diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index d0909642ce..abb9dc148f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -85,6 +85,13 @@ 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.startsWith("part-") & name.length() > 10) { + String tmp = name.substring(0, 10); + if (name.contains(".")) { + tmp += name.substring(name.indexOf(".")); + } + name = tmp; + } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index ab3b9593ed..40a17b4869 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -107,7 +107,6 @@ - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 6dca09b632..61167639ca 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -5,37 +5,40 @@ import java.util.Map; import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.common.ModelConstants; + public class Constants { - public static final Map accessRightsCoarMap = Maps.newHashMap(); - public static final Map coarCodeLabelMap = Maps.newHashMap(); + protected static final Map accessRightsCoarMap = Maps.newHashMap(); + protected static final Map coarCodeLabelMap = Maps.newHashMap(); public static final String INFERRED = "Inferred by OpenAIRE"; + public static final String CABF2 = "c_abf2"; public static final String HARVESTED = "Harvested"; public static final String DEFAULT_TRUST = "0.9"; public static final String USER_CLAIM = "Linked by user"; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - public static String RESEARCH_COMMUNITY = "Research Community"; + public static final String RESEARCH_COMMUNITY = "Research Community"; - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; static { - accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); - accessRightsCoarMap.put("CLOSED", "c_14cb"); - accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + accessRightsCoarMap.put("OPEN SOURCE", CABF2); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); } static { - coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index d20a3036e8..a714cea207 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,12 +11,14 @@ 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.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -37,7 +39,8 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); + execDump( + spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } @@ -55,7 +58,7 @@ public class DumpProducts implements Serializable { Utils .readPath(spark, inputPath, inputClazz) .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) - .filter(Objects::nonNull) + .filter((FilterFunction) value -> value != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") @@ -65,7 +68,7 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - String dumpType) { + String dumpType) throws NoAvailableEntityTypeException { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { @@ -89,11 +92,11 @@ public class DumpProducts implements Serializable { return c.getId(); } if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, 3); + return c.getId().substring(0, c.getId().indexOf("::")); } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.size() == 0) { + if (toDumpFor.isEmpty()) { return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java index 0d2df11fe6..b56849a3ab 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java @@ -57,16 +57,16 @@ public class MakeTar implements Serializable { public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) throws IOException { - RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - while (dir_iterator.hasNext()) { - LocatedFileStatus fileStatus = dir_iterator.next(); + while (dirIterator.hasNext()) { + LocatedFileStatus fileStatus = dirIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + String pathString = p.toString(); + String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - MakeTarArchive.tarMaxSize(fileSystem, p_string, outputPath + "/" + entity, entity, gBperSplit); + MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index dc740e8112..b972de6e9a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -18,10 +18,10 @@ public class QueryInformationSystem { private ISLookUpService isLookUp; - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + @@ -29,9 +29,22 @@ public class QueryInformationSystem { "{$x//CONFIGURATION/context/@label}" + ""; - public CommunityMap getCommunityMap() + private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//CONFIGURATION/context[./@id=%s] " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, DocumentException, SAXException { - return getMap(isLookUp.quickSearchProfile(XQUERY)); + if (singleCommunity) + return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); + return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 500fe5986e..49468540d9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -7,21 +7,28 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; +import eu.dnetlib.dhp.schema.dump.oaf.Author; +import eu.dnetlib.dhp.schema.dump.oaf.Country; +import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; +import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, String dumpType) { + E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { Result out; if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { @@ -33,113 +40,28 @@ public class ResultMapper implements Serializable { eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; Optional ort = Optional.ofNullable(input.getResulttype()); if (ort.isPresent()) { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + try { - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); + addTypeSpecificInformation(out, input, ort); + Optional> mes = Optional.ofNullable(input.getMeasures()); + if (mes.isPresent()) { + List measure = new ArrayList<>(); + mes + .get() + .forEach( + m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue())))); + out.setMeasures(measure); + } - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": + Optional + .ofNullable(input.getAuthor()) + .ifPresent( + ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); + // I do not map Access Right UNKNOWN or OTHER - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - } - - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); out .setBestaccessright( @@ -149,226 +71,340 @@ public class ResultMapper implements Serializable { Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); } - } - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - Country country = new Country(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - - out.setDateofcollection(input.getDateofcollection()); - - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); - - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getCommunityInstance).collect(Collectors.toList())); - } - } - - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setMaintitle(iTitle.get(0).getValue()); - } - - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setSubtitle(iTitle.get(0).getValue()); - } - - } - - List pids = new ArrayList<>(); - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> value - .stream() - .forEach( - p -> pids - .add( - ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())))); - out.setPid(pids); - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - - List sourceList = new ArrayList<>(); - Optional - .ofNullable(input.getSource()) - .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - - out.setType(input.getResulttype().getClassid()); - } - - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((CommunityResult) out) - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String community_id = c.getId(); - if (community_id.indexOf("::") > 0) { - community_id = community_id.substring(0, community_id.indexOf("::")); - } - if (communities.contains(community_id)) { - Context context = new Context(); - context.setCode(community_id); - context.setLabel(communityMap.get(community_id)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance .newInstance( - provenanceaction.getClassname(), di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); - context.setProvenance(getUniqueProvenance(provenance)); - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); - if (contextList.size() > 0) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + Optional> oInst = Optional + .ofNullable(input.getInstance()); + + if (oInst.isPresent()) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((GraphResult) out) + .setInstance( + oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); + } else { + ((CommunityResult) out) + .setInstance( + oInst + .get() + .stream() + .map(ResultMapper::getCommunityInstance) + .collect(Collectors.toList())); } - }); - ((CommunityResult) out).setContext(remainigContext); + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> out + .setPid( + value + .stream() + .map( + p -> ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + Optional + .ofNullable(input.getSource()) + .ifPresent( + value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); + + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((CommunityResult) out) + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + Set communities = communityMap.keySet(); + List contextList = Optional + .ofNullable( + input + .getContext()) + .map( + value -> value + .stream() + .map(c -> { + String communityId = c.getId(); + if (communityId.contains("::")) { + communityId = communityId.substring(0, communityId.indexOf("::")); + } + if (communities.contains(communityId)) { + Context context = new Context(); + context.setCode(communityId); + context.setLabel(communityMap.get(communityId)); + Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); + if (dataInfo.isPresent()) { + List provenance = new ArrayList<>(); + provenance + .addAll( + dataInfo + .get() + .stream() + .map( + di -> Optional + .ofNullable(di.getProvenanceaction()) + .map( + provenanceaction -> Provenance + .newInstance( + provenanceaction.getClassname(), + di.getTrust())) + .orElse(null)) + .filter(Objects::nonNull) + .collect(Collectors.toSet())); + + try { + context.setProvenance(getUniqueProvenance(provenance)); + } catch (NoAvailableEntityTypeException e) { + e.printStackTrace(); + } + } + return context; + } + return null; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); + + if (!contextList.isEmpty()) { + Set hashValue = new HashSet<>(); + List remainigContext = new ArrayList<>(); + contextList.forEach(c -> { + if (!hashValue.contains(c.hashCode())) { + remainigContext.add(c); + hashValue.add(c.hashCode()); + } + }); + ((CommunityResult) out).setContext(remainigContext); + } + } + } catch (ClassCastException cce) { + return out; } } + return out; } + private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, + Optional ort) throws NoAvailableEntityTypeException { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + Dataset id = (Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + Software is = (Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(Field::getValue) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + OtherResearchProduct ir = (OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + default: + throw new NoAvailableEntityTypeException(); + } + } + private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { Instance instance = new Instance(); @@ -397,21 +433,58 @@ public class ResultMapper implements Serializable { } private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional 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 opAr = Optional.ofNullable(i.getAccessright()); + + if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + if (opAr.get().getOpenAccessRoute() != null) { + switch (opAr.get().getOpenAccessRoute()) { + case hybrid: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); + break; + case gold: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); + break; + case green: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); + break; + case bronze: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); + break; + + } } + } + Optional + .ofNullable(i.getPid()) + .ifPresent( + pid -> instance + .setPid( + pid + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + Optional + .ofNullable(i.getAlternateIdentifier()) + .ifPresent( + ai -> instance + .setAlternateIdentifier( + ai + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + Optional .ofNullable(i.getLicense()) .ifPresent(value -> instance.setLicense(value.getValue())); @@ -424,11 +497,26 @@ public class ResultMapper implements Serializable { Optional .ofNullable(i.getInstancetype()) .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); + Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); + if (oPca.isPresent() && oPcc.isPresent()) { + Field pca = oPca.get(); + Field pcc = oPcc.get(); + if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { + APC apc = new APC(); + apc.setCurrency(oPcc.get().getValue()); + apc.setAmount(oPca.get().getValue()); + instance.setArticleprocessingcharge(apc); + } + + } Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); } - private static List getUniqueProvenance(List provenance) { + private static List getUniqueProvenance(List provenance) + throws NoAvailableEntityTypeException { Provenance iProv = new Provenance(); Provenance hProv = new Provenance(); @@ -450,6 +538,8 @@ public class ResultMapper implements Serializable { case Constants.USER_CLAIM: lProv = getHighestTrust(lProv, p); break; + default: + throw new NoAvailableEntityTypeException(); } } @@ -503,34 +593,67 @@ public class ResultMapper implements Serializable { return a; } - private static Pid getOrcid(List p) { - for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return Pid + private static Pid getAuthorPid(StructuredProperty pid) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - ); - } - - } + ); } + } + + private static Pid getOrcid(List p) { + List pidList = p.stream().map(pid -> { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || + (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { + return pid; + } + return null; + }).filter(Objects::nonNull).collect(Collectors.toList()); + + if (pidList.size() == 1) { + return getAuthorPid(pidList.get(0)); + } + + List orcid = pidList + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { + return getAuthorPid(orcid.get(0)); + } + orcid = pidList + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID_PENDING)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { + return getAuthorPid(orcid.get(0)); + } + return null; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index f86f6918f9..a6595d756d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -6,6 +6,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.Serializable; import java.nio.charset.StandardCharsets; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; @@ -18,6 +19,7 @@ import org.slf4j.LoggerFactory; import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; /** @@ -30,9 +32,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; public class SaveCommunityMap implements Serializable { private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final QueryInformationSystem queryInformationSystem; + private final transient QueryInformationSystem queryInformationSystem; - private final BufferedWriter writer; + private final transient BufferedWriter writer; public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { final Configuration conf = new Configuration(); @@ -70,13 +72,28 @@ public class SaveCommunityMap implements Serializable { final String isLookUpUrl = parser.get("isLookUpUrl"); log.info("isLookUpUrl: {}", isLookUpUrl); + final Boolean singleCommunity = Optional + .ofNullable(parser.get("singleDeposition")) + .map(Boolean::valueOf) + .orElse(false); + + final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); + final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); - scm.saveCommunityMap(); + scm.saveCommunityMap(singleCommunity, community_id); + } - private void saveCommunityMap() throws ISLookUpException, IOException, DocumentException, SAXException { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap())); + private void saveCommunityMap(boolean singleCommunity, String communityId) + throws ISLookUpException, IOException, DocumentException, SAXException { + final String communityMapString = Utils.OBJECT_MAPPER + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); + log.info("communityMap {} ", communityMapString); + writer + .write( + communityMapString); writer.close(); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index ba26b708a7..a19a3a5b60 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -5,15 +5,13 @@ import java.io.Serializable; import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.MissingConceptDoiException; import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; public class SendToZenodoHDFS implements Serializable { @@ -21,8 +19,6 @@ public class SendToZenodoHDFS implements Serializable { private static final String VERSION = "version"; // to be used to upload a new version of a published deposition private static final String UPDATE = "update"; // to upload content to an open deposition not published - private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); - public static void main(final String[] args) throws Exception, MissingConceptDoiException { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -48,15 +44,12 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); - RemoteIterator fileStatusListIterator = fileSystem .listFiles( new Path(hdfsPath), true); @@ -77,19 +70,17 @@ public class SendToZenodoHDFS implements Serializable { } zenodoApiClient.uploadOpenDeposition(depositionId); break; + default: + throw new NoAvailableEntityTypeException(); } while (fileStatusListIterator.hasNext()) { LocatedFileStatus fileStatus = fileStatusListIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - if (!p_string.endsWith("_SUCCESS")) { - String name = p_string.substring(p_string.lastIndexOf("/") + 1); - log.info("Sending information for community: " + name); - if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { - name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; - } + String pString = p.toString(); + if (!pString.endsWith("_SUCCESS")) { + String name = pString.substring(pString.lastIndexOf("/") + 1); FSDataInputStream inputStream = fileSystem.open(p); zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); @@ -101,7 +92,7 @@ public class SendToZenodoHDFS implements Serializable { zenodoApiClient.sendMretadata(metadata); } - if (publish) { + if (Boolean.TRUE.equals(publish)) { zenodoApiClient.publish(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index b92eb3e602..ee6341f843 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -4,9 +4,7 @@ package eu.dnetlib.dhp.oa.graph.dump.community; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.NoSuchElementException; import java.util.Optional; -import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; @@ -17,6 +15,7 @@ import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Context; /** * This class splits the dumped results according to the research community - research initiative/infrastructure they @@ -35,12 +34,13 @@ public class CommunitySplit implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execSplit(spark, inputPath, outputPath, Utils.getCommunityMap(spark, communityMapPath).keySet()); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + execSplit(spark, inputPath, outputPath, communityMap); }); } private static void execSplit(SparkSession spark, String inputPath, String outputPath, - Set communities) { + CommunityMap communities) { Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -49,34 +49,32 @@ public class CommunitySplit implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); communities - .forEach(c -> printResult(c, result, outputPath)); + .keySet() + .stream() + .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); } - private static void printResult(String community, Dataset result, String outputPath) { + private static void printResult(String c, Dataset result, String outputPath) { Dataset communityProducts = result - .filter((FilterFunction) r -> containsCommunity(r, community)); + .filter((FilterFunction) r -> containsCommunity(r, c)); + + communityProducts + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); - try { - communityProducts.first(); - communityProducts - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/" + community); - } catch (NoSuchElementException e) { - // ignoring it on purpose - } } - private static boolean containsCommunity(CommunityResult r, String community) { + private static boolean containsCommunity(CommunityResult r, String c) { if (Optional.ofNullable(r.getContext()).isPresent()) { - return !r + return r .getContext() .stream() - .filter(con -> con.getCode().equals(community)) + .map(Context::getCode) .collect(Collectors.toList()) - .isEmpty(); + .contains(c); } return false; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 0f2b4c2ed1..87ac20948a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -26,9 +26,11 @@ import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; +import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -78,7 +80,9 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); @@ -98,7 +102,7 @@ public class SparkPrepareResultProject implements Serializable { rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); - Project ps = getProject(p); + Project ps = getProject(p, first._2); List projList = new ArrayList<>(); projList.add(ps); @@ -107,7 +111,7 @@ public class SparkPrepareResultProject implements Serializable { eu.dnetlib.dhp.schema.oaf.Project op = c._1(); if (!projectSet.contains(op.getId())) { projList - .add(getProject(op)); + .add(getProject(op, c._2)); projectSet.add(op.getId()); @@ -122,7 +126,7 @@ public class SparkPrepareResultProject implements Serializable { .json(outputPath); } - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) { + private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { Project p = Project .newInstance( op.getId(), @@ -157,7 +161,9 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - + if (Boolean.TRUE.equals(relation.getValidated())) { + p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); + } return p; } @@ -173,8 +179,8 @@ public class SparkPrepareResultProject implements Serializable { f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream(((Node) node.get(0)).getText()); + List node = ((Node) o).selectNodes("./name"); + f.setFundingStream((node.get(0)).getText()); } return f; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java index 10f2014d00..a468e334da 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.*; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -38,6 +39,7 @@ public class CreateContextRelation implements Serializable { private final transient QueryInformationSystem queryInformationSystem; private static final String CONTEX_RELATION_DATASOURCE = "contentproviders"; + private static final String CONTEX_RELATION_PROJECT = "projects"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -72,6 +74,10 @@ public class CreateContextRelation implements Serializable { cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); log.info("Creating relations for projects... "); + cce + .execute( + Process::getRelation, CONTEX_RELATION_PROJECT, + ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); cce.close(); @@ -115,7 +121,7 @@ public class CreateContextRelation implements Serializable { writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); writer.newLine(); } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 36ced3a4ab..7f64db41cc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; +import static com.jayway.jsonpath.Filter.filter; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; @@ -9,7 +10,10 @@ import java.util.*; 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.ForeachFunction; 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; @@ -18,6 +22,8 @@ import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -453,13 +459,17 @@ public class DumpGraphEntities implements Serializable { .map( (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class)) + .filter((FilterFunction) o -> o != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); } - private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization( + eu.dnetlib.dhp.schema.oaf.Organization org) { + if (org.getDataInfo().getDeletedbyinference()) + return null; Organization organization = new Organization(); Optional diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index 31886d1b13..3e47ee6648 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -62,22 +62,7 @@ public class Extractor implements Serializable { .readPath(spark, inputPath, inputClazz) .flatMap((FlatMapFunction) value -> { List relationList = new ArrayList<>(); - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); + extractRelationsFromInstance(hashCodes, value, relationList); Set communities = communityMap.keySet(); Optional .ofNullable(value.getContext()) @@ -136,8 +121,28 @@ public class Extractor implements Serializable { } + private void extractRelationsFromInstance(Set hashCodes, R value, + List relationList) { + Optional + .ofNullable(value.getInstance()) + .ifPresent(inst -> inst.forEach(instance -> { + Optional + .ofNullable(instance.getCollectedfrom()) + .ifPresent( + cf -> getRelatioPair( + value, relationList, cf, + ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); + Optional + .ofNullable(instance.getHostedby()) + .ifPresent( + hb -> getRelatioPair( + value, relationList, hb, + Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); + })); + } + private static void getRelatioPair(R value, List relationList, KeyValue cf, - String result_dtasource, String datasource_result, + String resultDatasource, String datasourceResult, Set hashCodes) { Provenance provenance = Optional .ofNullable(cf.getDataInfo()) @@ -147,7 +152,7 @@ public class Extractor implements Serializable { .map( paction -> Provenance .newInstance( - paction.getClassid(), + paction.getClassname(), dinfo.getTrust())) .orElse( Provenance @@ -162,7 +167,7 @@ public class Extractor implements Serializable { Relation r = getRelation( value.getId(), cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - result_dtasource, ModelConstants.PROVISION, + resultDatasource, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { relationList @@ -173,7 +178,7 @@ public class Extractor implements Serializable { r = getRelation( cf.getKey(), value.getId(), Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasource_result, ModelConstants.PROVISION, + datasourceResult, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java index b0b8b8acdc..e1cb0e753f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java @@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; @@ -43,7 +44,7 @@ public class Process implements Serializable { return (R) ri; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } @@ -91,7 +92,7 @@ public class Process implements Serializable { return relationList; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 0ed5de67cc..fcc4bf39ce 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -13,6 +13,8 @@ import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -91,9 +93,9 @@ public class QueryInformationSystem { Element root = doc.getRootElement(); cinfo.setId(root.attributeValue("id")); - Iterator it = root.elementIterator(); + Iterator it = root.elementIterator(); while (it.hasNext()) { - Element el = (Element) it.next(); + Element el = it.next(); if (el.getName().equals("category")) { String categoryId = el.attributeValue("id"); categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); @@ -115,14 +117,79 @@ public class QueryInformationSystem { @NotNull private List getCategoryList(Element el, String prefix) { List datasourceList = new ArrayList<>(); - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - if (n.valueOf("./@name").equals("openaireId")) { - datasourceList.add(prefix + "|" + n.getText()); - } + for (Object node : el.selectNodes(".//concept")) { + String oid = getOpenaireId((Node) node, prefix); + if (oid != null) + datasourceList.add(oid); } return datasourceList; } + private String getOpenaireId(Node el, String prefix) { + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + if (n.valueOf("./@name").equals("openaireId")) { + return prefix + "|" + n.getText(); + } + } + + return makeOpenaireId(el, prefix); + + } + + private String makeOpenaireId(Node el, String prefix) { + if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { + return null; + } + String funder = ""; + String grantId = null; + String funding = null; + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + switch (n.valueOf("./@name")) { + case "funding": + funding = n.getText(); + break; + case "funder": + funder = n.getText(); + break; + case "CD_PROJECT_NUMBER": + grantId = n.getText(); + break; + default: + break; + } + } + String nsp = null; + + switch (funder.toLowerCase()) { + case "ec": + if (funding == null) { + return null; + } + if (funding.toLowerCase().contains("h2020")) { + nsp = "corda__h2020::"; + } else { + nsp = "corda_______::"; + } + break; + case "tubitak": + nsp = "tubitakf____::"; + break; + case "dfg": + nsp = "dfgf________::"; + break; + default: + StringBuilder bld = new StringBuilder(); + bld.append(funder.toLowerCase()); + for (int i = funder.length(); i < 12; i++) + bld.append("_"); + bld.append("::"); + nsp = bld.toString(); + } + + return prefix + "|" + nsp + DHPUtils.md5(grantId); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index 11c3600dd9..ddfd6592f9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -71,22 +71,22 @@ public class SparkDumpRelationJob implements Serializable { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel_new = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - rel_new + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); + relNew .setSource( Node .newInstance( relation.getSource(), ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - rel_new + relNew .setTarget( Node .newInstance( relation.getTarget(), ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - rel_new + relNew .setReltype( RelType .newInstance( @@ -96,26 +96,22 @@ public class SparkDumpRelationJob implements Serializable { Optional odInfo = Optional.ofNullable(relation.getDataInfo()); if (odInfo.isPresent()) { DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent()) { - if (Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - rel_new - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } + if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && + Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { + relNew + .setProvenance( + Provenance + .newInstance( + dInfo.getProvenanceaction().getClassname(), + dInfo.getTrust())); } } -// Optional -// .ofNullable(relation.getDataInfo()) -// .ifPresent( -// datainfo -> rel_new -// .setProvenance( -// Provenance -// .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust()))); + if (Boolean.TRUE.equals(relation.getValidated())) { + relNew.setValidated(relation.getValidated()); + relNew.setValidationDate(relation.getValidationDate()); + } - return rel_new; + return relNew; }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) .write() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java index 4365e861fe..f9d2123e2c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java @@ -58,7 +58,8 @@ public class SparkOrganizationRelation implements Serializable { final OrganizationMap organizationMap = new Gson() .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - log.info("organization map : {}", new Gson().toJson(organizationMap)); + final String serializedOrganizationMap = new Gson().toJson(organizationMap); + log.info("organization map : {}", serializedOrganizationMap); final String communityMapPath = parser.get("communityMapPath"); log.info("communityMapPath: {}", communityMapPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java new file mode 100644 index 0000000000..20f3fc4a7e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -0,0 +1,136 @@ + +package eu.dnetlib.dhp.oa.graph.dump.complete; + +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.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.Utils; +import eu.dnetlib.dhp.schema.oaf.*; + +/** + * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference + * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. + * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists + * with this view for both the source and the target + */ + +public class SparkSelectValidRelationsJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkSelectValidRelationsJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_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); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + selectValidRelation(spark, inputPath, outputPath); + + }); + + } + + private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { + Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); + Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); + Dataset dataset = Utils + .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); + Dataset other = Utils + .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); + Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); + Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); + Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); + + relation.createOrReplaceTempView("relation"); + publication.createOrReplaceTempView("publication"); + dataset.createOrReplaceTempView("dataset"); + other.createOrReplaceTempView("other"); + software.createOrReplaceTempView("software"); + organization.createOrReplaceTempView("organization"); + project.createOrReplaceTempView("project"); + datasource.createOrReplaceTempView("datasource"); + + spark + .sql( + "SELECT id " + + "FROM publication " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM dataset " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM other " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM software " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM organization " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM project " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM datasource " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ") + .createOrReplaceTempView("identifiers"); + + spark + .sql( + "SELECT relation.* " + + "FROM relation " + + "JOIN identifiers i1 " + + "ON source = i1.id " + + "JOIN identifiers i2 " + + "ON target = i2.id " + + "WHERE datainfo.deletedbyinference = false") + .as(Encoders.bean(Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java new file mode 100644 index 0000000000..e325c43347 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class MyRuntimeException extends RuntimeException { + + public MyRuntimeException() { + super(); + } + + public MyRuntimeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public MyRuntimeException(final String message, final Throwable cause) { + super(message, cause); + } + + public MyRuntimeException(final String message) { + super(message); + } + + public MyRuntimeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java new file mode 100644 index 0000000000..f3fbf740a3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class NoAvailableEntityTypeException extends Exception { + public NoAvailableEntityTypeException() { + super(); + } + + public NoAvailableEntityTypeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public NoAvailableEntityTypeException(final String message, final Throwable cause) { + super(message, cause); + } + + public NoAvailableEntityTypeException(final String message) { + super(message); + } + + public NoAvailableEntityTypeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index d8a1b5c212..6aed9d7a8c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -17,10 +17,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -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; /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC @@ -51,8 +49,8 @@ public class SparkDumpFunderResults implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("relationPath: {}", graphPath); SparkConf conf = new SparkConf(); @@ -61,18 +59,15 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, relationPath); + writeResultProjectList(spark, inputPath, outputPath, graphPath); }); } private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String relationPath) { + String graphPath) { - Dataset relation = Utils - .readPath(spark, relationPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils + .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -80,8 +75,8 @@ public class SparkDumpFunderResults implements Serializable { .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - List funderList = relation - .select("target") + List funderList = project + .select("id") .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) .distinct() .collectAsList(); @@ -99,19 +94,26 @@ public class SparkDumpFunderResults implements Serializable { } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } - writeFunderResult(funder, result, outputPath + "/" + funderdump); + writeFunderResult(funder, result, outputPath, funderdump); }); } - private static void writeFunderResult(String funder, Dataset results, String outputPath) { + private static void dumpResults(String nsp, Dataset results, String outputPath, + String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { return null; } for (Project p : r.getProjects()) { - if (p.getId().startsWith(funder)) { + if (p.getId().startsWith(nsp)) { + if (nsp.startsWith("40|irb")) { + if (p.getFunder().getShortName().equals(funderName)) + return r; + else + return null; + } return r; } } @@ -121,7 +123,18 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath); + .json(outputPath + "/" + funderName); + } + + private static void writeFunderResult(String funder, Dataset results, String outputPath, + String funderDump) { + + if (funder.startsWith("40|irb")) { + dumpResults(funder, results, outputPath, "HRZZ"); + dumpResults(funder, results, outputPath, "MZOS"); + } else + dumpResults(funder, results, outputPath, funderDump); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 2d2b04b5cc..d89b9e86dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -20,13 +20,13 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Project; 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 + * The code to perform the dump and to expend the dumped results with the information related to projects * is the one used for the dump of the community products */ public class SparkResultLinkedToProject implements Serializable { @@ -58,8 +58,8 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("graphPath: {}", graphPath); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); @@ -70,37 +70,47 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); }); } private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + String inputPath, String outputPath, String graphPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils - .readPath(spark, relationPath, Relation.class) + .readPath(spark, graphPath + "/relation", Relation.class) .filter( "dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - relations - .joinWith( - results, relations.col("source").equalTo(results.col("id")), - "inner") + results.createOrReplaceTempView("result"); + relations.createOrReplaceTempView("relation"); + project.createOrReplaceTempView("project"); + + Dataset tmp = spark + .sql( + "Select res.* " + + "from relation rel " + + "join result res " + + "on rel.source = res.id " + + "join project p " + + "on rel.target = p.id " + + "") + .as(Encoders.bean(inputClazz)); + tmp .groupByKey( - (MapFunction, String>) value -> value - ._2() + (MapFunction) value -> value .getId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, R>) (k, it) -> it.next()._2(), - Encoders.bean(inputClazz)) + .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json index 867fd5a779..03cbfb0744 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json @@ -1,6 +1,23 @@ { "$schema": "http://json-schema.org/draft-07/schema#", "definitions": { + "AccessRight":{ + "type":"object", + "properties":{ + "code": { + "type": "string", + "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" + }, + "label": { + "type": "string", + "description": "Label for the access mode" + }, + "scheme": { + "type": "string", + "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" + } + } + }, "ControlledField": { "type": "object", "properties": { @@ -266,6 +283,57 @@ ] } }, + "instance":{ + "type":"array", + "items":{ + "type":"object", + "properties":{ + "accessright":{ + "allOf":[ + { + "$ref":"#/definitions/AccessRight" + }, + { + "description":"The accessright of this materialization of the result" + } + ] + }, + "articleprocessingcharge":{ + "type":"object", + "properties":{ + "amount":{ + "type":"string" + }, + "currency":{ + "type":"string" + } + } + }, + "license":{ + "type":"string" + }, + "publicationdate":{ + "type":"string" + }, + "refereed":{ + "type":"string" + }, + "type":{ + "type":"string", + "description":"The specific sub-type of this materialization of the result (see https://api.openaire.eu/vocabularies/dnet:result_typologies following the links)" + }, + "url":{ + "description":"Description of url", + "type":"array", + "items":{ + "type":"string", + "description":"urls where it is possible to access the materialization of the result" + } + } + }, + "description":"One of the materialization for this result" + } + }, "programmingLanguage": { "type": "string", "description": "Only for results with type 'software': the programming language" @@ -302,7 +370,7 @@ "subject": { "allOf": [ {"$ref": "#/definitions/ControlledField"}, - {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."}, + {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."} ] } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 9a5a553b1f..5dc8e8910e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -18,8 +18,8 @@ "paramRequired": false }, { - "paramName": "rp", - "paramLongName": "relationPath", + "paramName": "gp", + "paramLongName": "graphPath", "paramDescription": "the relationPath", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json index 6e42bfa643..677715847c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json @@ -18,6 +18,18 @@ "paramLongName": "outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true + }, + { + "paramName": "sd", + "paramLongName": "singleDeposition", + "paramDescription": "true if the dump should be created for a single community", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "communityId", + "paramDescription": "the id of the community for which to create the dump", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index 1d986fc261..e86f6e3d25 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -35,7 +35,12 @@ "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 - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index fdd9492fe7..f5641bc456 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -24,8 +24,8 @@ "paramRequired": true }, { - "paramName":"rp", - "paramLongName":"relationPath", + "paramName":"gp", + "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json index 29812188a5..dec82bc973 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json @@ -25,7 +25,12 @@ "paramLongName": "isSparkSessionManaged", "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json index 683b6f4b73..b02062ede7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json @@ -12,12 +12,7 @@ "paramDescription": "The id of the concept record for a new version", "paramRequired": false }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": false - }, + { "paramName":"di", "paramLongName":"depositionId", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml new file mode 100644 index 0000000000..d262cb6e05 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt new file mode 100644 index 0000000000..bf55947d14 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt @@ -0,0 +1,4 @@ +## This is a classpath-based import file (this header is required) +dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app +dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app +dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml new file mode 100644 index 0000000000..2a612dec59 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml @@ -0,0 +1,306 @@ + + + + + singleDeposition + Indicates if it is a single community deposition + + + communityId + the id of the community to be dumped if a dump for a single community should be done + + + dumpType + the type of the dump one of {complete, community, funder} + + + onlyUpload + true if the dump is already done and should only be upload in zenodo + + + upload + true if the dump should be upload in zenodo + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + 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) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:conf('onlyUpload') eq true} + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + --singleDeposition${singleDeposition} + --communityId${communityId} + + + + + + + + ${wf:conf('dumpType') eq "funder"} + ${wf:conf('dumpType') eq "community"} + + + + + + + + ${wf:appPath()}/dump_complete + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + organizationCommunityMap + ${organizationCommunityMap} + + + isLookUpUrl + ${isLookUpUrl} + + + resultAggregation + ${resultAggregation} + + + + + + + + + + + ${wf:appPath()}/dump_community + + + + + sourcePath + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + + + + + + + + ${wf:appPath()}/dump_funder + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + dumpType + ${dumpType} + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + + ${wf:conf('upload') eq true} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml new file mode 100644 index 0000000000..5f954ff38a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml @@ -0,0 +1,347 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + communityMapPath + the path to the community map + + + selectedResults + the path the the possible subset ot results to be dumped + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt new file mode 100644 index 0000000000..15387e988d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml new file mode 100644 index 0000000000..319517026a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + + + yarn + cluster + Split dumped result for community + eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --communityMapPath${communityMapPath} + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml new file mode 100644 index 0000000000..f84ab7e1ad --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -0,0 +1,537 @@ + + + + sourcePath + the source path + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table organization + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/organization + --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization + --outputPath${outputPath}/organization + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${outputPath}/project + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table datasource + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/datasource + --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputPath${outputPath}/datasource + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Select valid table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath} + --outputPath${workingDir}/validrelation + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${workingDir}/validrelation + --outputPath${workingDir}/relation/relation + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities + --hdfsPath${outputPath}/communities_infrastructures/communities_infrastructure.json.gz + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation + --hdfsPath${workingDir}/relation/context + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/relation/contextOrg + --organizationCommunityMap${organizationCommunityMap} + --communityMapPath${communityMapPath} + + + + + + + + + + + + + + + + + yarn + cluster + Extract Relations from publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/relation/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/relation/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/relation/orp + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/relation/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Collect Results and Relations and put them in the right path + eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${workingDir} + --outputPath${outputPath} + --resultAggregation${resultAggregation} + + + + + + + + + Sub-workflow dump complete failed with error message ${wf:errorMessage()} + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt new file mode 100644 index 0000000000..15387e988d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml new file mode 100644 index 0000000000..b990f4e49b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -0,0 +1,256 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${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} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --graphPath${sourcePath} + + + + + + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${workingDir}/result + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults + dhp-graph-mapper-${projectVersion}.jar + + --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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --graphPath${sourcePath} + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 7c69c9635f..bf6301ec47 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -11,17 +11,21 @@ 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.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.core.JsonProcessingException; 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.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; 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; @@ -137,6 +141,512 @@ public class DumpJobTest { System.out.println(new Gson().toJson(map)); } + @Test + public void testPublicationDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getMeasures().size()); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("influence") + && m.getValue().equals("1.62759106106e-08"))); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("popularity") + && m.getValue().equals("0.22519296"))); + + Assertions.assertEquals(6, gr.getAuthor().size()); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Nikolaidou,Charitini") && + a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") + && a.getRank() == 1 && a.getPid() == null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Votsi,Nefta") && + a.getName().equals("Nefta") && a.getSurname().equals("Votsi") + && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Sgardelis,Steanos") && + a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") + && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Halley,John") && + a.getName().equals("John") && a.getSurname().equals("Halley") + && a.getRank() == 4 && a.getPid() == null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Pantis,John") && + a.getName().equals("John") && a.getSurname().equals("Pantis") + && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Tsiafouli,Maria") && + a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") + && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions.assertEquals("publication", gr.getType()); + + Assertions.assertEquals("eng", gr.getLanguage().getCode()); + Assertions.assertEquals("English", gr.getLanguage().getLabel()); + + Assertions.assertEquals(1, gr.getCountry().size()); + Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); + Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); + Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); + + Assertions.assertEquals(12, gr.getSubjects().size()); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") + && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Natura 2000") + && s.getSubject().getScheme().equals("") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + + Assertions + .assertEquals( + "Ecosystem Service capacity is higher in areas of multiple designation types", + gr.getMaintitle()); + + Assertions.assertEquals(null, gr.getSubtitle()); + + Assertions.assertEquals(1, gr.getDescription().size()); + + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .endsWith( + "start complying with new standards and demands for nature conservation and environmental management.")); + + Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); + + Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); + + Assertions.assertEquals(null, gr.getEmbargoenddate()); + + Assertions.assertEquals(1, gr.getSource().size()); + Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); + + Assertions.assertEquals(1, gr.getFormat().size()); + Assertions.assertEquals("text/html", gr.getFormat().get(0)); + + Assertions.assertEquals(0, gr.getContributor().size()); + + Assertions.assertEquals(0, gr.getCoverage().size()); + + Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); + Assertions + .assertEquals( + Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); + Assertions.assertEquals(null, gr.getBestaccessright().getOpenAccessRoute()); + + Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); + Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); + Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); + Assertions.assertEquals("", gr.getContainer().getIssnLinking()); + + Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); + + Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); + + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + + Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); + + Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); + + Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); + + Assertions.assertEquals(null, gr.getSize()); + + Assertions.assertEquals(null, gr.getVersion()); + + Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); + + Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); + + Assertions.assertEquals(2, gr.getOriginalId().size()); + Assertions + .assertTrue( + gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") + && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); + + Assertions.assertEquals(1, gr.getPid().size()); + Assertions + .assertTrue( + gr.getPid().get(0).getScheme().equals("doi") + && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); + + Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); + + Assertions.assertEquals(1, gr.getInstance().size()); + + Instance instance = gr.getInstance().get(0); + Assertions.assertEquals(0, instance.getPid().size()); + Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); + Assertions + .assertTrue( + instance.getAlternateIdentifier().get(0).getScheme().equals("doi") + && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); + Assertions.assertEquals(null, instance.getLicense()); + Assertions + .assertTrue( + instance + .getAccessright() + .getCode() + .equals( + Constants.accessRightsCoarMap + .get(ModelConstants.ACCESS_RIGHT_OPEN))); + Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); + Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); + Assertions.assertTrue(instance.getType().equals("Article")); + Assertions.assertEquals(2, instance.getUrl().size()); + Assertions + .assertTrue( + instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") + && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); + Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); + Assertions.assertEquals(null, instance.getArticleprocessingcharge()); + Assertions.assertEquals("peerReviewed", instance.getRefereed()); + } + + @Test + public void testDatasetDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Dataset.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); + + // the common fields in the result have been already checked. Now checking only + // community specific fields + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getGeolocation().size()); + Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) + .count()); + Assertions + .assertEquals( + 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) + .count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) + .count()); + + Assertions.assertEquals("1024Gb", gr.getSize()); + + Assertions.assertEquals("1.01", gr.getVersion()); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + + } + + @Test + public void testSoftwareDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Software.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getDocumentationUrl().size()); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); + + Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); + + Assertions.assertEquals("perl", gr.getProgrammingLanguage()); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testOrpDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, OtherResearchProduct.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getContactperson().size()); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); + + Assertions.assertEquals(1, gr.getContactgroup().size()); + Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); + + Assertions.assertEquals(2, gr.getTool().size()); + Assertions.assertTrue(gr.getTool().contains("tool1")); + Assertions.assertTrue(gr.getTool().contains("tool2")); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testPublicationDumpCommunity() throws JsonProcessingException { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); + + // the common fields in the result have been already checked. Now checking only + // community specific fields + + CommunityResult cr = verificationDataset.first(); + + Assertions.assertEquals(1, cr.getContext().size()); + Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); + Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); + Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); + Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); + Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); + + Assertions.assertEquals(1, cr.getCollectedfrom().size()); + Assertions + .assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); + Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); + + Assertions.assertEquals(1, cr.getInstance().size()); + Assertions + .assertEquals( + "10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", + cr.getInstance().get(0).getCollectedfrom().getKey()); + Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); + Assertions + .assertEquals( + "10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); + Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); + + } + @Test public void testDataset() { @@ -151,7 +661,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -166,10 +675,6 @@ public class DumpJobTest { Assertions.assertEquals(90, verificationDataset.count()); -// verificationDataset -// .filter("id = '50|DansKnawCris::1a960e20087cb46b93588e4e184e8a58'") -// .foreach((ForeachFunction) rec -> System.out.println(OBJECT_MAPPER.writeValueAsString(rec))); - Assertions .assertTrue( verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset @@ -198,8 +703,6 @@ public class DumpJobTest { Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) - } @Test @@ -231,8 +734,6 @@ public class DumpJobTest { Assertions.assertEquals(5, verificationDataset.count()); - verificationDataset - .foreach((ForeachFunction) res -> System.out.println(OBJECT_MAPPER.writeValueAsString(res))); } @Test @@ -249,7 +750,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -264,7 +764,6 @@ public class DumpJobTest { Assertions.assertEquals(0, verificationDataset.count()); - verificationDataset.show(false); } @Test @@ -299,8 +798,6 @@ public class DumpJobTest { Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) - } @Test @@ -333,9 +830,6 @@ public class DumpJobTest { Assertions.assertEquals(6, verificationDataset.count()); Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - verificationDataset.show(false); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -369,9 +863,6 @@ public class DumpJobTest { Assertions.assertEquals(3, verificationDataset.count()); Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - verificationDataset.show(false); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -388,7 +879,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -408,4 +898,51 @@ public class DumpJobTest { } + @Test + public void testArticlePCA() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(23, verificationDataset.count()); + + Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); + + verificationDataset.createOrReplaceTempView("check"); + + org.apache.spark.sql.Dataset temp = spark + .sql( + "select id " + + "from check " + + "lateral view explode (instance) i as inst " + + "where inst.articleprocessingcharge is not null"); + + Assertions.assertTrue(temp.count() == 2); + + Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); + + Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 03eed7a450..86d2f93c9c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -223,4 +223,102 @@ public class PrepareResultProjectJobTest { } + @Test + public void testMatchValidated() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + assertEquals(2, verificationDataset.count()); + + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + assertEquals(3, resultExplodedProvenance.count()); + assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); + assertEquals( + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); + + assertEquals( + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); + + assertEquals( + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java index 98902b618e..8391c89630 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java @@ -25,7 +25,7 @@ class QueryInformationSystemTest { private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + @@ -71,7 +71,7 @@ class QueryInformationSystemTest { lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); queryInformationSystem = new QueryInformationSystem(); queryInformationSystem.setIsLookUp(isLookUpService); - map = queryInformationSystem.getCommunityMap(); + map = queryInformationSystem.getCommunityMap(false, null); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java index e6f0e91069..4209caad34 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java @@ -79,7 +79,7 @@ public class SplitForCommunityTest { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/dh-ch") + .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark @@ -92,7 +92,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/egi") + .textFile(workingDir.toString() + "/split/EGI_Federation") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -105,7 +105,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/ni") + .textFile(workingDir.toString() + "/split/Neuroinformatics") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -118,7 +118,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/science-innovation-policy") + .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java index a164593ec3..9710e45537 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java @@ -5,11 +5,15 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; +import java.util.logging.Filter; +import java.util.stream.Collectors; 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.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -25,6 +29,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; public class UpdateProjectInfoTest { @@ -135,4 +141,96 @@ public class UpdateProjectInfoTest { resultExplodedProvenance.show(false); } + @Test + public void testValidatedRelation() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") + .getPath(); + + SparkUpdateProjectInfo.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-preparedInfoPath", sourcePath + "/preparedInfoValidated", + "-outputPath", workingDir.toString() + "/result", + "-sourcePath", sourcePath + "/publication_extendedmodel" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + verificationDataset.show(false); + + Assertions.assertEquals(2, verificationDataset.count()); + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " + + + "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " + + "from dataset " + + "lateral view explode(projects) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + + Assertions.assertEquals(2, resultExplodedProvenance.count()); + resultExplodedProvenance.show(false); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") + .count()); + + Project project = verificationDataset + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() != null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); + + Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); + Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); + Assertions.assertTrue(project.getFunder().getFundingStream() == null); + Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); + + project = verificationDataset + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() == null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); + + Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); + Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); + Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java index 69e550d45b..d2343d274f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java @@ -14,6 +14,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; class CreateRelationTest { @@ -203,6 +204,7 @@ class CreateRelationTest { " \n" + " oac_ni\n" + " 2018-03-01T12:00:00\n" + + " \n" + " \n" + " \n" + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + @@ -376,7 +378,7 @@ class CreateRelationTest { " \n" + " 675858\n" + " \n" + - " H2020-EINFRA-2015-1\n" + + " EC | H2020 | RIA\n" + " EC\n" + " West-Life\n" + " \n" + @@ -437,7 +439,65 @@ class CreateRelationTest { " \n" + " oaa_elixir-gr\n" + " 2018-03-01T12:00:00\n" + - " \n" + + " \n" + + " \n" + + " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" + + + " \n" + + " 1U24RR025736-01\n" + + " NIH\n" + + " \n" + + " \n" + + " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" + + + " \n" + + " 0223843\n" + + " NSF\n" + + " \n" + + " \n" + + " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" + + + " \n" + + " 5R01MH082795-05\n" + + " NIH\n" + + " \n" + + " \n" + + " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" + + + " \n" + + " 1P50MH096889-01A1\n" + + " NIH\n" + + " \n" + + " \n" + + " Enhancement of the 1000 Functional Connectome Project\n" + + + " \n" + + " 1R03MH096321-01A1\n" + + " TUBITAK\n" + + " \n" + + " \n" + + " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" + + + " \n" + + " 1131441\n" + + " NSF\n" + + " \n" + + " \n" + + " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" + + + " \n" + + " 0121950\n" + + " NSF\n" + + " \n" + + " \n" + + " Transforming statistical methodology for neuroimaging meta-analysis.\n" + + + " \n" + + " 100309\n" + + " WT\n" + + " \n" + + " " + + " \n" + " \n" + @@ -566,4 +626,98 @@ class CreateRelationTest { tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); } + + @Test + public void test2() { + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + + queryInformationSystem + .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); + + cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); + + List rList = new ArrayList<>(); + + cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); + + Assertions.assertEquals(44, rList.size()); + + Assertions + .assertFalse( + rList + .stream() + .map(r -> r.getSource().getId()) + .collect(Collectors.toSet()) + .contains( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getTarget() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Set tmp = rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .map(r -> r.getTarget().getId()) + .collect(Collectors.toSet()); + + Assertions + .assertTrue( + tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && + tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4")); + + rList.forEach(rel -> { + if (rel.getSource().getId().startsWith("40|")) { + String proj = rel.getSource().getId().substring(3); + Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); + } + }); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 69100a114e..80b5fd89e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Project; @@ -88,7 +89,7 @@ public class DumpOrganizationProjectDatasourceTest { org.apache.spark.sql.Dataset verificationDataset = spark .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - Assertions.assertEquals(34, verificationDataset.count()); + Assertions.assertEquals(15, verificationDataset.count()); verificationDataset .foreach( @@ -98,7 +99,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpProjectTest() { + public void dumpProjectTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") @@ -127,7 +128,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpDatasourceTest() { + public void dumpDatasourceTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") .getPath(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java index d80eb3ec6e..fe178795d7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java @@ -10,6 +10,7 @@ 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.api.java.function.ForeachFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; @@ -71,7 +72,7 @@ public class DumpRelationTest { public void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") .getPath(); SparkDumpRelationJob.main(new String[] { @@ -93,6 +94,9 @@ public class DumpRelationTest { verificationDataset.createOrReplaceTempView("table"); + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + Dataset check = spark .sql( "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " @@ -127,4 +131,76 @@ public class DumpRelationTest { .count()); } + @Test + public void test2() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + verificationDataset.createOrReplaceTempView("table"); + + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + Dataset check = spark + .sql( + "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " + + + "from table "); + + Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 20, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); + Assertions + .assertEquals( + 7, check + .filter( + "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + + "and provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); + Assertions + .assertEquals( + 1, check + .filter( + "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + + "and provenance = 'Inferred by OpenAIRE'") + .count()); + + Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); + Assertions + .assertEquals( + 2, check + .filter( + "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + + "and provenance = 'Harvested' and validated = true " + + "and validationDate = '2021-08-06'") + .count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java index 0499597046..08fcd49a86 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java @@ -13,6 +13,7 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -528,7 +529,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|"); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); Assertions.assertEquals(5, cInfoList.size()); } @@ -539,7 +541,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10"); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); cInfoList.forEach(contextInfo -> { switch (contextInfo.getId()) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java new file mode 100644 index 0000000000..3e4ab93c55 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java @@ -0,0 +1,100 @@ + +package eu.dnetlib.dhp.oa.graph.dump.complete; + +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.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Relation; +import net.sf.saxon.expr.instruct.ForEach; + +public class SelectRelationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(SelectRelationTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SelectRelationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SelectRelationTest.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(SelectRelationTest.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/selectrelations") + .getPath(); + + SparkSelectValidRelationsJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); + + Assertions.assertTrue(verificationDataset.count() == 7); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index d1e3b3acc5..4967ae5a53 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -75,8 +75,8 @@ public class ResultLinkedToProjectTest { .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") + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -84,7 +84,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", graphPath }); @@ -109,7 +109,7 @@ public class ResultLinkedToProjectTest { .getPath(); final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -117,7 +117,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", relationPath }); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 8ac0c552f4..477481c080 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -75,7 +75,7 @@ public class SplitPerFunderTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-outputPath", workingDir.toString() + "/split", "-sourcePath", sourcePath, - "-relationPath", sourcePath + "-graphPath", sourcePath }); @@ -137,5 +137,17 @@ public class SplitPerFunderTest { .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); + // MZOS 1 + tmp = sc + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // CONICYT 0 + tmp = sc + .textFile(workingDir.toString() + "/split/CONICYTF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(0, tmp.count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index 1bdcb60aaf..4613d56369 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -54,7 +54,7 @@ class TestApply extends java.io.Serializable{ assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy")) assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) - assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.gold)) assertTrue(pa.getBestaccessright.getClassid.equals("OPEN")) assertTrue(pa.getBestaccessright.getClassname.equals("Open Access")) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated new file mode 100644 index 0000000000..588bec8040 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated @@ -0,0 +1,2 @@ +{"resultId":"50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2","projectsList":[{"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","code":"123455","acronym":null,"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":{"validationDate":"2021-08-06","validatedByFunder":true}},{"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","code":"119027","acronym":null,"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer","funder":{"shortName":"EC","name":"European Commission","jurisdiction":"EU","fundingStream":"H2020"},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":null}]} +{"resultId":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80","projectsList":[{"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","code":"123455","acronym":null,"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":{"validationDate":"2021-08-04","validatedByFunder":true}}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel new file mode 100644 index 0000000000..6b146405a9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel @@ -0,0 +1,2 @@ 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b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json index d172419bf7..e141af7872 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json @@ -1,6 +1,5 @@ {"alternativeNames":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"value":"한국초등도덕교육학회"}],"collectedfrom":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"key":"10|openaire____::ff4a008470319a22d9cf3d14af485977","value":"GRID - Global Research Identifier 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)","New York University [Abu Dhabi] ; NYU System (NYU)","Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Muséum National d'Histoire Naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)","University of Washington [Seattle]","Université Libre de Bruxelles [Bruxelles] (ULB)","ANR-09-CEXC-0006,FOCEA,Excellence pour une synergie observation-modèle et l'évaluation de l'état écologique de la Méditerranée Nord Occidentale(2009)","ANR: 11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)","ANR: 11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011)","European Project: 624170,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IEF,SEAQUEST(2015)","Institut méditerranéen d'océanologie (MIO) ; Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)","Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)","Université libre de Bruxelles (ULB)","Processus et interactions de fine échelle océanique (PROTEO) ; Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)","ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011)"],"country":[{"code":"FR","label":"France","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2019-10-11T09:44:42.348Z","description":["International audience; Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Pensoft 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