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dnet-hadoop
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Merge branch 'master' into provision_indexing

This commit is contained in:
Claudio Atzori 2021-02-09 15:46:26 +01:00
parent ff72fcd91a f1a852f278
commit 62bd3c53ee
136 changed files with 10191 additions and 764 deletions
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4
dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
View File

@ -1,10 +1,10 @@
package eu.dnetlib.dhp.common;
import com.google.common.collect.Maps;
import java.util.Map;
import com.google.common.collect.Maps;
public class Constants {
public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();

695
dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java
View File

@ -1,6 +1,10 @@
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;
@ -10,406 +14,399 @@ import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
public class GraphResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) {
CommunityResult out = new CommunityResult();
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()));
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
.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":
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(v -> v.getValue())
.collect(Collectors.toList())));
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(v -> v.getValue())
.collect(Collectors.toList())));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break;
case "other":
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(cg -> cg.getValue()).collect(Collectors.toList()))
.orElse(null));
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(cg -> cg.getValue()).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break;
}
break;
}
Optional
.ofNullable(input.getAuthor())
.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
Optional
.ofNullable(input.getAuthor())
.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
// 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));
}
}
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);
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())));
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);
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());
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> 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());
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());
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(i -> getInstance(i)).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.size() > 0) {
out.setMaintitle(iTitle.get(0).getValue());
}
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.size() > 0) {
out.setMaintitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (iTitle.size() > 0) {
out.setSubtitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (iTitle.size() > 0) {
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<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))));
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.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid());
}
out.setType(input.getResulttype().getClassid());
}
out
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
out
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
return out;
return out;
}
}
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
setCommonValue(i, instance);
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
instance
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
setCommonValue(i, instance);
instance
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
instance
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
return instance;
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 <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());
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);
}
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
Pid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
}
return subject;
}
return a;
}
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());
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())
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;
}
}
}
return null;
}
}

35
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
@ -32,27 +33,33 @@ public class AuthorMerger {
}
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
if (pa == pb) {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
} else {
if (sa == sb) {
base = pa > pb ? a : b;
enrich = pa > pb ? b : a;
} else {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
}
enrichPidFromList(base, enrich);
enrichPidFromList(base, enrich, threshold);
return base;
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
return mergeAuthor(a, b, THRESHOLD);
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
if (base == null || enrich == null)
return;
// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
final Map<String, Author> basePidAuthorMap = base
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -63,6 +70,7 @@ public class AuthorMerger {
.map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
// <pid, Author> (list of pid that are missing in the other list)
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -83,10 +91,10 @@ public class AuthorMerger {
.max(Comparator.comparing(Tuple2::_1));
if (simAuthor.isPresent()) {
double th = THRESHOLD;
double th = threshold;
// increase the threshold if the surname is too short
if (simAuthor.get()._2().getSurname() != null
&& simAuthor.get()._2().getSurname().length() <= 3)
&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
th = 0.99;
if (simAuthor.get()._1() > th) {
@ -156,7 +164,7 @@ public class AuthorMerger {
}
private static String normalize(final String s) {
return nfd(s)
String[] normalized = nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
@ -166,7 +174,12 @@ public class AuthorMerger {
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
.trim()
.split(" ");
Arrays.sort(normalized);
return String.join(" ", normalized);
}
private static String nfd(final String s) {

100
dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java Normal file
View File

@ -0,0 +1,100 @@
package eu.dnetlib.dhp.oa.merge;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class AuthorMergerTest {
private String publicationsBasePath;
private List<List<Author>> authors;
@BeforeEach
public void setUp() throws Exception {
publicationsBasePath = Paths
.get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI())
.toFile()
.getAbsolutePath();
authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
}
@Test
public void mergeTest() { // used in the dedup: threshold set to 0.95
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = AuthorMerger.merge(authors);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(7, merge.size());
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
public String authorToString(Author a) {
String print = "Fullname = ";
print += a.getFullname() + " pid = [";
if (a.getPid() != null)
for (StructuredProperty sp : a.getPid()) {
print += sp.toComparableString() + " ";
}
print += "]";
return print;
}
}

3
dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json Normal file
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File diff suppressed because one or more lines are too long

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -105,6 +105,8 @@ public class ModelConstants {
public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
private static Qualifier qualifier(
final String classid,
final String classname,

29
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -49,23 +49,22 @@ public abstract class Oaf implements Serializable {
return;
}
setCollectedfrom(
Stream
.concat(
Optional
.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(o.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
mergeOAFDataInfo(o);
Stream
.concat(
Optional
.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(o.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
setLastupdatetimestamp(
Math.max(
Math
.max(
Optional.ofNullable(getLastupdatetimestamp()).orElse(0L),
Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L)));
}

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable {
? p.getFundedamount()
: fundedamount;
// programme = mergeLists(programme, p.getProgramme());
h2020classification = mergeLists(h2020classification, p.getH2020classification());
mergeOAFDataInfo(e);

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -243,7 +243,7 @@ public class Result extends OafEntity implements Serializable {
Result r = (Result) e;
// TODO consider merging also Measures
measures = mergeLists(measures, r.getMeasures());
instance = mergeLists(instance, r.getInstance());
@ -323,13 +323,13 @@ public class Result extends OafEntity implements Serializable {
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java Normal file
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@ -0,0 +1,28 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
/**
* Class that maps the model of the bipFinder! input data.
* Only needed for deserialization purposes
*/
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
public BipDeserialize() {
super();
}
public List<Score> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
/**
* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
*/
public class BipScore implements Serializable {
private String id; // doi
private List<Score> scoreList; // unit as given in the inputfile
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<Score> getScoreList() {
return scoreList;
}
public void setScoreList(List<Score> scoreList) {
this.scoreList = scoreList;
}
}

85
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java Normal file
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@ -0,0 +1,85 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Just collects all the atomic actions produced for the different results and saves them in
* outputpath for the ActionSet
*/
public class CollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
collectAndSave(spark, inputPath, outputPath);
});
}
private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
sc
.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

26
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java Normal file
View File

@ -0,0 +1,26 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
public class KeyValue implements Serializable {
private String key;
private String value;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java Normal file
View File

@ -0,0 +1,28 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
/**
* Subset of the information of the generic results that are needed to create the atomic action
*/
public class PreparedResult implements Serializable {
private String id; // openaire id
private String value; // doi
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java Normal file
View File

@ -0,0 +1,30 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
/**
* represents the score in the input file
*/
public class Score implements Serializable {
private String id;
private List<KeyValue> unit;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<KeyValue> getUnit() {
return unit;
}
public void setUnit(List<KeyValue> unit) {
this.unit = unit;
}
}

200
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java Normal file
View File

@ -0,0 +1,200 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import scala.Tuple2;
/**
* created the Atomic Action for each tipe of results
*/
public class SparkAtomicActionScoreJob implements Serializable {
private static String DOI = "doi";
private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkAtomicActionScoreJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String bipScorePath = parser.get("bipScorePath");
log.info("bipScorePath: {}", bipScorePath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
.textFile(bipScorePath)
.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
Dataset<BipScore> bipScores = spark
.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
System.out.println(bipScores.count());
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
Dataset<PreparedResult> preparedResult = spark
.sql(
"select pIde.value value, id " +
"from result " +
"lateral view explode (pid) p as pIde " +
"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
.as(Encoders.bean(PreparedResult.class));
bipScores
.joinWith(
preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
"inner")
.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
BipScore ret = value._1();
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
return ret;
}, Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
}
private static List<Measure> getMeasure(BipScore value) {
return value
.getScoreList()
.stream()
.map(score -> {
Measure m = new Measure();
m.setId(score.getId());
m
.setUnit(
score
.getUnit()
.stream()
.map(unit -> {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo());
return kv;
})
.collect(Collectors.toList()));
return m;
})
.collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json Normal file
View File

@ -0,0 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

32
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json Normal file
View File

@ -0,0 +1,32 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

171
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,171 @@
<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<description>the input path of the resources to be extended</description>
</property>
<property>
<name>bipScorePath</name>
<description>the path where to find the bipFinder scores</description>
</property>
<property>
<name>outputPath</name>
<description>the path where to store the actionset</description>
</property>
</parameters>
<start to="deleteoutputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="deleteoutputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
<delete path="${workingDir}"/>
<mkdir path="${workingDir}"/>
</fs>
<ok to="atomicactions"/>
<error to="Kill"/>
</action>
<fork name="atomicactions">
<path start="atomicactions_publication"/>
<path start="atomicactions_dataset"/>
<path start="atomicactions_orp"/>
<path start="atomicactions_software"/>
</fork>
<action name="atomicactions_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for publications</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for datasets</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for orp</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for software</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<join name="join_aa" to="collectandsave"/>
<action name="collectandsave">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>saves all the aa produced for the several types of results in the as output path</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

323
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java Normal file
View File

@ -0,0 +1,323 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class SparkAtomicActionScoreJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(SparkAtomicActionScoreJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void matchOne() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 1);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(2, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0));
}
@Test
public void matchOneWithTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 1);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
List<Row> tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList();
String tmp_influence = tmp_ds.get(0).getString(0);
Assertions
.assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
tmp_influence = tmp_ds.get(1).getString(0);
Assertions
.assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0)));
}
@Test
public void matchTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 2);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"1.98956540239e-08",
execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.282046161584",
execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
}
}

1101
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json Normal file
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7
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java
View File

@ -32,15 +32,15 @@ public class CheckDuplictedIdsJob {
IOUtils
.toString(
CheckDuplictedIdsJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json")));
parser.parseArgument(args);
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String countPath = parser.get("workingPath") + "/counts";
final String countPath = parser.get("outputDir") + "/counts";
log.info("countPath: {}", countPath);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
@ -59,6 +59,7 @@ public class CheckDuplictedIdsJob {
.map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(countPath);
;

13
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java
View File

@ -44,10 +44,10 @@ public class GenerateEventsJob {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String eventsPath = workingPath + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
@ -59,6 +59,9 @@ public class GenerateEventsJob {
final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ","));
final Set<String> topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist");
log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ","));
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@ -70,12 +73,12 @@ public class GenerateEventsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_events");
final Dataset<ResultGroup> groups = ClusterUtils
.readPath(spark, workingPath + "/duplicates", ResultGroup.class);
.readPath(spark, workingDir + "/duplicates", ResultGroup.class);
final Dataset<Event> dataset = groups
.map(
g -> EventFinder
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators),
Encoders
.bean(EventGroup.class))
.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));

2
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java
View File

@ -46,7 +46,7 @@ public class GenerateStatsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String dbUrl = parser.get("dbUrl");

22
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java
View File

@ -46,7 +46,7 @@ public class IndexEventSubsetJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -55,6 +55,18 @@ public class IndexEventSubsetJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic"));
log.info("maxEventsForTopic: {}", maxEventsForTopic);
@ -86,10 +98,10 @@ public class IndexEventSubsetJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

22
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java
View File

@ -54,7 +54,7 @@ public class IndexNotificationsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -63,6 +63,18 @@ public class IndexNotificationsJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
@ -92,10 +104,10 @@ public class IndexNotificationsJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

24
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java
View File

@ -36,7 +36,7 @@ public class IndexOnESJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -45,6 +45,18 @@ public class IndexOnESJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final JavaRDD<String> inputRdd = ClusterUtils
@ -53,15 +65,13 @@ public class IndexOnESJob {
.javaRDD();
final Map<String, String> esCfg = new HashMap<>();
// esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
}

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java
View File

@ -42,10 +42,10 @@ public class JoinStep0Job {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step0";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -57,10 +57,10 @@ public class JoinStep0Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class);
final Dataset<RelatedDatasource> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
.readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep1Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step1";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step1";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep1Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class);
final Dataset<RelatedProject> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class);
.readPath(spark, workingDir + "/relatedProjects", RelatedProject.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedProject>, OaBrokerMainEntity> aggr = new RelatedProjectAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java
View File

@ -39,10 +39,10 @@ public class JoinStep2Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step2";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step2";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -54,10 +54,10 @@ public class JoinStep2Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class);
final Dataset<RelatedSoftware> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class);
.readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedSoftware>, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep3Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step3";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step3";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep3Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class);
final Dataset<RelatedDataset> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class);
.readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDataset>, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep4Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step4";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step4";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep4Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class);
final Dataset<RelatedPublication> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class);
.readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedPublication>, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator()
.toColumn();

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java
View File

@ -36,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
public class PartitionEventsByDsIdJob {
private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class);
private static final String OPENDOAR_NSPREFIX = "10|opendoar____::";
private static final String OPENDOAR_NSPREFIX = "opendoar____::";
public static void main(final String[] args) throws Exception {
@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId";
log.info("partitionPath: {}", partitionPath);
final String opendoarIds = parser.get("opendoarIds");
@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob {
.write()
.partitionBy("group")
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(partitionPath);
});
@ -122,6 +123,7 @@ public class PartitionEventsByDsIdJob {
final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId();
res.setEventId(e.getEventId());
res.setOriginalId(payload.getResult().getOriginalId());
res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null));
res.setTopic(e.getTopic());

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java
View File

@ -45,10 +45,10 @@ public class PrepareGroupsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String groupsPath = workingPath + "/duplicates";
final String groupsPath = workingDir + "/duplicates";
log.info("groupsPath: {}", groupsPath);
final SparkConf conf = new SparkConf();
@ -60,10 +60,10 @@ public class PrepareGroupsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups");
final Dataset<OaBrokerMainEntity> results = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class);
final Dataset<Relation> mergedRels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<OaBrokerMainEntity, Relation>, ResultGroup> aggr = new ResultAggregator()

11
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java
View File

@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasets";
final String relsPath = workingDir + "/relatedDatasets";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob {
.map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob {
final Dataset<RelatedDataset> dataset = rels
.joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2);
final RelatedDataset rel = new RelatedDataset(t._1.getSource(),
t._2);
rel.getRelDataset().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedDataset.class));

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java
View File

@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasources";
final String relsPath = workingDir + "/relatedDatasources";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
View File

@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedProjects";
final String relsPath = workingDir + "/relatedProjects";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob {
.map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

11
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java
View File

@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedPublications";
final String relsPath = workingDir + "/relatedPublications";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob {
Encoders.bean(OaBrokerRelatedPublication.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob {
final Dataset<RelatedPublication> dataset = rels
.joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2);
final RelatedPublication rel = new RelatedPublication(
t._1.getSource(), t._2);
rel.getRelPublication().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedPublication.class));

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java
View File

@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedSoftwares";
final String relsPath = workingDir + "/relatedSoftwares";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob {
.map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java
View File

@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String simpleEntitiesPath = workingPath + "/simpleEntities";
final String simpleEntitiesPath = workingDir + "/simpleEntities";
log.info("simpleEntitiesPath: {}", simpleEntitiesPath);
final SparkConf conf = new SparkConf();

19
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java
View File

@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMissingSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MISSING_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MISSING_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MISSING_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MISSING_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MISSING_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

19
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
View File

@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMoreSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MORE_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MORE_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MORE_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MORE_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MORE_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

12
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java
View File

@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class ClusterUtils {
@ -30,6 +31,16 @@ public class ClusterUtils {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static Dataset<Relation> loadRelations(final String graphPath, final SparkSession spark) {
return ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.map(r -> {
r.setSource(ConversionUtils.cleanOpenaireId(r.getSource()));
r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget()));
return r;
}, Encoders.bean(Relation.class));
}
public static <R> Dataset<R> readPath(
final SparkSession spark,
final String inputPath,
@ -67,6 +78,7 @@ public class ClusterUtils {
.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(path);
}

16
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -74,7 +74,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
res.setOpenaireId(d.getId());
res.setOpenaireId(cleanOpenaireId(d.getId()));
res.setOriginalId(first(d.getOriginalId()));
res.setTitle(structPropValue(d.getTitle()));
res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -89,7 +89,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setOriginalId(first(p.getOriginalId()));
res.setTitle(structPropValue(p.getTitle()));
res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -106,7 +106,7 @@ public class ConversionUtils {
final OaBrokerMainEntity res = new OaBrokerMainEntity();
res.setOpenaireId(result.getId());
res.setOpenaireId(cleanOpenaireId(result.getId()));
res.setOriginalId(first(result.getOriginalId()));
res.setTypology(classId(result.getResulttype()));
res.setTitles(structPropList(result.getTitle()));
@ -129,6 +129,10 @@ public class ConversionUtils {
return res;
}
public static String cleanOpenaireId(final String id) {
return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
}
private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
if (author == null) {
return null;
@ -188,7 +192,7 @@ public class ConversionUtils {
}
final OaBrokerProject res = new OaBrokerProject();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setTitle(fieldValue(p.getTitle()));
res.setAcronym(fieldValue(p.getAcronym()));
res.setCode(fieldValue(p.getCode()));
@ -214,7 +218,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
res.setOpenaireId(sw.getId());
res.setOpenaireId(cleanOpenaireId(sw.getId()));
res.setName(structPropValue(sw.getTitle()));
res.setDescription(fieldValue(sw.getDescription()));
res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
@ -230,7 +234,7 @@ public class ConversionUtils {
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
res.setOpenaireId(ds.getId());
res.setOpenaireId(cleanOpenaireId(ds.getId()));
res.setType(classId(ds.getDatasourcetype()));
return res;
}

13
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java
View File

@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable {
final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
collectedFromSet
.stream()
.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.COLLECTED_FROM_REL))
.forEach(res::addTuple);
hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
hostedBySet
.stream()
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.HOSTED_BY_REL))
.forEach(res::addTuple);
return res;
}

9
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java
View File

@ -76,6 +76,7 @@ public class EventFinder {
final Set<String> dsIdWhitelist,
final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist,
final Set<String> topicWhitelist,
final Map<String, LongAccumulator> accumulators) {
final List<UpdateInfo<?>> list = new ArrayList<>();
@ -84,7 +85,13 @@ public class EventFinder {
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
for (final UpdateInfo<?> info : matcher
.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) {
if (topicWhitelist == null || topicWhitelist.isEmpty()
|| topicWhitelist.contains(info.getTopic().getPath())) {
list.add(info);
}
}
}
}
}

9
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json Normal file
View File

@ -0,0 +1,9 @@
[
{
"paramName": "o",
"paramLongName": "outputDir",
"paramDescription": "the path where the data are stored",
"paramRequired": true
}
]

2
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json
View File

@ -7,7 +7,7 @@
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data will be stored",
"paramRequired": true
}

75
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
View File

@ -6,7 +6,7 @@
<description>the path where the graph is stored</description>
</property>
<property>
<name>workingPath</name>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
@ -24,6 +24,11 @@
<value>-</value>
<description>a black list (comma separeted, - for empty list) of datasource ids</description>
</property>
<property>
<name>topicWhitelist</name>
<value>*</value>
<description>a white list (comma separeted, * for all) of topics</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
@ -36,6 +41,26 @@
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
@ -111,15 +136,15 @@
</configuration>
</global>
<start to="ensure_working_path"/>
<start to="ensure_output_dir"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ensure_working_path">
<action name="ensure_output_dir">
<fs>
<mkdir path='${workingPath}'/>
<mkdir path='${outputDir}'/>
</fs>
<ok to="start_entities_and_rels"/>
<error to="Kill"/>
@ -152,7 +177,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -176,7 +201,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -201,7 +226,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -225,7 +250,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -249,7 +274,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -273,7 +298,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -299,7 +324,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step1"/>
<error to="Kill"/>
@ -323,7 +348,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step2"/>
<error to="Kill"/>
@ -347,7 +372,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step3"/>
<error to="Kill"/>
@ -371,7 +396,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step4"/>
<error to="Kill"/>
@ -395,7 +420,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="prepare_groups"/>
<error to="Kill"/>
@ -419,7 +444,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="generate_events"/>
<error to="Kill"/>
@ -442,10 +467,12 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
<arg>--topicWhitelist</arg><arg>${topicWhitelist}</arg>
</spark>
<ok to="index_event_subset"/>
<error to="Kill"/>
@ -468,9 +495,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
@ -495,9 +526,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="stats"/>
@ -521,7 +556,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
<arg>--dbUser</arg><arg>${brokerDbUser}</arg>
<arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>

14
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json
View File

@ -1,7 +1,13 @@
[
{
"paramName": "wp",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data are stored",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "outputDir",
"paramDescription": "the path where the generated events will be stored",
"paramRequired": true
},
@ -22,5 +28,11 @@
"paramLongName": "datasourceIdBlacklist",
"paramDescription": "a black list (comma separeted, - for empty list) of datasource ids",
"paramRequired": true
},
{
"paramName": "topicWhitelist",
"paramLongName": "topicWhitelist",
"paramDescription": "a white list (comma separeted, * for all) of topics",
"paramRequired": true
}
]

28
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the data path",
"paramRequired": true
},
{
@ -16,5 +16,29 @@
"paramLongName": "esHost",
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
}
]

28
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the path where the generated data are stored",
"paramRequired": true
},
{
@ -16,7 +16,31 @@
"paramLongName": "esHost",
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "maxEventsForTopic",

28
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the dir that contains the events folder",
"paramRequired": true
},
{
@ -17,6 +17,30 @@
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "broker",
"paramLongName": "brokerApiBaseUrl",

30
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml
View File

@ -6,8 +6,8 @@
<description>the path where the graph is stored</description>
</property>
<property>
<name>workingPath</name>
<description>the path where the the generated data will be stored</description>
<name>outputDir</name>
<description>the path where the the generated data are stored</description>
</property>
<property>
<name>datasourceIdWhitelist</name>
@ -36,6 +36,26 @@
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
@ -122,9 +142,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>

4
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the path where the temporary data will be stored",
"paramLongName": "outputDir",
"paramDescription": "the path where the data will be stored",
"paramRequired": true
},
{

4
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml
View File

@ -6,7 +6,7 @@
<description>the opendoar IDs whitelist (comma separated)</description>
</property>
<property>
<name>workingPath</name>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
@ -87,7 +87,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
</spark>
<ok to="End"/>

18
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

140
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,140 @@
<workflow-app name="reindex_events" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
</property>
<property>
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
</property>
<property>
<name>brokerApiBaseUrl</name>
<description>the url of the broker service api</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="index_event_subset"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="index_event_subset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexEventSubsetOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

6
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "wp",
"paramLongName": "workingPath",
"paramDescription": "the working path",
"paramName": "o",
"paramLongName": "outputDir",
"paramDescription": "the path where generated data are stored",
"paramRequired": true
},
{

7
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -10,10 +10,11 @@ import java.io.Serializable;
import java.nio.file.Paths;
import java.util.*;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil;
@ -100,8 +101,8 @@ public class EntityMergerTest implements Serializable {
assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
// verify authors
assertEquals(pub_merged.getAuthor().size(), 9);
assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
assertEquals(13, pub_merged.getAuthor().size());
assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor()));
// verify title
int count = 0;

3
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
View File

@ -7,7 +7,6 @@ import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
@ -16,8 +15,8 @@ import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;

3
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java
View File

@ -10,7 +10,8 @@ import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf;

12
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import com.fasterxml.jackson.databind.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
@ -19,23 +18,18 @@ case class HostedByItemType(id: String, officialname: String, issn: String, eiss
case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
object DoiBoostMappingUtil {
def getUnknownCountry(): Qualifier = {
createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
}
def generateMAGAffiliationId(affId: String): String = {
s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
}
val logger: Logger = LoggerFactory.getLogger(getClass)
//STATIC STRING
val MAG = "microsoft"
val MAG_NAME = "Microsoft Academic Graph"
val ORCID = "ORCID"
val ORCID = "orcid"
val ORCID_PENDING = "orcid_pending"
val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall"
val GRID_AC = "grid.ac"

29
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala
View File

@ -39,33 +39,38 @@ object SparkGenerateDOIBoostActionSet {
val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath")
val workingDirPath = parser.get("targetPath")
val sequenceFilePath = parser.get("sFilePath")
spark.read.load(dbDatasetPath).as[OafDataset]
val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
.map(d =>DoiBoostMappingUtil.fixResult(d))
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
spark.read.load(dbPublicationPath).as[Publication]
val asPublication =spark.read.load(dbPublicationPath).as[Publication]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbOrganizationPath).as[Organization]
val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(crossRefRelation).as[Relation]
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbaffiliationRelationPath).as[Relation]
val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
// spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])

5
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -2,6 +2,7 @@ package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils
@ -30,7 +31,7 @@ object SparkGenerateDoiBoost {
import spark.implicits._
val hostedByMapPath = parser.get("hostedByMapPath")
val workingDirPath = parser.get("workingDirPath")
val workingDirPath = parser.get("workingPath")
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
@ -132,7 +133,7 @@ object SparkGenerateDoiBoost {
o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
if (affiliation.OfficialPage.isDefined)
o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
o.setCountry(DoiBoostMappingUtil.getUnknownCountry())
o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
o
}
else

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -200,7 +200,7 @@ case object Crossref2Oaf {
a.setSurname(family)
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava)
a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava)
a
}

46
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java
View File

@ -2,18 +2,16 @@
package eu.dnetlib.doiboost.crossref;
import java.io.ByteArrayOutputStream;
import java.util.Optional;
import java.util.zip.Inflater;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@ -30,34 +28,45 @@ public class CrossrefImporter {
parser.parseArgument(args);
final String hdfsuri = parser.get("namenode");
System.out.println("HDFS URI" + hdfsuri);
Path hdfswritepath = new Path(parser.get("targetPath"));
System.out.println("TargetPath: " + hdfsuri);
final String namenode = parser.get("namenode");
System.out.println("namenode: " + namenode);
final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))
? Long.parseLong(parser.get("timestamp"))
: -1;
Path targetPath = new Path(parser.get("targetPath"));
System.out.println("targetPath: " + targetPath);
if (timestamp > 0)
System.out.println("Timestamp added " + timestamp);
final Long timestamp = Optional
.ofNullable(parser.get("timestamp"))
.map(s -> {
try {
return Long.parseLong(s);
} catch (NumberFormatException e) {
return -1L;
}
})
.orElse(-1L);
System.out.println("timestamp: " + timestamp);
final String esServer = parser.get("esServer");
System.out.println("esServer: " + esServer);
final String esIndex = parser.get("esIndex");
System.out.println("esIndex: " + esIndex);
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
conf.set("fs.defaultFS", namenode);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
ESClient client = timestamp > 0
? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp)
: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
// "ip-90-147-167-25.ct1.garrservices.it", "crossref"
final ESClient client = new ESClient(esServer, esIndex, timestamp);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.file(targetPath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
@ -74,8 +83,7 @@ public class CrossrefImporter {
end = System.currentTimeMillis();
final float time = (end - start) / 1000.0F;
System.out
.println(
String.format("Imported %d records last 100000 imported in %f seconds", i, time));
.println(String.format("Imported %s records last 100000 imported in %s seconds", i, time));
start = System.currentTimeMillis();
}
}

63
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java
View File

@ -1,11 +1,11 @@
package eu.dnetlib.doiboost.crossref;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory;
import com.jayway.jsonpath.JsonPath;
public class ESClient implements Iterator<String> {
private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
static final String blobPath = "$.hits[*].hits[*]._source.blob";
static final String scrollIdPath = "$._scroll_id";
static final String JSON_NO_TS = "{\"size\":1000}";
static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
private static final String BLOB_PATH = "$.hits.hits[*]._source.blob";
private static final String SCROLL_ID_PATH = "$._scroll_id";
private static final String JSON_NO_TS = "{\"size\":1000}";
private static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
private static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
public static final String APPLICATION_JSON = "application/json";
public static final String ES_SEARCH_URL = "http://%s:9200/%s/_search?scroll=1m";
public static final String ES_SCROLL_URL = "http://%s:9200/_search/scroll";
private final String scrollId;
@ -31,47 +35,30 @@ public class ESClient implements Iterator<String> {
private final String esHost;
public ESClient(final String esHost, final String esIndex) throws IOException {
public ESClient(final String esHost, final String esIndex, final long timestamp) {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS);
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body);
}
public ESClient(final String esHost, final String esIndex, final long timestamp)
throws IOException {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
String.format(JSON_WITH_TS, timestamp));
scrollId = getJPathString(scrollIdPath, body);
final String body = timestamp > 0
? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp))
: getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS);
scrollId = getJPathString(SCROLL_ID_PATH, body);
buffer = getBlobs(body);
}
private String getResponse(final String url, final String json) {
CloseableHttpClient client = HttpClients.createDefault();
try {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpPost httpPost = new HttpPost(url);
if (json != null) {
StringEntity entity = new StringEntity(json);
httpPost.setEntity(entity);
httpPost.setHeader("Accept", "application/json");
httpPost.setHeader("Content-type", "application/json");
httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON);
httpPost.setHeader(HttpHeaders.CONTENT_TYPE, APPLICATION_JSON);
}
try (CloseableHttpResponse response = client.execute(httpPost)) {
return IOUtils.toString(response.getEntity().getContent());
}
CloseableHttpResponse response = client.execute(httpPost);
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
throw new RuntimeException("Error on executing request ", e);
} finally {
try {
client.close();
} catch (IOException e) {
throw new RuntimeException("Unable to close client ", e);
}
}
}
@ -87,7 +74,7 @@ public class ESClient implements Iterator<String> {
}
private List<String> getBlobs(final String body) {
final List<String> res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
final List<String> res = JsonPath.read(body, BLOB_PATH);
return res;
}
@ -102,11 +89,11 @@ public class ESClient implements Iterator<String> {
if (buffer.isEmpty()) {
final String json_param = String.format(JSON_SCROLL, scrollId);
final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
final String body = getResponse(String.format(ES_SCROLL_URL, esHost), json_param);
try {
buffer = getBlobs(body);
} catch (Throwable e) {
logger.error("Error on get next page: body:" + body);
System.out.println("Error on get next page: body:" + body);
}
}
return nextItem;

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala → dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala
View File

@ -11,7 +11,7 @@ import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkPreProcessMAG {
object SparkProcessMAG {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
View File

@ -1,11 +1,11 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
@ -18,7 +18,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err
case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
val mapper = new ObjectMapper
val mapper = new ObjectMapper()
def isJsonValid(inputStr: String): Boolean = {
import java.io.IOException

16
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java
View File

@ -3,10 +3,8 @@ package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
@ -18,11 +16,9 @@ import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.util.LongAccumulator;
import org.mortbay.log.Log;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -36,7 +32,7 @@ public class SparkDownloadOrcidAuthors {
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
static final String lastUpdate = "2020-09-29 00:00:00";
public static void main(String[] args) throws IOException, Exception {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors {
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath);
logger.info("workingPath: {}", workingPath);
final String outputPath = parser.get("outputPath");
logger.info("outputPath: ", outputPath);
logger.info("outputPath: {}", outputPath);
final String token = parser.get("token");
final String lambdaFileName = parser.get("lambdaFileName");
logger.info("lambdaFileName: ", lambdaFileName);
logger.info("lambdaFileName: {}", lambdaFileName);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors {
}
private static boolean isModified(String orcidId, String modifiedDate) {
Date modifiedDateDt = null;
Date lastUpdateDt = null;
Date modifiedDateDt;
Date lastUpdateDt;
try {
if (modifiedDate.length() != 19) {
modifiedDate = modifiedDate.substring(0, 19);

3
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json
View File

@ -5,5 +5,6 @@
{"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
{"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}
{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true},
{"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true}
]

2
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json
View File

@ -3,5 +3,5 @@
{"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true}
{"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true}
]

8
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json
View File

@ -1,5 +1,7 @@
[
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false}
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false},
{"paramName":"ess", "paramLongName":"esServer", "paramDescription": "elasticsearch server url", "paramRequired": true},
{"paramName":"esi", "paramLongName":"esIndex", "paramDescription": "elasticsearch index name", "paramRequired": true}
]

42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,42 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

335
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,335 @@
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorIntersectionMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<!-- Itersection Parameters -->
<property>
<name>workingPath</name>
<description>the working Path</description>
</property>
<property>
<name>hostedByMapPath</name>
<description>the hostedByMap Path</description>
</property>
<property>
<name>outputPath</name>
<description>the Path of the sequence file action set</description>
</property>
<!-- Crossref Parameters -->
<property>
<name>inputPathCrossref</name>
<description>the Crossref input path</description>
</property>
<property>
<name>crossrefTimestamp</name>
<description>Timestamp for the Crossref incremental Harvesting</description>
</property>
<property>
<name>esServer</name>
<description>elasticsearch server url for the Crossref Harvesting</description>
</property>
<property>
<name>esIndex</name>
<description>elasticsearch index name for the Crossref Harvesting</description>
</property>
<!-- MAG Parameters -->
<property>
<name>inputPathMAG</name>
<description>the MAG working path</description>
</property>
<!-- UnpayWall Parameters -->
<property>
<name>inputPathUnpayWall</name>
<description>the UnpayWall working path</description>
</property>
<!-- ORCID Parameters -->
<property>
<name>inputPathOrcid</name>
<description>the ORCID working path</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
<default to="ImportCrossRef"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportCrossRef">
<java>
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
<arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--esServer</arg><arg>${esServer}</arg>
<arg>--esIndex</arg><arg>${esIndex}</arg>
<arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>
</java>
<ok to="GenerateCrossrefDataset"/>
<error to="Kill"/>
</action>
<!-- CROSSREF SECTION -->
<action name="GenerateCrossrefDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateCrossrefDataset</name>
<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${inputPathCrossref}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="RenameDataset"/>
<error to="Kill"/>
</action>
<action name="RenameDataset">
<fs>
<delete path="${inputPathCrossref}/crossref_ds"/>
<move source="${inputPathCrossref}/crossref_ds_updated"
target="${inputPathCrossref}/crossref_ds"/>
</fs>
<ok to="ConvertCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ConvertCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ResetMagWorkingPath"/>
<error to="Kill"/>
</action>
<!-- MAG SECTION -->
<action name="ResetMagWorkingPath">
<fs>
<delete path="${inputPathMAG}/dataset"/>
<delete path="${inputPathMAG}/process"/>
<delete path="${inputPathMAG}/dataset"/>
</fs>
<ok to="ConvertMagToDataset"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathMAG}/input</arg>
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessMAG"/>
<error to="Kill"/>
</action>
<action name="ProcessMAG">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to OAF Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessUW"/>
<error to="Kill"/>
</action>
<!-- UnpayWall SECTION -->
<action name="ProcessUW">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert UnpayWall to Dataset</name>
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessORCID"/>
<error to="Kill"/>
</action>
<!-- ORCID SECTION -->
<action name="ProcessORCID">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="CreateDOIBoost"/>
<error to="Kill"/>
</action>
<!-- INTERSECTION SECTION-->
<action name="CreateDOIBoost">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create DOIBoost Infospace</name>
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorIntersectionMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--affiliationPath</arg><arg>${inputPathMAG}/process/Affiliations</arg>
<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/process/PaperAuthorAffiliations</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="GenerateActionSet"/>
<error to="Kill"/>
</action>
<action name="GenerateActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Generate DOIBoost ActionSet</name>
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
<arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
<arg>--sFilePath</arg><arg>${outputPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

2
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala
View File

@ -1,9 +1,9 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.codehaus.jackson.map.ObjectMapper
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java
View File

@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 {
+ " LATERAL VIEW EXPLODE (author) a AS MyT "
+ " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP "
+ " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or "
+ " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
+ " lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
+ " GROUP BY id) r_t "
+ " JOIN ("
+ " SELECT source, target "

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java
View File

@ -108,7 +108,7 @@ public class SparkResultToCommunityFromOrganizationJob {
.stream()
.map(con -> con.getId())
.collect(Collectors.toList());
Result res = new Result();
R res = (R) ret.getClass().newInstance();
res.setId(ret.getId());
List<Context> propagatedContexts = new ArrayList<>();
for (String cId : communitySet) {

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java
View File

@ -130,7 +130,7 @@ public class SparkResultToCommunityThroughSemRelJob {
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
Result r = new Result();
R r = (R) ret.getClass().newInstance();
r.setId(ret.getId());
r.setContext(contextList);
ret.mergeFrom(r);

3
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
View File

@ -24,7 +24,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.Dataset;
public class ResultToCommunityJobTest {
@ -66,7 +65,7 @@ public class ResultToCommunityJobTest {
}
@Test
public void test1() throws Exception {
public void testSparkResultToCommunityThroughSemRelJob() throws Exception {
SparkResultToCommunityThroughSemRelJob
.main(
new String[] {

87
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java
View File

@ -15,8 +15,11 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class CleaningFunctions {
public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/";
public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
public static final String DOI_PREFIX_REGEX = "^10\\.";
public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
public static final int ORCID_LEN = 19;
public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
public static final Set<String> PID_BLACKLIST = new HashSet<>();
@ -56,13 +59,19 @@ public class CleaningFunctions {
}
}
if (Objects.nonNull(r.getAuthor())) {
r.getAuthor().forEach(a -> {
if (Objects.nonNull(a.getPid())) {
a.getPid().forEach(p -> {
fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES);
});
}
});
r
.getAuthor()
.stream()
.filter(Objects::nonNull)
.forEach(a -> {
if (Objects.nonNull(a.getPid())) {
a
.getPid()
.stream()
.filter(Objects::nonNull)
.forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES));
}
});
}
if (value instanceof Publication) {
@ -86,7 +95,7 @@ public class CleaningFunctions {
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
}
} else if (value instanceof Relation) {
// nothing to clean here
@ -101,6 +110,16 @@ public class CleaningFunctions {
.setLanguage(
qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
}
if (Objects.nonNull(r.getCountry())) {
r
.setCountry(
r
.getCountry()
.stream()
.filter(Objects::nonNull)
.filter(c -> StringUtils.isNotBlank(c.getClassid()))
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getSubject())) {
r
.setSubject(
@ -153,12 +172,14 @@ public class CleaningFunctions {
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r
.setResourcetype(
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
}
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
i
.setAccessright(
qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
}
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
@ -173,12 +194,22 @@ public class CleaningFunctions {
if (Objects.isNull(bestaccessrights)) {
r
.setBestaccessright(
qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
} else {
r.setBestaccessright(bestaccessrights);
}
}
if (Objects.nonNull(r.getAuthor())) {
r
.setAuthor(
r
.getAuthor()
.stream()
.filter(a -> Objects.nonNull(a))
.filter(a -> StringUtils.isNotBlank(a.getFullname()))
.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
.collect(Collectors.toList()));
boolean nullRank = r
.getAuthor()
.stream()
@ -199,6 +230,7 @@ public class CleaningFunctions {
a
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(p -> Objects.nonNull(p.getQualifier()))
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.map(p -> {
@ -211,14 +243,31 @@ public class CleaningFunctions {
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
p.getQualifier().setClassid(ModelConstants.ORCID);
} else {
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
if (p
.getQualifier()
.getClassid()
.toLowerCase()
.contains(ModelConstants.ORCID)) {
if (pidProvenance
.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
p.getQualifier().setClassid(ModelConstants.ORCID);
} else {
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
}
final String orcid = p
.getValue()
.trim()
.toLowerCase()
.replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4");
if (orcid.length() == ORCID_LEN) {
p.setValue(orcid);
} else {
p.setValue("");
}
}
p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
return p;
})
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect(
Collectors
.toMap(
@ -286,7 +335,7 @@ public class CleaningFunctions {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, ""));
pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10."));
break;
}
return pid;

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java
View File

@ -21,6 +21,7 @@ import org.apache.spark.sql.expressions.Aggregator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.jayway.jsonpath.Configuration;
import com.jayway.jsonpath.DocumentContext;
@ -44,7 +45,8 @@ public class GroupEntitiesAndRelationsSparkJob {
private final static String SOURCE_JPATH = "$.source";
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public static void main(String[] args) throws Exception {

39
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -75,6 +75,8 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier MAG_PID_TYPE = qualifier(
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999";
protected static final Map<String, String> nsContext = new HashMap<>();
static {
@ -244,25 +246,54 @@ public abstract class AbstractMdRecordToOafMapper {
final String originalId = ((Node) o).getText();
final String validationdDate = ((Node) o).valueOf("@validationDate");
if (StringUtils.isNotBlank(originalId)) {
final String projectId = createOpenaireId(40, originalId, true);
res
.add(
getRelation(
getRelationWithValidationDate(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
lastUpdateTimestamp));
lastUpdateTimestamp, validationdDate));
res
.add(
getRelation(
getRelationWithValidationDate(
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
lastUpdateTimestamp));
lastUpdateTimestamp, validationdDate));
}
}
return res;
}
protected Relation getRelationWithValidationDate(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp,
final String validationDate) {
final Relation r = getRelation(
source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp);
r.setValidated(StringUtils.isNotBlank(validationDate));
r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
if (StringUtils.isNotBlank(validationDate)) {
r.setValidated(true);
r.setValidationDate(validationDate);
r.getDataInfo().setTrust(DEFAULT_TRUST_FOR_VALIDATED_RELS);
} else {
r.setValidated(false);
r.setValidationDate(null);
}
return r;
}
protected Relation getRelation(final String source,
final String target,
final String relType,

58
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.io.Closeable;
import java.io.IOException;
@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
return Arrays.asList(r);
} else {
final String validationDate = rs.getString("curation_date");
final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false);
final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
final Relation r1 = new Relation();
final Relation r2 = new Relation();
if (rs.getString(SOURCE_TYPE).equals("project")) {
r1.setCollectedfrom(collectedFrom);
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
r2.setCollectedfrom(collectedFrom);
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
} else {
r1.setCollectedfrom(collectedFrom);
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
r2.setCollectedfrom(collectedFrom);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
}
r1.setValidated(true);
r1.setValidationDate(validationDate);
r1.setCollectedfrom(collectedFrom);
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setValidationDate(validationDate);
r2.setValidated(true);
r2.setCollectedfrom(collectedFrom);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
if (rs.getString(SOURCE_TYPE).equals("project")) {
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
} else {
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
}
return Arrays.asList(r1, r2);
}

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

@ -51,31 +51,34 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Node n = (Node) o;
final Author author = new Author();
final String fullname = n.valueOf("./datacite:creatorName");
author.setFullname(fullname);
final PacePerson pp = new PacePerson(fullname, false);
final String name = n.valueOf("./datacite:givenName");
if (StringUtils.isBlank(name) & pp.isAccurate()) {
author.setName(pp.getNormalisedFirstName());
} else {
author.setName(name);
}
final String surname = n.valueOf("./datacite:familyName");
if (StringUtils.isBlank(surname) & pp.isAccurate()) {
author.setSurname(pp.getNormalisedSurname());
} else {
author.setSurname(surname);
}
if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) {
author.setFullname(fullname);
if (StringUtils.isBlank(author.getFullname())) {
author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
}
final PacePerson pp = new PacePerson(fullname, false);
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
author.setPid(preparePids(n, info));
author.setRank(pos++);
res.add(author);
if (StringUtils.isBlank(name) & pp.isAccurate()) {
author.setName(pp.getNormalisedFirstName());
} else {
author.setName(name);
}
if (StringUtils.isBlank(surname) & pp.isAccurate()) {
author.setSurname(pp.getNormalisedSurname());
} else {
author.setSurname(surname);
}
if (StringUtils.isBlank(author.getFullname())) {
author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
}
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
author.setPid(preparePids(n, info));
author.setRank(pos++);
res.add(author);
}
}
return res;
}

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java
View File

@ -11,7 +11,8 @@ import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql
View File

@ -1 +1 @@
SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;
SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE;

35
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -141,7 +141,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertTrue(r1.getValidated());
assertTrue(r2.getValidated());
assertEquals(r1.getValidationDate(), "2020-01-01");
assertEquals(r2.getValidationDate(), "2020-01-01");
// System.out.println(new ObjectMapper().writeValueAsString(p));
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
@ -246,6 +249,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertTrue(r1.getValidated());
assertTrue(r2.getValidated());
assertEquals(r1.getValidationDate(), "2020-01-01");
assertEquals(r2.getValidationDate(), "2020-01-01");
}
@Test
@ -355,7 +362,31 @@ public class MappersTest {
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
System.out.println(p.getTitle().get(0).getValue());
assertEquals(1, p.getAuthor().size());
assertEquals("OPEN", p.getBestaccessright().getClassid());
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue()));
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid()));
assertEquals("dataset", p.getResulttype().getClassname());
assertEquals(1, p.getInstance().size());
assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid());
assertValidId(p.getInstance().get(0).getCollectedfrom().getKey());
assertValidId(p.getInstance().get(0).getHostedby().getKey());
assertEquals(
"http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue());
assertEquals(1, p.getInstance().get(0).getUrl().size());
// System.out.println(p.getInstance().get(0).getUrl().get(0));
// System.out.println(p.getInstance().get(0).getHostedby().getValue());
System.out.println(p.getPid().get(0).getValue());
}
@Test
void testTextGridNoAuthor() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("textgrid-noauthor.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
}
@Test

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -35,7 +35,7 @@ public class MigrateDbEntitiesApplicationTest {
private MigrateDbEntitiesApplication app;
@Mock
@Mock(lenient = true)
private ResultSet rs;
@Mock

2
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml
View File

@ -51,7 +51,7 @@
<!--<dr:CobjCategory type="publication">0001</dr:CobjCategory>-->
<dr:CobjCategory>0001</dr:CobjCategory>
<oaf:dateAccepted>2017-01-01</oaf:dateAccepted>
<oaf:projectid>corda_______::226852</oaf:projectid>
<oaf:projectid validationDate="2020-01-01">corda_______::226852</oaf:projectid>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:hostedBy id="openaire____::issn226852" name="One Ecosystem"/>
<oaf:collectedFrom

2
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml
View File

@ -89,7 +89,7 @@
<oaf:language>und</oaf:language>
<oaf:concept id="https://zenodo.org/communities/epfl"/>
<oaf:hostedBy id="re3data_____::r3d100010468" name="Zenodo"/>
<oaf:projectid>corda_______::226852</oaf:projectid>
<oaf:projectid validationDate="2020-01-01">corda_______::226852</oaf:projectid>
<oaf:collectedFrom id="re3data_____::r3d100010468" name="Zenodo"/>
<oaf:refereed>0001</oaf:refereed>s
</metadata>

117
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml Normal file
View File

@ -0,0 +1,117 @@
<?xml version="1.0" encoding="UTF-8"?>
<record xmlns:datacite="http://datacite.org/schema/kernel-3"
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
<oai:header xmlns="http://namespace.openaire.eu/"
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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dri:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
<dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
<dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
<oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
<dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
</oai:header>
<metadata>
<datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-EE73-2</datacite:identifier>
<datacite:creators>
<datacite:creator>
<datacite:creatorName></datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id="></datacite:nameIdentifier>
</datacite:creator>
</datacite:creators>
<datacite:titles>
<datacite:title titleType="Other">Auf dem Trocknen</datacite:title>
<datacite:title titleType="Other">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
</datacite:titles>
<datacite:publisher>TextGrid</datacite:publisher>
<datacite:publicationYear>2012</datacite:publicationYear>
<datacite:contributors>
<datacite:contributor contributorType="DataManager">
<datacite:contributorName>tvitt@textgrid.de</datacite:contributorName>
</datacite:contributor>
<datacite:contributor contributorType="Other">
<datacite:contributorName>Digitale Bibliothek</datacite:contributorName>
<datacite:nameIdentifier nameIdentifierScheme="textgrid" schemeURI="http://www.textgridlab.org/schema/textgrid-metadata_2010.xsd">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
</datacite:contributor>
</datacite:contributors>
<datacite:dates>
<datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
</datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset"/>
<alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3">
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
</alternateIdentifiers>
<datacite:relatedIdentifiers>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-EE72-4</datacite:relatedIdentifier>
</datacite:relatedIdentifiers>
<datacite:sizes>
<datacite:size>527 Bytes</datacite:size>
</datacite:sizes>
<datacite:formats>
<datacite:format>text/tg.edition+tg.aggregation+xml</datacite:format>
</datacite:formats>
<datacite:version>0</datacite:version>
<datacite:rightsList>
<datacite:rights rightsURI="http://creativecommons.org/licenses/by/3.0/de/legalcode"> Der annotierte Datenbestand der Digitalen Bibliothek inklusive
Metadaten sowie davon einzeln zugängliche Teile sind eine Abwandlung
des Datenbestandes von www.editura.de durch TextGrid und werden
unter der Lizenz Creative Commons Namensnennung 3.0 Deutschland
Lizenz (by-Nennung TextGrid) veröffentlicht. Die Lizenz bezieht sich
nicht auf die der Annotation zu Grunde liegenden allgemeinfreien
Texte (Siehe auch Punkt 2 der Lizenzbestimmungen).</datacite:rights>
<datacite:rights rightsURI="info:eu-repo/semantics/openAccess"/>
</datacite:rightsList>
<datacite:descriptions>
<datacite:description descriptionType="Abstract"/>
</datacite:descriptions>
<datacite:geoLocations>
<datacite:geoLocation>
<datacite:geoLocationPlace
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin</datacite:geoLocationPlace>
</datacite:geoLocation>
</datacite:geoLocations>
</datacite:resource>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-EE73-2</oaf:identifier>
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:refereed>0002</oaf:refereed>
<oaf:dateAccepted>2012-01-29</oaf:dateAccepted>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
<oaf:language>und</oaf:language>
<oaf:country>DE</oaf:country>
<oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
<oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
</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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<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">
<originDescription altered="true" harvestDate="2020-12-16T10:04:03.148Z">
<baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
<identifier>textgrid:rn8z.0</identifier>
<datestamp>2012-01-29T20:54:12Z</datestamp>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>

58
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml
View File

@ -6,29 +6,29 @@
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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dri:objIdentifier>r3f52792889d::000051aa1f61d77d2c0b340091f8024e</dri:objIdentifier>
<dri:recordIdentifier>textgrid:q9cv.0</dri:recordIdentifier>
<dri:dateOfCollection>2020-11-17T09:34:11.128+01:00</dri:dateOfCollection>
<dri:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
<dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
<dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
<oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-21T13:35:20Z</datestamp>
<dr:dateOfTransformation>2020-11-17T19:08:56.703+01:00</dr:dateOfTransformation>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
<dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
</oai:header>
<metadata>
<datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-7664-F</datacite:identifier>
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-EE73-2</datacite:identifier>
<datacite:creators>
<datacite:creator>
<datacite:creatorName>Hoffmann von Fallersleben, August Heinrich</datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://de.dariah.eu/pnd-service">118552589</datacite:nameIdentifier>
<datacite:creatorName>Liliencron, Detlev von</datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id=">118572954</datacite:nameIdentifier>
</datacite:creator>
</datacite:creators>
<datacite:titles>
<datacite:title titleType="Other">Mailied</datacite:title>
<datacite:title titleType="Other">August Heinrich Hoffmann von Fallersleben: Unpolitische Lieder von Hoffmann von Fallersleben, 1. + 2. Theil, 1. Theil, Hamburg: Hoffmann und Campe, 1841.</datacite:title>
<datacite:title titleType="Other">Auf dem Trocknen</datacite:title>
<datacite:title titleType="Other">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
</datacite:titles>
<datacite:publisher>TextGrid</datacite:publisher>
<datacite:publicationYear>2012</datacite:publicationYear>
@ -38,21 +38,21 @@
</datacite:contributor>
<datacite:contributor contributorType="Other">
<datacite:contributorName>Digitale Bibliothek</datacite:contributorName>
<datacite:nameIdentifier nameIdentifierScheme="textgrid">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
<datacite:nameIdentifier nameIdentifierScheme="textgrid" schemeURI="http://www.textgridlab.org/schema/textgrid-metadata_2010.xsd">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
</datacite:contributor>
</datacite:contributors>
<datacite:dates>
<datacite:date dateType="Created">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Issued">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Updated">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
</datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset"/>
<alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3">
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F</alternateIdentifier>
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
</alternateIdentifiers>
<datacite:relatedIdentifiers>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-7666-B</datacite:relatedIdentifier>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-EE72-4</datacite:relatedIdentifier>
</datacite:relatedIdentifiers>
<datacite:sizes>
<datacite:size>527 Bytes</datacite:size>
@ -77,17 +77,18 @@
<datacite:geoLocations>
<datacite:geoLocation>
<datacite:geoLocationPlace
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Hamburg</datacite:geoLocationPlace>
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin</datacite:geoLocationPlace>
</datacite:geoLocation>
</datacite:geoLocations>
</datacite:resource>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-7664-F</oaf:identifier>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-EE73-2</oaf:identifier>
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:refereed>0002</oaf:refereed>
<oaf:dateAccepted>2012-01-21</oaf:dateAccepted>
<oaf:dateAccepted>2012-01-29</oaf:dateAccepted>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
<oaf:language>und</oaf:language>
<oaf:country>DE</oaf:country>
<oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
<oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
</metadata>
@ -95,11 +96,11 @@
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<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">
<originDescription altered="true" harvestDate="2020-11-17T09:34:11.128+01:00">
<originDescription altered="true" harvestDate="2020-12-16T10:04:03.148Z">
<baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
<identifier>textgrid:q9cv.0</identifier>
<datestamp>2012-01-21T13:35:20Z</datestamp>
<metadataNamespace>http://schema.datacite.org/oai/oai-1.0/</metadataNamespace>
<identifier>textgrid:rn8z.0</identifier>
<datestamp>2012-01-29T20:54:12Z</datestamp>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
@ -107,9 +108,10 @@
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk"
classname="sysimport:crosswalk"
<oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>
</record>

6
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
View File

@ -1,15 +1,15 @@
package eu.dnetlib.dhp.export
import com.fasterxml.jackson.databind.ObjectMapper
import java.time.LocalDateTime
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._
import scala.collection.JavaConverters._

17
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala
View File

@ -1,27 +1,21 @@
package eu.dnetlib.dhp.`export`
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions._
import org.apache.spark.sql.expressions.Window
import org.apache.spark.{SparkConf, SparkContext}
import org.codehaus.jackson.map.ObjectMapper
import org.apache.spark.SparkConf
import scala.collection.mutable.ArrayBuffer
import scala.collection.JavaConverters._
object SparkExportContentForOpenAire {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json")))
@ -178,11 +172,4 @@ object SparkExportContentForOpenAire {
fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

3
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java
View File

@ -10,7 +10,8 @@ import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;

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