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[Graph Dump] changed to mirror the changes in the model

This commit is contained in:
Miriam Baglioni 2021-11-19 11:25:50 +01:00
parent 5dc5792722
commit 9fae872181
4 changed files with 25 additions and 441 deletions
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413
dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java
View File

@ -1,413 +0,0 @@
package eu.dnetlib.dhp.common;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class GraphResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) {
CommunityResult out = new CommunityResult();
eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in;
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
if (ort.isPresent()) {
switch (ort.get().getClassid()) {
case "publication":
Optional<Journal> journal = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
if (journal.isPresent()) {
Journal j = journal.get();
Container c = new Container();
c.setConferencedate(j.getConferencedate());
c.setConferenceplace(j.getConferenceplace());
c.setEdition(j.getEdition());
c.setEp(j.getEp());
c.setIss(j.getIss());
c.setIssnLinking(j.getIssnLinking());
c.setIssnOnline(j.getIssnOnline());
c.setIssnPrinted(j.getIssnPrinted());
c.setName(j.getName());
c.setSp(j.getSp());
c.setVol(j.getVol());
out.setContainer(c);
out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
}
break;
case "dataset":
eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input;
Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue()));
Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
out
.setGeolocation(
Optional
.ofNullable(id.getGeolocation())
.map(
igl -> igl
.stream()
.filter(Objects::nonNull)
.map(gli -> {
GeoLocation gl = new GeoLocation();
gl.setBox(gli.getBox());
gl.setPlace(gli.getPlace());
gl.setPoint(gli.getPoint());
return gl;
})
.collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
break;
case "software":
eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
Optional
.ofNullable(is.getCodeRepositoryUrl())
.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
Optional
.ofNullable(is.getDocumentationUrl())
.ifPresent(
value -> out
.setDocumentationUrl(
value
.stream()
.map(Field::getValue)
.collect(Collectors.toList())));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break;
case "other":
eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
out
.setContactgroup(
Optional
.ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break;
}
Optional
.ofNullable(input.getAuthor())
.ifPresent(
ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
if (oar.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
out
.setBestaccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
final List<String> contributorList = new ArrayList<>();
Optional
.ofNullable(input.getContributor())
.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
out.setContributor(contributorList);
Optional
.ofNullable(input.getCountry())
.ifPresent(
value -> out
.setCountry(
value
.stream()
.map(
c -> {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null;
}
Country country = new Country();
country.setCode(c.getClassid());
country.setLabel(c.getClassname());
Optional
.ofNullable(c.getDataInfo())
.ifPresent(
provenance -> country
.setProvenance(
Provenance
.newInstance(
provenance
.getProvenanceaction()
.getClassname(),
c.getDataInfo().getTrust())));
return country;
})
.filter(Objects::nonNull)
.collect(Collectors.toList())));
final List<String> coverageList = new ArrayList<>();
Optional
.ofNullable(input.getCoverage())
.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
out.setCoverage(coverageList);
out.setDateofcollection(input.getDateofcollection());
final List<String> descriptionList = new ArrayList<>();
Optional
.ofNullable(input.getDescription())
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
out.setDescription(descriptionList);
Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
if (oStr.isPresent()) {
out.setEmbargoenddate(oStr.get().getValue());
}
final List<String> formatList = new ArrayList<>();
Optional
.ofNullable(input.getFormat())
.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
out.setFormat(formatList);
out.setId(input.getId());
out.setOriginalId(input.getOriginalId());
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
}
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
}
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) {
out.setLastupdatetimestamp(oLong.get());
}
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
if (otitle.isPresent()) {
List<StructuredProperty> iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setMaintitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setSubtitle(iTitle.get(0).getValue());
}
}
List<ControlledField> pids = new ArrayList<>();
Optional
.ofNullable(input.getPid())
.ifPresent(
value -> value
.stream()
.forEach(
p -> pids
.add(
ControlledField
.newInstance(p.getQualifier().getClassid(), p.getValue()))));
out.setPid(pids);
oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue());
}
oStr = Optional.ofNullable(input.getPublisher());
if (oStr.isPresent()) {
out.setPublisher(oStr.get().getValue());
}
List<String> sourceList = new ArrayList<>();
Optional
.ofNullable(input.getSource())
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
List<Subject> subjectList = new ArrayList<>();
Optional
.ofNullable(input.getSubject())
.ifPresent(
value -> value
.forEach(s -> subjectList.add(getSubject(s))));
out.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid());
}
out
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
return out;
}
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
setCommonValue(i, instance);
instance
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
instance
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
return instance;
}
private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
.ofNullable(i.getAccessright());
if (opAr.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
instance
.setAccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
Optional
.ofNullable(i.getLicense())
.ifPresent(value -> instance.setLicense(value.getValue()));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
Optional
.ofNullable(i.getRefereed())
.ifPresent(value -> instance.setRefereed(value.getClassname()));
Optional
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
}
private static Subject getSubject(StructuredProperty s) {
Subject subject = new Subject();
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
if (di.isPresent()) {
Provenance p = new Provenance();
p.setProvenance(di.get().getProvenanceaction().getClassname());
p.setTrust(di.get().getTrust());
subject.setProvenance(p);
}
return subject;
}
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
Author a = new Author();
a.setFullname(oa.getFullname());
a.setName(oa.getName());
a.setSurname(oa.getSurname());
a.setRank(oa.getRank());
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
Pid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
}
return a;
}
private static Pid getOrcid(List<StructuredProperty> p) {
for (StructuredProperty pid : p) {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue()),
Provenance
.newInstance(
di.get().getProvenanceaction().getClassname(),
di.get().getTrust()));
} else {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue())
);
}
}
}
return null;
}
}

45
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java
View File

@ -16,6 +16,7 @@ import eu.dnetlib.dhp.schema.dump.oaf.Country;
import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
import eu.dnetlib.dhp.schema.dump.oaf.Measure;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
import eu.dnetlib.dhp.schema.dump.oaf.Result;
@ -82,7 +83,7 @@ public class ResultMapper implements Serializable {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null;
}
Country country = new Country();
ResultCountry country = new ResultCountry();
country.setCode(c.getClassid());
country.setLabel(c.getClassname());
Optional
@ -136,10 +137,6 @@ public class ResultMapper implements Serializable {
.stream()
.filter(s -> !s.startsWith("50|"))
.collect(Collectors.toList())));
// Optional
// .ofNullable(
// input.getOriginalId().stream().filter(s -> !s.startsWith("50|")).collect(Collectors.toList()))
// .ifPresent(v -> out.setOriginalId(v));
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
@ -163,7 +160,7 @@ public class ResultMapper implements Serializable {
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname()));
}
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) {
@ -199,7 +196,7 @@ public class ResultMapper implements Serializable {
value
.stream()
.map(
p -> ControlledField
p -> ResultPid
.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
@ -452,14 +449,14 @@ public class ResultMapper implements Serializable {
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
Optional<List<Measure>> mes = Optional.ofNullable(i.getMeasures());
if (mes.isPresent()){
List<KeyValue> measure = new ArrayList<>();
Optional<List<eu.dnetlib.dhp.schema.oaf.Measure>> mes = Optional.ofNullable(i.getMeasures());
if (mes.isPresent()) {
List<Measure> measure = new ArrayList<>();
mes
.get()
.forEach(
m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue()))));
instance.setMeasures(measure );
.get()
.forEach(
m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue()))));
instance.setMeasures(measure);
}
if (opAr.get().getOpenAccessRoute() != null) {
@ -489,7 +486,7 @@ public class ResultMapper implements Serializable {
.setPid(
pid
.stream()
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
.map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional
@ -499,7 +496,7 @@ public class ResultMapper implements Serializable {
.setAlternateIdentifier(
ai
.stream()
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
.map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional
@ -579,7 +576,7 @@ public class ResultMapper implements Serializable {
private static Subject getSubject(StructuredProperty s) {
Subject subject = new Subject();
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
if (di.isPresent()) {
Provenance p = new Provenance();
@ -601,7 +598,7 @@ public class ResultMapper implements Serializable {
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
Pid pid = getOrcid(oPids.get());
AuthorPid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
@ -610,12 +607,12 @@ public class ResultMapper implements Serializable {
return a;
}
private static Pid getAuthorPid(StructuredProperty pid) {
private static AuthorPid getAuthorPid(StructuredProperty pid) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return Pid
return AuthorPid
.newInstance(
ControlledField
AuthorPidSchemeValue
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue()),
@ -624,9 +621,9 @@ public class ResultMapper implements Serializable {
di.get().getProvenanceaction().getClassname(),
di.get().getTrust()));
} else {
return Pid
return AuthorPid
.newInstance(
ControlledField
AuthorPidSchemeValue
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue())
@ -635,7 +632,7 @@ public class ResultMapper implements Serializable {
}
}
private static Pid getOrcid(List<StructuredProperty> p) {
private static AuthorPid getOrcid(List<StructuredProperty> p) {
List<StructuredProperty> pidList = p.stream().map(pid -> {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) ||
(pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) {

6
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java
View File

@ -140,7 +140,7 @@ public class DumpGraphEntities implements Serializable {
.ofNullable(d.getDatasourcetype())
.ifPresent(
dsType -> datasource
.setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname())));
.setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname())));
Optional
.ofNullable(d.getOpenairecompatibility())
@ -499,7 +499,7 @@ public class DumpGraphEntities implements Serializable {
.ifPresent(
value -> {
if (!value.getClassid().equals(Constants.UNKNOWN)) {
organization.setCountry(Qualifier.newInstance(value.getClassid(), value.getClassname()));
organization.setCountry(Country.newInstance(value.getClassid(), value.getClassname()));
}
});
@ -515,7 +515,7 @@ public class DumpGraphEntities implements Serializable {
.setPid(
value
.stream()
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
.map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
return organization;

2
pom.xml
View File

@ -753,7 +753,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.9.23]</dhp-schemas.version>
<dhp-schemas.version>[2.9.24-SNAPSHOT]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>