Merge pull request 'dump of the results related to at least one project' (#61) from miriam.baglioni/dnet-hadoop:dump into master
LGTM
This commit is contained in:
commit
ada21ad920
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@ -0,0 +1,30 @@
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package eu.dnetlib.dhp.common;
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import com.google.common.collect.Maps;
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import java.util.Map;
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public class Constants {
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public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
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public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
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public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
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static {
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accessRightsCoarMap.put("OPEN", "c_abf2");
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accessRightsCoarMap.put("RESTRICTED", "c_16ec");
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accessRightsCoarMap.put("OPEN SOURCE", "c_abf2");
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accessRightsCoarMap.put("CLOSED", "c_14cb");
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accessRightsCoarMap.put("EMBARGO", "c_f1cf");
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}
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static {
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coarCodeLabelMap.put("c_abf2", "OPEN");
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coarCodeLabelMap.put("c_16ec", "RESTRICTED");
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coarCodeLabelMap.put("c_14cb", "CLOSED");
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coarCodeLabelMap.put("c_f1cf", "EMBARGO");
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}
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}
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@ -0,0 +1,415 @@
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package eu.dnetlib.dhp.common;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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public class GraphResultMapper implements Serializable {
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public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
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E in) {
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CommunityResult out = new CommunityResult();
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eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in;
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
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if (ort.isPresent()) {
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switch (ort.get().getClassid()) {
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case "publication":
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Optional<Journal> journal = Optional
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.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
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if (journal.isPresent()) {
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Journal j = journal.get();
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Container c = new Container();
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c.setConferencedate(j.getConferencedate());
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c.setConferenceplace(j.getConferenceplace());
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c.setEdition(j.getEdition());
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c.setEp(j.getEp());
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c.setIss(j.getIss());
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c.setIssnLinking(j.getIssnLinking());
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c.setIssnOnline(j.getIssnOnline());
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c.setIssnPrinted(j.getIssnPrinted());
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c.setName(j.getName());
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c.setSp(j.getSp());
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c.setVol(j.getVol());
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out.setContainer(c);
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out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
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}
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break;
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case "dataset":
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eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input;
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Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue()));
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Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
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out
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.setGeolocation(
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Optional
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.ofNullable(id.getGeolocation())
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.map(
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igl -> igl
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.stream()
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.filter(Objects::nonNull)
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.map(gli -> {
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GeoLocation gl = new GeoLocation();
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gl.setBox(gli.getBox());
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gl.setPlace(gli.getPlace());
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gl.setPoint(gli.getPoint());
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return gl;
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})
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.collect(Collectors.toList()))
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.orElse(null));
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out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
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break;
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case "software":
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eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
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Optional
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.ofNullable(is.getCodeRepositoryUrl())
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.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
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Optional
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.ofNullable(is.getDocumentationUrl())
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.ifPresent(
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value -> out
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.setDocumentationUrl(
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value
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.stream()
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.map(v -> v.getValue())
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.collect(Collectors.toList())));
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Optional
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.ofNullable(is.getProgrammingLanguage())
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.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
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out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
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break;
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case "other":
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eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
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out
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.setContactgroup(
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Optional
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.ofNullable(ir.getContactgroup())
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.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
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.orElse(null));
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out
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.setContactperson(
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Optional
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.ofNullable(ir.getContactperson())
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.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
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.orElse(null));
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out
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.setTool(
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Optional
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.ofNullable(ir.getTool())
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.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
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.orElse(null));
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out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
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break;
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}
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Optional
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.ofNullable(input.getAuthor())
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.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
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// I do not map Access Right UNKNOWN or OTHER
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
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if (oar.isPresent()) {
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if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
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String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
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out
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.setBestaccessright(
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AccessRight
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.newInstance(
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code,
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Constants.coarCodeLabelMap.get(code),
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Constants.COAR_ACCESS_RIGHT_SCHEMA));
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}
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}
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final List<String> contributorList = new ArrayList<>();
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Optional
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.ofNullable(input.getContributor())
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.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
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out.setContributor(contributorList);
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Optional
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.ofNullable(input.getCountry())
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.ifPresent(
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value -> out
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.setCountry(
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value
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.stream()
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.map(
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c -> {
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if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
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return null;
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}
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Country country = new Country();
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country.setCode(c.getClassid());
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country.setLabel(c.getClassname());
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Optional
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.ofNullable(c.getDataInfo())
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.ifPresent(
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provenance -> country
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.setProvenance(
|
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Provenance
|
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.newInstance(
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provenance
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.getProvenanceaction()
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.getClassname(),
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c.getDataInfo().getTrust())));
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return country;
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})
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.filter(Objects::nonNull)
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.collect(Collectors.toList())));
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final List<String> coverageList = new ArrayList<>();
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Optional
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.ofNullable(input.getCoverage())
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.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
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out.setCoverage(coverageList);
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out.setDateofcollection(input.getDateofcollection());
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final List<String> descriptionList = new ArrayList<>();
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Optional
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.ofNullable(input.getDescription())
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.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
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out.setDescription(descriptionList);
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Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
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if (oStr.isPresent()) {
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out.setEmbargoenddate(oStr.get().getValue());
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}
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|
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final List<String> formatList = new ArrayList<>();
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Optional
|
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.ofNullable(input.getFormat())
|
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.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
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out.setFormat(formatList);
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out.setId(input.getId());
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out.setOriginalId(input.getOriginalId());
|
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|
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Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
|
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.ofNullable(input.getInstance());
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|
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if (oInst.isPresent()) {
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out
|
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.setInstance(
|
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oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
|
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|
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}
|
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|
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
|
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if (oL.isPresent()) {
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eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
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out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
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}
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Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
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if (oLong.isPresent()) {
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out.setLastupdatetimestamp(oLong.get());
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}
|
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Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
|
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if (otitle.isPresent()) {
|
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List<StructuredProperty> iTitle = otitle
|
||||
.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
|
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.collect(Collectors.toList());
|
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if (iTitle.size() > 0) {
|
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out.setMaintitle(iTitle.get(0).getValue());
|
||||
}
|
||||
|
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iTitle = otitle
|
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.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
|
||||
.collect(Collectors.toList());
|
||||
if (iTitle.size() > 0) {
|
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out.setSubtitle(iTitle.get(0).getValue());
|
||||
}
|
||||
|
||||
}
|
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|
||||
List<ControlledField> pids = new ArrayList<>();
|
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Optional
|
||||
.ofNullable(input.getPid())
|
||||
.ifPresent(
|
||||
value -> value
|
||||
.stream()
|
||||
.forEach(
|
||||
p -> pids
|
||||
.add(
|
||||
ControlledField
|
||||
.newInstance(p.getQualifier().getClassid(), p.getValue()))));
|
||||
out.setPid(pids);
|
||||
oStr = Optional.ofNullable(input.getDateofacceptance());
|
||||
if (oStr.isPresent()) {
|
||||
out.setPublicationdate(oStr.get().getValue());
|
||||
}
|
||||
oStr = Optional.ofNullable(input.getPublisher());
|
||||
if (oStr.isPresent()) {
|
||||
out.setPublisher(oStr.get().getValue());
|
||||
}
|
||||
|
||||
List<String> sourceList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getSource())
|
||||
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
|
||||
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
|
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List<Subject> subjectList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getSubject())
|
||||
.ifPresent(
|
||||
value -> value
|
||||
.forEach(s -> subjectList.add(getSubject(s))));
|
||||
|
||||
out.setSubjects(subjectList);
|
||||
|
||||
out.setType(input.getResulttype().getClassid());
|
||||
}
|
||||
|
||||
out
|
||||
.setCollectedfrom(
|
||||
input
|
||||
.getCollectedfrom()
|
||||
.stream()
|
||||
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
|
||||
.collect(Collectors.toList()));
|
||||
|
||||
|
||||
return out;
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
|
||||
CommunityInstance instance = new CommunityInstance();
|
||||
|
||||
setCommonValue(i, instance);
|
||||
|
||||
instance
|
||||
.setCollectedfrom(
|
||||
KeyValue
|
||||
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
|
||||
|
||||
instance
|
||||
.setHostedby(
|
||||
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
|
||||
|
||||
return instance;
|
||||
|
||||
}
|
||||
|
||||
private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
|
||||
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
|
||||
.ofNullable(i.getAccessright());
|
||||
if (opAr.isPresent()) {
|
||||
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
|
||||
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
|
||||
instance
|
||||
.setAccessright(
|
||||
AccessRight
|
||||
.newInstance(
|
||||
code,
|
||||
Constants.coarCodeLabelMap.get(code),
|
||||
Constants.COAR_ACCESS_RIGHT_SCHEMA));
|
||||
}
|
||||
}
|
||||
|
||||
Optional
|
||||
.ofNullable(i.getLicense())
|
||||
.ifPresent(value -> instance.setLicense(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getDateofacceptance())
|
||||
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getRefereed())
|
||||
.ifPresent(value -> instance.setRefereed(value.getClassname()));
|
||||
Optional
|
||||
.ofNullable(i.getInstancetype())
|
||||
.ifPresent(value -> instance.setType(value.getClassname()));
|
||||
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static Subject getSubject(StructuredProperty s) {
|
||||
Subject subject = new Subject();
|
||||
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
|
||||
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
|
||||
if (di.isPresent()) {
|
||||
Provenance p = new Provenance();
|
||||
p.setProvenance(di.get().getProvenanceaction().getClassname());
|
||||
p.setTrust(di.get().getTrust());
|
||||
subject.setProvenance(p);
|
||||
}
|
||||
|
||||
return subject;
|
||||
}
|
||||
|
||||
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
|
||||
Author a = new Author();
|
||||
a.setFullname(oa.getFullname());
|
||||
a.setName(oa.getName());
|
||||
a.setSurname(oa.getSurname());
|
||||
a.setRank(oa.getRank());
|
||||
|
||||
Optional<List<StructuredProperty>> oPids = Optional
|
||||
.ofNullable(oa.getPid());
|
||||
if (oPids.isPresent()) {
|
||||
Pid pid = getOrcid(oPids.get());
|
||||
if (pid != null) {
|
||||
a.setPid(pid);
|
||||
}
|
||||
}
|
||||
|
||||
return a;
|
||||
}
|
||||
|
||||
private static Pid getOrcid(List<StructuredProperty> p) {
|
||||
for (StructuredProperty pid : p) {
|
||||
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
|
||||
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
|
||||
if (di.isPresent()) {
|
||||
return Pid
|
||||
.newInstance(
|
||||
ControlledField
|
||||
.newInstance(
|
||||
pid.getQualifier().getClassid(),
|
||||
pid.getValue()),
|
||||
Provenance
|
||||
.newInstance(
|
||||
di.get().getProvenanceaction().getClassname(),
|
||||
di.get().getTrust()));
|
||||
} else {
|
||||
return Pid
|
||||
.newInstance(
|
||||
ControlledField
|
||||
.newInstance(
|
||||
pid.getQualifier().getClassid(),
|
||||
pid.getValue())
|
||||
|
||||
);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -90,9 +90,6 @@ public class MakeTarArchive implements Serializable {
|
|||
String p_string = p.toString();
|
||||
if (!p_string.endsWith("_SUCCESS")) {
|
||||
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
|
||||
if (name.trim().equalsIgnoreCase("communities_infrastructures")) {
|
||||
name = "communities_infrastructures.json";
|
||||
}
|
||||
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
|
||||
entry.setSize(fileStatus.getLen());
|
||||
current_size += fileStatus.getLen();
|
||||
|
|
|
|||
|
|
@ -170,6 +170,7 @@ public class OrcidPropagationJobTest {
|
|||
.filter(
|
||||
"id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' "
|
||||
+ "and name = 'Vajinder' and surname = 'Kumar' and pidType = '" +
|
||||
|
||||
ModelConstants.ORCID_PENDING + "'")
|
||||
.count());
|
||||
|
||||
|
|
|
|||
|
|
@ -40,4 +40,18 @@ public class Constants {
|
|||
coarCodeLabelMap.put("c_14cb", "CLOSED");
|
||||
coarCodeLabelMap.put("c_f1cf", "EMBARGO");
|
||||
}
|
||||
|
||||
public enum DUMPTYPE {
|
||||
COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder");
|
||||
|
||||
private String type;
|
||||
|
||||
DUMPTYPE(String type) {
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -11,17 +11,12 @@ import java.util.Set;
|
|||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
/**
|
||||
|
|
@ -33,7 +28,7 @@ public class DumpProducts implements Serializable {
|
|||
public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath,
|
||||
Class<? extends OafEntity> inputClazz,
|
||||
Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> outputClazz,
|
||||
boolean graph) {
|
||||
String dumpType) {
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
|
|
@ -42,7 +37,7 @@ public class DumpProducts implements Serializable {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph);
|
||||
execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
|
||||
});
|
||||
}
|
||||
|
||||
|
|
@ -53,13 +48,13 @@ public class DumpProducts implements Serializable {
|
|||
String communityMapPath,
|
||||
Class<I> inputClazz,
|
||||
Class<O> outputClazz,
|
||||
boolean graph) {
|
||||
String dumpType) {
|
||||
|
||||
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
|
||||
|
||||
Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.map((MapFunction<I, O>) value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz))
|
||||
.map((MapFunction<I, O>) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
|
|
@ -70,18 +65,18 @@ public class DumpProducts implements Serializable {
|
|||
|
||||
private static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> O execMap(I value,
|
||||
CommunityMap communityMap,
|
||||
boolean graph) {
|
||||
String dumpType) {
|
||||
|
||||
Optional<DataInfo> odInfo = Optional.ofNullable(value.getDataInfo());
|
||||
if (odInfo.isPresent()) {
|
||||
if (odInfo.get().getDeletedbyinference()) {
|
||||
if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) {
|
||||
return null;
|
||||
}
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
|
||||
if (!graph) {
|
||||
if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) {
|
||||
Set<String> communities = communityMap.keySet();
|
||||
|
||||
Optional<List<Context>> inputContext = Optional
|
||||
|
|
@ -102,7 +97,8 @@ public class DumpProducts implements Serializable {
|
|||
return null;
|
||||
}
|
||||
}
|
||||
return (O) ResultMapper.map(value, communityMap, graph);
|
||||
|
||||
return (O) ResultMapper.map(value, communityMap, dumpType);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -21,10 +21,10 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
|||
public class ResultMapper implements Serializable {
|
||||
|
||||
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
|
||||
E in, Map<String, String> communityMap, boolean graph) {
|
||||
E in, Map<String, String> communityMap, String dumpType) {
|
||||
|
||||
Result out;
|
||||
if (graph) {
|
||||
if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
|
||||
out = new GraphResult();
|
||||
} else {
|
||||
out = new CommunityResult();
|
||||
|
|
@ -217,7 +217,7 @@ public class ResultMapper implements Serializable {
|
|||
.ofNullable(input.getInstance());
|
||||
|
||||
if (oInst.isPresent()) {
|
||||
if (graph) {
|
||||
if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
|
||||
((GraphResult) out)
|
||||
.setInstance(oInst.get().stream().map(i -> getGraphInstance(i)).collect(Collectors.toList()));
|
||||
} else {
|
||||
|
|
@ -296,7 +296,7 @@ public class ResultMapper implements Serializable {
|
|||
out.setType(input.getResulttype().getClassid());
|
||||
}
|
||||
|
||||
if (!graph) {
|
||||
if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
|
||||
((CommunityResult) out)
|
||||
.setCollectedfrom(
|
||||
input
|
||||
|
|
|
|||
|
|
@ -9,6 +9,7 @@ import java.util.Set;
|
|||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
|
@ -54,7 +55,7 @@ public class CommunitySplit implements Serializable {
|
|||
|
||||
private static void printResult(String c, Dataset<CommunityResult> result, String outputPath) {
|
||||
Dataset<CommunityResult> community_products = result
|
||||
.filter(r -> containsCommunity(r, c));
|
||||
.filter((FilterFunction<CommunityResult>) r -> containsCommunity(r, c));
|
||||
|
||||
try {
|
||||
community_products.first();
|
||||
|
|
|
|||
|
|
@ -4,12 +4,15 @@ package eu.dnetlib.dhp.oa.graph.dump.community;
|
|||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import javax.swing.text.html.Option;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
|
|
@ -48,6 +51,11 @@ public class SparkDumpCommunityProducts implements Serializable {
|
|||
|
||||
String communityMapPath = parser.get("communityMapPath");
|
||||
|
||||
final String dumpType = Optional
|
||||
.ofNullable(parser.get("dumpType"))
|
||||
.map(String::valueOf)
|
||||
.orElse("community");
|
||||
|
||||
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
|
||||
DumpProducts dump = new DumpProducts();
|
||||
|
|
@ -55,7 +63,7 @@ public class SparkDumpCommunityProducts implements Serializable {
|
|||
dump
|
||||
.run(
|
||||
isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class,
|
||||
false);
|
||||
dumpType);
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ import scala.Tuple2;
|
|||
|
||||
/**
|
||||
* Preparation of the Project information to be added to the dumped results. For each result associated to at least one
|
||||
* Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the
|
||||
* Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the
|
||||
* list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to
|
||||
*/
|
||||
public class SparkPrepareResultProject implements Serializable {
|
||||
|
|
@ -76,16 +76,16 @@ public class SparkPrepareResultProject implements Serializable {
|
|||
private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) {
|
||||
Dataset<Relation> relation = Utils
|
||||
.readPath(spark, inputPath + "/relation", Relation.class)
|
||||
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
|
||||
.filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'");
|
||||
Dataset<eu.dnetlib.dhp.schema.oaf.Project> projects = Utils
|
||||
.readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
|
||||
|
||||
projects
|
||||
.joinWith(relation, projects.col("id").equalTo(relation.col("source")))
|
||||
.joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner")
|
||||
.groupByKey(
|
||||
(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation>, String>) value -> value
|
||||
._2()
|
||||
.getTarget(),
|
||||
.getSource(),
|
||||
Encoders.STRING())
|
||||
.mapGroups(
|
||||
(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation>, ResultProject>) (s,
|
||||
|
|
@ -93,7 +93,7 @@ public class SparkPrepareResultProject implements Serializable {
|
|||
Set<String> projectSet = new HashSet<>();
|
||||
Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation> first = it.next();
|
||||
ResultProject rp = new ResultProject();
|
||||
rp.setResultId(first._2().getTarget());
|
||||
rp.setResultId(s);
|
||||
eu.dnetlib.dhp.schema.oaf.Project p = first._1();
|
||||
projectSet.add(p.getId());
|
||||
Project ps = getProject(p);
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ import java.util.Optional;
|
|||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
|
|
@ -20,6 +21,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkUpdateProjectInfo implements Serializable {
|
||||
|
||||
|
|
@ -73,7 +75,7 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
.joinWith(
|
||||
resultProject, result.col("id").equalTo(resultProject.col("resultId")),
|
||||
"left")
|
||||
.map(value -> {
|
||||
.map((MapFunction<Tuple2<CommunityResult, ResultProject>, CommunityResult>) value -> {
|
||||
CommunityResult r = value._1();
|
||||
Optional.ofNullable(value._2()).ifPresent(rp -> {
|
||||
r.setProjects(rp.getProjectsList());
|
||||
|
|
|
|||
|
|
@ -1,22 +1,25 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.complete;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStreamWriter;
|
||||
import java.io.Serializable;
|
||||
import java.io.*;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.function.Consumer;
|
||||
import java.util.function.Function;
|
||||
|
||||
import org.apache.commons.crypto.utils.IoUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.compress.CompressionCodec;
|
||||
import org.apache.hadoop.io.compress.CompressionCodecFactory;
|
||||
import org.apache.hadoop.io.compress.CompressionOutputStream;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
|
||||
|
|
@ -76,8 +79,11 @@ public class CreateContextEntities implements Serializable {
|
|||
} else {
|
||||
fsDataOutputStream = fileSystem.create(hdfsWritePath);
|
||||
}
|
||||
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
|
||||
CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec");
|
||||
|
||||
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
|
||||
this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream),
|
||||
StandardCharsets.UTF_8));
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ public class DumpGraphEntities implements Serializable {
|
|||
d
|
||||
.run(
|
||||
isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class,
|
||||
true);
|
||||
eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType());
|
||||
break;
|
||||
case "40":
|
||||
runWithSparkSession(
|
||||
|
|
|
|||
|
|
@ -0,0 +1,130 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.funderresults;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.api.zenodo.Community;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Constants;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC
|
||||
* for the EC it specifies also the fundingStream (FP7 or H2020)
|
||||
*/
|
||||
public class SparkDumpFunderResults implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkDumpFunderResults.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/funder_result_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("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String relationPath = parser.get("relationPath");
|
||||
log.info("relationPath: {}", relationPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
writeResultProjectList(spark, inputPath, outputPath, relationPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath,
|
||||
String relationPath) {
|
||||
|
||||
Dataset<Relation> relation = Utils
|
||||
.readPath(spark, relationPath + "/relation", Relation.class)
|
||||
.filter(
|
||||
"dataInfo.deletedbyinference = false and lower(relClass) = '"
|
||||
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
|
||||
|
||||
Dataset<CommunityResult> result = Utils
|
||||
.readPath(spark, inputPath + "/publication", CommunityResult.class)
|
||||
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
|
||||
|
||||
List<String> funderList = relation
|
||||
.select("target")
|
||||
.map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING())
|
||||
.distinct()
|
||||
.collectAsList();
|
||||
|
||||
funderList.forEach(funder -> {
|
||||
String fundernsp = funder.substring(3);
|
||||
String funderdump;
|
||||
if (fundernsp.startsWith("corda")) {
|
||||
funderdump = "EC_";
|
||||
if (fundernsp.endsWith("h2020")) {
|
||||
funderdump += "H2020";
|
||||
} else {
|
||||
funderdump += "FP7";
|
||||
}
|
||||
} else {
|
||||
funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase();
|
||||
}
|
||||
writeFunderResult(funder, result, outputPath + "/" + funderdump);
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath) {
|
||||
|
||||
results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
|
||||
if (!Optional.ofNullable(r.getProjects()).isPresent()) {
|
||||
return null;
|
||||
}
|
||||
for (Project p : r.getProjects()) {
|
||||
if (p.getId().startsWith(funder)) {
|
||||
return r;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}, Encoders.bean(CommunityResult.class))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,106 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.funderresults;
|
||||
|
||||
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.spark.SparkConf;
|
||||
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.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Constants;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* Selects the results linked to projects. Only for these results the dump will be performed.
|
||||
* The code to perform the dump and to expend the dumped results with the informaiton related to projects
|
||||
* is the one used for the dump of the community products
|
||||
*/
|
||||
public class SparkResultLinkedToProject implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkResultLinkedToProject.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.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("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
final String relationPath = parser.get("relationPath");
|
||||
log.info("relationPath: {}", relationPath);
|
||||
|
||||
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result> void writeResultsLinkedToProjects(SparkSession spark, Class<R> inputClazz,
|
||||
String inputPath, String outputPath, String relationPath) {
|
||||
|
||||
Dataset<R> results = Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.filter("dataInfo.deletedbyinference = false and datainfo.invisible = false");
|
||||
Dataset<Relation> relations = Utils
|
||||
.readPath(spark, relationPath, Relation.class)
|
||||
.filter(
|
||||
"dataInfo.deletedbyinference = false and lower(relClass) = '"
|
||||
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
|
||||
|
||||
relations
|
||||
.joinWith(
|
||||
results, relations.col("source").equalTo(results.col("id")),
|
||||
"inner")
|
||||
.groupByKey(
|
||||
(MapFunction<Tuple2<Relation, R>, String>) value -> value
|
||||
._2()
|
||||
.getId(),
|
||||
Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Tuple2<Relation, R>, R>) (k, it) -> {
|
||||
return it.next()._2();
|
||||
}, Encoders.bean(inputClazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
}
|
||||
|
|
@ -26,8 +26,8 @@
|
|||
<description> the metadata associated to the deposition</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>newDeposition</name>
|
||||
<description>true if it is a brand new depositon. false for new version of an old deposition</description>
|
||||
<name>depositionType</name>
|
||||
<description>one among {new, update, version}</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>conceptRecordId</name>
|
||||
|
|
@ -419,6 +419,7 @@
|
|||
<arg>--metadata</arg><arg>${metadata}</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
|
||||
<arg>--depositionId</arg><arg>${depositionId}</arg>
|
||||
<arg>--depositionType</arg><arg>${depositionType}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="dump_whole_graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="dump_complete_graph" xmlns="uri:oozie:workflow:0.5">
|
||||
|
||||
<parameters>
|
||||
<property>
|
||||
|
|
@ -368,7 +368,7 @@
|
|||
<action name="create_entities_fromcontext">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/collect/communities_infrastructures</arg>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/collect/communities_infrastructures/communities_infrastructure.json.gz</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</java>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the path of the sequencial file to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path used to store temporary output files",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "ssm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rp",
|
||||
"paramLongName": "relationPath",
|
||||
"paramDescription": "the relationPath",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
<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>hiveMetastoreUris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveJdbcUrl</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveDbName</name>
|
||||
<value>openaire</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,563 @@
|
|||
<workflow-app name="dump_funder_results" xmlns="uri:oozie:workflow:0.5">
|
||||
|
||||
<parameters>
|
||||
<property>
|
||||
<name>upload</name>
|
||||
<value>false</value>
|
||||
<description>true to upload the dump for the funders in Zenodo</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookUpUrl</name>
|
||||
<description>the isLookup service endpoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the output path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>accessToken</name>
|
||||
<description>the access token used for the deposition in Zenodo</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>connectionUrl</name>
|
||||
<description>the connection url for Zenodo</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>metadata</name>
|
||||
<description> the metadata associated to the deposition</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>depositionType</name>
|
||||
<description>the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided)</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>conceptRecordId</name>
|
||||
<description>for new version, the id of the record for the old deposition</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>depositionId</name>
|
||||
<description>the depositionId of a deposition open that has to be added content</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveDbName</name>
|
||||
<description>the target hive database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveJdbcUrl</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveMetastoreUris</name>
|
||||
<description>hive server metastore URIs</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="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="reset_outputpath">
|
||||
<fs>
|
||||
<delete path="${outputPath}"/>
|
||||
<mkdir path="${outputPath}"/>
|
||||
</fs>
|
||||
<ok to="save_community_map"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="save_community_map">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</java>
|
||||
<ok to="fork_result_linked_to_projects"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_result_linked_to_projects">
|
||||
<path start="select_publication_linked_to_projects"/>
|
||||
<path start="select_dataset_linked_to_projects"/>
|
||||
<path start="select_orp_linked_to_project"/>
|
||||
<path start="select_software_linked_to_projects"/>
|
||||
</fork>
|
||||
|
||||
<action name="select_publication_linked_to_projects">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump funder results </name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
|
||||
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||
</spark>
|
||||
<ok to="join_link"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="select_dataset_linked_to_projects">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump funder results </name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
|
||||
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||
</spark>
|
||||
<ok to="join_link"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="select_orp_linked_to_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump funder results </name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||
</spark>
|
||||
<ok to="join_link"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="select_software_linked_to_projects">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump funder results </name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
|
||||
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
|
||||
</spark>
|
||||
<ok to="join_link"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="join_link" to="fork_dump"/>
|
||||
|
||||
<fork name="fork_dump">
|
||||
<path start="dump_publication"/>
|
||||
<path start="dump_dataset"/>
|
||||
<path start="dump_orp"/>
|
||||
<path start="dump_software"/>
|
||||
</fork>
|
||||
|
||||
<action name="dump_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump table publication for community related products</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/result/publication</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/dump/publication</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--dumpType</arg><arg>funder</arg>
|
||||
</spark>
|
||||
<ok to="join_dump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dump_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump table dataset for community related products</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/result/dataset</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--dumpType</arg><arg>funder</arg>
|
||||
</spark>
|
||||
<ok to="join_dump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dump_orp">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump table ORP for community related products</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--dumpType</arg><arg>funder</arg>
|
||||
</spark>
|
||||
<ok to="join_dump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dump_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump table software for community related products</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/result/software</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/dump/software</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--dumpType</arg><arg>funder</arg>
|
||||
</spark>
|
||||
<ok to="join_dump"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="join_dump" to="prepareResultProject"/>
|
||||
|
||||
<action name="prepareResultProject">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Prepare association result subset of project info</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||
</spark>
|
||||
<ok to="fork_extendWithProject"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_extendWithProject">
|
||||
<path start="extend_publication"/>
|
||||
<path start="extend_dataset"/>
|
||||
<path start="extend_orp"/>
|
||||
<path start="extend_software"/>
|
||||
</fork>
|
||||
|
||||
<action name="extend_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extend dumped publications with information about project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/dump/publication</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/ext/publication</arg>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||
</spark>
|
||||
<ok to="join_extend"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="extend_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extend dumped dataset with information about project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/ext/dataset</arg>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||
</spark>
|
||||
<ok to="join_extend"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="extend_orp">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extend dumped ORP with information about project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/ext/orp</arg>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||
</spark>
|
||||
<ok to="join_extend"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="extend_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extend dumped software with information about project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||
<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/dump/software</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/ext/software</arg>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||
</spark>
|
||||
<ok to="join_extend"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<join name="join_extend" to="dump_funder_results"/>
|
||||
|
||||
<action name="dump_funder_results">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dump funder results </name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/ext</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/resultperfunder</arg>
|
||||
<arg>--relationPath</arg><arg>${sourcePath}</arg>
|
||||
</spark>
|
||||
<ok to="make_archive"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="make_archive">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/resultperfunder</arg>
|
||||
</java>
|
||||
<ok to="should_upload"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<decision name="should_upload">
|
||||
<switch>
|
||||
<case to="send_zenodo">${wf:conf('upload') eq true}</case>
|
||||
<default to="End"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="send_zenodo">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--accessToken</arg><arg>${accessToken}</arg>
|
||||
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
|
||||
<arg>--metadata</arg><arg>${metadata}</arg>
|
||||
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
|
||||
<arg>--depositionType</arg><arg>${depositionType}</arg>
|
||||
<arg>--depositionId</arg><arg>${depositionId}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
||||
|
|
@ -29,6 +29,12 @@
|
|||
"paramLongName":"resultTableName",
|
||||
"paramDescription": "the name of the result table we are currently working on",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"dt",
|
||||
"paramLongName":"dumpType",
|
||||
"paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,35 @@
|
|||
[
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the path of the sequencial file to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path used to store temporary output files",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "ssm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName":"tn",
|
||||
"paramLongName":"resultTableName",
|
||||
"paramDescription": "the name of the result table we are currently working on",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"rp",
|
||||
"paramLongName":"relationPath",
|
||||
"paramDescription": "the path to the relations",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
||||
|
||||
|
||||
|
|
@ -8,7 +8,6 @@ import java.util.Arrays;
|
|||
import java.util.List;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
|
|
@ -23,7 +22,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
import com.google.gson.Gson;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
|
|
@ -155,7 +153,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -220,7 +218,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
GraphResult.class, true);
|
||||
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -253,7 +251,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -285,7 +283,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -321,7 +319,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -357,7 +355,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -392,7 +390,7 @@ public class DumpJobTest {
|
|||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
CommunityResult.class, false);
|
||||
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
|
|||
|
|
@ -3,15 +3,24 @@ package eu.dnetlib.dhp.oa.graph.dump.complete;
|
|||
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStreamWriter;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.nio.file.Files;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.function.Consumer;
|
||||
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.compress.CompressionCodec;
|
||||
import org.apache.hadoop.io.compress.CompressionCodecFactory;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
|
@ -60,6 +69,8 @@ public class CreateEntityTest {
|
|||
|
||||
private QueryInformationSystem queryInformationSystem;
|
||||
|
||||
private static String workingDir;
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws ISLookUpException {
|
||||
lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap);
|
||||
|
|
@ -67,6 +78,13 @@ public class CreateEntityTest {
|
|||
queryInformationSystem.setIsLookUp(isLookUpService);
|
||||
}
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName())
|
||||
.toString();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test1() throws ISLookUpException, IOException {
|
||||
List<ContextInfo> cInfoList = new ArrayList<>();
|
||||
|
|
@ -123,4 +141,33 @@ public class CreateEntityTest {
|
|||
|
||||
riList.forEach(c -> System.out.println(new Gson().toJson(c)));
|
||||
}
|
||||
|
||||
@Test
|
||||
@Disabled
|
||||
public void test2() throws IOException, ISLookUpException {
|
||||
LocalFileSystem fs = FileSystem.getLocal(new Configuration());
|
||||
|
||||
Path hdfsWritePath = new Path(workingDir + "/prova");
|
||||
FSDataOutputStream fsDataOutputStream = null;
|
||||
if (fs.exists(hdfsWritePath)) {
|
||||
fsDataOutputStream = fs.append(hdfsWritePath);
|
||||
} else {
|
||||
fsDataOutputStream = fs.create(hdfsWritePath);
|
||||
}
|
||||
CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf());
|
||||
CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec");
|
||||
|
||||
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream),
|
||||
StandardCharsets.UTF_8));
|
||||
|
||||
List<ContextInfo> cInfoList = new ArrayList<>();
|
||||
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
|
||||
queryInformationSystem.getContextInformation(consumer);
|
||||
|
||||
for (ContextInfo cInfo : cInfoList) {
|
||||
writer.write(new Gson().toJson(Process.getEntity(cInfo)));
|
||||
}
|
||||
writer.close();
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,137 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.funderresult;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.HashMap;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
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.oa.graph.dump.funderresults.SparkResultLinkedToProject;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class ResultLinkedToProjectTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class);
|
||||
|
||||
private static HashMap<String, String> map = new HashMap<>();
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(
|
||||
eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.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(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNoMatch() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
|
||||
.getPath();
|
||||
|
||||
final String relationPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json")
|
||||
.getPath();
|
||||
|
||||
SparkResultLinkedToProject.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||
"-sourcePath", sourcePath,
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-relationPath", relationPath
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Result> tmp = sc
|
||||
.textFile(workingDir.toString() + "/preparedInfo")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Result> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(Result.class));
|
||||
|
||||
Assertions.assertEquals(0, verificationDataset.count());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMatchOne() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json")
|
||||
.getPath();
|
||||
|
||||
final String relationPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json")
|
||||
.getPath();
|
||||
|
||||
SparkResultLinkedToProject.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||
"-sourcePath", sourcePath,
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-relationPath", relationPath
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Publication> tmp = sc
|
||||
.textFile(workingDir.toString() + "/preparedInfo")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
|
||||
|
||||
Assertions.assertEquals(1, verificationDataset.count());
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,141 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.funderresult;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
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.oa.graph.dump.DumpJobTest;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
|
||||
|
||||
public class SplitPerFunderTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(SplitPerFunderTest.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(SplitPerFunderTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test1() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump")
|
||||
.getPath();
|
||||
|
||||
SparkDumpFunderResults.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/split",
|
||||
"-sourcePath", sourcePath,
|
||||
"-relationPath", sourcePath
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
// FP7 3
|
||||
JavaRDD<CommunityResult> tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/EC_FP7")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
||||
|
||||
Assertions.assertEquals(3, verificationDataset.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count());
|
||||
|
||||
// CIHR 2
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/CIHR")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
|
||||
// NWO 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NWO")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// NIH 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NIH")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
|
||||
// NSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// SNSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/SNSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// NHMRC 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NHMRC")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// H2020 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/EC_H2020")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(3, tmp.count());
|
||||
|
||||
}
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,8 @@
|
|||
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:project:semrel","classname":"Propagation of result to project through semantic relation","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"trust":"0.85"},"lastupdatetimestamp":null,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::7f0f296b5e4ec1a1d61cfe4da63406c7","subRelType":"outcome","source":"50|dedup_wf_001::595ab3bf9261fbd616fb0240fb78add2"}
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Reference in New Issue