package eu.dnetlib.dhp.oa.graph.dump; import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.eosc.model.EoscInteroperabilityFramework; import eu.dnetlib.dhp.eosc.model.EoscResult; import eu.dnetlib.dhp.oa.graph.dump.exceptions.CardinalityTooHighException; import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.oa.model.*; import eu.dnetlib.dhp.oa.model.AccessRight; import eu.dnetlib.dhp.oa.model.Author; import eu.dnetlib.dhp.oa.model.GeoLocation; import eu.dnetlib.dhp.oa.model.Instance; import eu.dnetlib.dhp.oa.model.Measure; import eu.dnetlib.dhp.oa.model.OpenAccessRoute; import eu.dnetlib.dhp.oa.model.Result; import eu.dnetlib.dhp.oa.model.community.CfHbKeyValue; import eu.dnetlib.dhp.oa.model.community.CommunityInstance; import eu.dnetlib.dhp.oa.model.community.CommunityResult; import eu.dnetlib.dhp.oa.model.community.Context; import eu.dnetlib.dhp.oa.model.graph.GraphResult; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; public class ResultMapper implements Serializable { public static Result map( E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException, CardinalityTooHighException { Result out; if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { out = new GraphResult(); } else if (Constants.DUMPTYPE.EOSC.getType().equals(dumpType)) { out = new EoscResult(); } else { out = new CommunityResult(); } eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; Optional ort = Optional.ofNullable(input.getResulttype()); if (ort.isPresent()) { try { addTypeSpecificInformation(out, input, ort); Optional .ofNullable(input.getAuthor()) .ifPresent( ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); // I do not map Access Right UNKNOWN or OTHER Optional oar = Optional.ofNullable(input.getBestaccessright()); if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); out .setBestaccessright( BestAccessRight .newInstance( code, Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); } final List contributorList = new ArrayList<>(); Optional .ofNullable(input.getContributor()) .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); out.setContributor(contributorList); Optional .ofNullable(input.getCountry()) .ifPresent( value -> out .setCountry( value .stream() .map( c -> { if (c.getClassid().equals((ModelConstants.UNKNOWN))) { return null; } ResultCountry country = new ResultCountry(); country.setCode(c.getClassid()); country.setLabel(c.getClassname()); Optional .ofNullable(c.getDataInfo()) .ifPresent( provenance -> country .setProvenance( Provenance .newInstance( provenance .getProvenanceaction() .getClassname(), c.getDataInfo().getTrust()))); return country; }) .filter(Objects::nonNull) .collect(Collectors.toList()))); final List coverageList = new ArrayList<>(); Optional .ofNullable(input.getCoverage()) .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); out.setCoverage(coverageList); out.setDateofcollection(input.getDateofcollection()); final List descriptionList = new ArrayList<>(); Optional .ofNullable(input.getDescription()) .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); out.setDescription(descriptionList); Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); if (oStr.isPresent()) { out.setEmbargoenddate(oStr.get().getValue()); } final List formatList = new ArrayList<>(); Optional .ofNullable(input.getFormat()) .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); out.setFormat(formatList); out.setId(input.getId()); out.setOriginalId(new ArrayList<>()); Optional .ofNullable(input.getOriginalId()) .ifPresent( v -> out .setOriginalId( input .getOriginalId() .stream() .filter(s -> !s.startsWith("50|")) .collect(Collectors.toList()))); Optional> oInst = Optional .ofNullable(input.getInstance()); if (oInst.isPresent()) { if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((GraphResult) out) .setInstance( oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); } else { ((CommunityResult) out) .setInstance( oInst .get() .stream() .map(ResultMapper::getCommunityInstance) .collect(Collectors.toList())); } } Optional oL = Optional.ofNullable(input.getLanguage()); if (oL.isPresent()) { eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname())); } Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); if (oLong.isPresent()) { out.setLastupdatetimestamp(oLong.get()); } Optional> otitle = Optional.ofNullable(input.getTitle()); if (otitle.isPresent()) { List iTitle = otitle .get() .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) .collect(Collectors.toList()); if (!iTitle.isEmpty()) { out.setMaintitle(iTitle.get(0).getValue()); } iTitle = otitle .get() .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) .collect(Collectors.toList()); if (!iTitle.isEmpty()) { out.setSubtitle(iTitle.get(0).getValue()); } } Optional .ofNullable(input.getPid()) .ifPresent( value -> out .setPid( value .stream() .map( p -> ResultPid .newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); oStr = Optional.ofNullable(input.getDateofacceptance()); if (oStr.isPresent()) { out.setPublicationdate(oStr.get().getValue()); } oStr = Optional.ofNullable(input.getPublisher()); if (oStr.isPresent()) { out.setPublisher(oStr.get().getValue()); } Optional .ofNullable(input.getSource()) .ifPresent( value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); List subjectList = new ArrayList<>(); Optional .ofNullable(input.getSubject()) .ifPresent( value -> value .forEach(s -> subjectList.add(getSubject(s)))); out.setSubjects(subjectList); out.setType(input.getResulttype().getClassid()); if (Constants.DUMPTYPE.EOSC.getType().equals(dumpType)) { if (Optional.ofNullable(input.getEoscifguidelines()).isPresent()) { List gei = input.getEoscifguidelines(); if (gei.size() > 1) { throw new CardinalityTooHighException( "EOSC IF in the result has cardinality greater than one. Change dump!"); } if (gei.size() == 1) { EoscInteroperabilityFramework eif = new EoscInteroperabilityFramework(); eif.setCode(gei.get(0).getCode()); eif.setLabel(gei.get(0).getLabel()); eif.setUrl(gei.get(0).getUrl()); eif.setSemanticRelation(gei.get(0).getSemanticRelation()); ((EoscResult) out).setEoscIF(eif); } } } else if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((CommunityResult) out) .setCollectedfrom( input .getCollectedfrom() .stream() .map(cf -> CfHbKeyValue.newInstance(cf.getKey(), cf.getValue())) .collect(Collectors.toList())); Set communities = communityMap.keySet(); List contextList = Optional .ofNullable( input .getContext()) .map( value -> value .stream() .map(c -> { String communityId = c.getId(); if (communityId.contains("::")) { communityId = communityId.substring(0, communityId.indexOf("::")); } if (communities.contains(communityId)) { Context context = new Context(); context.setCode(communityId); context.setLabel(communityMap.get(communityId)); Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); if (dataInfo.isPresent()) { List provenance = new ArrayList<>(); provenance .addAll( dataInfo .get() .stream() .map( di -> Optional .ofNullable(di.getProvenanceaction()) .map( provenanceaction -> Provenance .newInstance( provenanceaction.getClassname(), di.getTrust())) .orElse(null)) .filter(Objects::nonNull) .collect(Collectors.toSet())); try { context.setProvenance(getUniqueProvenance(provenance)); } catch (NoAvailableEntityTypeException e) { e.printStackTrace(); } } return context; } return null; }) .filter(Objects::nonNull) .collect(Collectors.toList())) .orElse(new ArrayList<>()); if (!contextList.isEmpty()) { Set hashValue = new HashSet<>(); List remainigContext = new ArrayList<>(); contextList.forEach(c -> { if (!hashValue.contains(c.hashCode())) { remainigContext.add(c); hashValue.add(c.hashCode()); } }); ((CommunityResult) out).setContext(remainigContext); } } } catch (ClassCastException cce) { return out; } } return out; } private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, Optional ort) throws NoAvailableEntityTypeException { switch (ort.get().getClassid()) { case "publication": Optional journal = Optional .ofNullable(((Publication) input).getJournal()); if (journal.isPresent()) { Journal j = journal.get(); Container c = new Container(); c.setConferencedate(j.getConferencedate()); c.setConferenceplace(j.getConferenceplace()); c.setEdition(j.getEdition()); c.setEp(j.getEp()); c.setIss(j.getIss()); c.setIssnLinking(j.getIssnLinking()); c.setIssnOnline(j.getIssnOnline()); c.setIssnPrinted(j.getIssnPrinted()); c.setName(j.getName()); c.setSp(j.getSp()); c.setVol(j.getVol()); out.setContainer(c); out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); } break; case "dataset": Dataset id = (Dataset) input; Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); out .setGeolocation( Optional .ofNullable(id.getGeolocation()) .map( igl -> igl .stream() .filter(Objects::nonNull) .map(gli -> { GeoLocation gl = new GeoLocation(); gl.setBox(gli.getBox()); gl.setPlace(gli.getPlace()); gl.setPoint(gli.getPoint()); return gl; }) .collect(Collectors.toList())) .orElse(null)); out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); break; case "software": Software is = (Software) input; Optional .ofNullable(is.getCodeRepositoryUrl()) .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); Optional .ofNullable(is.getDocumentationUrl()) .ifPresent( value -> out .setDocumentationUrl( value .stream() .map(Field::getValue) .collect(Collectors.toList()))); Optional .ofNullable(is.getProgrammingLanguage()) .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); break; case "other": OtherResearchProduct ir = (OtherResearchProduct) input; out .setContactgroup( Optional .ofNullable(ir.getContactgroup()) .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) .orElse(null)); out .setContactperson( Optional .ofNullable(ir.getContactperson()) .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) .orElse(null)); out .setTool( Optional .ofNullable(ir.getTool()) .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) .orElse(null)); out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); break; default: throw new NoAvailableEntityTypeException(); } } private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { Instance instance = new Instance(); setCommonValue(i, instance); return instance; } private static CommunityInstance getCommunityInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { CommunityInstance instance = new CommunityInstance(); setCommonValue(i, instance); instance .setCollectedfrom( CfHbKeyValue .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); instance .setHostedby( CfHbKeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); return instance; } private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { Optional opAr = Optional.ofNullable(i.getAccessright()); if (opAr.isPresent() && 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> mes = Optional.ofNullable(i.getMeasures()); if (mes.isPresent()) { List measure = new ArrayList<>(); mes .get() .forEach( m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue())))); instance.setMeasures(measure); } if (opAr.get().getOpenAccessRoute() != null) { switch (opAr.get().getOpenAccessRoute()) { case hybrid: instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); break; case gold: instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); break; case green: instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); break; case bronze: instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); break; } } } Optional .ofNullable(i.getPid()) .ifPresent( pid -> instance .setPid( pid .stream() .map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); Optional .ofNullable(i.getAlternateIdentifier()) .ifPresent( ai -> instance .setAlternateIdentifier( ai .stream() .map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); 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)); Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); if (oPca.isPresent() && oPcc.isPresent()) { Field pca = oPca.get(); Field pcc = oPcc.get(); if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { APC apc = new APC(); apc.setCurrency(oPcc.get().getValue()); apc.setAmount(oPca.get().getValue()); instance.setArticleprocessingcharge(apc); } } Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); } private static List getUniqueProvenance(List provenance) throws NoAvailableEntityTypeException { Provenance iProv = new Provenance(); Provenance hProv = new Provenance(); Provenance lProv = new Provenance(); for (Provenance p : provenance) { switch (p.getProvenance()) { case Constants.HARVESTED: hProv = getHighestTrust(hProv, p); break; case Constants.INFERRED: iProv = getHighestTrust(iProv, p); // To be removed as soon as the new beta run has been done // this fixex issue of not set trust during bulktagging if (StringUtils.isEmpty(iProv.getTrust())) { iProv.setTrust(Constants.DEFAULT_TRUST); } break; case Constants.USER_CLAIM: lProv = getHighestTrust(lProv, p); break; default: throw new NoAvailableEntityTypeException(); } } return Arrays .asList(iProv, hProv, lProv) .stream() .filter(p -> !StringUtils.isEmpty(p.getProvenance())) .collect(Collectors.toList()); } private static Provenance getHighestTrust(Provenance hProv, Provenance p) { if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust())) return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p; return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p; } private static Subject getSubject(StructuredProperty s) { Subject subject = new Subject(); subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue())); Optional di = Optional.ofNullable(s.getDataInfo()); if (di.isPresent()) { Provenance p = new Provenance(); p.setProvenance(di.get().getProvenanceaction().getClassname()); p.setTrust(di.get().getTrust()); subject.setProvenance(p); } return subject; } private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { Author a = new Author(); a.setFullname(oa.getFullname()); a.setName(oa.getName()); a.setSurname(oa.getSurname()); a.setRank(oa.getRank()); Optional> oPids = Optional .ofNullable(oa.getPid()); if (oPids.isPresent()) { AuthorPid pid = getOrcid(oPids.get()); if (pid != null) { a.setPid(pid); } } return a; } private static AuthorPid getAuthorPid(StructuredProperty pid) { Optional di = Optional.ofNullable(pid.getDataInfo()); if (di.isPresent()) { return AuthorPid .newInstance( AuthorPidSchemeValue .newInstance( pid.getQualifier().getClassid(), pid.getValue()), Provenance .newInstance( di.get().getProvenanceaction().getClassname(), di.get().getTrust())); } else { return AuthorPid .newInstance( AuthorPidSchemeValue .newInstance( pid.getQualifier().getClassid(), pid.getValue()) ); } } private static AuthorPid getOrcid(List p) { List pidList = p.stream().map(pid -> { if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { return pid; } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); if (pidList.size() == 1) { return getAuthorPid(pidList.get(0)); } List orcid = pidList .stream() .filter( ap -> ap .getQualifier() .getClassid() .equals(ModelConstants.ORCID)) .collect(Collectors.toList()); if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } orcid = pidList .stream() .filter( ap -> ap .getQualifier() .getClassid() .equals(ModelConstants.ORCID_PENDING)) .collect(Collectors.toList()); if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } return null; } }