLicenses(doc, info));
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER); s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); oafs.add(s);
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); break;
o.setTool(prepareOtherResearchProductTools(doc, info)); case "otherresearchproducts":
oafs.add(o); default:
break; final OtherResearchProduct o = new OtherResearchProduct();
} populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
if (!oafs.isEmpty()) { o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); o.setTool(prepareOtherResearchProductTools(doc, info));
} oafs.add(o);
break;
return oafs; }
}
if (!oafs.isEmpty()) {
private List<Oaf> addProjectRels( oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
final Document doc, oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
final KeyValue collectedFrom, }
final DataInfo info,
final long lastUpdateTimestamp) { return oafs;
}
final List<Oaf> res = new ArrayList<>();
private List<Oaf> addProjectRels(
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); final Document doc,
final KeyValue collectedFrom,
for (final Object o : doc.selectNodes("//oaf:projectid")) { final DataInfo info,
final String projectId = createOpenaireId(40, ((Node) o).getText(), true); final long lastUpdateTimestamp) {
final Relation r1 = new Relation(); final List<Oaf> res = new ArrayList<>();
r1.setRelType("resultProject");
r1.setSubRelType("outcome"); final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
r1.setRelClass("isProducedBy");
r1.setSource(docId); for (final Object o : doc.selectNodes("//oaf:projectid")) {
r1.setTarget(projectId); final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
r1.setCollectedfrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info); final Relation r1 = new Relation();
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setRelType("resultProject");
res.add(r1); r1.setSubRelType("outcome");
r1.setRelClass("isProducedBy");
final Relation r2 = new Relation(); r1.setSource(docId);
r2.setRelType("resultProject"); r1.setTarget(projectId);
r2.setSubRelType("outcome"); r1.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setRelClass("produces"); r1.setDataInfo(info);
r2.setSource(projectId); r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setTarget(docId); res.add(r1);
r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info); final Relation r2 = new Relation();
r2.setLastupdatetimestamp(lastUpdateTimestamp); r2.setRelType("resultProject");
res.add(r2); r2.setSubRelType("outcome");
} r2.setRelClass("produces");
r2.setSource(projectId);
return res; r2.setTarget(docId);
} r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info);
protected abstract List<Oaf> addOtherResultRels( r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Document doc, res.add(r2);
final KeyValue collectedFrom, }
final DataInfo info,
final long lastUpdateTimestamp); return res;
}
private void populateResultFields(
final Result r, protected abstract List<Oaf> addOtherResultRels(
final Document doc, final Document doc,
final KeyValue collectedFrom, final KeyValue collectedFrom,
final KeyValue hostedBy, final DataInfo info,
final DataInfo info, final long lastUpdateTimestamp);
final long lastUpdateTimestamp) {
r.setDataInfo(info); private void populateResultFields(
r.setLastupdatetimestamp(lastUpdateTimestamp); final Result r,
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); final Document doc,
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); final KeyValue collectedFrom,
r.setCollectedfrom(Arrays.asList(collectedFrom)); final KeyValue hostedBy,
r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); final DataInfo info,
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); final long lastUpdateTimestamp) {
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setDataInfo(info);
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setOaiprovenance(prepareOAIprovenance(doc)); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setAuthor(prepareAuthors(doc, info)); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setLanguage(prepareLanguages(doc)); r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setPid(
r.setSubject(prepareSubjects(doc, info)); prepareListStructProps(
r.setTitle(prepareTitles(doc, info)); doc,
r.setRelevantdate(prepareRelevantDates(doc, info)); "//oaf:identifier",
r.setDescription(prepareDescriptions(doc, info)); "@identifierType",
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); "dnet:pid_types",
r.setPublisher(preparePublisher(doc, info)); "dnet:pid_types",
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); info));
r.setSource(prepareSources(doc, info)); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setFormat(prepareFormats(doc, info)); r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setContributor(prepareContributors(doc, info)); r.setOaiprovenance(prepareOAIprovenance(doc));
r.setResourcetype(prepareResourceType(doc, info)); r.setAuthor(prepareAuthors(doc, info));
r.setCoverage(prepareCoverages(doc, info)); r.setLanguage(prepareLanguages(doc));
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setSubject(prepareSubjects(doc, info));
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); r.setTitle(prepareTitles(doc, info));
} r.setRelevantdate(prepareRelevantDates(doc, info));
r.setDescription(prepareDescriptions(doc, info));
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
r.setPublisher(preparePublisher(doc, info));
protected abstract List<Instance> prepareInstances( r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
Document doc, r.setSource(prepareSources(doc, info));
DataInfo info, r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
KeyValue collectedfrom, r.setFormat(prepareFormats(doc, info));
KeyValue hostedby); r.setContributor(prepareContributors(doc, info));
r.setResourcetype(prepareResourceType(doc, info));
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info); r.setCoverage(prepareCoverages(doc, info));
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info); r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info); }
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info); protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info); protected abstract List<Instance> prepareInstances(
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
protected abstract Qualifier prepareLanguages(Document doc);
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools(
Document doc, protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
DataInfo info);
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc, protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
DataInfo info);
protected abstract Qualifier prepareLanguages(Document doc);
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
Document doc, protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools(
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); Document doc, DataInfo info);
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
Document doc, protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
DataInfo info); Document doc, DataInfo info);
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls( protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
Document doc,
DataInfo info); protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info); protected abstract List<StructuredProperty> prepareSoftwareLicenses(
Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
Document doc, protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
DataInfo info); Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info); protected abstract Field<String> prepareDatasetMetadataVersionNumber(
Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
private Journal prepareJournal(final Document doc, final DataInfo info) {
final Node n = doc.selectSingleNode("//oaf:journal"); protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
if (n != null) {
final String name = n.getText(); protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
final String issnPrinted = n.valueOf("@issn");
final String issnOnline = n.valueOf("@eissn"); private Journal prepareJournal(final Document doc, final DataInfo info) {
final String issnLinking = n.valueOf("@lissn"); final Node n = doc.selectSingleNode("//oaf:journal");
final String ep = n.valueOf("@ep"); if (n != null) {
final String iss = n.valueOf("@iss"); final String name = n.getText();
final String sp = n.valueOf("@sp"); final String issnPrinted = n.valueOf("@issn");
final String vol = n.valueOf("@vol"); final String issnOnline = n.valueOf("@eissn");
final String edition = n.valueOf("@edition"); final String issnLinking = n.valueOf("@lissn");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } final String ep = n.valueOf("@ep");
} final String iss = n.valueOf("@iss");
return null; final String sp = n.valueOf("@sp");
} final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition");
protected Qualifier prepareQualifier( if (StringUtils.isNotBlank(name)) {
final Node node, return journal(
final String xpath, name,
final String schemeId, issnPrinted,
final String schemeName) { issnOnline,
final String classId = node.valueOf(xpath); issnLinking,
final String className = code2name.get(classId); ep,
return qualifier(classId, className, schemeId, schemeName); iss,
} sp,
vol,
protected List<StructuredProperty> prepareListStructProps( edition,
final Node node, null,
final String xpath, null,
final String xpathClassId, info);
final String schemeId, }
final String schemeName, }
final DataInfo info) { return null;
final List<StructuredProperty> res = new ArrayList<>(); }
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o; protected Qualifier prepareQualifier(
final String classId = n.valueOf(xpathClassId); final Node node, final String xpath, final String schemeId, final String schemeName) {
final String className = code2name.get(classId); final String classId = node.valueOf(xpath);
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); final String className = code2name.get(classId);
} return qualifier(classId, className, schemeId, schemeName);
return res; }
}
protected List<StructuredProperty> prepareListStructProps(
protected List<StructuredProperty> prepareListStructProps( final Node node,
final Node node, final String xpath,
final String xpath, final String xpathClassId,
final Qualifier qualifier, final String schemeId,
final DataInfo info) { final String schemeName,
final List<StructuredProperty> res = new ArrayList<>(); final DataInfo info) {
for (final Object o : node.selectNodes(xpath)) { final List<StructuredProperty> res = new ArrayList<>();
final Node n = (Node) o; for (final Object o : node.selectNodes(xpath)) {
res.add(structuredProperty(n.getText(), qualifier, info)); final Node n = (Node) o;
} final String classId = n.valueOf(xpathClassId);
return res; final String className = code2name.get(classId);
} res.add(
structuredProperty(
protected List<StructuredProperty> prepareListStructProps( n.getText(), classId, className, schemeId, schemeName, info));
final Node node, }
final String xpath, return res;
final DataInfo info) { }
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) { protected List<StructuredProperty> prepareListStructProps(
final Node n = (Node) o; final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); final List<StructuredProperty> res = new ArrayList<>();
} for (final Object o : node.selectNodes(xpath)) {
return res; final Node n = (Node) o;
} res.add(structuredProperty(n.getText(), qualifier, info));
}
protected OAIProvenance prepareOAIprovenance(final Document doc) { return res;
final Node n = }
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
protected List<StructuredProperty> prepareListStructProps(
if (n == null) { return null; } final Node node, final String xpath, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
final String identifier = n.valueOf("./*[local-name()='identifier']"); for (final Object o : node.selectNodes(xpath)) {
final String baseURL = n.valueOf("./*[local-name()='baseURL']");; final Node n = (Node) o;
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; res.add(
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); structuredProperty(
final String datestamp = n.valueOf("./*[local-name()='datestamp']");; n.getText(),
final String harvestDate = n.valueOf("@harvestDate");; n.valueOf("@classid"),
n.valueOf("@classname"),
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); n.valueOf("@schemeid"),
} n.valueOf("@schemename"),
info));
protected DataInfo prepareDataInfo(final Document doc) { }
final Node n = doc.selectSingleNode("//oaf:datainfo"); return res;
}
if (n == null) { return dataInfo(false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final Node n =
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); doc.selectSingleNode(
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); "//*[local-name()='provenance']/*[local-name()='originDescription']");
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
if (n == null) {
final boolean deletedbyinference = return null;
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); }
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String identifier = n.valueOf("./*[local-name()='identifier']");
final String trust = n.valueOf("./oaf:trust"); final String baseURL = n.valueOf("./*[local-name()='baseURL']");
;
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
} ;
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) { final String datestamp = n.valueOf("./*[local-name()='datestamp']");
return field(node.valueOf(xpath), info); ;
} final String harvestDate = n.valueOf("@harvestDate");
;
protected List<Field<String>> prepareListFields(
final Node node, return oaiIProvenance(
final String xpath, identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
final DataInfo info) { }
return listFields(info, prepareListString(node, xpath));
} protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
protected List<String> prepareListString(final Node node, final String xpath) {
final List<String> res = new ArrayList<>(); if (n == null) {
for (final Object o : node.selectNodes(xpath)) { return dataInfo(
final String s = ((Node) o).getText().trim(); false,
if (StringUtils.isNotBlank(s)) { null,
res.add(s); false,
} false,
} MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS,
return res; "0.9");
} }
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
final boolean deletedbyinference =
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
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);
}
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
return field(node.valueOf(xpath), info);
}
protected List<Field<String>> prepareListFields(
final Node node, final String xpath, final DataInfo info) {
return listFields(info, prepareListString(node, xpath));
}
protected List<String> prepareListString(final Node node, final String xpath) {
final List<String> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final String s = ((Node) o).getText().trim();
if (StringUtils.isNotBlank(s)) {
res.add(s);
}
}
return res;
}
} }

View File

@ -1,8 +1,19 @@
package eu.dnetlib.dhp.oa.graph.raw; 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.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
@ -62,33 +73,44 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final DataInfo info, final DataInfo info,
final KeyValue collectedfrom, final KeyValue collectedfrom,
final KeyValue hostedby) { final KeyValue hostedby) {
final List<Instance> res = new ArrayList<>();
final Instance instance = new Instance();
instance.setUrl(new ArrayList<>());
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(
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(
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
for (final Object o : for (final Object o :
doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
final Instance instance = new Instance(); instance.getUrl().add(((Node) o).getText().trim());
instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
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(
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(
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
res.add(instance);
} }
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 @Override

View File

@ -6,17 +6,28 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class MigrationConstants { public class MigrationConstants {
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); qualifier(
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER = "publication",
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); "publication",
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = "dnet:result_typologies",
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); "dnet:result_typologies");
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER = public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS = public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions"); qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenanceActions", "dnet:provenanceActions"); 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");
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
qualifier(
"sysimport:crosswalk:entityregistry",
"sysimport:crosswalk:entityregistry",
"dnet:provenanceActions",
"dnet:provenanceActions");
} }

View File

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