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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
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import com.google.common.collect.Maps;
import java.util.Map; import java.util.Map;
import com.google.common.collect.Maps;
public class Constants { public class Constants {
public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap(); 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; 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.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; 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.Journal;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; 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 class GraphResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map( public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) { E in) {
CommunityResult out = new CommunityResult(); CommunityResult out = new CommunityResult();
eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; 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()); Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
if (ort.isPresent()) { if (ort.isPresent()) {
switch (ort.get().getClassid()) { switch (ort.get().getClassid()) {
case "publication": case "publication":
Optional<Journal> journal = Optional Optional<Journal> journal = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
if (journal.isPresent()) { if (journal.isPresent()) {
Journal j = journal.get(); Journal j = journal.get();
Container c = new Container(); Container c = new Container();
c.setConferencedate(j.getConferencedate()); c.setConferencedate(j.getConferencedate());
c.setConferenceplace(j.getConferenceplace()); c.setConferenceplace(j.getConferenceplace());
c.setEdition(j.getEdition()); c.setEdition(j.getEdition());
c.setEp(j.getEp()); c.setEp(j.getEp());
c.setIss(j.getIss()); c.setIss(j.getIss());
c.setIssnLinking(j.getIssnLinking()); c.setIssnLinking(j.getIssnLinking());
c.setIssnOnline(j.getIssnOnline()); c.setIssnOnline(j.getIssnOnline());
c.setIssnPrinted(j.getIssnPrinted()); c.setIssnPrinted(j.getIssnPrinted());
c.setName(j.getName()); c.setName(j.getName());
c.setSp(j.getSp()); c.setSp(j.getSp());
c.setVol(j.getVol()); c.setVol(j.getVol());
out.setContainer(c); out.setContainer(c);
out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
} }
break; break;
case "dataset": case "dataset":
eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; 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.getSize()).ifPresent(v -> out.setSize(v.getValue()));
Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
out out
.setGeolocation( .setGeolocation(
Optional Optional
.ofNullable(id.getGeolocation()) .ofNullable(id.getGeolocation())
.map( .map(
igl -> igl igl -> igl
.stream() .stream()
.filter(Objects::nonNull) .filter(Objects::nonNull)
.map(gli -> { .map(gli -> {
GeoLocation gl = new GeoLocation(); GeoLocation gl = new GeoLocation();
gl.setBox(gli.getBox()); gl.setBox(gli.getBox());
gl.setPlace(gli.getPlace()); gl.setPlace(gli.getPlace());
gl.setPoint(gli.getPoint()); gl.setPoint(gli.getPoint());
return gl; return gl;
}) })
.collect(Collectors.toList())) .collect(Collectors.toList()))
.orElse(null)); .orElse(null));
out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
break; break;
case "software": case "software":
eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
Optional Optional
.ofNullable(is.getCodeRepositoryUrl()) .ofNullable(is.getCodeRepositoryUrl())
.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
Optional Optional
.ofNullable(is.getDocumentationUrl()) .ofNullable(is.getDocumentationUrl())
.ifPresent( .ifPresent(
value -> out value -> out
.setDocumentationUrl( .setDocumentationUrl(
value value
.stream() .stream()
.map(v -> v.getValue()) .map(v -> v.getValue())
.collect(Collectors.toList()))); .collect(Collectors.toList())));
Optional Optional
.ofNullable(is.getProgrammingLanguage()) .ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); .ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break; break;
case "other": case "other":
eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
out out
.setContactgroup( .setContactgroup(
Optional Optional
.ofNullable(ir.getContactgroup()) .ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
.orElse(null)); .orElse(null));
out out
.setContactperson( .setContactperson(
Optional Optional
.ofNullable(ir.getContactperson()) .ofNullable(ir.getContactperson())
.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
.orElse(null)); .orElse(null));
out out
.setTool( .setTool(
Optional Optional
.ofNullable(ir.getTool()) .ofNullable(ir.getTool())
.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
.orElse(null)); .orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break; break;
} }
Optional Optional
.ofNullable(input.getAuthor()) .ofNullable(input.getAuthor())
.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); .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()); Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
if (oar.isPresent()) { if (oar.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
out out
.setBestaccessright( .setBestaccessright(
AccessRight AccessRight
.newInstance( .newInstance(
code, code,
Constants.coarCodeLabelMap.get(code), Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA)); Constants.COAR_ACCESS_RIGHT_SCHEMA));
} }
} }
final List<String> contributorList = new ArrayList<>(); final List<String> contributorList = new ArrayList<>();
Optional Optional
.ofNullable(input.getContributor()) .ofNullable(input.getContributor())
.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
out.setContributor(contributorList); out.setContributor(contributorList);
Optional Optional
.ofNullable(input.getCountry()) .ofNullable(input.getCountry())
.ifPresent( .ifPresent(
value -> out value -> out
.setCountry( .setCountry(
value value
.stream() .stream()
.map( .map(
c -> { c -> {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) { if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null; return null;
} }
Country country = new Country(); Country country = new Country();
country.setCode(c.getClassid()); country.setCode(c.getClassid());
country.setLabel(c.getClassname()); country.setLabel(c.getClassname());
Optional Optional
.ofNullable(c.getDataInfo()) .ofNullable(c.getDataInfo())
.ifPresent( .ifPresent(
provenance -> country provenance -> country
.setProvenance( .setProvenance(
Provenance Provenance
.newInstance( .newInstance(
provenance provenance
.getProvenanceaction() .getProvenanceaction()
.getClassname(), .getClassname(),
c.getDataInfo().getTrust()))); c.getDataInfo().getTrust())));
return country; return country;
}) })
.filter(Objects::nonNull) .filter(Objects::nonNull)
.collect(Collectors.toList()))); .collect(Collectors.toList())));
final List<String> coverageList = new ArrayList<>(); final List<String> coverageList = new ArrayList<>();
Optional Optional
.ofNullable(input.getCoverage()) .ofNullable(input.getCoverage())
.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
out.setCoverage(coverageList); out.setCoverage(coverageList);
out.setDateofcollection(input.getDateofcollection()); out.setDateofcollection(input.getDateofcollection());
final List<String> descriptionList = new ArrayList<>(); final List<String> descriptionList = new ArrayList<>();
Optional Optional
.ofNullable(input.getDescription()) .ofNullable(input.getDescription())
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
out.setDescription(descriptionList); out.setDescription(descriptionList);
Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate()); Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
if (oStr.isPresent()) { if (oStr.isPresent()) {
out.setEmbargoenddate(oStr.get().getValue()); out.setEmbargoenddate(oStr.get().getValue());
} }
final List<String> formatList = new ArrayList<>(); final List<String> formatList = new ArrayList<>();
Optional Optional
.ofNullable(input.getFormat()) .ofNullable(input.getFormat())
.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
out.setFormat(formatList); out.setFormat(formatList);
out.setId(input.getId()); out.setId(input.getId());
out.setOriginalId(input.getOriginalId()); out.setOriginalId(input.getOriginalId());
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance()); .ofNullable(input.getInstance());
if (oInst.isPresent()) { if (oInst.isPresent()) {
out out
.setInstance( .setInstance(
oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
} }
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage()); Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) { if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
} }
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp()); Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) { if (oLong.isPresent()) {
out.setLastupdatetimestamp(oLong.get()); out.setLastupdatetimestamp(oLong.get());
} }
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle()); Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
if (otitle.isPresent()) { if (otitle.isPresent()) {
List<StructuredProperty> iTitle = otitle List<StructuredProperty> iTitle = otitle
.get() .get()
.stream() .stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList()); .collect(Collectors.toList());
if (iTitle.size() > 0) { if (iTitle.size() > 0) {
out.setMaintitle(iTitle.get(0).getValue()); out.setMaintitle(iTitle.get(0).getValue());
} }
iTitle = otitle iTitle = otitle
.get() .get()
.stream() .stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList()); .collect(Collectors.toList());
if (iTitle.size() > 0) { if (iTitle.size() > 0) {
out.setSubtitle(iTitle.get(0).getValue()); out.setSubtitle(iTitle.get(0).getValue());
} }
} }
List<ControlledField> pids = new ArrayList<>(); List<ControlledField> pids = new ArrayList<>();
Optional Optional
.ofNullable(input.getPid()) .ofNullable(input.getPid())
.ifPresent( .ifPresent(
value -> value value -> value
.stream() .stream()
.forEach( .forEach(
p -> pids p -> pids
.add( .add(
ControlledField ControlledField
.newInstance(p.getQualifier().getClassid(), p.getValue())))); .newInstance(p.getQualifier().getClassid(), p.getValue()))));
out.setPid(pids); out.setPid(pids);
oStr = Optional.ofNullable(input.getDateofacceptance()); oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) { if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue()); out.setPublicationdate(oStr.get().getValue());
} }
oStr = Optional.ofNullable(input.getPublisher()); oStr = Optional.ofNullable(input.getPublisher());
if (oStr.isPresent()) { if (oStr.isPresent()) {
out.setPublisher(oStr.get().getValue()); out.setPublisher(oStr.get().getValue());
} }
List<String> sourceList = new ArrayList<>(); List<String> sourceList = new ArrayList<>();
Optional Optional
.ofNullable(input.getSource()) .ofNullable(input.getSource())
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
List<Subject> subjectList = new ArrayList<>(); List<Subject> subjectList = new ArrayList<>();
Optional Optional
.ofNullable(input.getSubject()) .ofNullable(input.getSubject())
.ifPresent( .ifPresent(
value -> value value -> value
.forEach(s -> subjectList.add(getSubject(s)))); .forEach(s -> subjectList.add(getSubject(s))));
out.setSubjects(subjectList); out.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid()); out.setType(input.getResulttype().getClassid());
} }
out out
.setCollectedfrom( .setCollectedfrom(
input input
.getCollectedfrom() .getCollectedfrom()
.stream() .stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList())); .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) { instance
CommunityInstance instance = new CommunityInstance(); .setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
setCommonValue(i, instance); instance
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
instance return instance;
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
instance }
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
return instance; private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
.ofNullable(i.getAccessright());
if (opAr.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
instance
.setAccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
} Optional
.ofNullable(i.getLicense())
.ifPresent(value -> instance.setLicense(value.getValue()));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
Optional
.ofNullable(i.getRefereed())
.ifPresent(value -> instance.setRefereed(value.getClassname()));
Optional
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
private static <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 private static Subject getSubject(StructuredProperty s) {
.ofNullable(i.getLicense()) Subject subject = new Subject();
.ifPresent(value -> instance.setLicense(value.getValue())); subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
.ofNullable(i.getDateofacceptance()) if (di.isPresent()) {
.ifPresent(value -> instance.setPublicationdate(value.getValue())); Provenance p = new Provenance();
Optional p.setProvenance(di.get().getProvenanceaction().getClassname());
.ofNullable(i.getRefereed()) p.setTrust(di.get().getTrust());
.ifPresent(value -> instance.setRefereed(value.getClassname())); subject.setProvenance(p);
Optional }
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
} 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) { Optional<List<StructuredProperty>> oPids = Optional
Subject subject = new Subject(); .ofNullable(oa.getPid());
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); if (oPids.isPresent()) {
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo()); Pid pid = getOrcid(oPids.get());
if (di.isPresent()) { if (pid != null) {
Provenance p = new Provenance(); a.setPid(pid);
p.setProvenance(di.get().getProvenanceaction().getClassname()); }
p.setTrust(di.get().getTrust()); }
subject.setProvenance(p);
}
return subject; return a;
} }
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { private static Pid getOrcid(List<StructuredProperty> p) {
Author a = new Author(); for (StructuredProperty pid : p) {
a.setFullname(oa.getFullname()); if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
a.setName(oa.getName()); Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
a.setSurname(oa.getSurname()); if (di.isPresent()) {
a.setRank(oa.getRank()); 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; }
} }
return null;
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;
}
} }

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

100
dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java Normal file
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@ -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
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@ -105,6 +105,8 @@ public class ModelConstants {
public static final KeyValue UNKNOWN_REPOSITORY = keyValue( public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository"); "10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
private static Qualifier qualifier( private static Qualifier qualifier(
final String classid, final String classid,
final String classname, 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; return;
} }
setCollectedfrom( setCollectedfrom(
Stream Stream
.concat( .concat(
Optional Optional
.ofNullable(getCollectedfrom()) .ofNullable(getCollectedfrom())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty()), .orElse(Stream.empty()),
Optional Optional
.ofNullable(o.getCollectedfrom()) .ofNullable(o.getCollectedfrom())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty())) .orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals .distinct() // relies on KeyValue.equals
.collect(Collectors.toList())); .collect(Collectors.toList()));
mergeOAFDataInfo(o);
setLastupdatetimestamp( setLastupdatetimestamp(
Math.max( Math
.max(
Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), Optional.ofNullable(getLastupdatetimestamp()).orElse(0L),
Optional.ofNullable(o.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() ? p.getFundedamount()
: fundedamount; : fundedamount;
// programme = mergeLists(programme, p.getProgramme());
h2020classification = mergeLists(h2020classification, p.getH2020classification()); h2020classification = mergeLists(h2020classification, p.getH2020classification());
mergeOAFDataInfo(e); 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; Result r = (Result) e;
// TODO consider merging also Measures measures = mergeLists(measures, r.getMeasures());
instance = mergeLists(instance, r.getInstance()); instance = mergeLists(instance, r.getInstance());
@ -323,13 +323,13 @@ public class Result extends OafEntity implements Serializable {
if (a.size() == b.size()) { if (a.size() == b.size()) {
int msa = a int msa = a
.stream() .stream()
.filter(i -> i.getValue() != null) .filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length()) .map(i -> i.getValue().length())
.max(Comparator.naturalOrder()) .max(Comparator.naturalOrder())
.orElse(0); .orElse(0);
int msb = b int msb = b
.stream() .stream()
.filter(i -> i.getValue() != null) .filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length()) .map(i -> i.getValue().length())
.max(Comparator.naturalOrder()) .max(Comparator.naturalOrder())
.orElse(0); .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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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 IOUtils
.toString( .toString(
CheckDuplictedIdsJob.class CheckDuplictedIdsJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json")));
parser.parseArgument(args); parser.parseArgument(args);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String countPath = parser.get("workingPath") + "/counts"; final String countPath = parser.get("outputDir") + "/counts";
log.info("countPath: {}", countPath); log.info("countPath: {}", countPath);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); 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())) .map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(countPath); .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); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String eventsPath = workingPath + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist"); final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
@ -59,6 +59,9 @@ public class GenerateEventsJob {
final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist"); final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ",")); 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(); final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> { runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@ -70,12 +73,12 @@ public class GenerateEventsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_events"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_events");
final Dataset<ResultGroup> groups = ClusterUtils final Dataset<ResultGroup> groups = ClusterUtils
.readPath(spark, workingPath + "/duplicates", ResultGroup.class); .readPath(spark, workingDir + "/duplicates", ResultGroup.class);
final Dataset<Event> dataset = groups final Dataset<Event> dataset = groups
.map( .map(
g -> EventFinder g -> EventFinder
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators),
Encoders Encoders
.bean(EventGroup.class)) .bean(EventGroup.class))
.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.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
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@ -46,7 +46,7 @@ public class GenerateStatsJob {
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String dbUrl = parser.get("dbUrl"); 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 SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index"); final String index = parser.get("index");
@ -55,6 +55,18 @@ public class IndexEventSubsetJob {
final String indexHost = parser.get("esHost"); final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost); 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")); final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic"));
log.info("maxEventsForTopic: {}", maxEventsForTopic); log.info("maxEventsForTopic: {}", maxEventsForTopic);
@ -86,10 +98,10 @@ public class IndexEventSubsetJob {
esCfg.put("es.index.auto.create", "false"); esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost); esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8"); esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", "60s"); esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", "200"); esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", "true"); esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing"); log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

22
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java
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@ -54,7 +54,7 @@ public class IndexNotificationsJob {
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index"); final String index = parser.get("index");
@ -63,6 +63,18 @@ public class IndexNotificationsJob {
final String indexHost = parser.get("esHost"); final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost); 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"); final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
@ -92,10 +104,10 @@ public class IndexNotificationsJob {
esCfg.put("es.index.auto.create", "false"); esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost); esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8"); esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", "60s"); esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", "200"); esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", "true"); esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing"); log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

24
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java
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@ -36,7 +36,7 @@ public class IndexOnESJob {
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index"); final String index = parser.get("index");
@ -45,6 +45,18 @@ public class IndexOnESJob {
final String indexHost = parser.get("esHost"); final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost); 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 SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final JavaRDD<String> inputRdd = ClusterUtils final JavaRDD<String> inputRdd = ClusterUtils
@ -53,15 +65,13 @@ public class IndexOnESJob {
.javaRDD(); .javaRDD();
final Map<String, String> esCfg = new HashMap<>(); 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.index.auto.create", "false");
esCfg.put("es.nodes", indexHost); esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8"); esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", "60s"); esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", "200"); esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", "true"); esCfg.put("es.nodes.wan.only", esNodesWanOnly);
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
} }

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

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java
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@ -40,10 +40,10 @@ public class JoinStep1Job {
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step1"; final String joinedEntitiesPath = workingDir + "/joinedEntities_step1";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath); log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep1Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class); .readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class);
final Dataset<RelatedProject> typedRels = ClusterUtils 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() final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedProject>, OaBrokerMainEntity> aggr = new RelatedProjectAggregator()
.toColumn(); .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); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step2"; final String joinedEntitiesPath = workingDir + "/joinedEntities_step2";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath); log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -54,10 +54,10 @@ public class JoinStep2Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class); .readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class);
final Dataset<RelatedSoftware> typedRels = ClusterUtils 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() final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedSoftware>, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator()
.toColumn(); .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); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step3"; final String joinedEntitiesPath = workingDir + "/joinedEntities_step3";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath); log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep3Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class); .readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class);
final Dataset<RelatedDataset> typedRels = ClusterUtils 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() final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDataset>, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator()
.toColumn(); .toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java
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@ -40,10 +40,10 @@ public class JoinStep4Job {
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step4"; final String joinedEntitiesPath = workingDir + "/joinedEntities_step4";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath); log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep4Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class); .readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class);
final Dataset<RelatedPublication> typedRels = ClusterUtils 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() final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedPublication>, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator()
.toColumn(); .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 { public class PartitionEventsByDsIdJob {
private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class); 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 { public static void main(final String[] args) throws Exception {
@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob {
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events"; final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId";
log.info("partitionPath: {}", partitionPath); log.info("partitionPath: {}", partitionPath);
final String opendoarIds = parser.get("opendoarIds"); final String opendoarIds = parser.get("opendoarIds");
@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob {
.write() .write()
.partitionBy("group") .partitionBy("group")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(partitionPath); .json(partitionPath);
}); });
@ -122,6 +123,7 @@ public class PartitionEventsByDsIdJob {
final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId(); final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId();
res.setEventId(e.getEventId());
res.setOriginalId(payload.getResult().getOriginalId()); res.setOriginalId(payload.getResult().getOriginalId());
res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null)); res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null));
res.setTopic(e.getTopic()); 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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String groupsPath = workingPath + "/duplicates"; final String groupsPath = workingDir + "/duplicates";
log.info("groupsPath: {}", groupsPath); log.info("groupsPath: {}", groupsPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -60,10 +60,10 @@ public class PrepareGroupsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups"); final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups");
final Dataset<OaBrokerMainEntity> results = ClusterUtils final Dataset<OaBrokerMainEntity> results = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class); .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class);
final Dataset<Relation> mergedRels = ClusterUtils final Dataset<Relation> mergedRels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class) .loadRelations(graphPath, spark)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<OaBrokerMainEntity, Relation>, ResultGroup> aggr = new ResultAggregator() 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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasets"; final String relsPath = workingDir + "/relatedDatasets";
log.info("relsPath: {}", relsPath); log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob {
.map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class)); .map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class));
final Dataset<Relation> rels = ClusterUtils final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class) .loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob {
final Dataset<RelatedDataset> dataset = rels final Dataset<RelatedDataset> dataset = rels
.joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> { .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()); rel.getRelDataset().setRelType(t._1.getRelClass());
return rel; return rel;
}, Encoders.bean(RelatedDataset.class)); }, 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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasources"; final String relsPath = workingDir + "/relatedDatasources";
log.info("relsPath: {}", relsPath); log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf(); 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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedProjects"; final String relsPath = workingDir + "/relatedProjects";
log.info("relsPath: {}", relsPath); log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob {
.map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class)); .map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class));
final Dataset<Relation> rels = ClusterUtils final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class) .loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedPublications"; final String relsPath = workingDir + "/relatedPublications";
log.info("relsPath: {}", relsPath); log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob {
Encoders.bean(OaBrokerRelatedPublication.class)); Encoders.bean(OaBrokerRelatedPublication.class));
final Dataset<Relation> rels = ClusterUtils final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class) .loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob {
final Dataset<RelatedPublication> dataset = rels final Dataset<RelatedPublication> dataset = rels
.joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> { .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()); rel.getRelPublication().setRelType(t._1.getRelClass());
return rel; return rel;
}, Encoders.bean(RelatedPublication.class)); }, 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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedSoftwares"; final String relsPath = workingDir + "/relatedSoftwares";
log.info("relsPath: {}", relsPath); log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob {
.map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class)); .map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class));
final Dataset<Relation> rels = ClusterUtils final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class) .loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .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"); final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath); log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath"); final String workingDir = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingDir: {}", workingDir);
final String simpleEntitiesPath = workingPath + "/simpleEntities"; final String simpleEntitiesPath = workingDir + "/simpleEntities";
log.info("simpleEntitiesPath: {}", simpleEntitiesPath); log.info("simpleEntitiesPath: {}", simpleEntitiesPath);
final SparkConf conf = new SparkConf(); 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() { public EnrichMissingSubject() {
super(20, 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), (p, s) -> p.getSubjects().add(s),
s -> subjectAsString(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() { public EnrichMoreSubject() {
super(20, 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), (p, s) -> p.getSubjects().add(s),
s -> subjectAsString(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.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class ClusterUtils { public class ClusterUtils {
@ -30,6 +31,16 @@ public class ClusterUtils {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); 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( public static <R> Dataset<R> readPath(
final SparkSession spark, final SparkSession spark,
final String inputPath, final String inputPath,
@ -67,6 +78,7 @@ public class ClusterUtils {
.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz)) .map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(path); .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(); final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
res.setOpenaireId(d.getId()); res.setOpenaireId(cleanOpenaireId(d.getId()));
res.setOriginalId(first(d.getOriginalId())); res.setOriginalId(first(d.getOriginalId()));
res.setTitle(structPropValue(d.getTitle())); res.setTitle(structPropValue(d.getTitle()));
res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid)); res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -89,7 +89,7 @@ public class ConversionUtils {
} }
final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication(); final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
res.setOpenaireId(p.getId()); res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setOriginalId(first(p.getOriginalId())); res.setOriginalId(first(p.getOriginalId()));
res.setTitle(structPropValue(p.getTitle())); res.setTitle(structPropValue(p.getTitle()));
res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid)); res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -106,7 +106,7 @@ public class ConversionUtils {
final OaBrokerMainEntity res = new OaBrokerMainEntity(); final OaBrokerMainEntity res = new OaBrokerMainEntity();
res.setOpenaireId(result.getId()); res.setOpenaireId(cleanOpenaireId(result.getId()));
res.setOriginalId(first(result.getOriginalId())); res.setOriginalId(first(result.getOriginalId()));
res.setTypology(classId(result.getResulttype())); res.setTypology(classId(result.getResulttype()));
res.setTitles(structPropList(result.getTitle())); res.setTitles(structPropList(result.getTitle()));
@ -129,6 +129,10 @@ public class ConversionUtils {
return res; return res;
} }
public static String cleanOpenaireId(final String id) {
return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
}
private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) { private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
if (author == null) { if (author == null) {
return null; return null;
@ -188,7 +192,7 @@ public class ConversionUtils {
} }
final OaBrokerProject res = new OaBrokerProject(); final OaBrokerProject res = new OaBrokerProject();
res.setOpenaireId(p.getId()); res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setTitle(fieldValue(p.getTitle())); res.setTitle(fieldValue(p.getTitle()));
res.setAcronym(fieldValue(p.getAcronym())); res.setAcronym(fieldValue(p.getAcronym()));
res.setCode(fieldValue(p.getCode())); res.setCode(fieldValue(p.getCode()));
@ -214,7 +218,7 @@ public class ConversionUtils {
} }
final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware(); final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
res.setOpenaireId(sw.getId()); res.setOpenaireId(cleanOpenaireId(sw.getId()));
res.setName(structPropValue(sw.getTitle())); res.setName(structPropValue(sw.getTitle()));
res.setDescription(fieldValue(sw.getDescription())); res.setDescription(fieldValue(sw.getDescription()));
res.setRepository(fieldValue(sw.getCodeRepositoryUrl())); res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
@ -230,7 +234,7 @@ public class ConversionUtils {
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource(); final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname()))); res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
res.setOpenaireId(ds.getId()); res.setOpenaireId(cleanOpenaireId(ds.getId()));
res.setType(classId(ds.getDatasourcetype())); res.setType(classId(ds.getDatasourcetype()));
return res; 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(); final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
collectedFromSet collectedFromSet
.stream() .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); .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; 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> dsIdWhitelist,
final Set<String> dsIdBlacklist, final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist, final Set<String> dsTypeWhitelist,
final Set<String> topicWhitelist,
final Map<String, LongAccumulator> accumulators) { final Map<String, LongAccumulator> accumulators) {
final List<UpdateInfo<?>> list = new ArrayList<>(); final List<UpdateInfo<?>> list = new ArrayList<>();
@ -84,7 +85,13 @@ public class EventFinder {
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) { for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) { if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) { 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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "workingDir",
"paramDescription": "the path where the temporary data will be stored", "paramDescription": "the path where the temporary data will be stored",
"paramRequired": true "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> <description>the path where the graph is stored</description>
</property> </property>
<property> <property>
<name>workingPath</name> <name>outputDir</name>
<description>the path where the the generated data will be stored</description> <description>the path where the the generated data will be stored</description>
</property> </property>
<property> <property>
@ -24,6 +24,11 @@
<value>-</value> <value>-</value>
<description>a black list (comma separeted, - for empty list) of datasource ids</description> <description>a black list (comma separeted, - for empty list) of datasource ids</description>
</property> </property>
<property>
<name>topicWhitelist</name>
<value>*</value>
<description>a white list (comma separeted, * for all) of topics</description>
</property>
<property> <property>
<name>esEventIndexName</name> <name>esEventIndexName</name>
<description>the elasticsearch index name for events</description> <description>the elasticsearch index name for events</description>
@ -36,6 +41,26 @@
<name>esIndexHost</name> <name>esIndexHost</name>
<description>the elasticsearch host</description> <description>the elasticsearch host</description>
</property> </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> <property>
<name>maxIndexedEventsForDsAndTopic</name> <name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description> <description>the max number of events for each couple (ds/topic)</description>
@ -111,15 +136,15 @@
</configuration> </configuration>
</global> </global>
<start to="ensure_working_path"/> <start to="ensure_output_dir"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="ensure_working_path"> <action name="ensure_output_dir">
<fs> <fs>
<mkdir path='${workingPath}'/> <mkdir path='${outputDir}'/>
</fs> </fs>
<ok to="start_entities_and_rels"/> <ok to="start_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -152,7 +177,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -176,7 +201,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -201,7 +226,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -225,7 +250,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -249,7 +274,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -273,7 +298,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="wait_entities_and_rels"/> <ok to="wait_entities_and_rels"/>
<error to="Kill"/> <error to="Kill"/>
@ -299,7 +324,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="join_entities_step1"/> <ok to="join_entities_step1"/>
<error to="Kill"/> <error to="Kill"/>
@ -323,7 +348,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="join_entities_step2"/> <ok to="join_entities_step2"/>
<error to="Kill"/> <error to="Kill"/>
@ -347,7 +372,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="join_entities_step3"/> <ok to="join_entities_step3"/>
<error to="Kill"/> <error to="Kill"/>
@ -371,7 +396,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="join_entities_step4"/> <ok to="join_entities_step4"/>
<error to="Kill"/> <error to="Kill"/>
@ -395,7 +420,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="prepare_groups"/> <ok to="prepare_groups"/>
<error to="Kill"/> <error to="Kill"/>
@ -419,7 +444,7 @@
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg> <arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingDir</arg><arg>${workingDir}</arg>
</spark> </spark>
<ok to="generate_events"/> <ok to="generate_events"/>
<error to="Kill"/> <error to="Kill"/>
@ -442,10 +467,12 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </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>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg> <arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg> <arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
<arg>--topicWhitelist</arg><arg>${topicWhitelist}</arg>
</spark> </spark>
<ok to="index_event_subset"/> <ok to="index_event_subset"/>
<error to="Kill"/> <error to="Kill"/>
@ -468,9 +495,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg> <arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg> <arg>--esHost</arg><arg>${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>${maxIndexedEventsForDsAndTopic}</arg> <arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg> <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark> </spark>
@ -495,9 +526,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg> <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg> <arg>--esHost</arg><arg>${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>${brokerApiBaseUrl}</arg> <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark> </spark>
<ok to="stats"/> <ok to="stats"/>
@ -521,7 +556,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</arg> <arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
<arg>--dbUser</arg><arg>${brokerDbUser}</arg> <arg>--dbUser</arg><arg>${brokerDbUser}</arg>
<arg>--dbPassword</arg><arg>${brokerDbPassword}</arg> <arg>--dbPassword</arg><arg>${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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the path where the generated events will be stored", "paramDescription": "the path where the generated events will be stored",
"paramRequired": true "paramRequired": true
}, },
@ -22,5 +28,11 @@
"paramLongName": "datasourceIdBlacklist", "paramLongName": "datasourceIdBlacklist",
"paramDescription": "a black list (comma separeted, - for empty list) of datasource ids", "paramDescription": "a black list (comma separeted, - for empty list) of datasource ids",
"paramRequired": true "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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the workinh path", "paramDescription": "the data path",
"paramRequired": true "paramRequired": true
}, },
{ {
@ -16,5 +16,29 @@
"paramLongName": "esHost", "paramLongName": "esHost",
"paramDescription": "the ES host", "paramDescription": "the ES host",
"paramRequired": true "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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the workinh path", "paramDescription": "the path where the generated data are stored",
"paramRequired": true "paramRequired": true
}, },
{ {
@ -16,7 +16,31 @@
"paramLongName": "esHost", "paramLongName": "esHost",
"paramDescription": "the ES host", "paramDescription": "the ES host",
"paramRequired": true "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", "paramName": "n",
"paramLongName": "maxEventsForTopic", "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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the workinh path", "paramDescription": "the dir that contains the events folder",
"paramRequired": true "paramRequired": true
}, },
{ {
@ -17,6 +17,30 @@
"paramDescription": "the ES host", "paramDescription": "the ES host",
"paramRequired": true "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", "paramName": "broker",
"paramLongName": "brokerApiBaseUrl", "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> <description>the path where the graph is stored</description>
</property> </property>
<property> <property>
<name>workingPath</name> <name>outputDir</name>
<description>the path where the the generated data will be stored</description> <description>the path where the the generated data are stored</description>
</property> </property>
<property> <property>
<name>datasourceIdWhitelist</name> <name>datasourceIdWhitelist</name>
@ -36,6 +36,26 @@
<name>esIndexHost</name> <name>esIndexHost</name>
<description>the elasticsearch host</description> <description>the elasticsearch host</description>
</property> </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> <property>
<name>maxIndexedEventsForDsAndTopic</name> <name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description> <description>the max number of events for each couple (ds/topic)</description>
@ -122,9 +142,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg> <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg> <arg>--esHost</arg><arg>${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>${brokerApiBaseUrl}</arg> <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark> </spark>
<ok to="End"/> <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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the path where the temporary data will be stored", "paramDescription": "the path where the data will be stored",
"paramRequired": true "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> <description>the opendoar IDs whitelist (comma separated)</description>
</property> </property>
<property> <property>
<name>workingPath</name> <name>outputDir</name>
<description>the path where the the generated data will be stored</description> <description>the path where the the generated data will be stored</description>
</property> </property>
<property> <property>
@ -87,7 +87,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--opendoarIds</arg><arg>${opendoarIds}</arg> <arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
</spark> </spark>
<ok to="End"/> <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", "paramName": "o",
"paramLongName": "workingPath", "paramLongName": "outputDir",
"paramDescription": "the working path", "paramDescription": "the path where generated data are stored",
"paramRequired": true "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.nio.file.Paths;
import java.util.*; import java.util.*;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil; import eu.dnetlib.pace.util.MapDocumentUtil;
@ -100,8 +101,8 @@ public class EntityMergerTest implements Serializable {
assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
// verify authors // verify authors
assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(13, pub_merged.getAuthor().size());
assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor()));
// verify title // verify title
int count = 0; 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.commons.io.IOUtils;
import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD; 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.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction; 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.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; 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 com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent; 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.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; 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.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf; 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.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import org.json4s import org.json4s
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
import scala.io.Source
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} 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]){} case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
object DoiBoostMappingUtil { object DoiBoostMappingUtil {
def getUnknownCountry(): Qualifier = {
createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
}
def generateMAGAffiliationId(affId: String): String = { def generateMAGAffiliationId(affId: String): String = {
s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}" s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
} }
val logger: Logger = LoggerFactory.getLogger(getClass) val logger: Logger = LoggerFactory.getLogger(getClass)
//STATIC STRING //STATIC STRING
val MAG = "microsoft" val MAG = "microsoft"
val MAG_NAME = "Microsoft Academic Graph" val MAG_NAME = "Microsoft Academic Graph"
val ORCID = "ORCID" val ORCID = "orcid"
val ORCID_PENDING = "orcid_pending"
val CROSSREF = "Crossref" val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall" val UNPAYWALL = "UnpayWall"
val GRID_AC = "grid.ac" 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 dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath") val dbOrganizationPath = parser.get("dbOrganizationPath")
val workingDirPath = parser.get("targetPath") 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.fixResult(d))
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) .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)) .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)) .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)) .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)) .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.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger 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.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.doiboost.mag.ConversionUtil import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
@ -30,7 +31,7 @@ object SparkGenerateDoiBoost {
import spark.implicits._ import spark.implicits._
val hostedByMapPath = parser.get("hostedByMapPath") val hostedByMapPath = parser.get("hostedByMapPath")
val workingDirPath = parser.get("workingDirPath") val workingDirPath = parser.get("workingPath")
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
@ -132,7 +133,7 @@ object SparkGenerateDoiBoost {
o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get)) o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
if (affiliation.OfficialPage.isDefined) if (affiliation.OfficialPage.isDefined)
o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get)) o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
o.setCountry(DoiBoostMappingUtil.getUnknownCountry()) o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
o o
} }
else 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.setSurname(family)
a.setFullname(s"$given $family") a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid)) 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 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; package eu.dnetlib.doiboost.crossref;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
import java.util.Optional;
import java.util.zip.Inflater; import java.util.zip.Inflater;
import org.apache.commons.codec.binary.Base64; import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@ -30,34 +28,45 @@ public class CrossrefImporter {
parser.parseArgument(args); parser.parseArgument(args);
final String hdfsuri = parser.get("namenode"); final String namenode = parser.get("namenode");
System.out.println("HDFS URI" + hdfsuri); System.out.println("namenode: " + namenode);
Path hdfswritepath = new Path(parser.get("targetPath"));
System.out.println("TargetPath: " + hdfsuri);
final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp")) Path targetPath = new Path(parser.get("targetPath"));
? Long.parseLong(parser.get("timestamp")) System.out.println("targetPath: " + targetPath);
: -1;
if (timestamp > 0) final Long timestamp = Optional
System.out.println("Timestamp added " + timestamp); .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 // ====== Init HDFS File System Object
Configuration conf = new Configuration(); Configuration conf = new Configuration();
// Set FileSystem URI // Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri); conf.set("fs.defaultFS", namenode);
// Because of Maven // Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
ESClient client = timestamp > 0 // "ip-90-147-167-25.ct1.garrservices.it", "crossref"
? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp) final ESClient client = new ESClient(esServer, esIndex, timestamp);
: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
try (SequenceFile.Writer writer = SequenceFile try (SequenceFile.Writer writer = SequenceFile
.createWriter( .createWriter(
conf, conf,
SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.file(targetPath),
SequenceFile.Writer.keyClass(IntWritable.class), SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) { SequenceFile.Writer.valueClass(Text.class))) {
@ -74,8 +83,7 @@ public class CrossrefImporter {
end = System.currentTimeMillis(); end = System.currentTimeMillis();
final float time = (end - start) / 1000.0F; final float time = (end - start) / 1000.0F;
System.out System.out
.println( .println(String.format("Imported %s records last 100000 imported in %s seconds", i, time));
String.format("Imported %d records last 100000 imported in %f seconds", i, time));
start = System.currentTimeMillis(); 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; package eu.dnetlib.doiboost.crossref;
import java.io.IOException;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost; import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity; import org.apache.http.entity.StringEntity;
@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory;
import com.jayway.jsonpath.JsonPath; import com.jayway.jsonpath.JsonPath;
public class ESClient implements Iterator<String> { public class ESClient implements Iterator<String> {
private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
static final String blobPath = "$.hits[*].hits[*]._source.blob"; private static final String BLOB_PATH = "$.hits.hits[*]._source.blob";
static final String scrollIdPath = "$._scroll_id"; private static final String SCROLL_ID_PATH = "$._scroll_id";
static final String JSON_NO_TS = "{\"size\":1000}"; private static final String JSON_NO_TS = "{\"size\":1000}";
static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; private 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 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; private final String scrollId;
@ -31,47 +35,30 @@ public class ESClient implements Iterator<String> {
private final String esHost; 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; 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) final String body = timestamp > 0
throws IOException { ? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp))
this.esHost = esHost; : getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS);
final String body = getResponse( scrollId = getJPathString(SCROLL_ID_PATH, body);
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
String.format(JSON_WITH_TS, timestamp));
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body); buffer = getBlobs(body);
} }
private String getResponse(final String url, final String json) { private String getResponse(final String url, final String json) {
CloseableHttpClient client = HttpClients.createDefault(); try (CloseableHttpClient client = HttpClients.createDefault()) {
try {
HttpPost httpPost = new HttpPost(url); HttpPost httpPost = new HttpPost(url);
if (json != null) { if (json != null) {
StringEntity entity = new StringEntity(json); StringEntity entity = new StringEntity(json);
httpPost.setEntity(entity); httpPost.setEntity(entity);
httpPost.setHeader("Accept", "application/json"); httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON);
httpPost.setHeader("Content-type", "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) { } catch (Throwable e) {
throw new RuntimeException("Error on executing request ", 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) { 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; return res;
} }
@ -102,11 +89,11 @@ public class ESClient implements Iterator<String> {
if (buffer.isEmpty()) { if (buffer.isEmpty()) {
final String json_param = String.format(JSON_SCROLL, scrollId); 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 { try {
buffer = getBlobs(body); buffer = getBlobs(body);
} catch (Throwable e) { } catch (Throwable e) {
logger.error("Error on get next page: body:" + body); System.out.println("Error on get next page: body:" + body);
} }
} }
return nextItem; 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._ import scala.collection.JavaConverters._
object SparkPreProcessMAG { object SparkProcessMAG {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass) 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 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.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier} import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import org.apache.commons.lang.StringUtils import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ 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]) {} case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
object ORCIDToOAF { object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass) val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
val mapper = new ObjectMapper val mapper = new ObjectMapper()
def isJsonValid(inputStr: String): Boolean = { def isJsonValid(inputStr: String): Boolean = {
import java.io.IOException 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 static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
import java.util.Date; import java.util.Date;
import java.util.List;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; 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.http.impl.client.HttpClients;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD; 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.JavaSparkContext;
import org.apache.spark.api.java.function.Function; import org.apache.spark.api.java.function.Function;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.mortbay.log.Log;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; 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 DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
static final String lastUpdate = "2020-09-29 00:00:00"; 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( final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils IOUtils
@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors {
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath); logger.info("workingPath: {}", workingPath);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
logger.info("outputPath: ", outputPath); logger.info("outputPath: {}", outputPath);
final String token = parser.get("token"); final String token = parser.get("token");
final String lambdaFileName = parser.get("lambdaFileName"); final String lambdaFileName = parser.get("lambdaFileName");
logger.info("lambdaFileName: ", lambdaFileName); logger.info("lambdaFileName: {}", lambdaFileName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors {
} }
private static boolean isModified(String orcidId, String modifiedDate) { private static boolean isModified(String orcidId, String modifiedDate) {
Date modifiedDateDt = null; Date modifiedDateDt;
Date lastUpdateDt = null; Date lastUpdateDt;
try { try {
if (modifiedDate.length() != 19) { if (modifiedDate.length() != 19) {
modifiedDate = modifiedDate.substring(0, 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": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
{"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG 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": "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": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, {"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation 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":"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":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false} {"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 package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.Publication import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass
import org.apache.spark.sql.{Encoder, Encoders, SparkSession} 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.Assertions._
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory} 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 (author) a AS MyT "
+ " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP "
+ " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or " + " 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 " + " GROUP BY id) r_t "
+ " JOIN (" + " JOIN ("
+ " SELECT source, target " + " 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() .stream()
.map(con -> con.getId()) .map(con -> con.getId())
.collect(Collectors.toList()); .collect(Collectors.toList());
Result res = new Result(); R res = (R) ret.getClass().newInstance();
res.setId(ret.getId()); res.setId(ret.getId());
List<Context> propagatedContexts = new ArrayList<>(); List<Context> propagatedContexts = new ArrayList<>();
for (String cId : communitySet) { 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) .filter(Objects::nonNull)
.collect(Collectors.toList()); .collect(Collectors.toList());
Result r = new Result(); R r = (R) ret.getClass().newInstance();
r.setId(ret.getId()); r.setId(ret.getId());
r.setContext(contextList); r.setContext(contextList);
ret.mergeFrom(r); 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 com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
public class ResultToCommunityJobTest { public class ResultToCommunityJobTest {
@ -66,7 +65,7 @@ public class ResultToCommunityJobTest {
} }
@Test @Test
public void test1() throws Exception { public void testSparkResultToCommunityThroughSemRelJob() throws Exception {
SparkResultToCommunityThroughSemRelJob SparkResultToCommunityThroughSemRelJob
.main( .main(
new String[] { 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 class CleaningFunctions {
public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; public static final String DOI_PREFIX_REGEX = "^10\\.";
public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
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 String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
public static final Set<String> PID_BLACKLIST = new HashSet<>(); public static final Set<String> PID_BLACKLIST = new HashSet<>();
@ -56,13 +59,19 @@ public class CleaningFunctions {
} }
} }
if (Objects.nonNull(r.getAuthor())) { if (Objects.nonNull(r.getAuthor())) {
r.getAuthor().forEach(a -> { r
if (Objects.nonNull(a.getPid())) { .getAuthor()
a.getPid().forEach(p -> { .stream()
fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES); .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) { if (value instanceof Publication) {
@ -86,7 +95,7 @@ public class CleaningFunctions {
} else if (value instanceof Organization) { } else if (value instanceof Organization) {
Organization o = (Organization) value; Organization o = (Organization) value;
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) { 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) { } else if (value instanceof Relation) {
// nothing to clean here // nothing to clean here
@ -101,6 +110,16 @@ public class CleaningFunctions {
.setLanguage( .setLanguage(
qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES)); 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())) { if (Objects.nonNull(r.getSubject())) {
r r
.setSubject( .setSubject(
@ -153,12 +172,14 @@ public class CleaningFunctions {
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r r
.setResourcetype( .setResourcetype(
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE)); qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
} }
if (Objects.nonNull(r.getInstance())) { if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) { for (Instance i : r.getInstance()) {
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) { 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())) { if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY); i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
@ -173,12 +194,22 @@ public class CleaningFunctions {
if (Objects.isNull(bestaccessrights)) { if (Objects.isNull(bestaccessrights)) {
r r
.setBestaccessright( .setBestaccessright(
qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
} else { } else {
r.setBestaccessright(bestaccessrights); r.setBestaccessright(bestaccessrights);
} }
} }
if (Objects.nonNull(r.getAuthor())) { 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 boolean nullRank = r
.getAuthor() .getAuthor()
.stream() .stream()
@ -199,6 +230,7 @@ public class CleaningFunctions {
a a
.getPid() .getPid()
.stream() .stream()
.filter(Objects::nonNull)
.filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> Objects.nonNull(p.getQualifier()))
.filter(p -> StringUtils.isNotBlank(p.getValue())) .filter(p -> StringUtils.isNotBlank(p.getValue()))
.map(p -> { .map(p -> {
@ -211,14 +243,31 @@ public class CleaningFunctions {
.map(Qualifier::getClassid) .map(Qualifier::getClassid)
.orElse("")) .orElse(""))
.orElse(""); .orElse("");
if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { if (p
p.getQualifier().setClassid(ModelConstants.ORCID); .getQualifier()
} else { .getClassid()
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); .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; return p;
}) })
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect( .collect(
Collectors Collectors
.toMap( .toMap(
@ -286,7 +335,7 @@ public class CleaningFunctions {
// TODO add cleaning for more PID types as needed // TODO add cleaning for more PID types as needed
case "doi": case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, "")); pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10."));
break; break;
} }
return pid; 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.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.jayway.jsonpath.Configuration; import com.jayway.jsonpath.Configuration;
import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.DocumentContext;
@ -44,7 +45,8 @@ public class GroupEntitiesAndRelationsSparkJob {
private final static String SOURCE_JPATH = "$.source"; private final static String SOURCE_JPATH = "$.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 { 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( protected static final Qualifier MAG_PID_TYPE = qualifier(
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); "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<>(); protected static final Map<String, String> nsContext = new HashMap<>();
static { static {
@ -244,25 +246,54 @@ public abstract class AbstractMdRecordToOafMapper {
final String originalId = ((Node) o).getText(); final String originalId = ((Node) o).getText();
final String validationdDate = ((Node) o).valueOf("@validationDate");
if (StringUtils.isNotBlank(originalId)) { if (StringUtils.isNotBlank(originalId)) {
final String projectId = createOpenaireId(40, originalId, true); final String projectId = createOpenaireId(40, originalId, true);
res res
.add( .add(
getRelation( getRelationWithValidationDate(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
lastUpdateTimestamp)); lastUpdateTimestamp, validationdDate));
res res
.add( .add(
getRelation( getRelationWithValidationDate(
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
lastUpdateTimestamp)); lastUpdateTimestamp, validationdDate));
} }
} }
return res; 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, protected Relation getRelation(final String source,
final String target, final String target,
final String relType, 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.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; 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.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.Closeable;
import java.io.IOException; import java.io.IOException;
@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
return Arrays.asList(r); return Arrays.asList(r);
} else { } else {
final String validationDate = rs.getString("curation_date");
final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false); 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 String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
final Relation r1 = new Relation(); final Relation r1 = new Relation();
final Relation r2 = new Relation(); final Relation r2 = new Relation();
if (rs.getString(SOURCE_TYPE).equals("project")) { r1.setValidated(true);
r1.setCollectedfrom(collectedFrom); r1.setValidationDate(validationDate);
r1.setRelType(RESULT_PROJECT); r1.setCollectedfrom(collectedFrom);
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.setSource(sourceId); r1.setSource(sourceId);
r1.setTarget(targetId); r1.setTarget(targetId);
r1.setDataInfo(info); r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setValidationDate(validationDate);
r2.setValidated(true);
r2.setCollectedfrom(collectedFrom);
r2.setSource(targetId); r2.setSource(targetId);
r2.setTarget(sourceId); r2.setTarget(sourceId);
r2.setDataInfo(info); r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp); 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); 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 Node n = (Node) o;
final Author author = new Author(); final Author author = new Author();
final String fullname = n.valueOf("./datacite:creatorName"); final String fullname = n.valueOf("./datacite:creatorName");
author.setFullname(fullname);
final PacePerson pp = new PacePerson(fullname, false);
final String name = n.valueOf("./datacite:givenName"); 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"); final String surname = n.valueOf("./datacite:familyName");
if (StringUtils.isBlank(surname) & pp.isAccurate()) { if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) {
author.setSurname(pp.getNormalisedSurname()); author.setFullname(fullname);
} else {
author.setSurname(surname);
}
if (StringUtils.isBlank(author.getFullname())) { final PacePerson pp = new PacePerson(fullname, false);
author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
}
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); if (StringUtils.isBlank(name) & pp.isAccurate()) {
author.setPid(preparePids(n, info)); author.setName(pp.getNormalisedFirstName());
author.setRank(pos++); } else {
res.add(author); 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; 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.fs.Path;
import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text; 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; 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(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.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(p));
// System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2)); // System.out.println(new ObjectMapper().writeValueAsString(r2));
@ -246,6 +249,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.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 @Test
@ -355,7 +362,31 @@ public class MappersTest {
assertValidId(p.getId()); assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey()); assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); 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 @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; private MigrateDbEntitiesApplication app;
@Mock @Mock(lenient = true)
private ResultSet rs; private ResultSet rs;
@Mock @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 type="publication">0001</dr:CobjCategory>-->
<dr:CobjCategory>0001</dr:CobjCategory> <dr:CobjCategory>0001</dr:CobjCategory>
<oaf:dateAccepted>2017-01-01</oaf:dateAccepted> <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:accessrights>OPEN</oaf:accessrights>
<oaf:hostedBy id="openaire____::issn226852" name="One Ecosystem"/> <oaf:hostedBy id="openaire____::issn226852" name="One Ecosystem"/>
<oaf:collectedFrom <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:language>und</oaf:language>
<oaf:concept id="https://zenodo.org/communities/epfl"/> <oaf:concept id="https://zenodo.org/communities/epfl"/>
<oaf:hostedBy id="re3data_____::r3d100010468" name="Zenodo"/> <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:collectedFrom id="re3data_____::r3d100010468" name="Zenodo"/>
<oaf:refereed>0001</oaf:refereed>s <oaf:refereed>0001</oaf:refereed>s
</metadata> </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:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri" 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"> 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:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
<dri:recordIdentifier>textgrid:q9cv.0</dri:recordIdentifier> <dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
<dri:dateOfCollection>2020-11-17T09:34:11.128+01:00</dri:dateOfCollection> <dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
<oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix> <oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</identifier> <identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-21T13:35:20Z</datestamp> <datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
<dr:dateOfTransformation>2020-11-17T19:08:56.703+01:00</dr:dateOfTransformation> <dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
</oai:header> </oai:header>
<metadata> <metadata>
<datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/" <datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri" 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"> 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:creators>
<datacite:creator> <datacite:creator>
<datacite:creatorName>Hoffmann von Fallersleben, August Heinrich</datacite:creatorName> <datacite:creatorName>Liliencron, Detlev von</datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://de.dariah.eu/pnd-service">118552589</datacite:nameIdentifier> <datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id=">118572954</datacite:nameIdentifier>
</datacite:creator> </datacite:creator>
</datacite:creators> </datacite:creators>
<datacite:titles> <datacite:titles>
<datacite:title titleType="Other">Mailied</datacite:title> <datacite:title titleType="Other">Auf dem Trocknen</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">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
</datacite:titles> </datacite:titles>
<datacite:publisher>TextGrid</datacite:publisher> <datacite:publisher>TextGrid</datacite:publisher>
<datacite:publicationYear>2012</datacite:publicationYear> <datacite:publicationYear>2012</datacite:publicationYear>
@ -38,21 +38,21 @@
</datacite:contributor> </datacite:contributor>
<datacite:contributor contributorType="Other"> <datacite:contributor contributorType="Other">
<datacite:contributorName>Digitale Bibliothek</datacite:contributorName> <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:contributor>
</datacite:contributors> </datacite:contributors>
<datacite:dates> <datacite:dates>
<datacite:date dateType="Created">2012-01-21T13:35:20Z</datacite:date> <datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Issued">2012-01-21T13:35:20Z</datacite:date> <datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Updated">2012-01-21T13:35:20Z</datacite:date> <datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
</datacite:dates> </datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset"/> <datacite:resourceType resourceTypeGeneral="Dataset"/>
<alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3"> <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> <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:11858/00-1734-0000-0003-7664-F</alternateIdentifier> <alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
</alternateIdentifiers> </alternateIdentifiers>
<datacite:relatedIdentifiers> <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:relatedIdentifiers>
<datacite:sizes> <datacite:sizes>
<datacite:size>527 Bytes</datacite:size> <datacite:size>527 Bytes</datacite:size>
@ -77,17 +77,18 @@
<datacite:geoLocations> <datacite:geoLocations>
<datacite:geoLocation> <datacite:geoLocation>
<datacite:geoLocationPlace <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:geoLocation>
</datacite:geoLocations> </datacite:geoLocations>
</datacite:resource> </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> <dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:refereed>0002</oaf:refereed> <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:accessrights>OPEN</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license> <oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
<oaf:language>und</oaf:language> <oaf:language>und</oaf:language>
<oaf:country>DE</oaf:country>
<oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/> <oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
<oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/> <oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
</metadata> </metadata>
@ -95,11 +96,11 @@
xmlns:dri="http://www.driver-repository.eu/namespace/dri" 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"> 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"> <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> <baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
<identifier>textgrid:q9cv.0</identifier> <identifier>textgrid:rn8z.0</identifier>
<datestamp>2012-01-21T13:35:20Z</datestamp> <datestamp>2012-01-29T20:54:12Z</datestamp>
<metadataNamespace>http://schema.datacite.org/oai/oai-1.0/</metadataNamespace> <metadataNamespace/>
</originDescription> </originDescription>
</provenance> </provenance>
<oaf:datainfo> <oaf:datainfo>
@ -107,9 +108,10 @@
<oaf:deletedbyinference>false</oaf:deletedbyinference> <oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust> <oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/> <oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk" <oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk" classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/> schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo> </oaf:datainfo>
</about> </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 package eu.dnetlib.dhp.export
import com.fasterxml.jackson.databind.ObjectMapper
import java.time.LocalDateTime import java.time.LocalDateTime
import java.time.format.DateTimeFormatter import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction 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.schema.scholexplorer.{DLIDataset, DLIPublication}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._ import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._
import scala.collection.JavaConverters._ 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` package eu.dnetlib.dhp.`export`
import eu.dnetlib.dhp.application.ArgumentApplicationParser 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 eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.Text import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat 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.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions._ import org.apache.spark.sql.functions._
import org.apache.spark.sql.expressions.Window import org.apache.spark.sql.expressions.Window
import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.SparkConf
import org.codehaus.jackson.map.ObjectMapper
import scala.collection.mutable.ArrayBuffer import scala.collection.mutable.ArrayBuffer
import scala.collection.JavaConverters._
object SparkExportContentForOpenAire { object SparkExportContentForOpenAire {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf() val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json"))) 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"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$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.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients; 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; import eu.dnetlib.dhp.application.ArgumentApplicationParser;

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