diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java deleted file mode 100644 index 8ceee5c8a0..0000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ /dev/null @@ -1,413 +0,0 @@ - -package eu.dnetlib.dhp.common; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.*; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -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; - -public class GraphResultMapper implements Serializable { - - public static Result map( - E in) { - - CommunityResult out = new CommunityResult(); - - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - 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())); - - 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": - - 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()))); - - 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(GraphResultMapper::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())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } - - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); - - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - 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()) { - out - .setInstance( - oInst.get().stream().map(GraphResultMapper::getInstance).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.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()); - } - - } - - 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()); - } - - out - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - return out; - - } - - private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); - - setCommonValue(i, instance); - - instance - .setCollectedfrom( - KeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - - instance - .setHostedby( - KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - - return instance; - - } - - private static 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 - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - - } - - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } - - return subject; - } - - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); - - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - Pid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } - - 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 - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - - } - } - return null; - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/index.md b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md index 240617f912..6c4e05d5fa 100644 --- a/dhp-workflows/dhp-aggregation/src/site/markdown/index.md +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md @@ -16,5 +16,5 @@ It defines [mappings](mappings.md) for transformation of different datasource (S ### Integration of external information in the result -The workflows create new entity in the OpenAIRE format (OAF) which aim is to enrich the result already contained in the graph. +The workflows create new entity in the OpenAIRE format (OAF) whose aim is to enrich the result already contained in the graph. See integration section for more insight diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md index baf232e40f..7b763c6810 100644 --- a/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md @@ -9,7 +9,7 @@ The information integrated so far is: 1. Article impact measures 1. [Bip!Finder](https://dl.acm.org/doi/10.1145/3357384.3357850) scores 2. Result Subjects - 1. Integration of Fields od Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in + 1. Integration of Fields of Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in results subjects. @@ -18,7 +18,7 @@ and the element in the OAF model that should be used to map the information we w The id is set by using a particular encoding of the given PID -*unresolved:[pid]:[pidtype]* +*unresolved::[pid]::[pidtype]* where @@ -31,6 +31,6 @@ Such entities are matched against those available in the graph using the result. This mechanism can be used to integrate enrichments produced as associated by a given PID. If a match will be found with one of the results already in the graph that said result will be enriched with the information present in the new OAF. -All the objects for which a match is not found are discarded. +All the entities for which a match is not found are discarded. 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 1beea5cb48..aad3a87062 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 @@ -12,13 +12,12 @@ 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.Measure; 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.CfHbKeyValue; 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; @@ -56,7 +55,8 @@ public class ResultMapper implements Serializable { String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); out .setBestaccessright( - AccessRight + + BestAccessRight .newInstance( code, Constants.coarCodeLabelMap.get(code), @@ -81,7 +81,7 @@ public class ResultMapper implements Serializable { if (c.getClassid().equals((ModelConstants.UNKNOWN))) { return null; } - Country country = new Country(); + ResultCountry country = new ResultCountry(); country.setCode(c.getClassid()); country.setLabel(c.getClassname()); Optional @@ -124,7 +124,17 @@ public class ResultMapper implements Serializable { .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); out.setFormat(formatList); out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); + out.setOriginalId(new ArrayList<>()); + Optional + .ofNullable(input.getOriginalId()) + .ifPresent( + v -> out + .setOriginalId( + input + .getOriginalId() + .stream() + .filter(s -> !s.startsWith("50|")) + .collect(Collectors.toList()))); Optional> oInst = Optional .ofNullable(input.getInstance()); @@ -148,7 +158,7 @@ public class ResultMapper implements Serializable { 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())); + out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname())); } Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); if (oLong.isPresent()) { @@ -184,7 +194,7 @@ public class ResultMapper implements Serializable { value .stream() .map( - p -> ControlledField + p -> ResultPid .newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); @@ -219,7 +229,7 @@ public class ResultMapper implements Serializable { input .getCollectedfrom() .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .map(cf -> CfHbKeyValue.newInstance(cf.getKey(), cf.getValue())) .collect(Collectors.toList())); Set communities = communityMap.keySet(); @@ -412,12 +422,12 @@ public class ResultMapper implements Serializable { instance .setCollectedfrom( - KeyValue + CfHbKeyValue .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); instance .setHostedby( - KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + CfHbKeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); return instance; @@ -436,6 +446,17 @@ public class ResultMapper implements Serializable { code, Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); + + Optional> mes = Optional.ofNullable(i.getMeasures()); + if (mes.isPresent()) { + List measure = new ArrayList<>(); + mes + .get() + .forEach( + m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue())))); + instance.setMeasures(measure); + } + if (opAr.get().getOpenAccessRoute() != null) { switch (opAr.get().getOpenAccessRoute()) { case hybrid: @@ -463,7 +484,7 @@ public class ResultMapper implements Serializable { .setPid( pid .stream() - .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); Optional @@ -473,7 +494,7 @@ public class ResultMapper implements Serializable { .setAlternateIdentifier( ai .stream() - .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); Optional @@ -553,7 +574,7 @@ public class ResultMapper implements Serializable { private static Subject getSubject(StructuredProperty s) { Subject subject = new Subject(); - subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue())); Optional di = Optional.ofNullable(s.getDataInfo()); if (di.isPresent()) { Provenance p = new Provenance(); @@ -575,7 +596,7 @@ public class ResultMapper implements Serializable { Optional> oPids = Optional .ofNullable(oa.getPid()); if (oPids.isPresent()) { - Pid pid = getOrcid(oPids.get()); + AuthorPid pid = getOrcid(oPids.get()); if (pid != null) { a.setPid(pid); } @@ -584,12 +605,12 @@ public class ResultMapper implements Serializable { return a; } - private static Pid getAuthorPid(StructuredProperty pid) { + private static AuthorPid getAuthorPid(StructuredProperty pid) { Optional di = Optional.ofNullable(pid.getDataInfo()); if (di.isPresent()) { - return Pid + return AuthorPid .newInstance( - ControlledField + AuthorPidSchemeValue .newInstance( pid.getQualifier().getClassid(), pid.getValue()), @@ -598,9 +619,9 @@ public class ResultMapper implements Serializable { di.get().getProvenanceaction().getClassname(), di.get().getTrust())); } else { - return Pid + return AuthorPid .newInstance( - ControlledField + AuthorPidSchemeValue .newInstance( pid.getQualifier().getClassid(), pid.getValue()) @@ -609,7 +630,7 @@ public class ResultMapper implements Serializable { } } - private static Pid getOrcid(List p) { + private static AuthorPid getOrcid(List p) { List pidList = p.stream().map(pid -> { if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java index 120de9327b..c422c3b404 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java @@ -41,7 +41,7 @@ public class CreateContextEntities implements Serializable { .toString( CreateContextEntities.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); 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 a468e334da..03f53de641 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 @@ -48,7 +48,7 @@ public class CreateContextRelation implements Serializable { .requireNonNull( CreateContextRelation.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json"))); + "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); 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 7f64db41cc..c9de866139 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 @@ -1,7 +1,6 @@ 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; @@ -11,9 +10,7 @@ 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; @@ -22,8 +19,6 @@ 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; @@ -133,14 +128,14 @@ public class DumpGraphEntities implements Serializable { .ifPresent( pids -> pids .stream() - .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .map(p -> DatasourcePid.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList())); Optional .ofNullable(d.getDatasourcetype()) .ifPresent( dsType -> datasource - .setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname()))); + .setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname()))); Optional .ofNullable(d.getOpenairecompatibility()) @@ -499,7 +494,7 @@ public class DumpGraphEntities implements Serializable { .ifPresent( value -> { if (!value.getClassid().equals(Constants.UNKNOWN)) { - organization.setCountry(Qualifier.newInstance(value.getClassid(), value.getClassname())); + organization.setCountry(Country.newInstance(value.getClassid(), value.getClassname())); } }); @@ -515,7 +510,7 @@ public class DumpGraphEntities implements Serializable { .setPid( value .stream() - .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue())) .collect(Collectors.toList()))); return organization; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java index 671bccd25c..1c98ea6cb9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java @@ -31,7 +31,7 @@ public class SparkCollectAndSave implements Serializable { .toString( SparkCollectAndSave.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java index 8b282386f8..7cc05a821d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java @@ -22,7 +22,7 @@ public class SparkDumpEntitiesJob implements Serializable { .toString( SparkDumpEntitiesJob.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); 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 ddfd6592f9..0ac97dcb64 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 @@ -4,10 +4,11 @@ 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 java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -37,7 +38,7 @@ public class SparkDumpRelationJob implements Serializable { .toString( SparkDumpRelationJob.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -54,6 +55,12 @@ public class SparkDumpRelationJob implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); + Optional rs = Optional.ofNullable(parser.get("removeSet")); + final Set removeSet = new HashSet<>(); + if (rs.isPresent()) { + Collections.addAll(removeSet, rs.get().split(";")); + } + SparkConf conf = new SparkConf(); runWithSparkSession( @@ -61,15 +68,16 @@ public class SparkDumpRelationJob implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - dumpRelation(spark, inputPath, outputPath); + dumpRelation(spark, inputPath, outputPath, removeSet); }); } - private static void dumpRelation(SparkSession spark, String inputPath, String outputPath) { + private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set removeSet) { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations + .filter((FilterFunction) r -> !removeSet.contains(r.getRelClass())) .map((MapFunction) relation -> { eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); relNew 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 f9d2123e2c..dff1a1066e 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 @@ -39,7 +39,7 @@ public class SparkOrganizationRelation implements Serializable { .toString( SparkOrganizationRelation.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); 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 index 20f3fc4a7e..1e5675e5ff 100644 --- 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 @@ -35,7 +35,7 @@ public class SparkSelectValidRelationsJob implements Serializable { .toString( SparkSelectValidRelationsJob.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0aee..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - 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/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml deleted file mode 100644 index fcef2547ac..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml +++ /dev/null @@ -1,431 +0,0 @@ - - - - - sourcePath - the source path - - - isLookUpUrl - the isLookup service endpoint - - - outputPath - the output path - - - accessToken - the access token used for the deposition in Zenodo - - - connectionUrl - the connection url for Zenodo - - - metadata - the metadata associated to the deposition - - - depositionType - one among {new, update, version} - - - conceptRecordId - for new version, the id of the record for the old deposition - - - 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())}] - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap - --outputPath${workingDir}/communityMap - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${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=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/publication - --communityMapPath${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table dataset 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${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dataset - --communityMapPath${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${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=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/otherresearchproduct - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/software - --communityMapPath${workingDir}/communityMap - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${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}/publication - --outputPath${workingDir}/ext/publication - --preparedInfoPath${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${workingDir}/dataset - --outputPath${workingDir}/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}/otherresearchproduct - --outputPath${workingDir}/ext/orp - --preparedInfoPath${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${workingDir}/software - --outputPath${workingDir}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - yarn - cluster - Split dumped result for community - eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity - dhp-graph-mapper-${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${workingDir}/split - --communityMapPath${workingDir}/communityMap - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/split - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --communityMapPath${workingDir}/communityMap - --conceptRecordId${conceptRecordId} - --depositionId${depositionId} - --depositionType${depositionType} - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0aee..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - 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/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml deleted file mode 100644 index 8189e25945..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ /dev/null @@ -1,586 +0,0 @@ - - - - - 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())}] - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap - --outputPath${workingDir}/communityMap - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - - - - - - - - - - - - yarn - cluster - Dump table publication - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${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${workingDir}/result/publication - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table ORP - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${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${workingDir}/result/otherresearchproduct - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table organization - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${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${workingDir}/collect/organization - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${sourcePath}/project - --resultTableNameeu.dnetlib.dhp.schema.oaf.Project - --outputPath${workingDir}/collect/project - --communityMapPath${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table datasource - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${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${workingDir}/collect/datasource - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${sourcePath}/relation - --outputPath${workingDir}/relation/relation - - - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${workingDir}/collect/communities_infrastructures/communities_infrastructure.json.gz - --nameNode${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${organizationCommunityMap} - --communityMapPath${workingDir}/communityMap - - - - - - - - - - - - - - - - - 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${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table dataset - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${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${workingDir}/relation/dataset - --communityMapPath${workingDir}/communityMap - - - - - - - - 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${workingDir}/communityMap - - - - - - - - yarn - cluster - Dump table software - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${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${workingDir}/relation/software - --communityMapPath${workingDir}/communityMap - - - - - - - - - - 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${workingDir} - --outputPath${workingDir}/collect - --resultAggregation${resultAggregation} - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/collect - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --communityMapPath${workingDir}/communityMap - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/community_infrastructure_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/community_infrastructure_schema.json deleted file mode 100644 index d2f1792125..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/community_infrastructure_schema.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "description": { - "type": "string", - "description": "Description of the research community/research infrastructure" - }, - "id": { - "type": "string", - "description": "OpenAIRE id of the research community/research infrastructure" - }, - "name": { - "type": "string", - "description": "The long name of the community" - }, - "originalId": { - "type": "string", - "description": "The acronym of the community" - }, - "subject": { - "description": "Only for research communities: the list of the subjects associated to the research community", - "type": "array", - "items": { - "type": "string" - } - }, - "type": { - "type": "string", - "description": "One of {Research Community, Research infrastructure}" - }, - "zenodo_community": { - "type": "string", - "description": "The URL of the Zenodo community associated to the Research community/Research infrastructure" - } - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/datasource_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/datasource_schema.json deleted file mode 100644 index b9c15d9219..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/datasource_schema.json +++ /dev/null @@ -1,192 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "definitions": { - "ControlledField": { - "type": "object", - "properties": { - "scheme": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "description": "To represent the information described by a scheme and a value in that scheme (i.e. pid)" - } - }, - "type": "object", - "properties": { - "accessrights": { - "type": "string", - "description": "Type of access to the data source, as defined by re3data.org. Possible values: {open, restricted, closed}" - }, - "certificates": { - "type": "string", - "description": "The certificate, seal or standard the data source complies with. As defined by re3data.org." - }, - "citationguidelineurl": { - "type": "string", - "description":"The URL of the data source providing information on how to cite its items. As defined by re3data.org." - }, - "contenttypes": { - "description": "Types of content in the data source, as defined by OpenDOAR", - "type": "array", - "items": { - "type": "string" - } - }, - "databaseaccessrestriction": { - "type": "string", - "description": "Access restrinctions to the data source, as defined by re3data.org. One of {feeRequired, registration, other}" - }, - "datasourcetype": { - "allOf": [ - { - "$ref": "#/definitions/ControlledField" - }, - { - "description": "The type of the datasource. See https://api.openaire.eu/vocabularies/dnet:datasource_typologies" - } - ] - }, - "datauploadrestriction": { - "type": "string", - "description": "Upload restrictions applied by the datasource, as defined by re3data.org. One of {feeRequired, registration, other}" - }, - "dateofvalidation": { - "type": "string", - "description": "The date of last validation against the OpenAIRE guidelines for the datasource records" - }, - "description": { - "type": "string" - }, - "englishname": { - "type": "string", - "description": "The English name of the datasource" - }, - "id": { - "type": "string", - "description": "The OpenAIRE id of the data source" - }, - "journal": { - "type": "object", - "properties": { - "conferencedate": { - "type": "string" - }, - "conferenceplace": { - "type": "string" - }, - "edition": { - "type": "string" - }, - "ep": { - "type": "string", - "description": "End page" - }, - "iss": { - "type": "string", - "description": "Issue number" - }, - "issnLinking": { - "type": "string" - }, - "issnOnline": { - "type": "string" - }, - "issnPrinted": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sp": { - "type": "string", - "description": "Start page" - }, - "vol": { - "type": "string", - "description": "Volume" - } - }, - "description": "Information about the journal, if this data source is of type Journal." - }, - "languages": { - "description": "The languages present in the data source's content, as defined by OpenDOAR.", - "type": "array", - "items": { - "type": "string" - } - }, - "logourl": { - "type": "string" - }, - "missionstatementurl": { - "type": "string", - "description":"The URL of a mission statement describing the designated community of the data source. As defined by re3data.org" - }, - "officialname": { - "type": "string", - "description": "The official name of the datasource" - }, - "openairecompatibility": { - "type": "string", - "description": "OpenAIRE guidelines the data source comply with. See also https://guidelines.openaire.eu." - }, - "originalId": { - "description": "Original identifiers for the datasource" - "type": "array", - "items": { - "type": "string" - } - }, - "pid": { - "description": "Persistent identifiers of the datasource", - "type": "array", - "items": { - "allOf": [ - { - "$ref": "#/definitions/ControlledField" - } - ] - } - }, - "pidsystems": { - "type": "string", - "description": "The persistent identifier system that is used by the data source. As defined by re3data.org" - }, - "policies": { - "description": "Policies of the data source, as defined in OpenDOAR.", - "type": "array", - "items": { - "type": "string" - } - }, - "releaseenddate": { - "type": "string", - "description": "Date when the data source went offline or stopped ingesting new research data. As defined by re3data.org" - }, - "releasestartdate": { - "type": "string", - "description": "Releasing date of the data source, as defined by re3data.org" - }, - "subjects": { - "description": "List of subjects associated to the datasource", - "type": "array", - "items": { - "type": "string" - } - }, - "uploadrights": { - "type": "string", - "description": "Type of data upload. As defined by re3data.org: one of {open, restricted,closed}" - }, - "versioning": { - "type": "boolean", - "description": "As defined by redata.org: 'yes' if the data source supports versioning, 'no' otherwise." - }, - "websiteurl": { - "type": "string" - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/organization_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/organization_schema.json deleted file mode 100644 index 16afa386d5..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/organization_schema.json +++ /dev/null @@ -1,57 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "alternativenames": { - "description": "Alternative names that identify the organisation", - "type": "array", - "items": { - "type": "string" - } - }, - "country": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "The organisation country code" - }, - "label": { - "type": "string", - "description": "The organisation country label" - } - }, - "description": "The country of the organisation" - }, - "id": { - "type": "string", - "description": "The OpenAIRE id for the organisation" - }, - "legalname": { - "type": "string" - }, - "legalshortname": { - "type": "string" - }, - "pid": { - "description": "Persistent identifiers for the organisation i.e. isni 0000000090326370", - "type": "array", - "items": { - "type": "object", - "properties": { - "scheme": { - "type": "string", - "description": "The scheme of the identifier (i.e. isni)" - }, - "value": { - "type": "string", - "description": "the value in the schema (i.e. 0000000090326370)" - } - } - } - }, - "websiteurl": { - "type": "string" - } - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/project_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/project_schema.json deleted file mode 100644 index c81187258e..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/project_schema.json +++ /dev/null @@ -1,119 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "acronym": { - "type": "string" - }, - "callidentifier": { - "type": "string" - }, - "code": { - "type": "string", - "description": "The grant agreement number" - }, - "enddate": { - "type": "string" - }, - "funding": { - "description": "Funding information for the project", - "type": "array", - "items": { - "type": "object", - "properties": { - "funding_stream": { - "type": "object", - "properties": { - "description": { - "type": "string", - "description": "Description of the funding stream" - }, - "id": { - "type": "string", - "description": "Id of the funding stream" - } - } - }, - "jurisdiction": { - "type": "string", - "description": "The jurisdiction of the funder (i.e. EU)" - }, - "name": { - "type": "string", - "description": "The name of the funder (European Commission)" - }, - "shortName": { - "type": "string", - "description": "The short name of the funder (EC)" - } - } - } - }, - "granted": { - "type": "object", - "properties": { - "currency": { - "type": "string", - "description": "The currency of the granted amount (e.g. EUR)" - }, - "fundedamount": { - "type": "number", - "description": "The funded amount" - }, - "totalcost": { - "type": "number", - "description": "The total cost of the project" - } - }, - "description": "The money granted to the project" - }, - "h2020programme": { - "description": "The h2020 programme funding the project", - "type": "array", - "items": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "The code of the programme" - }, - "description": { - "type": "string", - "description": "The description of the programme" - } - } - } - }, - "id": { - "type": "string", - "description": "OpenAIRE id for the project" - }, - "keywords": { - "type": "string" - }, - "openaccessmandatefordataset": { - "type": "boolean" - }, - "openaccessmandateforpublications": { - "type": "boolean" - }, - "startdate": { - "type": "string" - }, - "subject": { - "type": "array", - "items": { - "type": "string" - } - }, - "summary": { - "type": "string" - }, - "title": { - "type": "string" - }, - "websiteurl": { - "type": "string" - } - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/relation_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/relation_schema.json deleted file mode 100644 index 7c7de9c98d..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/relation_schema.json +++ /dev/null @@ -1,60 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "definitions": { - "Node": { - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "The OpenAIRE id of the entity" - }, - "type": { - "type": "string", - "description": "The type of the entity (i.e. organisation)" - } - } - } - }, - "type": "object", - "properties": { - "provenance": { - "type": "object", - "properties": { - "provenance": { - "type": "string", - "description": "The reason why OpenAIRE holds the relation " - }, - "trust": { - "type": "string", - "description": "The trust of the relation in the range of [0,1]. Where greater the number, more the trust. Harvested relationships have typically a high trust (0.9). The trust of inferred relationship is calculated by the inference algorithm that generated them, as described in https://graph.openaire.eu/about#architecture (Enrichment --> Mining)" - } - } - }, - "reltype": { - "type": "object", - "properties": { - "name": { - "type": "string", - "description": "The semantics of the relation (i.e. isAuthorInstitutionOf). " - }, - "type": { - "type": "string", - "description": "the type of the relation (i.e. affiliation)" - } - }, - "description": "To represent the semantics of a relation between two entities" - }, - "source": { - "allOf": [ - {"$ref": "#/definitions/Node"}, - {"description": "The node source in the relation"} - ] - }, - "target": { - "allOf": [ - {"$ref": "#/definitions/Node"}, - {"description": "The node target in the relation"} - ] - } - } -} \ No newline at end of file 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 deleted file mode 100644 index 03cbfb0744..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json +++ /dev/null @@ -1,398 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "definitions": { - "AccessRight":{ - "type":"object", - "properties":{ - "code": { - "type": "string", - "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" - }, - "label": { - "type": "string", - "description": "Label for the access mode" - }, - "scheme": { - "type": "string", - "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" - } - } - }, - "ControlledField": { - "type": "object", - "properties": { - "scheme": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "description": "To represent the information described by a scheme and a value in that scheme (i.e. pid)" - }, - "Provenance": { - "type": "object", - "properties": { - "provenance": { - "type": "string", - "description": "The process that produced/provided the information" - }, - "trust": { - "type": "string" - } - }, - "description": "Indicates the process that produced (or provided) the information, and the trust associated to the information" - } - }, - "type": "object", - "properties": { - "author": { - "type": "array", - "items": { - "type": "object", - "properties": { - "fullname": { - "type": "string" - }, - "name": { - "type": "string" - }, - "pid": { - "type": "object", - "properties": { - "id": { - "allOf": [ - {"$ref": "#/definitions/ControlledField"}, - {"description": "The author's id and scheme. OpenAIRE currently supports 'ORCID'"} - ] - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Provenance of author's pid"} - ] - } - } - }, - "rank": { - "type": "integer" - }, - "surname": { - "type": "string" - } - } - } - }, - "bestaccessright": { - "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/" - } - }, - "description": "The openest access right associated to the manifestations of this research results" - }, - "codeRepositoryUrl": { - "type": "string", - "description": "Only for results with type 'software': the URL to the repository with the source code" - }, - "contactgroup": { - "description": "Only for results with type 'software': Information on the group responsible for providing further information regarding the resource", - "type": "array", - "items": { - "type": "string" - } - }, - "contactperson": { - "description": "Only for results with type 'software': Information on the person responsible for providing further information regarding the resource", - "type": "array", - "items": { - "type": "string" - } - }, - "container": { - "type": "object", - "properties": { - "conferencedate": { - "type": "string" - }, - "conferenceplace": { - "type": "string" - }, - "edition": { - "type": "string", - "description": "Edition of the journal or conference proceeding" - }, - "ep": { - "type": "string", - "description": "End page" - }, - "iss": { - "type": "string", - "description": "Journal issue" - }, - "issnLinking": { - "type": "string" - }, - "issnOnline": { - "type": "string" - }, - "issnPrinted": { - "type": "string" - }, - "name": { - "type": "string", - "description": "Name of the journal or conference" - }, - "sp": { - "type": "string", - "description": "start page" - }, - "vol": { - "type": "string" - } - }, - "description": "Container has information about the conference or journal where the result has been presented or published" - }, - "contributor": { - "type": "array", - "items": { - "type": "string", - "description": "Description of contributor" - } - }, - "country": { - "type": "array", - "items": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "ISO 3166-1 alpha-2 country code" - }, - "label": { - "type": "string" - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this result is associated to the country."} - ] - } - } - } - }, - "coverage": { - "type": "array", - "items": { - "type": "string" - } - }, - "dateofcollection": { - "type": "string", - "description": "When OpenAIRE collected the record the last time" - }, - "description": { - "type": "array", - "items": { - "type": "string" - } - }, - "documentationUrl": { - "description": "Only for results with type 'software': URL to the software documentation", - "type": "array", - "items": { - "type": "string" - } - }, - "embargoenddate": { - "type": "string", - "description": "Date when the embargo ends and this result turns Open Access" - }, - "format": { - "type": "array", - "items": { - "type": "string" - } - }, - "geolocation": { - "description": "Geolocation information", - "type": "array", - "items": { - "type": "object", - "properties": { - "box": { - "type": "string" - }, - "place": { - "type": "string" - }, - "point": { - "type": "string" - } - } - } - }, - "id": { - "type": "string", - "description": "OpenAIRE Identifier" - }, - "language": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "alpha-3/ISO 639-2 code of the language" - }, - "label": { - "type": "string", - "description": "English label" - } - } - }, - "lastupdatetimestamp": { - "type": "integer", - "description": "Timestamp of last update of the record in OpenAIRE" - }, - "maintitle": { - "type": "string" - }, - "originalId": { - "description": "Identifiers of the record at the original sources", - "type": "array", - "items": { - "type": "string" - } - }, - "pid": { - "description": "Persistent identifiers of the result", - "type": "array", - "items": { - "allOf": [ - {"$ref": "#/definitions/ControlledField"}, - {"description": "scheme: list of available schemes are at https://api.openaire.eu/vocabularies/dnet:pid_types, value: the PID of the result "} - ] - } - }, - "instance":{ - "type":"array", - "items":{ - "type":"object", - "properties":{ - "accessright":{ - "allOf":[ - { - "$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" - }, - "publicationdate": { - "type": "string" - }, - "publisher": { - "type": "string" - }, - "size": { - "type": "string", - "description": "Only for results with type 'dataset': the declared size of the dataset" - }, - "source": { - "description": "See definition of Dublin Core field dc:source", - "type": "array", - "items": { - "type": "string" - } - }, - "subjects": { - "description": "Keywords associated to the result", - "type": "array", - "items": { - "type": "object", - "properties": { - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this subject is associated to the result"} - ] - }, - "subject": { - "allOf": [ - {"$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)."} - ] - } - } - } - }, - "subtitle": { - "type": "string" - }, - "tool": { - "description": "Only for results with type 'other': tool useful for the interpretation and/or re-used of the research product", - "type": "array", - "items": { - "type": "string" - } - }, - "type": { - "type": "string", - "description": "Type of the result: one of 'publication', 'dataset', 'software', 'other' (see also https://api.openaire.eu/vocabularies/dnet:result_typologies)" - }, - "version": { - "type": "string", - "description": "Version of the result" - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0aee..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - 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/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml deleted file mode 100644 index 650b972fa3..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ /dev/null @@ -1,563 +0,0 @@ - - - - - upload - false - true to upload the dump for the funders in Zenodo - - - sourcePath - the source path - - - isLookUpUrl - the isLookup service endpoint - - - outputPath - the output path - - - 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 - - - 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())}] - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap - --outputPath${workingDir}/communityMap - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${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${workingDir}/result/publication - --relationPath${sourcePath}/relation - - - - - - - - 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 - --relationPath${sourcePath}/relation - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${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${workingDir}/result/otherresearchproduct - --relationPath${sourcePath}/relation - - - - - - - - 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 - --relationPath${sourcePath}/relation - - - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${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=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/result/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${workingDir}/communityMap - --dumpTypefunder - - - - - - - - yarn - cluster - Dump table dataset 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${workingDir}/result/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${workingDir}/communityMap - --dumpTypefunder - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${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=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/result/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${workingDir}/communityMap - --dumpTypefunder - - - - - - - - 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${workingDir}/result/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${workingDir}/communityMap - --dumpTypefunder - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${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${workingDir}/ext/publication - --preparedInfoPath${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${workingDir}/dump/dataset - --outputPath${workingDir}/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${workingDir}/ext/orp - --preparedInfoPath${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${workingDir}/dump/software - --outputPath${workingDir}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults - dhp-graph-mapper-${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${workingDir}/resultperfunder - --relationPath${sourcePath} - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/resultperfunder - - - - - - - - ${wf:conf('upload') eq true} - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --communityMapPath${workingDir}/communityMap - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json similarity index 73% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json index 2bfcac3bce..5c26ea7d1e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json @@ -19,6 +19,12 @@ "paramLongName": "isSparkSessionManaged", "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false + }, + { + "paramName": "rs", + "paramLongName": "removeSet", + "paramDescription": "the list of classname relations, split by ';', not to be dumped", + "paramRequired": false } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json deleted file mode 100644 index cb092110ec..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json +++ /dev/null @@ -1,542 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "definitions": { - "AccessRight": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" - }, - "label": { - "type": "string", - "description": "Label for the access mode" - }, - "scheme": { - "type": "string", - "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" - } - } - }, - "ControlledField": { - "type": "object", - "properties": { - "scheme": { - "type": "string", - "description": "The scheme for the resource" - }, - "value": { - "type": "string", - "description": "the value in the scheme" - } - } - }, - "KeyValue": { - "type": "object", - "properties": { - "key": { - "type": "string", - "description": "Description of key" - }, - "value": { - "type": "string", - "description": "Description of value" - } - } - }, - "Provenance": { - "type": "object", - "properties": { - "provenance": { - "type": "string", - "description": "The provenance of the information" - }, - "trust": { - "type": "string", - "description": "The trust associated to the information" - } - } - } - }, - "type": "object", - "properties": { - "author": { - "description": "List of authors of the research results", - "type": "array", - "items": { - "type": "object", - "properties": { - "affiliation": { - "description": "Affiliations of the author", - "type": "array", - "items": { - "type": "string", - "description": "One of the affiliation of the author" - } - }, - "fullname": { - "type": "string", - "description": "Fullname of the author" - }, - "name": { - "type": "string", - "description": "First name of the author" - }, - "pid": { - "type": "object", - "properties": { - "id": { - "allOf": [ - {"$ref": "#/definitions/ControlledField"}, - {"description": "The author's id and scheme. OpenAIRE currently supports 'ORCID'"} - ] - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "The provenance of the author's pid"} - ] - } - }, - "description": "Persistent identifier of the author (e.g. ORCID)" - }, - "rank": { - "type": "integer", - "description": "Order in which the author appears in the authors list" - }, - "surname": { - "type": "string", - "description": "Surname of the author" - } - }, - "description": "One of the author of the research result" - } - }, - "bestaccessright": { - "allOf": [ - {"$ref": "#/definitions/AccessRight"}, - {"description": "The openest access right associated to the manifestations of this research results"} - ] - }, - "codeRepositoryUrl": { - "type": "string", - "description": "Only for results with type 'software': the URL to the repository with the source code" - }, - "collectedfrom": { - "description": "Information about the sources from which the record has been collected", - "type": "array", - "items": { - "allOf": [ - {"$ref": "#/definitions/KeyValue"}, - {"description": "Key is the OpenAIRE identifier of the data source, value is its name"} - ] - } - }, - "contactgroup": { - "description": "Only for results with type 'software': Information on the group responsible for providing further information regarding the resource", - "type": "array", - "items": { - "type": "string" - } - }, - "contactperson": { - "description": "Only for results with type 'software': Information on the person responsible for providing further information regarding the resource", - "type": "array", - "items": { - "type": "string" - } - }, - "container": { - "type": "object", - "properties": { - "conferencedate": { - "type": "string", - "description": "Date of the conference" - }, - "conferenceplace": { - "type": "string", - "description": "Place of the conference" - }, - "edition": { - "type": "string", - "description": "Edition of the journal or conference proceeding" - }, - "ep": { - "type": "string", - "description": "End page" - }, - "iss": { - "type": "string", - "description": "Journal issue" - }, - "issnLinking": { - "type": "string", - "description": "Journal linking iisn" - }, - "issnOnline": { - "type": "string", - "description": "Journal online issn" - }, - "issnPrinted": { - "type": "string", - "description": "Journal printed issn" - }, - "name": { - "type": "string", - "description": "Name of the journal or conference" - }, - "sp": { - "type": "string", - "description": "Start page" - }, - "vol": { - "type": "string", - "description": "Volume" - } - }, - "description": "Container has information about the conference or journal where the result has been presented or published" - }, - "context": { - "description": "Reference to a relevant research infrastructure, initiative or community (RI/RC) among those collaborating with OpenAIRE. Please see https://connect.openaire.eu", - "type": "array", - "items": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "Code identifying the RI/RC" - }, - "label": { - "type": "string", - "description": "Label of the RI/RC" - }, - "provenance": { - "description": "Why this result is associated to the RI/RC.", - "type": "array", - "items": { - "allOf": [ - {"$ref": "#/definitions/Provenance"} - - ] - } - } - } - } - }, - "contributor": { - "description": "Contributors of this result", - "type": "array", - "items": { - "type": "string" - } - }, - "country": { - "description": "Country associated to this result", - "type": "array", - "items": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "ISO 3166-1 alpha-2 country code" - }, - "label": { - "type": "string", - "description": "English label of the country" - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this result is associated to the country."} - ] - } - } - } - }, - "coverage": { - "type": "array", - "items": { - "type": "string" - } - }, - "dateofcollection": { - "type": "string", - "description": "When OpenAIRE collected the record the last time" - }, - "description": { - "type": "array", - "items": { - "type": "string" - } - }, - "documentationUrl": { - "description": "Only for results with type 'software': URL to the software documentation", - "type": "array", - "items": { - "type": "string" - - } - }, - "embargoenddate": { - "type": "string", - "description": "Date when the embargo ends and this result turns Open Access" - }, - "externalReference": { - "description": "Links to external resources like entries from thematic databases (e.g. Protein Data Bank)", - "type": "array", - "items": { - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this result is linked to the external resource"} - ] - }, - "typology": { - "type": "string" - }, - "value": { - "type": "string" - } - } - } - }, - "format": { - - "type": "array", - "items": { - "type": "string" - } - }, - "geolocation": { - "description": "Geolocation information", - "type": "array", - "items": { - "type": "object", - "properties": { - "box": { - "type": "string" - }, - "place": { - "type": "string" - }, - "point": { - "type": "string" - } - } - } - }, - "id": { - "type": "string", - "description": "OpenAIRE identifier" - }, - "instance": { - "description": "Manifestations (i.e. different versions) of the result. For example: the pre-print and the published versions are two manifestations of the same research result", - "type": "array", - "items": { - "type": "object", - "properties": { - "accessright": { - "allOf": [ - {"$ref": "#/definitions/AccessRight"}, - {"description": "Access right of this instance"} - ] - }, - "collectedfrom": { - "allOf": [ - {"$ref": "#/definitions/KeyValue"}, - {"description": "Information about the source from which the instance has been collected. Key is the OpenAIRE identifier of the data source, value is its name"} - ] - }, - "hostedby": { - "allOf": [ - {"$ref": "#/definitions/KeyValue"}, - {"description": "Information about the source from which the instance can be viewed or downloaded. Key is the OpenAIRE identifier of the data source, value is its name"} - ] - }, - "license": { - "type": "string", - "description": "License applied to the instance" - }, - "publicationdate": { - "type": "string", - "description": "Publication date of the instance" - }, - "refereed": { - "type": "string", - "description": "Was the instance subject to peer-review? Possible values are 'Unknown', 'nonPeerReviewed', 'peerReviewed' (see also https://api.openaire.eu/vocabularies/dnet:review_levels)" - }, - "type": { - "type": "string", - "description": "Type of the instance. Possible values are listed at https://api.openaire.eu/vocabularies/dnet:publication_resource" - }, - "url": { - "description":"Location where the instance is accessible", - "type": "array", - "items": { - "type": "string" - } - } - } - } - }, - "language": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "alpha-3/ISO 639-2 code of the language" - }, - "label": { - "type": "string", - "description": "English label" - } - } - }, - "lastupdatetimestamp": { - "type": "integer", - "description": "Timestamp of last update of the record in OpenAIRE" - }, - "maintitle": { - "type": "string", - "description": "Title" - }, - "originalId": { - "description": "Identifiers of the record at the original sources", - "type": "array", - "items": { - "type": "string" - } - }, - "pid": { - "description": "Persistent identifiers of the result", - "type": "array", - "items": { - "allOf": [ - {"$ref": "#/definitions/ControlledField"}, - {"description": "scheme: list of available schemes are at https://api.openaire.eu/vocabularies/dnet:pid_types, value: the PID of the result "} - ] - } - }, - "programmingLanguage": { - "type": "string", - "description": "Only for results with type 'software': the programming language" - }, - "projects": { - "description": "List of projects (i.e. grants) that (co-)funded the production ofn the research results", - "type": "array", - "items": { - "type": "object", - "properties": { - "acronym": { - "type": "string", - "description": "Project acronym" - }, - "code": { - "type": "string", - "description": "Grant code" - }, - "funder": { - "type": "object", - "properties": { - "fundingStream": { - "type": "string", - "description": "Stream of funding (e.g. for European Commission can be H2020 or FP7)" - }, - "jurisdiction": { - "type": "string", - "description": "Geographical jurisdiction (e.g. for European Commission is EU, for Croatian Science Foundation is HR)" - }, - "name": { - "type": "string", - "description": "Name of the funder" - }, - "shortName": { - "type": "string", - "description": "Short name or acronym of the funder" - } - }, - "description": "Information about the funder funding the project" - }, - "id": { - "type": "string", - "description": "OpenAIRE identifier of the project" - }, - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this project is associated to the result"} - ] - }, - "title": { - "type": "string", - "description": "Title of the project" - } - } - } - }, - "publicationdate": { - "type": "string", - "description": "Date of publication" - }, - "publisher": { - "type": "string", - "description": "Publisher" - }, - "size": { - "type": "string", - "description": "Only for results with type 'dataset': the declared size of the dataset" - }, - "source": { - "description": "See definition of Dublin Core field dc:source", - "type": "array", - "items": { - "type": "string" - } - }, - "subjects": { - "description": "Keywords associated to the result", - "type": "array", - "items": { - "type": "object", - "properties": { - "provenance": { - "allOf": [ - {"$ref": "#/definitions/Provenance"}, - {"description": "Why this subject is associated to the result"} - ] - }, - "subject": { - "allOf": [ - {"$ref": "#/definitions/ControlledField"}, - {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary). "} - ] - } - } - } - }, - "subtitle": { - "type": "string", - "description": "Sub-title of the result" - }, - "tool": { - "description": "Only for results with type 'other': tool useful for the interpretation and/or re-used of the research product", - "type": "array", - "items": { - "type": "string" - } - }, - "type": { - "type": "string", - "description": "Type of the result: one of 'publication', 'dataset', 'software', 'other' (see also https://api.openaire.eu/vocabularies/dnet:result_typologies)" - }, - "version": { - "type": "string", - "description": "Version of the result" - } - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index f84ab7e1ad..8eab569928 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -325,6 +325,7 @@ --sourcePath${workingDir}/validrelation --outputPath${workingDir}/relation/relation + --removeSet${removeSet} 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 07f6638965..7300ce860f 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 @@ -339,11 +339,10 @@ public class DumpJobTest { Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); - Assertions.assertEquals(2, gr.getOriginalId().size()); + Assertions.assertEquals(1, gr.getOriginalId().size()); Assertions .assertTrue( - gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") - && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); + gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); Assertions.assertEquals(1, gr.getPid().size()); Assertions @@ -892,7 +891,6 @@ 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, GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); @@ -924,6 +922,46 @@ public class DumpJobTest { Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); + temp = spark + .sql( + "select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " + + "from check " + + "lateral view explode (instance) i as inst " + + "where inst.articleprocessingcharge is not null"); + + Assertions + .assertEquals( + "3131.64", + temp + .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") + .collectAsList() + .get(0) + .getString(1)); + Assertions + .assertEquals( + "EUR", + temp + .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") + .collectAsList() + .get(0) + .getString(2)); + + Assertions + .assertEquals( + "2578.35", + temp + .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") + .collectAsList() + .get(0) + .getString(1)); + Assertions + .assertEquals( + "EUR", + temp + .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") + .collectAsList() + .get(0) + .getString(2)); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java index 697ec705f0..2cc53027e5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java @@ -9,7 +9,7 @@ import com.github.victools.jsonschema.generator.*; import eu.dnetlib.dhp.schema.dump.oaf.graph.*; -@Disabled +//@Disabled class GenerateJsonSchema { @Test @@ -21,7 +21,7 @@ class GenerateJsonSchema { configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName()); SchemaGeneratorConfig config = configBuilder.build(); SchemaGenerator generator = new SchemaGenerator(config); - JsonNode jsonSchema = generator.generateSchema(Relation.class); + JsonNode jsonSchema = generator.generateSchema(GraphResult.class); System.out.println(jsonSchema.toString()); } 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 fe178795d7..763318ae49 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 @@ -81,8 +81,6 @@ public class DumpRelationTest { "-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 @@ -144,8 +142,6 @@ public class DumpRelationTest { "-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 @@ -203,4 +199,107 @@ public class DumpRelationTest { "and validationDate = '2021-08-06'") .count()); } + + @Test + public void test3() throws Exception {// + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath, + "-removeSet", "isParticipant" + }); + + 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(22, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 22, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(0, check.filter("name = 'isParticipant'").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()); + } + + @Test + public void test4() throws Exception {// + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath, + "-removeSet", "isParticipant;isAuthorInstitutionOf" + }); + + 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(22, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 22, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); + + Assertions.assertEquals(0, check.filter("name = 'isAuthorInstitutionOf'").count()); + + } + } 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 index b56b30fa52..979cbf1684 100644 --- 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 @@ -1,2 +1,2 @@ -{"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem Services hotspots"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Natura 2000"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Quiet Protected Areas"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Biodiversity"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Agriculture"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Elevation"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Slope"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Ecosystem Service trade-offs and synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. 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."],"publicationdate":"2017-01-01","publisher":"Pensoft Publishers","embargoenddate":null,"source":["One Ecosystem 2: e13718"],"format":["text/html"],"contributor":[],"coverage":[],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"container":{"name":"One 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concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. 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 Publishers","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"}}},"embargoenddate":null,"source":[{"value":"One Ecosystem 2: e13718","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"}}}],"fulltext":[],"format":[{"value":"text/html","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"}}}],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"}],"id":"dh-ch"}],"externalReference":[],"instance":[{"measures":[{"id": "influence", "unit": [{"value": "1.62759106106e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.22519296", "key": "score"}]}],"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":"green"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd","value":"One Ecosystem","dataInfo":null},"url":["https://doi.org/10.3897/oneeco.2.e13718","https://oneecosystem.pensoft.net/article/13718/"],"distributionlocation":"","collectedfrom":{"key":"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db","value":"Pensoft","dataInfo":null},"pid":[],"alternateIdentifier":[{"value":"10.3897/oneeco.2.e13718","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"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"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":{"classid":"0001","classname":"peerReviewed","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"}}],"journal":{"name":"One Ecosystem","issnPrinted":"","issnOnline":"2367-8194","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":null,"conferencedate":null,"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"}}}} \ No newline at end of file diff --git a/pom.xml b/pom.xml index 9e9bbaa167..b95bd9acbb 100644 --- a/pom.xml +++ b/pom.xml @@ -758,7 +758,7 @@ 3.3.3 3.4.2 [2.12,3.0) - 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