diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java new file mode 100644 index 0000000000..2b8ef4e300 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.common; + +import java.util.Map; + +import com.google.common.collect.Maps; + +public class Constants { + + public static final Map accessRightsCoarMap = Maps.newHashMap(); + public static final Map coarCodeLabelMap = Maps.newHashMap(); + + public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + + static { + accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put("RESTRICTED", "c_16ec"); + accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); + accessRightsCoarMap.put("CLOSED", "c_14cb"); + accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + } + + static { + coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put("c_16ec", "RESTRICTED"); + coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_f1cf", "EMBARGO"); + } + +} 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 new file mode 100644 index 0000000000..44599eb83f --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -0,0 +1,412 @@ + +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(v -> v.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(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.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(at -> getAuthor(at)).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(i -> getInstance(i)).collect(Collectors.toList())); + + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + } + + 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-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 4047fdca4f..76017d5b70 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,9 +90,6 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); - if (name.trim().equalsIgnoreCase("communities_infrastructures")) { - name = "communities_infrastructures.json"; - } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index b04d62dd29..73efeabb44 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp 1.2.4-SNAPSHOT - ../ + ../pom.xml dhp-schemas diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index d759f0d553..1efa865862 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -7,6 +7,10 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier; public class ModelConstants { + public static final String ORCID = "orcid"; + public static final String ORCID_PENDING = "orcid_pending"; + public static final String ORCID_CLASSNAME = "Open Researcher and Contributor ID"; + public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies"; public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies"; public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource"; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 3496492e8e..f4f5baa7bb 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -2,8 +2,12 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Collection; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; public abstract class Oaf implements Serializable { @@ -40,9 +44,36 @@ public abstract class Oaf implements Serializable { this.lastupdatetimestamp = lastupdatetimestamp; } - public void mergeOAFDataInfo(Oaf e) { - if (e.getDataInfo() != null && compareTrust(this, e) < 0) - dataInfo = e.getDataInfo(); + public void mergeFrom(Oaf o) { + if (Objects.isNull(o)) { + return; + } + setCollectedfrom( + Stream + .concat( + Optional + .ofNullable(getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(o.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + + mergeOAFDataInfo(o); + + setLastupdatetimestamp( + Math + .max( + Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), + Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); + } + + public void mergeOAFDataInfo(Oaf o) { + if (o.getDataInfo() != null && compareTrust(this, o) < 0) + dataInfo = o.getDataInfo(); } protected String extractTrust(Oaf e) { @@ -62,7 +93,7 @@ public abstract class Oaf implements Serializable { if (o == null || getClass() != o.getClass()) return false; Oaf oaf = (Oaf) o; - return Objects.equals(dataInfo, oaf.dataInfo) + return Objects.equals(getDataInfo(), oaf.getDataInfo()) && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 2823ee49dd..17c3e6bddc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -78,14 +78,10 @@ public abstract class OafEntity extends Oaf implements Serializable { } public void mergeFrom(OafEntity e) { - - if (e == null) - return; + super.mergeFrom(e); originalId = mergeLists(originalId, e.getOriginalId()); - collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom()); - pid = mergeLists(pid, e.getPid()); if (e.getDateofcollection() != null && compareTrust(this, e) < 0) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 17a50d7aca..0de34dbecc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -130,19 +130,7 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedfrom( - Stream - .concat( - Optional - .ofNullable(getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty()), - Optional - .ofNullable(r.getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + super.mergeFrom(r); } @Override diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java similarity index 64% rename from dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java rename to dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java index 29551c347a..6c94cdb13e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java @@ -1,7 +1,14 @@ -package eu.dnetlib.doiboost.orcid.model; +package eu.dnetlib.dhp.schema.orcid; import java.io.Serializable; +import java.util.List; + +import com.google.common.collect.Lists; + +/** + * This class models the data that are retrieved from orcid publication + */ public class AuthorData implements Serializable { @@ -10,6 +17,7 @@ public class AuthorData implements Serializable { private String surname; private String creditName; private String errorCode; + private List otherNames; public String getErrorCode() { return errorCode; @@ -50,4 +58,15 @@ public class AuthorData implements Serializable { public void setOid(String oid) { this.oid = oid; } + + public List getOtherNames() { + return otherNames; + } + + public void setOtherNames(List otherNames) { + if (this.otherNames == null) { + this.otherNames = Lists.newArrayList(); + } + this.otherNames = otherNames; + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java new file mode 100644 index 0000000000..cf372c12aa --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.schema.orcid; + +import java.util.List; + +public class OrcidDOI { + private String doi; + private List authors; + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public List getAuthors() { + return authors; + } + + public void setAuthors(List authors) { + this.authors = authors; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index da2c5bb78a..e9644122f3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -4,8 +4,13 @@ package eu.dnetlib.dhp.broker.oa; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; +import java.util.Arrays; +import java.util.HashSet; import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; +import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; @@ -13,6 +18,8 @@ import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; @@ -29,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; public class PartitionEventsByDsIdJob { private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class); - private static final String OPENDOAR_NSPREFIX = "opendoar____::"; + private static final String OPENDOAR_NSPREFIX = "10|opendoar____::"; public static void main(final String[] args) throws Exception { @@ -37,7 +44,7 @@ public class PartitionEventsByDsIdJob { IOUtils .toString( PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -54,14 +61,32 @@ public class PartitionEventsByDsIdJob { final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; log.info("partitionPath: {}", partitionPath); + final String opendoarIds = parser.get("opendoarIds"); + log.info("opendoarIds: {}", opendoarIds); + + final Set validOpendoarIds = new HashSet<>(); + if (!opendoarIds.trim().equals("-")) { + validOpendoarIds + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); + } + log.info("validOpendoarIds: {}", validOpendoarIds); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { ClusterUtils .readPath(spark, eventsPath, Event.class) - .filter(e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) - .filter(e -> e.getMap().getTargetDatasourceId().contains(OPENDOAR_NSPREFIX)) - .limit(10000) - .map(e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) + .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) + .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) + .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) + .map( + (MapFunction) e -> messageFromNotification(e), + Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json new file mode 100644 index 0000000000..10ba926abf --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "o", + "paramLongName": "workingPath", + "paramDescription": "the path where the temporary data will be stored", + "paramRequired": true + }, + { + "paramName": "list", + "paramLongName": "opendoarIds", + "paramDescription": "the opendoar IDs whitelist (comma separated)", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml similarity index 61% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 8bae626f17..dba3c9f73b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -1,60 +1,13 @@ - + - graphInputPath - the path where the graph is stored + opendoarIds + the opendoar IDs whitelist (comma separated) workingPath the path where the the generated data will be stored - - - datasourceIdWhitelist - - - a white list (comma separeted, - for empty list) of datasource ids - - - datasourceTypeWhitelist - - - a white list (comma separeted, - for empty list) of datasource types - - - datasourceIdBlacklist - - - a black list (comma separeted, - for empty list) of datasource ids - - - esEventIndexName - the elasticsearch index name for events - - - esNotificationsIndexName - the elasticsearch index name for notifications - - - esIndexHost - the elasticsearch host - - - maxIndexedEventsForDsAndTopic - the max number of events for each couple (ds/topic) - - - brokerApiBaseUrl - the url of the broker service api - - - brokerDbUrl - the url of the broker database - - - brokerDbUser - the user of the broker database - - - brokerDbPassword - the password of the broker database sparkDriverMemory @@ -111,13 +64,13 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + yarn cluster @@ -134,8 +87,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --graphPath${graphInputPath} --workingPath${workingPath} + --opendoarIds${opendoarIds} diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 3299c1496c..624dd7b319 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -14,7 +14,7 @@ net.alchim31.maven scala-maven-plugin - 4.0.1 + ${net.alchim31.maven.version} scala-compile-first @@ -51,7 +51,6 @@ org.apache.httpcomponents httpclient - 4.3.4 eu.dnetlib.dhp @@ -84,6 +83,11 @@ spark-sql_2.11 + + org.apache.commons + commons-text + + diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index a29809fc0a..860254527a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -62,7 +62,7 @@ object SparkGenerateDoiBoost { val orcidPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p)) fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/secondJoin") - logger.info("Phase 3) Join Result with MAG") + logger.info("Phase 4) Join Result with MAG") val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index d1f6d86134..5ba01357e7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -200,7 +200,7 @@ case object Crossref2Oaf { a.setSurname(family) a.setFullname(s"$given $family") if (StringUtils.isNotBlank(orcid)) - a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava) a } @@ -248,7 +248,7 @@ case object Crossref2Oaf { def snsfRule(award:String): String = { - var tmp1 = StringUtils.substringAfter(award,"_") + val tmp1 = StringUtils.substringAfter(award,"_") val tmp2 = StringUtils.substringBefore(tmp1,"/") logger.debug(s"From $award to $tmp2") tmp2 @@ -294,7 +294,7 @@ case object Crossref2Oaf { } def getProjectId (nsPrefix:String, targetId:String):String = { - "40|$nsPrefix::$targetId" + s"40|$nsPrefix::$targetId" } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala index 996ba55855..4a39a2987b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala @@ -2,6 +2,7 @@ package eu.dnetlib.doiboost.crossref import eu.dnetlib.dhp.application.ArgumentApplicationParser import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.{IntWritable, Text} import org.apache.spark.SparkConf import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} @@ -12,21 +13,23 @@ import org.slf4j.{Logger, LoggerFactory} object CrossrefDataset { + val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) - def extractTimestamp(input:String): Long = { + + def to_item(input:String):CrossrefDT = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = parse(input) - - (json\"indexed"\"timestamp").extractOrElse[Long](0) + val ts:Long = (json \ "indexed" \ "timestamp").extract[Long] + val doi:String = (json \ "DOI").extract[String] + CrossrefDT(doi, input, ts) } - def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) + val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json"))) parser.parseArgument(args) @@ -49,9 +52,8 @@ object CrossrefDataset { if (a == null) return b - val tb = extractTimestamp(b.json) - val ta = extractTimestamp(a.json) - if(ta >tb) { + + if(a.timestamp >b.timestamp) { return a } b @@ -63,9 +65,7 @@ object CrossrefDataset { if (a == null) return b - val tb = extractTimestamp(b.json) - val ta = extractTimestamp(a.json) - if(ta >tb) { + if(a.timestamp >b.timestamp) { return a } b @@ -78,15 +78,21 @@ object CrossrefDataset { override def finish(reduction: CrossrefDT): CrossrefDT = reduction } - val sourcePath:String = parser.get("sourcePath") - val targetPath:String = parser.get("targetPath") + val workingPath:String = parser.get("workingPath") - val ds:Dataset[CrossrefDT] = spark.read.load(sourcePath).as[CrossrefDT] - ds.groupByKey(_.doi) + val main_ds:Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT] + + + val update = + spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text]) + .map(i =>CrossrefImporter.decompressBlob(i._2.toString)) + .map(i =>to_item(i))) + + main_ds.union(update).groupByKey(_.doi) .agg(crossrefAggregator.toColumn) .map(s=>s._2) - .write.mode(SaveMode.Overwrite).save(targetPath) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated") } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala index 08319058c7..0272cb1a64 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala @@ -34,85 +34,21 @@ object SparkMapDumpIntoOAF { implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation] implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset] - val sc = spark.sparkContext val targetPath = parser.get("targetPath") import spark.implicits._ - spark.read.load(parser.get("sourcePath")).as[CrossrefDT] .flatMap(k => Crossref2Oaf.convert(k.json)) .filter(o => o != null) .write.mode(SaveMode.Overwrite).save(s"$targetPath/mixObject") - val ds:Dataset[Oaf] = spark.read.load(s"$targetPath/mixObject").as[Oaf] - ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.save(s"$targetPath/publication") + ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefPublication") - ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.save(s"$targetPath/relation") + ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefRelation") - ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.save(s"$targetPath/dataset") - - - -// -// -// -// sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text]) -// .map(k => k._2.toString).map(CrossrefImporter.decompressBlob) -// .flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject") -// -// val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null) -// -// val distinctPubs:RDD[Publication] = inputRDD.filter(k => k != null && k.isInstanceOf[Publication]) -// .map(k => k.asInstanceOf[Publication]).map { p: Publication => Tuple2(p.getId, p) }.reduceByKey { case (p1: Publication, p2: Publication) => -// var r = if (p1 == null) p2 else p1 -// if (p1 != null && p2 != null) { -// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) { -// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp) -// r = p2 -// else -// r = p1 -// } else { -// r = if (p1.getLastupdatetimestamp == null) p2 else p1 -// } -// } -// r -// }.map(_._2) -// -// val pubs:Dataset[Publication] = spark.createDataset(distinctPubs) -// pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication") -// -// -// val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset]) -// .map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) => -// var r = if (p1 == null) p2 else p1 -// if (p1 != null && p2 != null) { -// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) { -// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp) -// r = p2 -// else -// r = p1 -// } else { -// r = if (p1.getLastupdatetimestamp == null) p2 else p1 -// } -// } -// r -// }.map(_._2) -// -// spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset") -// -// -// -// val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation]) -// .map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r)) -// .reduceByKey { case (p1: Relation, p2: Relation) => -// if (p1 == null) p2 else p1 -// }.map(_._2) -// -// val rels: Dataset[Relation] = spark.createDataset(distinctRels) -// -// rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations") + ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefDataset") } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala index f291a92f99..88fee72b7d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala @@ -21,15 +21,17 @@ object SparkImportMagIntoDataset { val stream = Map( - "Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), - "Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), - "ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")), + "Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), "ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), "EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")), "FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")), "FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")), - "FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), - "Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + // ['FieldOfStudyId:long', 'Rank:uint', 'NormalizedName:string', 'DisplayName:string', 'MainType:string', 'Level:int', 'PaperCount:long', 'PaperFamilyCount:long', 'CitationCount:long', 'CreatedDate:DateTime'] + "FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "CreatedDate:DateTime")), "PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")), "PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")), "PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")), @@ -39,7 +41,7 @@ object SparkImportMagIntoDataset { "PaperReferences" -> Tuple2("mag/PaperReferences.txt", Seq("PaperId:long", "PaperReferenceId:long")), "PaperResources" -> Tuple2("mag/PaperResources.txt", Seq("PaperId:long", "ResourceType:int", "ResourceUrl:string", "SourceUrl:string", "RelationshipType:int")), "PaperUrls" -> Tuple2("mag/PaperUrls.txt", Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")), - "Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "CreatedDate:DateTime")), + "Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "OnlineDate:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "FamilyRank:uint?", "CreatedDate:DateTime")), "RelatedFieldOfStudy" -> Tuple2("advanced/RelatedFieldOfStudy.txt", Seq("FieldOfStudyId1:long", "Type1:string", "FieldOfStudyId2:long", "Type2:string", "Rank:float")) ) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala index a24f0e6bb4..02dc4979af 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala @@ -26,12 +26,15 @@ object SparkPreProcessMAG { .master(parser.get("master")).getOrCreate() val sourcePath = parser.get("sourcePath") + val workingPath = parser.get("workingPath") + val targetPath = parser.get("targetPath") + import spark.implicits._ implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication] implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) logger.info("Phase 1) make uninque DOI in Papers:") - val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers] + val d: Dataset[MagPapers] = spark.read.load(s"$sourcePath/Papers").as[MagPapers] // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one val result: RDD[MagPapers] = d.where(col("Doi").isNotNull) @@ -41,11 +44,12 @@ object SparkPreProcessMAG { .map(_._2) val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) - distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct") + + distinctPaper.write.mode(SaveMode.Overwrite).save(s"$workingPath/Papers_distinct") logger.info("Phase 0) Enrich Publication with description") - val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] - pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") + val pa = spark.read.load(s"$sourcePath/PaperAbstractsInvertedIndex").as[MagPaperAbstract] + pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"$workingPath/PaperAbstract") logger.info("Phase 3) Group Author by PaperId") val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor] @@ -64,24 +68,24 @@ object SparkPreProcessMAG { } else mpa }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors")) - .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors") + .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_1_paper_authors") logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors") val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal] - val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers] + val papers = spark.read.load((s"$workingPath/Papers_distinct")).as[MagPapers] - val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList] + val paperWithAuthors = spark.read.load(s"$workingPath/merge_step_1_paper_authors").as[MagPaperWithAuthorList] val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left") firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left") .map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) } - .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2") + .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_2") var magPubs: Dataset[(String, Publication)] = - spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication] + spark.read.load(s"$workingPath/merge_step_2").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] @@ -95,10 +99,10 @@ object SparkPreProcessMAG { .map(item => ConversionUtil.updatePubsWithConferenceInfo(item)) .write .mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/merge_step_2_conference") + .save(s"$workingPath/merge_step_2_conference") - magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication] + magPubs= spark.read.load(s"$workingPath/merge_step_2_conference").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] @@ -108,27 +112,27 @@ object SparkPreProcessMAG { magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } .write.mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/merge_step_3") + .save(s"$workingPath/merge_step_3") // logger.info("Phase 6) Enrich Publication with description") // val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] // pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") - val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract] + val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract] - magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication] + magPubs = spark.read.load(s"$workingPath/merge_step_3").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left") .map(item => ConversionUtil.updatePubsWithDescription(item) - ).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4") + ).write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_4") logger.info("Phase 7) Enrich Publication with FieldOfStudy") - magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication] + magPubs = spark.read.load(s"$workingPath/merge_step_4").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType") @@ -144,14 +148,14 @@ object SparkPreProcessMAG { .equalTo(paperField("PaperId")), "left") .map(item => ConversionUtil.updatePubsWithSubject(item)) .write.mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/mag_publication") + .save(s"$workingPath/mag_publication") - val s:RDD[Publication] = spark.read.load(s"${parser.get("targetPath")}/mag_publication").as[Publication] + val s:RDD[Publication] = spark.read.load(s"$workingPath/mag_publication").as[Publication] .map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b)) .map(_._2) - spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication_u") + spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication") } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java index 570fdef17c..420c363ec4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java @@ -17,11 +17,12 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.GzipCodec; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcid.json.JsonWriter; import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class ActivitiesDecompressor { @@ -143,4 +144,64 @@ public class ActivitiesDecompressor { Log.info("Error from Orcid found: " + errorFromOrcidFound); Log.info("Error parsing xml work found: " + xmlParserErrorFound); } + + public static void extractXML(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + int counter = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + if (entry.isDirectory() || !filename.contains("works")) { + } else { + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + String xml = buffer.toString(); + String[] filenameParts = filename.split("/"); + final Text key = new Text( + XMLRecordParser + .retrieveOrcidIdFromActivity( + xml.getBytes(), filenameParts[filenameParts.length - 1])); + final Text value = new Text(xml); + writer.append(key, value); + if ((counter % 100000) == 0) { + Log.info("Current xml works extracted: " + counter); + } + } + } + } + } + Log.info("Activities extraction completed"); + Log.info("Total XML works parsed: " + counter); + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java new file mode 100644 index 0000000000..c834efa205 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork; + +public class ExtractXMLActivitiesData extends OrcidDSManager { + private String outputWorksPath; + private String activitiesFileNameTarGz; + + public static void main(String[] args) throws IOException, Exception { + ExtractXMLActivitiesData extractXMLActivitiesData = new ExtractXMLActivitiesData(); + extractXMLActivitiesData.loadArgs(args); + extractXMLActivitiesData.extractWorks(); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); + Log.info("Activities File Name: " + activitiesFileNameTarGz); + outputWorksPath = parser.get("outputWorksPath"); + Log.info("Output Author Work Data: " + outputWorksPath); + } + + private void extractWorks() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputWorksPath)); + ActivitiesDecompressor.extractXML(conf, tarGzUri, outputPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java new file mode 100644 index 0000000000..8438891087 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java @@ -0,0 +1,56 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork; + +public class ExtractXMLSummariesData extends OrcidDSManager { + + private String outputAuthorsPath; + private String summariesFileNameTarGz; + + public static void main(String[] args) throws IOException, Exception { + ExtractXMLSummariesData extractXMLSummariesData = new ExtractXMLSummariesData(); + extractXMLSummariesData.loadArgs(args); + extractXMLSummariesData.extractAuthors(); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); + Log.info("Summaries File Name: " + summariesFileNameTarGz); + outputAuthorsPath = parser.get("outputAuthorsPath"); + Log.info("Output Authors Data: " + outputAuthorsPath); + } + + public void extractAuthors() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz); + Path outputPath = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputAuthorsPath) + .concat("xml_authors.seq")); + SummariesDecompressor.extractXML(conf, tarGzUri, outputPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala index f230c604f7..f7255e5591 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -1,6 +1,7 @@ package eu.dnetlib.doiboost.orcid -import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication} +import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier} import org.apache.commons.lang.StringUtils @@ -43,16 +44,19 @@ object ORCIDToOAF { } - def convertTOOAF(input:ORCIDElement) :Publication = { - val doi = input.doi + def convertTOOAF(input:OrcidDOI) :Publication = { + val doi = input.getDoi val pub:Publication = new Publication - pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava) + pub.setPid(List(createSP(doi.toLowerCase, "doi", PID_TYPES)).asJava) pub.setDataInfo(generateDataInfo()) pub.setId(generateIdentifier(pub, doi.toLowerCase)) try{ - pub.setAuthor(input.authors.map(a=> { - generateAuthor(a.name, a.surname, a.creditName, a.oid) - }).asJava) + + val l:List[Author]= input.getAuthors.asScala.map(a=> { + generateAuthor(a.getName, a.getSurname, a.getCreditName, a.getOid) + })(collection.breakOut) + + pub.setAuthor(l.asJava) pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava) pub.setDataInfo(DoiBoostMappingUtil.generateDataInfo()) pub @@ -63,6 +67,13 @@ object ORCIDToOAF { } } + def generateOricPIDDatainfo():DataInfo = { + val di =DoiBoostMappingUtil.generateDataInfo("0.91") + di.getProvenanceaction.setClassid("sysimport:crosswalk:entityregistry") + di.getProvenanceaction.setClassname("Harvested") + di + } + def generateAuthor(given: String, family: String, fullName:String, orcid: String): Author = { val a = new Author a.setName(given) @@ -72,7 +83,7 @@ object ORCIDToOAF { else a.setFullname(s"$given $family") if (StringUtils.isNotBlank(orcid)) - a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateOricPIDDatainfo())).asJava) a } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java index 70528a8f60..2ec4fe59db 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java @@ -25,8 +25,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager { public void generateAuthorsDOIsData() throws Exception { Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(activitiesFileNameTarGz); - Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsDOIsPath)); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputAuthorsDOIsPath)); ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath); } @@ -41,8 +41,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager { hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Default Path: " + workingPath); activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); Log.info("Activities File Name: " + activitiesFileNameTarGz); outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java index 4f846bdf3c..bf13db0219 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -15,7 +15,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class OrcidDSManager { protected String hdfsServerUri; - protected String hdfsOrcidDefaultPath; + protected String workingPath; private String summariesFileNameTarGz; private String outputAuthorsPath; @@ -28,10 +28,10 @@ public class OrcidDSManager { public void generateAuthors() throws Exception { Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz); Path outputPath = new Path( hdfsServerUri - .concat(hdfsOrcidDefaultPath) + .concat(workingPath) .concat(outputAuthorsPath) .concat("authors.seq")); SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath); @@ -41,22 +41,18 @@ public class OrcidDSManager { // ====== Init HDFS File System Object Configuration conf = new Configuration(); // Set FileSystem URI - conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath)); + conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath)); // Because of Maven conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); return conf; } - protected FileSystem initFileSystemObject(Configuration conf) { + protected FileSystem initFileSystemObject(Configuration conf) throws IOException { // Get the filesystem - HDFS + // if there is an exception, it will be propagate FileSystem fs = null; - try { - fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf); - } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } + fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); return fs; } @@ -66,13 +62,13 @@ public class OrcidDSManager { .toString( OrcidDSManager.class .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json"))); + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json"))); parser.parseArgument(args); hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); Log.info("Summaries File Name: " + summariesFileNameTarGz); outputAuthorsPath = parser.get("outputAuthorsPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java index 2e1a199da9..be727ab9fe 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java @@ -1,14 +1,15 @@ package eu.dnetlib.doiboost.orcid; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; +import java.io.*; import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.Date; import java.util.List; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataInputStream; @@ -16,6 +17,7 @@ import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; @@ -27,10 +29,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class OrcidDownloader extends OrcidDSManager { static final int REQ_LIMIT = 24; -// static final int REQ_MAX_TEST = 100; - static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 10000; + static final int REQ_MAX_TEST = -1; + static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 500; static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; - static final String lastUpdate = "2019-09-30 00:00:00"; + static final String lastUpdate = "2020-09-29 00:00:00"; private String lambdaFileName; private String outputPath; private String token; @@ -41,7 +43,7 @@ public class OrcidDownloader extends OrcidDSManager { orcidDownloader.parseLambdaFile(); } - private String downloadRecord(String orcidId) { + private String downloadRecord(String orcidId) throws IOException { try (CloseableHttpClient client = HttpClients.createDefault()) { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); @@ -49,17 +51,23 @@ public class OrcidDownloader extends OrcidDSManager { CloseableHttpResponse response = client.execute(httpGet); if (response.getStatusLine().getStatusCode() != 200) { Log - .warn( + .info( "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); return new String(""); } - return IOUtils.toString(response.getEntity().getContent()); - - } catch (Throwable e) { - Log.warn("Downloading " + orcidId, e.getMessage()); - +// return IOUtils.toString(response.getEntity().getContent()); + return xmlStreamToString(response.getEntity().getContent()); } - return new String(""); + } + + private String xmlStreamToString(InputStream xmlStream) throws IOException { + BufferedReader br = new BufferedReader(new InputStreamReader(xmlStream)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + return buffer.toString(); } public void parseLambdaFile() throws Exception { @@ -69,97 +77,94 @@ public class OrcidDownloader extends OrcidDSManager { long startDownload = 0; Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName); + String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName); Path hdfsreadpath = new Path(lambdaFileUri); FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath); Path hdfsoutputPath = new Path( hdfsServerUri - .concat(hdfsOrcidDefaultPath) + .concat(workingPath) .concat(outputPath) - .concat("orcid_records.seq")); - - try (SequenceFile.Writer writer = SequenceFile - .createWriter( - conf, - SequenceFile.Writer.file(hdfsoutputPath), - SequenceFile.Writer.keyClass(Text.class), - SequenceFile.Writer.valueClass(Text.class))) { - - try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) { - String line; - int nReqTmp = 0; + .concat("updated_xml_authors.seq")); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(lambdaFileStream))) { + TarArchiveEntry entry = null; + StringBuilder sb = new StringBuilder(); + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(hdfsoutputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { startDownload = System.currentTimeMillis(); - long startReqTmp = System.currentTimeMillis(); - while ((line = br.readLine()) != null) { - parsedRecordsCounter++; - // skip headers line - if (parsedRecordsCounter == 1) { - continue; - } - String[] values = line.split(","); - List recordInfo = Arrays.asList(values); - String orcidId = recordInfo.get(0); - if (isModified(orcidId, recordInfo.get(3))) { - String record = downloadRecord(orcidId); - downloadedRecordsCounter++; - if (!record.isEmpty()) { - String compressRecord = ArgumentApplicationParser.compressArgument(record); - final Text key = new Text(recordInfo.get(0)); - final Text value = new Text(compressRecord); - - try { + while ((entry = tais.getNextTarEntry()) != null) { + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + int nReqTmp = 0; + long startReqTmp = System.currentTimeMillis(); + // skip headers line + if (parsedRecordsCounter == 0) { + parsedRecordsCounter++; + continue; + } + parsedRecordsCounter++; + String orcidId = recordInfo.get(0); + if (isModified(orcidId, recordInfo.get(3))) { + String record = downloadRecord(orcidId); + downloadedRecordsCounter++; + if (!record.isEmpty()) { +// String compressRecord = ArgumentApplicationParser.compressArgument(record); + final Text key = new Text(recordInfo.get(0)); + final Text value = new Text(record); writer.append(key, value); savedRecordsCounter++; - } catch (IOException e) { - Log.warn("Writing to sequence file: " + e.getMessage()); - Log.warn(e); - throw new RuntimeException(e); + } + } else { + break; + } + long endReq = System.currentTimeMillis(); + nReqTmp++; + if (nReqTmp == REQ_LIMIT) { + long reqSessionDuration = endReq - startReqTmp; + if (reqSessionDuration <= 1000) { + Log + .info( + "\nreqSessionDuration: " + + reqSessionDuration + + " nReqTmp: " + + nReqTmp + + " wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } else { + nReqTmp = 0; + startReqTmp = System.currentTimeMillis(); + } + } + if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log + .info( + "Current parsed: " + + parsedRecordsCounter + + " downloaded: " + + downloadedRecordsCounter + + " saved: " + + savedRecordsCounter); + if (REQ_MAX_TEST != -1 && parsedRecordsCounter > REQ_MAX_TEST) { + break; } } } - long endReq = System.currentTimeMillis(); - nReqTmp++; - if (nReqTmp == REQ_LIMIT) { - long reqSessionDuration = endReq - startReqTmp; - if (reqSessionDuration <= 1000) { - Log - .warn( - "\nreqSessionDuration: " - + reqSessionDuration - + " nReqTmp: " - + nReqTmp - + " wait ...."); - Thread.sleep(1000 - reqSessionDuration); - } else { - nReqTmp = 0; - startReqTmp = System.currentTimeMillis(); - } - } - -// if (parsedRecordsCounter > REQ_MAX_TEST) { -// break; -// } - if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) { - Log - .info( - "Current parsed: " - + parsedRecordsCounter - + " downloaded: " - + downloadedRecordsCounter - + " saved: " - + savedRecordsCounter); -// if (parsedRecordsCounter > REQ_MAX_TEST) { -// break; -// } - } + long endDownload = System.currentTimeMillis(); + long downloadTime = endDownload - startDownload; + Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); } - long endDownload = System.currentTimeMillis(); - long downloadTime = endDownload - startDownload; - Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); } } - lambdaFileStream.close(); Log.info("Download started at: " + new Date(startDownload).toString()); + Log.info("Download ended at: " + new Date(System.currentTimeMillis()).toString()); Log.info("Parsed Records Counter: " + parsedRecordsCounter); Log.info("Downloaded Records Counter: " + downloadedRecordsCounter); Log.info("Saved Records Counter: " + savedRecordsCounter); @@ -176,8 +181,8 @@ public class OrcidDownloader extends OrcidDSManager { hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Default Path: " + workingPath); lambdaFileName = parser.get("lambdaFileName"); Log.info("Lambda File Name: " + lambdaFileName); outputPath = parser.get("outputPath"); @@ -185,7 +190,7 @@ public class OrcidDownloader extends OrcidDSManager { token = parser.get("token"); } - private boolean isModified(String orcidId, String modifiedDate) { + public boolean isModified(String orcidId, String modifiedDate) { Date modifiedDateDt = null; Date lastUpdateDt = null; try { @@ -195,7 +200,7 @@ public class OrcidDownloader extends OrcidDSManager { modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); } catch (Exception e) { - Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); + Log.info("[" + orcidId + "] Parsing date: ", e.getMessage()); return true; } return modifiedDateDt.after(lastUpdateDt); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala index 1cd9ba4d42..f1c7c58b4e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -1,21 +1,72 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.rdd.RDD +import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} object SparkConvertORCIDToOAF { + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + + def getPublicationAggregator(): Aggregator[(String, Publication), Publication, Publication] = new Aggregator[(String, Publication), Publication, Publication]{ + + override def zero: Publication = new Publication() + + override def reduce(b: Publication, a: (String, Publication)): Publication = { + b.mergeFrom(a._2) + b.setAuthor(AuthorMerger.mergeAuthor(a._2.getAuthor, b.getAuthor)) + if (b.getId == null) + b.setId(a._2.getId) + b + } + override def merge(wx: Publication, wy: Publication): Publication = { + wx.mergeFrom(wy) + wx.setAuthor(AuthorMerger.mergeAuthor(wy.getAuthor, wx.getAuthor)) + if(wx.getId == null && wy.getId.nonEmpty) + wx.setId(wy.getId) + wx + } + override def finish(reduction: Publication): Publication = reduction + + override def bufferEncoder: Encoder[Publication] = + Encoders.kryo(classOf[Publication]) + + override def outputEncoder: Encoder[Publication] = + Encoders.kryo(classOf[Publication]) + } + +def run(spark:SparkSession,sourcePath:String, targetPath:String):Unit = { + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + implicit val mapOrcid: Encoder[OrcidDOI] = Encoders.kryo[OrcidDOI] + implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) + + val mapper = new ObjectMapper() + mapper.getDeserializationConfig.withFeatures(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES) + + val dataset:Dataset[OrcidDOI] = spark.createDataset(spark.sparkContext.textFile(sourcePath).map(s => mapper.readValue(s,classOf[OrcidDOI]))) + + logger.info("Converting ORCID to OAF") + dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null) + .map(d => (d.getId, d)) + .groupByKey(_._1)(Encoders.STRING) + .agg(getPublicationAggregator().toColumn) + .map(p => p._2) + .write.mode(SaveMode.Overwrite).save(targetPath) +} def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) parser.parseArgument(args) @@ -26,19 +77,12 @@ object SparkConvertORCIDToOAF { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] - implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) - import spark.implicits._ + + val sourcePath = parser.get("sourcePath") val targetPath = parser.get("targetPath") - val dataset:Dataset[ORCIDElement] = spark.read.json(sourcePath).as[ORCIDElement] + run(spark, sourcePath, targetPath) - - logger.info("Converting ORCID to OAF") - val d:RDD[Publication] = dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null).map(p=>(p.getId,p)).rdd.reduceByKey(ConversionUtil.mergePublication) - .map(_._2) - - spark.createDataset(d).as[Publication].write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java new file mode 100644 index 0000000000..598835a000 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -0,0 +1,188 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.util.LongAccumulator; +import org.mortbay.log.Log; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; +import scala.Tuple2; + +public class SparkDownloadOrcidAuthors { + + static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class); + static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + static final String lastUpdate = "2020-09-29 00:00:00"; + + public static void main(String[] args) throws IOException, Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkDownloadOrcidAuthors.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String workingPath = parser.get("workingPath"); + logger.info("workingPath: ", workingPath); + final String outputPath = parser.get("outputPath"); + logger.info("outputPath: ", outputPath); + final String token = parser.get("token"); + final String lambdaFileName = parser.get("lambdaFileName"); + logger.info("lambdaFileName: ", lambdaFileName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsed_records"); + LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records"); + LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records"); + LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403"); + LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409"); + LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503"); + LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525"); + LongAccumulator errorHTTPGenericAcc = spark.sparkContext().longAccumulator("error_HTTP_Generic"); + + logger.info("Retrieving data from lamda sequence file"); + JavaPairRDD lamdaFileRDD = sc + .sequenceFile(workingPath + lambdaFileName, Text.class, Text.class); + logger.info("Data retrieved: " + lamdaFileRDD.count()); + + Function, Boolean> isModifiedAfterFilter = data -> { + String orcidId = data._1().toString(); + String lastModifiedDate = data._2().toString(); + parsedRecordsAcc.add(1); + if (isModified(orcidId, lastModifiedDate)) { + modifiedRecordsAcc.add(1); + return true; + } + return false; + }; + + Function, Tuple2> downloadRecordFunction = data -> { + String orcidId = data._1().toString(); + String lastModifiedDate = data._2().toString(); + final DownloadedRecordData downloaded = new DownloadedRecordData(); + downloaded.setOrcidId(orcidId); + downloaded.setLastModifiedDate(lastModifiedDate); + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", String.format("Bearer %s", token)); + long startReq = System.currentTimeMillis(); + CloseableHttpResponse response = client.execute(httpGet); + long endReq = System.currentTimeMillis(); + long reqTime = endReq - startReq; + if (reqTime < 1000) { + Thread.sleep(1000 - reqTime); + } + int statusCode = response.getStatusLine().getStatusCode(); + downloaded.setStatusCode(statusCode); + if (statusCode != 200) { + switch (statusCode) { + case 403: + errorHTTP403Acc.add(1); + case 409: + errorHTTP409Acc.add(1); + case 503: + errorHTTP503Acc.add(1); + throw new RuntimeException("Orcid request rate limit reached (HTTP 503)"); + case 525: + errorHTTP525Acc.add(1); + default: + errorHTTPGenericAcc.add(1); + logger + .info( + "Downloading " + orcidId + " status code: " + + response.getStatusLine().getStatusCode()); + } + return downloaded.toTuple2(); + } + downloadedRecordsAcc.add(1); + downloaded + .setCompressedData( + ArgumentApplicationParser + .compressArgument(IOUtils.toString(response.getEntity().getContent()))); + } catch (Throwable e) { + logger.info("Downloading " + orcidId, e.getMessage()); + downloaded.setErrorMessage(e.getMessage()); + return downloaded.toTuple2(); + } + return downloaded.toTuple2(); + }; + + sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); + + logger.info("Start execution ..."); + JavaPairRDD authorsModifiedRDD = lamdaFileRDD.filter(isModifiedAfterFilter); + logger.info("Authors modified count: " + authorsModifiedRDD.count()); + logger.info("Start downloading ..."); + authorsModifiedRDD + .repartition(10) + .map(downloadRecordFunction) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + workingPath.concat(outputPath), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); + logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString()); + logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString()); + logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); + logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString()); + logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString()); + logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString()); + logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString()); + logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString()); + }); + + } + + private static boolean isModified(String orcidId, String modifiedDate) { + Date modifiedDateDt = null; + Date lastUpdateDt = null; + try { + if (modifiedDate.length() != 19) { + modifiedDate = modifiedDate.substring(0, 19); + } + modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); + lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); + } catch (Exception e) { + logger.info("[" + orcidId + "] Parsing date: ", e.getMessage()); + return true; + } + return modifiedDateDt.after(lastUpdateDt); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java new file mode 100644 index 0000000000..f710635abe --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java @@ -0,0 +1,99 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.URI; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class SparkGenLastModifiedSeq { + private static String hdfsServerUri; + private static String workingPath; + private static String outputPath; + private static String lambdaFileName; + + public static void main(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkGenLastModifiedSeq.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + hdfsServerUri = parser.get("hdfsServerUri"); + workingPath = parser.get("workingPath"); + outputPath = parser.get("outputPath"); + lambdaFileName = parser.get("lambdaFileName"); + String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName); + + SparkConf sparkConf = new SparkConf(); + runWithSparkSession( + sparkConf, + isSparkSessionManaged, + spark -> { + int rowsNum = 0; + Path output = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputPath)); + Path hdfsreadpath = new Path(lambdaFileUri); + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath)); + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); + FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(lambdaFileStream))) { + TarArchiveEntry entry = null; + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(output), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { + while ((entry = tais.getNextTarEntry()) != null) { + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + while ((line = br.readLine()) != null) { + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + final Text key = new Text(orcidId); + final Text value = new Text(recordInfo.get(3)); + writer.append(key, value); + rowsNum++; + } + } + } + } + Log.info("Saved rows from lamda csv tar file: " + rowsNum); + }); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java index b4239bba29..011c153ec6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java @@ -13,9 +13,6 @@ import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.hadoop.mapreduce.Job; -import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; @@ -33,7 +30,7 @@ import com.google.gson.JsonElement; import com.google.gson.JsonParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; import scala.Tuple2; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java deleted file mode 100644 index 4e18ab8401..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java +++ /dev/null @@ -1,165 +0,0 @@ - -package eu.dnetlib.doiboost.orcid; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; -import java.util.List; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.impl.client.HttpClients; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.Function; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.util.LongAccumulator; -import org.mortbay.log.Log; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; -import scala.Tuple2; - -public class SparkOrcidGenerateAuthors { - - static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; - static final String lastUpdate = "2019-09-30 00:00:00"; - - public static void main(String[] args) throws IOException, Exception { - Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); - logger.info("[ SparkOrcidGenerateAuthors STARTED]"); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkOrcidGenerateAuthors.class - .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - logger.info("workingPath: ", workingPath); - final String outputAuthorsPath = parser.get("outputAuthorsPath"); - logger.info("outputAuthorsPath: ", outputAuthorsPath); - final String token = parser.get("token"); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - LongAccumulator parsedRecordsAcc = sc.sc().longAccumulator("parsedRecords"); - LongAccumulator modifiedRecordsAcc = sc.sc().longAccumulator("modifiedRecords"); - LongAccumulator downloadedRecordsAcc = sc.sc().longAccumulator("downloadedRecords"); - LongAccumulator alreadyDownloadedRecords = sc.sc().longAccumulator("alreadyDownloadedRecords"); - JavaRDD lamdaFileRDD = sc.textFile(workingPath + "lamdafiles"); - - JavaRDD downloadedRDD = sc.textFile(workingPath + "downloaded"); - Function getOrcidIdFunction = line -> { - try { - String[] values = line.split(","); - return values[0].substring(1); - } catch (Exception e) { - return new String(""); - } - }; - List downloadedRecords = downloadedRDD.map(getOrcidIdFunction).collect(); - - Function isModifiedAfterFilter = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - parsedRecordsAcc.add(1); - if (isModified(orcidId, values[3])) { - modifiedRecordsAcc.add(1); - return true; - } - return false; - }; - Function isNotDownloadedFilter = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - if (downloadedRecords.contains(orcidId)) { - alreadyDownloadedRecords.add(1); - return false; - } - return true; - }; - Function> downloadRecordFunction = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - String modifiedDate = values[3]; - return downloadRecord(orcidId, modifiedDate, token, downloadedRecordsAcc); - }; - - lamdaFileRDD - .filter(isModifiedAfterFilter) - .filter(isNotDownloadedFilter) - .map(downloadRecordFunction) - .rdd() - .saveAsTextFile(workingPath.concat(outputAuthorsPath)); - }); - - } - - private static boolean isModified(String orcidId, String modifiedDate) { - Date modifiedDateDt = null; - Date lastUpdateDt = null; - try { - if (modifiedDate.length() != 19) { - modifiedDate = modifiedDate.substring(0, 19); - } - modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); - lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); - } catch (Exception e) { - Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); - return true; - } - return modifiedDateDt.after(lastUpdateDt); - } - - private static Tuple2 downloadRecord(String orcidId, String modifiedDate, String token, - LongAccumulator downloadedRecordsAcc) { - final DownloadedRecordData data = new DownloadedRecordData(); - data.setOrcidId(orcidId); - data.setModifiedDate(modifiedDate); - try (CloseableHttpClient client = HttpClients.createDefault()) { - HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); - httpGet.addHeader("Accept", "application/vnd.orcid+xml"); - httpGet.addHeader("Authorization", String.format("Bearer %s", token)); - CloseableHttpResponse response = client.execute(httpGet); - int statusCode = response.getStatusLine().getStatusCode(); - data.setStatusCode(statusCode); - if (statusCode != 200) { - Log - .warn( - "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); - return data.toTuple2(); - } - downloadedRecordsAcc.add(1); - data - .setCompressedData( - ArgumentApplicationParser.compressArgument(IOUtils.toString(response.getEntity().getContent()))); - } catch (Throwable e) { - Log.warn("Downloading " + orcidId, e.getMessage()); - data.setErrorMessage(e.getMessage()); - return data.toTuple2(); - } - return data.toTuple2(); - } -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java deleted file mode 100644 index ca6f0f6c4c..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.doiboost.orcid; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.IOException; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -public class SparkPartitionLambdaFile { - - public static void main(String[] args) throws IOException, Exception { - Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkOrcidGenerateAuthors.class - .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - final String workingPath = parser.get("workingPath"); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD lamdaFileRDD = sc.textFile(workingPath + "last_modified.csv"); - - lamdaFileRDD - .repartition(20) - .saveAsTextFile(workingPath.concat("lamdafiles")); - }); - } - -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java index f0bbb5c327..c16899977d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -17,11 +17,12 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.GzipCodec; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcid.json.JsonWriter; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class SummariesDecompressor { @@ -56,6 +57,7 @@ public class SummariesDecompressor { int nameFound = 0; int surnameFound = 0; int creditNameFound = 0; + int otherNamesFound = 0; int errorFromOrcidFound = 0; int xmlParserErrorFound = 0; try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { @@ -117,6 +119,9 @@ public class SummariesDecompressor { if (authorData.getCreditName() != null) { creditNameFound += 1; } + if (authorData.getOtherNames() != null && authorData.getOtherNames().size() > 1) { + otherNamesFound += authorData.getOtherNames().size(); + } } else { Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); @@ -152,7 +157,71 @@ public class SummariesDecompressor { Log.info("Name found: " + nameFound); Log.info("Surname found: " + surnameFound); Log.info("Credit name found: " + creditNameFound); + Log.info("Other names found: " + otherNamesFound); Log.info("Error from Orcid found: " + errorFromOrcidFound); Log.info("Error parsing xml record found: " + xmlParserErrorFound); } + + public static void extractXML(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + int counter = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + CompressionCodec Codec = new GzipCodec(); + org.apache.hadoop.io.SequenceFile.Writer.Option optCom = SequenceFile.Writer + .compression(SequenceFile.CompressionType.RECORD, Codec); + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), optCom)) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + if (entry.isDirectory()) { + Log.debug("Directory entry name: " + entry.getName()); + } else { + Log.debug("XML record entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + String xml = buffer.toString(); + final Text key = new Text( + XMLRecordParser + .retrieveOrcidIdFromSummary( + xml.getBytes(), filename.split("/")[2].substring(0, 19))); + final Text value = new Text(xml); + writer.append(key, value); + } + if ((counter % 100000) == 0) { + Log.info("Current xml records extracted: " + counter); + } + } + } + } + Log.info("Summaries extract completed"); + Log.info("Total XML records parsed: " + counter); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java new file mode 100644 index 0000000000..94f7d8c913 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java @@ -0,0 +1,13 @@ + +package eu.dnetlib.doiboost.orcid.json; + +import com.google.gson.Gson; + +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +public class JsonHelper { + + public static String createOidWork(WorkDataNoDoi workData) { + return new Gson().toJson(workData); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java deleted file mode 100644 index 35676d5bab..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.doiboost.orcid.json; - -import com.google.gson.JsonObject; - -import eu.dnetlib.doiboost.orcid.model.AuthorData; -import eu.dnetlib.doiboost.orcid.model.WorkData; - -public class JsonWriter { - - public static String create(AuthorData authorData) { - JsonObject author = new JsonObject(); - author.addProperty("oid", authorData.getOid()); - author.addProperty("name", authorData.getName()); - author.addProperty("surname", authorData.getSurname()); - if (authorData.getCreditName() != null) { - author.addProperty("creditname", authorData.getCreditName()); - } - return author.toString(); - } - - public static String create(WorkData workData) { - JsonObject work = new JsonObject(); - work.addProperty("oid", workData.getOid()); - work.addProperty("doi", workData.getDoi()); - return work.toString(); - } -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java index f66ef82a2f..da1a79b199 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java @@ -3,8 +3,6 @@ package eu.dnetlib.doiboost.orcid.model; import java.io.Serializable; -import org.apache.hadoop.io.Text; - import com.google.gson.JsonObject; import scala.Tuple2; @@ -12,7 +10,7 @@ import scala.Tuple2; public class DownloadedRecordData implements Serializable { private String orcidId; - private String modifiedDate; + private String lastModifiedDate; private String statusCode; private String compressedData; private String errorMessage; @@ -20,7 +18,7 @@ public class DownloadedRecordData implements Serializable { public Tuple2 toTuple2() { JsonObject data = new JsonObject(); data.addProperty("statusCode", getStatusCode()); - data.addProperty("modifiedDate", getModifiedDate()); + data.addProperty("lastModifiedDate", getLastModifiedDate()); if (getCompressedData() != null) { data.addProperty("compressedData", getCompressedData()); } @@ -66,11 +64,11 @@ public class DownloadedRecordData implements Serializable { this.compressedData = compressedData; } - public String getModifiedDate() { - return modifiedDate; + public String getLastModifiedDate() { + return lastModifiedDate; } - public void setModifiedDate(String modifiedDate) { - this.modifiedDate = modifiedDate; + public void setLastModifiedDate(String lastModifiedDate) { + this.lastModifiedDate = lastModifiedDate; } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java index 2e43f4d3e6..cc9abb6213 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -4,6 +4,8 @@ package eu.dnetlib.doiboost.orcid.xml; import java.util.Arrays; import java.util.List; +import org.mortbay.log.Log; + import com.ximpleware.AutoPilot; import com.ximpleware.EOFException; import com.ximpleware.EncodingException; @@ -14,7 +16,7 @@ import com.ximpleware.VTDNav; import eu.dnetlib.dhp.parser.utility.VtdException; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; public class XMLRecordParser { @@ -81,6 +83,12 @@ public class XMLRecordParser { if (!creditNames.isEmpty()) { authorData.setCreditName(creditNames.get(0)); } + + final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); + if (!otherNames.isEmpty()) { + authorData.setOtherNames(otherNames); + } + return authorData; } @@ -120,4 +128,33 @@ public class XMLRecordParser { } return workData; } + + public static String retrieveOrcidIdFromSummary(byte[] bytes, String defaultValue) + throws VtdException, ParseException { + return retrieveOrcidId(bytes, defaultValue, NS_RECORD, NS_RECORD_URL, "//record:record", "path").substring(1); + } + + public static String retrieveOrcidIdFromActivity(byte[] bytes, String defaultValue) + throws VtdException, ParseException { + return retrieveOrcidId(bytes, defaultValue, NS_WORK, NS_WORK_URL, "//work:work", "put-code"); + } + + private static String retrieveOrcidId(byte[] bytes, String defaultValue, String ns, String nsUrl, String xpath, + String idAttributeName) + throws VtdException, ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(ns, nsUrl); + List recordNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, xpath, Arrays.asList(idAttributeName)); + if (!recordNodes.isEmpty()) { + return (recordNodes.get(0).getAttributes().get(idAttributeName)); + } + Log.info("id not found - default: " + defaultValue); + return defaultValue; + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java new file mode 100644 index 0000000000..c2cfafd874 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -0,0 +1,154 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.URI; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.mortbay.log.Log; + +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; + +/** + * This class write on hdfs one sequence file, the key is an orcid identifier and the + * value is an orcid publication in json format + */ + +public class ActivitiesDumpReader { + + private static final int MAX_XML_WORKS_PARSED = -1; + private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000; + + public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + parseTarActivities(fs, conf, gzipInputStream, outputPath); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + + private static void parseTarActivities( + FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) { + int counter = 0; + int noDoiFound = 0; + int errorFromOrcidFound = 0; + int xmlParserErrorFound = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + StringBuffer buffer = new StringBuffer(); + try { + if (entry.isDirectory() || !filename.contains("works")) { + + } else { + Log.debug("XML work entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from + // tarInput + String line; + buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi + .VTDParseWorkData(buffer.toString().getBytes()); + if (workDataNoDoi != null) { + if (workDataNoDoi.getErrorCode() != null) { + errorFromOrcidFound += 1; + Log + .debug( + "error from Orcid with code " + + workDataNoDoi.getErrorCode() + + " for entry " + + entry.getName()); + continue; + } + boolean isDoiFound = workDataNoDoi + .getExtIds() + .stream() + .filter(e -> e.getType() != null) + .anyMatch(e -> e.getType().equals("doi")); + if (!isDoiFound) { + String jsonData = JsonHelper.createOidWork(workDataNoDoi); + Log.debug("oid: " + workDataNoDoi.getOid() + " data: " + jsonData); + + final Text key = new Text(workDataNoDoi.getOid()); + final Text value = new Text(jsonData); + + try { + writer.append(key, value); + } catch (IOException e) { + Log.debug("Writing to sequence file: " + e.getMessage()); + Log.debug(e); + throw new RuntimeException(e); + } + noDoiFound += 1; + } + + } else { + Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); + xmlParserErrorFound += 1; + } + } + } catch (Exception e) { + throw new Exception(filename, e); + } + + if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log.info("Current xml works parsed: " + counter); + } + + if ((MAX_XML_WORKS_PARSED > -1) && (counter > MAX_XML_WORKS_PARSED)) { + break; + } + } + } + } catch (Exception e) { + Log.warn("Parsing work from gzip archive: " + e.getMessage()); + Log.warn(e); + throw new RuntimeException(e); + } + Log.info("Activities parse completed"); + Log.info("Total XML works parsed: " + counter); + Log.info("Total no doi work found: " + noDoiFound); + Log.info("Error from Orcid found: " + errorFromOrcidFound); + Log.info("Error parsing xml work found: " + xmlParserErrorFound); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java new file mode 100644 index 0000000000..d3e9aeaefc --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -0,0 +1,57 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.OrcidDSManager; + +/** + * This job generates one sequence file, the key is an orcid identifier and the + * value is an orcid publication in json format + */ + +public class GenOrcidAuthorWork extends OrcidDSManager { + + private String activitiesFileNameTarGz; + private String outputWorksPath; + + public static void main(String[] args) throws IOException, Exception { + GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork(); + genOrcidAuthorWork.loadArgs(args); + genOrcidAuthorWork.generateAuthorsDOIsData(); + } + + public void generateAuthorsDOIsData() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputWorksPath)); + ActivitiesDumpReader.parseGzActivities(conf, tarGzUri, outputPath); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); + Log.info("Activities File Name: " + activitiesFileNameTarGz); + outputWorksPath = parser.get("outputWorksPath"); + Log.info("Output Author Work Data: " + outputWorksPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java new file mode 100644 index 0000000000..a92d534d8d --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -0,0 +1,180 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.util.Objects; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.util.LongAccumulator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.orcid.AuthorData; +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; +import scala.Tuple2; + +/** + * This spark job generates one parquet file, containing orcid publications dataset + */ + +public class SparkGenEnrichedOrcidWorks { + + static Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws IOException, Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkGenEnrichedOrcidWorks.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + final String workingPath = parser.get("workingPath"); + final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath"); + final String outputWorksPath = parser.get("outputWorksPath"); + final String hdfsServerUri = parser.get("hdfsServerUri"); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaPairRDD summariesRDD = sc + .sequenceFile(workingPath + "authors/authors.seq", Text.class, Text.class); + Dataset summariesDataset = spark + .createDataset( + summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(AuthorData.class)); + logger.info("Authors data loaded: " + summariesDataset.count()); + + JavaPairRDD activitiesRDD = sc + .sequenceFile(workingPath + outputWorksPath + "*.seq", Text.class, Text.class); + Dataset activitiesDataset = spark + .createDataset( + activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(WorkDataNoDoi.class)); + logger.info("Works data loaded: " + activitiesDataset.count()); + + JavaRDD> enrichedWorksRDD = activitiesDataset + .joinWith( + summariesDataset, + activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") + .map( + (MapFunction, Tuple2>) value -> { + WorkDataNoDoi w = value._1; + AuthorData a = value._2; + AuthorMatcher.match(a, w.getContributors()); + return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w)); + }, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())) + .filter(Objects::nonNull) + .toJavaRDD(); + logger.info("Enriched works RDD ready."); + + final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications"); + final LongAccumulator enrichedPublications = spark + .sparkContext() + .longAccumulator("enrichedPublications"); + final LongAccumulator errorsGeneric = spark.sparkContext().longAccumulator("errorsGeneric"); + final LongAccumulator errorsInvalidTitle = spark.sparkContext().longAccumulator("errorsInvalidTitle"); + final LongAccumulator errorsNotFoundAuthors = spark + .sparkContext() + .longAccumulator("errorsNotFoundAuthors"); + final LongAccumulator errorsInvalidType = spark.sparkContext().longAccumulator("errorsInvalidType"); + final PublicationToOaf publicationToOaf = new PublicationToOaf( + parsedPublications, + enrichedPublications, + errorsGeneric, + errorsInvalidTitle, + errorsNotFoundAuthors, + errorsInvalidType); + JavaRDD oafPublicationRDD = enrichedWorksRDD + .map( + e -> { + return (Publication) publicationToOaf + .generatePublicationActionsFromJson(e._2()); + }) + .filter(p -> p != null); + + sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); + + oafPublicationRDD + .mapToPair( + p -> new Tuple2<>(p.getClass().toString(), + OBJECT_MAPPER.writeValueAsString(new AtomicAction<>(Publication.class, (Publication) p)))) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + workingPath.concat(outputEnrichedWorksPath), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); + + logger.info("parsedPublications: " + parsedPublications.value().toString()); + logger.info("enrichedPublications: " + enrichedPublications.value().toString()); + logger.info("errorsGeneric: " + errorsGeneric.value().toString()); + logger.info("errorsInvalidTitle: " + errorsInvalidTitle.value().toString()); + logger.info("errorsNotFoundAuthors: " + errorsNotFoundAuthors.value().toString()); + logger.info("errorsInvalidType: " + errorsInvalidType.value().toString()); + }); + } + + private static AuthorData loadAuthorFromJson(Text orcidId, Text json) { + AuthorData authorData = new AuthorData(); + authorData.setOid(orcidId.toString()); + JsonElement jElement = new JsonParser().parse(json.toString()); + authorData.setName(getJsonValue(jElement, "name")); + authorData.setSurname(getJsonValue(jElement, "surname")); + authorData.setCreditName(getJsonValue(jElement, "creditname")); + return authorData; + } + + private static WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) { + + WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class); + return workData; + } + + private static String getJsonValue(JsonElement jElement, String property) { + if (jElement.getAsJsonObject().has(property)) { + JsonElement name = null; + name = jElement.getAsJsonObject().get(property); + if (name != null && !name.isJsonNull()) { + return name.getAsString(); + } + } + return new String(""); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java new file mode 100644 index 0000000000..982fb6316f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.doiboost.orcidnodoi.json; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.JsonObject; + +import eu.dnetlib.dhp.schema.orcid.AuthorData; +import eu.dnetlib.doiboost.orcid.model.WorkData; + +/** + * This class converts an object to json and viceversa + */ + +public class JsonWriter { + + public static final com.fasterxml.jackson.databind.ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .setSerializationInclusion(JsonInclude.Include.NON_NULL);; + + public static String create(AuthorData authorData) throws JsonProcessingException { + return OBJECT_MAPPER.writeValueAsString(authorData); + } + + public static String create(WorkData workData) { + JsonObject work = new JsonObject(); + work.addProperty("oid", workData.getOid()); + work.addProperty("doi", workData.getDoi()); + return work.toString(); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java new file mode 100644 index 0000000000..9222c1cc40 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +import java.io.Serializable; + +import eu.dnetlib.dhp.schema.orcid.AuthorData; + +/** + * This class models the data related to a contributor, that are retrieved from an orcid publication + */ + +public class Contributor extends AuthorData implements Serializable { + private String sequence; + private String role; + private transient boolean simpleMatch = false; + private transient Double score = 0.0; + private transient boolean bestMatch = false; + + public String getSequence() { + return sequence; + } + + public void setSequence(String sequence) { + this.sequence = sequence; + } + + public String getRole() { + return role; + } + + public void setRole(String role) { + this.role = role; + } + + public boolean isSimpleMatch() { + return simpleMatch; + } + + public void setSimpleMatch(boolean simpleMatch) { + this.simpleMatch = simpleMatch; + } + + public Double getScore() { + return score; + } + + public void setScore(Double score) { + this.score = score; + } + + public boolean isBestMatch() { + return bestMatch; + } + + public void setBestMatch(boolean bestMatch) { + this.bestMatch = bestMatch; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java new file mode 100644 index 0000000000..7fe50ce25a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +/** + * This class models the data related to external id, that are retrieved from an orcid publication + */ + +public class ExternalId { + private String type; + private String value; + private String relationShip; + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getRelationShip() { + return relationShip; + } + + public void setRelationShip(String relationShip) { + this.relationShip = relationShip; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java new file mode 100644 index 0000000000..5f794d8eb6 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +/** + * This class models the data related to a publication date, that are retrieved from an orcid publication + */ + +public class PublicationDate { + private String year; + private String month; + private String day; + + public String getYear() { + return year; + } + + public void setYear(String year) { + this.year = year; + } + + public String getMonth() { + return month; + } + + public void setMonth(String month) { + this.month = month; + } + + public String getDay() { + return day; + } + + public void setDay(String day) { + this.day = day; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java new file mode 100644 index 0000000000..58f992d12a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java @@ -0,0 +1,104 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +import java.io.Serializable; +import java.util.List; + +/** + * This class models the data that are retrieved from orcid publication + */ + +public class WorkDataNoDoi implements Serializable { + + private String oid; + private String id; + private String sourceName; + private String type; + private List titles; + private List urls; + List extIds; + List publicationDates; + List contributors; + + public String getOid() { + return oid; + } + + public void setOid(String oid) { + this.oid = oid; + } + + public String getErrorCode() { + return errorCode; + } + + public void setErrorCode(String errorCode) { + this.errorCode = errorCode; + } + + private String errorCode; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getTitles() { + return titles; + } + + public void setTitles(List titles) { + this.titles = titles; + } + + public String getSourceName() { + return sourceName; + } + + public void setSourceName(String sourceName) { + this.sourceName = sourceName; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public List getUrls() { + return urls; + } + + public void setUrls(List urls) { + this.urls = urls; + } + + public List getExtIds() { + return extIds; + } + + public void setExtIds(List extIds) { + this.extIds = extIds; + } + + public List getPublicationDates() { + return publicationDates; + } + + public void setPublicationDates(List publicationDates) { + this.publicationDates = publicationDates; + } + + public List getContributors() { + return contributors; + } + + public void setContributors(List contributors) { + this.contributors = contributors; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java new file mode 100644 index 0000000000..1aed66dfd2 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -0,0 +1,543 @@ + +package eu.dnetlib.doiboost.orcidnodoi.oaf; + +import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.util.LongAccumulator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.*; + +import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; +import eu.dnetlib.doiboost.orcidnodoi.util.Pair; + +/** + * This class converts an orcid publication from json format to oaf + */ + +public class PublicationToOaf implements Serializable { + + static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class); + + public static final String ORCID = "ORCID"; + public final static String orcidPREFIX = "orcid_______"; + public static final String OPENAIRE_PREFIX = "openaire____"; + public static final String SEPARATOR = "::"; + + private final LongAccumulator parsedPublications; + private final LongAccumulator enrichedPublications; + private final LongAccumulator errorsGeneric; + private final LongAccumulator errorsInvalidTitle; + private final LongAccumulator errorsNotFoundAuthors; + private final LongAccumulator errorsInvalidType; + + public PublicationToOaf( + LongAccumulator parsedPublications, + LongAccumulator enrichedPublications, + LongAccumulator errorsGeneric, + LongAccumulator errorsInvalidTitle, + LongAccumulator errorsNotFoundAuthors, + LongAccumulator errorsInvalidType) { + this.parsedPublications = parsedPublications; + this.enrichedPublications = enrichedPublications; + this.errorsGeneric = errorsGeneric; + this.errorsInvalidTitle = errorsInvalidTitle; + this.errorsNotFoundAuthors = errorsNotFoundAuthors; + this.errorsInvalidType = errorsInvalidType; + } + + public PublicationToOaf() { + this.parsedPublications = null; + this.enrichedPublications = null; + this.errorsGeneric = null; + this.errorsInvalidTitle = null; + this.errorsNotFoundAuthors = null; + this.errorsInvalidType = null; + } + + private static Map> datasources = new HashMap>() { + + { + put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); + + } + }; + + // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname + private static Map> externalIds = new HashMap>() { + + { + put("ark".toLowerCase(), new Pair<>("ark", "ark")); + put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); + put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); + put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); + put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); + put("urn".toLowerCase(), new Pair<>("urn", "urn")); + } + }; + + static Map> typologiesMapping; + + static { + try { + final String tt = IOUtils + .toString( + PublicationToOaf.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json")); + typologiesMapping = new Gson().fromJson(tt, Map.class); + } catch (Exception e) { + throw new RuntimeException("loading typologies", e); + } + } + + public static final String PID_TYPES = "dnet:pid_types"; + + public Oaf generatePublicationActionsFromJson(final String json) { + try { + if (parsedPublications != null) { + parsedPublications.add(1); + } + JsonElement jElement = new JsonParser().parse(json); + JsonObject jObject = jElement.getAsJsonObject(); + return generatePublicationActionsFromDump(jObject); + } catch (Throwable t) { + logger.error("creating publication: " + t.getMessage()); + if (errorsGeneric != null) { + errorsGeneric.add(1); + } + return null; + } + } + + public Oaf generatePublicationActionsFromDump(final JsonObject rootElement) { + + if (!isValid(rootElement)) { + return null; + } + + Publication publication = new Publication(); + + final DataInfo dataInfo = new DataInfo(); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferred(false); + dataInfo.setTrust("0.9"); + dataInfo + .setProvenanceaction( + mapQualifier( + "sysimport:actionset:orcidworks-no-doi", + "sysimport:actionset:orcidworks-no-doi", + "dnet:provenanceActions", + "dnet:provenanceActions")); + publication.setDataInfo(dataInfo); + + publication.setLastupdatetimestamp(new Date().getTime()); + + publication.setDateofcollection("2020-10-14"); + publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601()); + + // Adding external ids + externalIds + .keySet() + .stream() + .forEach(jsonExtId -> { + final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); + final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); + final String extId = getStringValue(rootElement, jsonExtId); + if (StringUtils.isNotBlank(extId)) { + publication + .getExternalReference() + .add( + convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types")); + } + }); + + // Adding source + final String source = getStringValue(rootElement, "sourceName"); + if (StringUtils.isNotBlank(source)) { + Field sourceField = mapStringField(source, null); + if (sourceField == null) { + publication.setSource(null); + } else { + publication.setSource(Arrays.asList(sourceField)); + } + } + + // Adding titles + final List titles = createRepeatedField(rootElement, "titles"); + if (titles == null || titles.isEmpty()) { + if (errorsInvalidTitle != null) { + errorsInvalidTitle.add(1); + } + return null; + } + Qualifier q = mapQualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + publication + .setTitle( + titles + .stream() + .map(t -> { + return mapStructuredProperty(t, q, null); + }) + .filter(s -> s != null) + .collect(Collectors.toList())); + // Adding identifier + final String id = getStringValue(rootElement, "id"); + String sourceId = null; + if (id != null) { + publication.setOriginalId(Arrays.asList(id)); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(id.toLowerCase())); + } else { + String mergedTitle = titles.stream().map(Object::toString).collect(Collectors.joining(",")); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(mergedTitle.toLowerCase())); + } + publication.setId(sourceId); + + // Adding relevant date + settingRelevantDate(rootElement, publication, "publication_date", "issued", true); + + // Adding collectedfrom + publication.setCollectedfrom(Arrays.asList(createCollectedFrom())); + + // Adding type + final String type = getStringValue(rootElement, "type"); + String cobjValue = ""; + if (StringUtils.isNotBlank(type)) { + publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource")); + + final String typeValue = typologiesMapping.get(type).get("value"); + cobjValue = typologiesMapping.get(type).get("cobj"); + final Instance instance = new Instance(); + + // Adding hostedby + instance.setHostedby(createHostedBy()); + + // Adding url + final List urls = createRepeatedField(rootElement, "urls"); + if (urls != null && !urls.isEmpty()) { + instance.setUrl(urls); + } else { + dataInfo.setInvisible(true); + } + + final String pubDate = getPublicationDate(rootElement, "publicationDates"); + if (StringUtils.isNotBlank(pubDate)) { + instance.setDateofacceptance(mapStringField(pubDate, null)); + } + + instance.setCollectedfrom(createCollectedFrom()); + + // Adding accessright + instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes")); + + // Adding type + instance + .setInstancetype( + mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource")); + + publication.setInstance(Arrays.asList(instance)); + } else { + if (errorsInvalidType != null) { + errorsInvalidType.add(1); + } + return null; + } + + // Adding authors + final List authors = createAuthors(rootElement); + if (authors != null && authors.size() > 0) { + publication.setAuthor(authors); + } else { + if (errorsNotFoundAuthors != null) { + errorsNotFoundAuthors.add(1); + } + return null; + } + String classValue = getDefaultResulttype(cobjValue); + publication + .setResulttype(mapQualifier(classValue, classValue, "dnet:result_typologies", "dnet:result_typologies")); + if (enrichedPublications != null) { + enrichedPublications.add(1); + } + return publication; + } + + public List createAuthors(final JsonObject root) { + + final String authorsJSONFieldName = "contributors"; + + if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { + + final List authors = new ArrayList<>(); + final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); + int firstCounter = 0; + int defaultCounter = 0; + int rank = 1; + int currentRank = 0; + + for (final JsonElement item : jsonAuthors) { + final JsonObject jsonAuthor = item.getAsJsonObject(); + final Author author = new Author(); + if (item.isJsonObject()) { + final String creditname = getStringValue(jsonAuthor, "creditName"); + final String surname = getStringValue(jsonAuthor, "surname"); + final String name = getStringValue(jsonAuthor, "name"); + final String oid = getStringValue(jsonAuthor, "oid"); + final String seq = getStringValue(jsonAuthor, "sequence"); + if (StringUtils.isNotBlank(seq)) { + if (seq.equals("first")) { + firstCounter += 1; + rank = firstCounter; + + } else if (seq.equals("additional")) { + rank = currentRank + 1; + } else { + defaultCounter += 1; + rank = defaultCounter; + } + } + if (StringUtils.isNotBlank(oid)) { + author.setPid(Arrays.asList(mapAuthorId(oid))); + author.setFullname(name + " " + surname); + if (StringUtils.isNotBlank(name)) { + author.setName(name); + } + if (StringUtils.isNotBlank(surname)) { + author.setSurname(surname); + } + } else { + PacePerson p = new PacePerson(creditname, false); + if (p.isAccurate()) { + author.setName(p.getNormalisedFirstName()); + author.setSurname(p.getNormalisedSurname()); + author.setFullname(p.getNormalisedFullname()); + } else { + author.setFullname(creditname); + } + } + } + author.setRank(rank); + authors.add(author); + currentRank = rank; + } + return authors; + + } + return null; + } + + private List createRepeatedField(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { + return null; + } + if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { + return null; + } + if (rootElement.get(fieldName).isJsonArray()) { + if (!isValidJsonArray(rootElement, fieldName)) { + return null; + } + return getArrayValues(rootElement, fieldName); + } else { + String field = getStringValue(rootElement, fieldName); + return Arrays.asList(cleanField(field)); + } + } + + private String cleanField(String value) { + if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') { + value = value.substring(1, value.length() - 1); + } + return value; + } + + private void settingRelevantDate(final JsonObject rootElement, + final Publication publication, + final String jsonKey, + final String dictionaryKey, + final boolean addToDateOfAcceptance) { + + final String pubDate = getPublicationDate(rootElement, "publication_date"); + if (StringUtils.isNotBlank(pubDate)) { + if (addToDateOfAcceptance) { + publication.setDateofacceptance(mapStringField(pubDate, null)); + } + Qualifier q = mapQualifier(dictionaryKey, dictionaryKey, "dnet:dataCite_date", "dnet:dataCite_date"); + publication + .setRelevantdate( + Arrays + .asList(pubDate) + .stream() + .map(r -> { + return mapStructuredProperty(r, q, null); + }) + .filter(s -> s != null) + .collect(Collectors.toList())); + } + } + + private String getPublicationDate(final JsonObject rootElement, + final String jsonKey) { + + JsonObject pubDateJson = null; + try { + pubDateJson = rootElement.getAsJsonObject(jsonKey); + } catch (Exception e) { + return null; + } + if (pubDateJson == null) { + return null; + } + final String year = getStringValue(pubDateJson, "year"); + final String month = getStringValue(pubDateJson, "month"); + final String day = getStringValue(pubDateJson, "day"); + + if (StringUtils.isBlank(year)) { + return null; + } + String pubDate = "".concat(year); + if (StringUtils.isNotBlank(month)) { + pubDate = pubDate.concat("-" + month); + if (StringUtils.isNotBlank(day)) { + pubDate = pubDate.concat("-" + day); + } else { + pubDate += "-01"; + } + } else { + pubDate += "-01-01"; + } + if (isValidDate(pubDate)) { + return pubDate; + } + return null; + } + + protected boolean isValid(final JsonObject rootElement/* , final Reporter context */) { + + final String type = getStringValue(rootElement, "type"); + if (!typologiesMapping.containsKey(type)) { + logger.error("unknowntype_" + type); + if (errorsInvalidType != null) { + errorsInvalidType.add(1); + } + return false; + } + + if (!isValidJsonArray(rootElement, "titles")) { + if (errorsInvalidTitle != null) { + errorsInvalidTitle.add(1); + } + return false; + } + return true; + } + + private boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { + return false; + } + final JsonElement jsonElement = rootElement.get(fieldName); + if (jsonElement.isJsonNull()) { + return false; + } + if (jsonElement.isJsonArray()) { + final JsonArray jsonArray = jsonElement.getAsJsonArray(); + if (jsonArray.isJsonNull()) { + return false; + } + if (jsonArray.get(0).isJsonNull()) { + return false; + } + } + return true; + } + + private Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { + final Qualifier qualifier = new Qualifier(); + qualifier.setClassid(classId); + qualifier.setClassname(className); + qualifier.setSchemeid(schemeId); + qualifier.setSchemename(schemeName); + return qualifier; + } + + private ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, + String schemeName) { + ExternalReference ex = new ExternalReference(); + ex.setRefidentifier(extId); + ex.setQualifier(mapQualifier(classId, className, schemeId, schemeName)); + return ex; + } + + private StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { + if (value == null | StringUtils.isBlank(value)) { + return null; + } + + final StructuredProperty structuredProperty = new StructuredProperty(); + structuredProperty.setValue(value); + structuredProperty.setQualifier(qualifier); + structuredProperty.setDataInfo(dataInfo); + return structuredProperty; + } + + private Field mapStringField(String value, DataInfo dataInfo) { + if (value == null || StringUtils.isBlank(value)) { + return null; + } + + final Field stringField = new Field<>(); + stringField.setValue(value); + stringField.setDataInfo(dataInfo); + return stringField; + } + + private KeyValue createCollectedFrom() { + KeyValue cf = new KeyValue(); + cf.setValue(ORCID); + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); + return cf; + } + + private KeyValue createHostedBy() { + KeyValue hb = new KeyValue(); + hb.setValue("Unknown Repository"); + hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c"); + return hb; + } + + private StructuredProperty mapAuthorId(String orcidId) { + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(orcidId); + final Qualifier q = new Qualifier(); + q.setClassid(ORCID.toLowerCase()); + q.setClassname(ORCID.toLowerCase()); + q.setSchemeid(ModelConstants.DNET_PID_TYPES); + q.setSchemename(ModelConstants.DNET_PID_TYPES); + sp.setQualifier(q); + final DataInfo dataInfo = new DataInfo(); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferred(false); + dataInfo.setTrust("0.9"); + dataInfo + .setProvenanceaction( + mapQualifier( + "sysimport:crosswalk:entityregistry", + "Harvested", + "dnet:provenanceActions", + "dnet:provenanceActions")); + sp.setDataInfo(dataInfo); + return sp; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java new file mode 100644 index 0000000000..c0f6178684 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -0,0 +1,217 @@ + +package eu.dnetlib.doiboost.orcidnodoi.similarity; + +import java.io.IOException; +import java.text.Normalizer; +import java.util.*; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.text.similarity.JaroWinklerSimilarity; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.schema.orcid.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +/** + * This class is used for searching from a list of publication contributors a + * specific author making a similarity check on both name and surname of the + * author with the credit name of each contributor of the list; as soon as + * the match is found (if exist) author informations are used to enrich the + * matched contribuotr inside contributors list + */ + +public class AuthorMatcher { + + private static final Logger logger = LoggerFactory.getLogger(AuthorMatcher.class); + public static final Double threshold = 0.8; + + public static void match(AuthorData author, List contributors) + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + + int matchCounter = 0; + List matchCounters = Arrays.asList(matchCounter); + Contributor contributor = null; + contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (simpleMatch(c.getCreditName(), author.getName()) || + simpleMatch(c.getCreditName(), author.getSurname()) || + simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); + if (matchCounters.get(0) == 1) { + updateAuthorsSimpleMatch(contributors, author); + } else if (matchCounters.get(0) == 0) { + Optional optCon = contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .map(c -> { + c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); + return c; + }) + .filter(c -> c.getScore() >= threshold) + .max(Comparator.comparing(c -> c.getScore())); + Contributor bestMatchContributor = null; + if (optCon.isPresent()) { + bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + updateAuthorsSimilarityMatch(contributors, author); + } + } else if (matchCounters.get(0) > 1) { + Optional optCon = contributors + .stream() + .filter(c -> c.isSimpleMatch()) + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .map(c -> { + c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); + return c; + }) + .filter(c -> c.getScore() >= threshold) + .max(Comparator.comparing(c -> c.getScore())); + Contributor bestMatchContributor = null; + if (optCon.isPresent()) { + bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + updateAuthorsSimilarityMatch(contributors, author); + } + } + + } + + public static boolean simpleMatchOnOtherNames(String name, List otherNames) { + if (otherNames == null || (otherNames != null && otherNames.isEmpty())) { + return false; + } + return otherNames.stream().filter(o -> simpleMatch(name, o)).count() > 0; + } + + public static boolean simpleMatch(String name, String searchValue) { + if (searchValue == null) { + return false; + } + return normalize(name).contains(normalize(searchValue)); + } + + public static Double bestMatch(String authorSurname, String authorName, String contributor) { + String[] contributorSplitted = contributor.split(" "); + if (contributorSplitted.length == 0) { + return 0.0; + } + final String contributorName = contributorSplitted[contributorSplitted.length - 1]; + String contributorSurname = ""; + if (contributorSplitted.length > 1) { + StringJoiner joiner = new StringJoiner(" "); + for (int i = 0; i < contributorSplitted.length - 1; i++) { + joiner.add(contributorSplitted[i]); + } + contributorSurname = joiner.toString(); + } + String authorNameNrm = normalize(authorName); + String authorSurnameNrm = normalize(authorSurname); + String contributorNameNrm = normalize(contributorName); + String contributorSurnameNrm = normalize(contributorSurname); + Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm); + Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm); + if (sm1.compareTo(sm2) >= 0) { + return sm1; + } + return sm2; + } + + public static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { + Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); + return score; + } + + private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) { + return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); + } + + public static String normalize(final String s) { + if (s == null) { + return new String(""); + } + return nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } + + private static String parse(String name, String surname) { + return surname + " " + name; + } + + public static void updateAuthorsSimpleMatch(List contributors, AuthorData author) { + contributors.forEach(c -> { + if (c.isSimpleMatch()) { + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + } + }); + updateRanks(contributors); + } + + public static void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { + contributors + .stream() + .filter(c -> c.isBestMatch()) + .forEach(c -> { + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + }); + updateRanks(contributors); + } + + private static void updateRanks(List contributors) { + boolean seqFound = false; + if (contributors + .stream() + .filter( + c -> c.getRole() != null && c.getSequence() != null && + c.getRole().equals("author") && (c.getSequence().equals("first") || + c.getSequence().equals("additional"))) + .count() > 0) { + seqFound = true; + } + if (!seqFound) { + List seqIds = Arrays.asList(0); + contributors.forEach(c -> { + int currentSeq = seqIds.get(0) + 1; + seqIds.set(0, currentSeq); + c.setSequence(Integer.toString(seqIds.get(0))); + }); + } + } + + private static String toJson(WorkDataNoDoi work) { + GsonBuilder builder = new GsonBuilder(); + Gson gson = builder.create(); + return gson.toJson(work); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java new file mode 100644 index 0000000000..8096c4e8e0 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java @@ -0,0 +1,113 @@ + +package eu.dnetlib.doiboost.orcidnodoi.util; + +import java.text.SimpleDateFormat; +import java.util.*; + +import org.apache.commons.lang3.StringUtils; + +import com.google.gson.JsonArray; +import com.google.gson.JsonObject; + +/** + * Utility class + */ + +public class DumpToActionsUtility { + + private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US); + + public static String getStringValue(final JsonObject root, final String key) { + if (root.has(key) && !root.get(key).isJsonNull()) + return root.get(key).getAsString(); + return new String(""); + } + + public static List getArrayValues(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + + asJsonArray.forEach(it -> { + if (StringUtils.isNotBlank(it.getAsString())) { + result.add(it.getAsString()); + } + }); + return result; + } + return new ArrayList<>(); + } + + public static List getArrayObjects(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + asJsonArray.forEach(it -> { + if (it.getAsJsonObject() != null) { + result.add(it.getAsJsonObject()); + } + }); + return result; + } + return new ArrayList<>(); + } + + public static boolean isValidDate(final String date) { + return date.matches("\\d{4}-\\d{2}-\\d{2}"); + } + + public static String now_ISO8601() { // NOPMD + String result; + synchronized (ISO8601FORMAT) { + result = ISO8601FORMAT.format(new Date()); + } + // convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00 + // - note the added colon for the Timezone + return result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2); + } + + public static String getDefaultResulttype(final String cobjcategory) { + switch (cobjcategory) { + case "0029": + return "software"; + case "0021": + case "0024": + case "0025": + case "0030": + return "dataset"; + case "0000": + case "0010": + case "0018": + case "0020": + case "0022": + case "0023": + case "0026": + case "0027": + case "0028": + case "0037": + return "other"; + case "0001": + case "0002": + case "0004": + case "0005": + case "0006": + case "0007": + case "0008": + case "0009": + case "0011": + case "0012": + case "0013": + case "0014": + case "0015": + case "0016": + case "0017": + case "0019": + case "0031": + case "0032": + return "publication"; + default: + return "publication"; + } + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java new file mode 100644 index 0000000000..8883d00f5d --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.doiboost.orcidnodoi.util; + +public class Pair { + + private K k; + + private V v; + + public Pair(K k, V v) { + this.k = k; + this.v = v; + } + + public K getKey() { + return k; + } + + public V getValue() { + return v; + } + + @Override + public boolean equals(Object obj) { + if (obj instanceof Pair) { + Pair tmp = (Pair) obj; + return k.equals(tmp.getKey()) && v.equals(tmp.getValue()); + } else + return false; + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java new file mode 100644 index 0000000000..f4b0934020 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java @@ -0,0 +1,217 @@ + +package eu.dnetlib.doiboost.orcidnodoi.xml; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.ximpleware.*; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId; +import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +/** + * This class is used for parsing xml data with vtd parser + */ + +public class XMLRecordParserNoDoi { + + private static final Logger logger = LoggerFactory.getLogger(XMLRecordParserNoDoi.class); + + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; + private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; + private static final String NS_PERSON = "person"; + private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; + private static final String NS_DETAILS = "personal-details"; + private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; + private static final String NS_OTHER = "other-name"; + private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; + private static final String NS_RECORD = "record"; + private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; + + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + + private static final String NS_ERROR = "error"; + + public static WorkDataNoDoi VTDParseWorkData(byte[] bytes) + throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException, + NavException, XPathEvalException { + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + + WorkDataNoDoi workData = new WorkDataNoDoi(); + final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); + if (!errors.isEmpty()) { + workData.setErrorCode(errors.get(0)); + return workData; + } + + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "put-code")); + if (!workNodes.isEmpty()) { + final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + workData.setOid(oid); + final String id = (workNodes.get(0).getAttributes().get("put-code")); + workData.setId(id); + } else { + return null; + } + + final List titles = VtdUtilityParser + .getTextValue( + ap, vn, "//common:title"); + if (!titles.isEmpty()) { + workData.setTitles(titles); + } + + final List sourceNames = VtdUtilityParser + .getTextValue( + ap, vn, "//common:source-name"); + if (!sourceNames.isEmpty()) { + workData.setSourceName(sourceNames.get(0)); + } + + final List types = VtdUtilityParser + .getTextValue( + ap, vn, "//work:type"); + if (!types.isEmpty()) { + workData.setType(types.get(0)); + } + + final List urls = VtdUtilityParser + .getTextValue( + ap, vn, "//common:url"); + if (!urls.isEmpty()) { + workData.setUrls(urls); + } + + workData.setPublicationDates(getPublicationDates(vg, vn, ap)); + workData.setExtIds(getExternalIds(vg, vn, ap)); + workData.setContributors(getContributors(vg, vn, ap)); + return workData; + + } + + private static List getPublicationDates(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List publicationDates = new ArrayList(); + int yearIndex = 0; + ap.selectXPath("//common:publication-date/common:year"); + while (ap.evalXPath() != -1) { + PublicationDate publicationDate = new PublicationDate(); + int t = vn.getText(); + if (t >= 0) { + publicationDate.setYear(vn.toNormalizedString(t)); + publicationDates.add(yearIndex, publicationDate); + yearIndex++; + } + } + int monthIndex = 0; + ap.selectXPath("//common:publication-date/common:month"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + publicationDates.get(monthIndex).setMonth(vn.toNormalizedString(t)); + monthIndex++; + } + } + int dayIndex = 0; + ap.selectXPath("//common:publication-date/common:day"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + publicationDates.get(dayIndex).setDay(vn.toNormalizedString(t)); + dayIndex++; + } + } + return publicationDates; + } + + private static List getExternalIds(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List extIds = new ArrayList(); + int typeIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-type"); + while (ap.evalXPath() != -1) { + ExternalId extId = new ExternalId(); + int t = vn.getText(); + if (t >= 0) { + extId.setType(vn.toNormalizedString(t)); + extIds.add(typeIndex, extId); + typeIndex++; + } + } + int valueIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-value"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + extIds.get(valueIndex).setValue(vn.toNormalizedString(t)); + valueIndex++; + } + } + int relationshipIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-relationship"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + extIds.get(relationshipIndex).setRelationShip(vn.toNormalizedString(t)); + relationshipIndex++; + } + } + if (typeIndex == valueIndex) { + return extIds; + } + return new ArrayList(); + } + + private static List getContributors(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List contributors = new ArrayList(); + ap.selectXPath("//work:contributors/work:contributor"); + while (ap.evalXPath() != -1) { + Contributor contributor = new Contributor(); + if (vn.toElement(VTDNav.FIRST_CHILD, "work:credit-name")) { + int val = vn.getText(); + if (val != -1) { + contributor.setCreditName(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); + } + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-attributes")) { + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-sequence")) { + int val = vn.getText(); + if (val != -1) { + contributor.setSequence(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); + } + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-role")) { + int val = vn.getText(); + if (val != -1) { + contributor.setRole(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); + } + vn.toElement(VTDNav.PARENT); + } + contributors.add(contributor); + } + return contributors; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json index 131c301257..b2f0fdedac 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml index a9cc9ea3cd..63c2e9ef29 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml @@ -16,88 +16,86 @@ sparkExecutorCores number of cores used by single executor - - - - + + timestamp + Timestamp for incremental Harvesting + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.crossref.CrossrefImporter + -t${workingPath}/input/crossref/index_update + -n${nameNode} + -ts${timestamp} + + + + + + + + yarn-cluster + cluster + ExtractCrossrefToOAF + eu.dnetlib.doiboost.crossref.CrossrefDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --workingPath/data/doiboost/input/crossref + --masteryarn-cluster + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + yarn-cluster cluster - ExtractCrossrefToOAF + ConvertCrossrefToOAF eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF dhp-doiboost-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 ${sparkExtraOPT} --sourcePath${workingPath}/input/crossref/crossref_ds - --targetPath${workingPath}/input/crossref + --targetPath${workingPath}/process/ --masteryarn-cluster - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json index 312bd0751e..23c0fdabc0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json @@ -1,6 +1,5 @@ [ - {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true}, {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json index 444e487f7b..8c69b168b5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json new file mode 100644 index 0000000000..c3a8f92ecf --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json @@ -0,0 +1,7 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, + {"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, + {"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json similarity index 76% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json index bf992b5086..6f213e4150 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json deleted file mode 100644 index 35bfe1b415..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json +++ /dev/null @@ -1,4 +0,0 @@ -[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}, - {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write the authors data", "paramRequired": true} -] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json new file mode 100644 index 0000000000..c3a8f92ecf --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json @@ -0,0 +1,7 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, + {"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, + {"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml index e35f88abd5..dcde62c9d9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml @@ -39,14 +39,7 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - + diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml index 2277b79b0f..9d19dddc71 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml @@ -8,6 +8,10 @@ targetPath the working dir base path + + workingPath + the working dir base path + sparkDriverMemory memory for driver process @@ -31,10 +35,10 @@ - - + + - + @@ -52,10 +56,10 @@ ${sparkExtraOPT} --sourcePath${sourcePath} - --targetPath${targetPath} + --targetPath${workingPath} --masteryarn-cluster - + @@ -65,7 +69,7 @@ yarn-cluster cluster - Convert Mag to Dataset + Convert Mag to OAF Dataset eu.dnetlib.doiboost.mag.SparkPreProcessMAG dhp-doiboost-${projectVersion}.jar @@ -75,7 +79,8 @@ --conf spark.sql.shuffle.partitions=3840 ${sparkExtraOPT} - --sourcePath${sourcePath} + --sourcePath${workingPath} + --workingPath${workingPath}/process --targetPath${targetPath} --masteryarn-cluster diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json index bf0b80f69f..d45f7269fc 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json @@ -1,6 +1,7 @@ [ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target dir path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true}, {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml deleted file mode 100644 index fe14bb8cb5..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - hadoop-rm3.garr-pa1.d4science.org:8032 - - - nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://hadoop-edge2.garr-pa1.d4science.org:9083 - - - spark2YarnHistoryServerAddress - http://hadoop-edge1.garr-pa1.d4science.org:18089/ - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml new file mode 100644 index 0000000000..05fe6d014f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml @@ -0,0 +1,31 @@ + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx2g + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml new file mode 100644 index 0000000000..ea4d33296c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml @@ -0,0 +1,542 @@ + + + + workingPath + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2020_10_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/25002232 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_0.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_0.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_0.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 0 + + + shell_cmd_1 + wget -O /tmp/ORCID_2020_10_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/25002088 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_1.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_1.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_1.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 1 + + + shell_cmd_2 + wget -O /tmp/ORCID_2020_10_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/25000596 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_2.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_2.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_2.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 2 + + + shell_cmd_3 + wget -O /tmp/ORCID_2020_10_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/25015150 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_3.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_3.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_3.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 3 + + + shell_cmd_4 + wget -O /tmp/ORCID_2020_10_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/25033643 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_4.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_4.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_4.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 4 + + + shell_cmd_5 + wget -O /tmp/ORCID_2020_10_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/25005483 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_5.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_5.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_5.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 5 + + + shell_cmd_6 + wget -O /tmp/ORCID_2020_10_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/25005425 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_6.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_6.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_6.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 6 + + + shell_cmd_7 + wget -O /tmp/ORCID_2020_10_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/25012016 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_7.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_7.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_7.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 7 + + + shell_cmd_8 + wget -O /tmp/ORCID_2020_10_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/25012079 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_8.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_8.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_8.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 8 + + + shell_cmd_9 + wget -O /tmp/ORCID_2020_10_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/25010727 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_9.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_9.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_9.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 9 + + + shell_cmd_X + wget -O /tmp/ORCID_2020_10_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/25011025 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_X.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_X.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_X.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file X + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_0.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_0.tar.gz + -owno_doi_works/works_0.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_1.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_1} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_1.tar.gz + -owno_doi_works/works_1.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_2.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_2} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_2.tar.gz + -owno_doi_works/works_2.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_3.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_3} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_3.tar.gz + -owno_doi_works/works_3.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_4.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_4} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_4.tar.gz + -owno_doi_works/works_4.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_5.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_5} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_5.tar.gz + -owno_doi_works/works_5.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_6.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_6} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_6.tar.gz + -owno_doi_works/works_6.seq + -oewno_doi_enriched_works/ + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_7.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_7} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_7.tar.gz + -owno_doi_works/works_7.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_8.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_8} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_8.tar.gz + -owno_doi_works/works_8.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_9.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_9} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_9.tar.gz + -owno_doi_works/works_9.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_X.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_X} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_X.tar.gz + -owno_doi_works/works_X.seq + -oewno_doi_enriched_works/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml deleted file mode 100644 index 1f9adeb4d8..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - - workingPathOrcid - the working dir base path - - - token - access token - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidDownloader - -d${workingPathOrcid}/ - -n${nameNode} - -flast_modified.csv - -odownload/ - -t${token} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml new file mode 100644 index 0000000000..6f629c7540 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml @@ -0,0 +1,232 @@ + + + + workingPath + the working dir base path + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.java + ${oozieActionShareLibForSpark2} + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx2g + + + oozie.use.system.libpath + true + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_0.tar.gz + -owxml/works/xml_works_0.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_1.tar.gz + -owxml/works/xml_works_1.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_2.tar.gz + -owxml/works/xml_works_2.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_3.tar.gz + -owxml/works/xml_works_3.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_4.tar.gz + -owxml/works/xml_works_4.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_5.tar.gz + -owxml/works/xml_works_5.seq + -oew--- + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_6.tar.gz + -owxml/works/xml_works_6.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_7.tar.gz + -owxml/works/xml_works_7.seq + -oew--- + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_8.tar.gz + -owxml/works/xml_works_8.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_9.tar.gz + -owxml/works/xml_works_9.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_X.tar.gz + -owxml/works/xml_works_X.seq + -oew--- + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml new file mode 100644 index 0000000000..191654378a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml @@ -0,0 +1,26 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx8g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml similarity index 55% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml index 7a8d041870..68d468ab33 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml @@ -1,41 +1,40 @@ - + workingPath the working dir base path - + - - + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - - + + - + - - - - + + ${jobTracker} ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidDSManager - -d${workingPath}/ + eu.dnetlib.doiboost.orcid.ExtractXMLSummariesData + -w${workingPath}/ -n${nameNode} - -fORCID_2019_summaries.tar.gz - -ooutput/ + -fORCID_2020_10_summaries.tar.gz + -oxml/authors/ + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml deleted file mode 100644 index a720e75923..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - jobTracker - hadoop-rm3.garr-pa1.d4science.org:8032 - - - nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - - - queueName - default - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml deleted file mode 100644 index 7ebc5f0a0b..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - workingPath - the working dir base path - - - token - access token - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - outputPath - the working dir base path - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - yarn - cluster - Split_Lambda_File - eu.dnetlib.doiboost.orcid.SparkPartitionLambdaFile - dhp-doiboost-1.2.1-SNAPSHOT.jar - --num-executors 24 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - - -w${workingPath}/ - -oauthors/ - -t${token} - - - - - - - - ${jobTracker} - ${nameNode} - yarn - cluster - Gen_Orcid_Authors - eu.dnetlib.doiboost.orcid.SparkOrcidGenerateAuthors - dhp-doiboost-1.2.1-SNAPSHOT.jar - --num-executors 20 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - - -w${workingPath}/ - -oauthors/ - -t${token} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml new file mode 100644 index 0000000000..191654378a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml @@ -0,0 +1,26 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx8g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml new file mode 100644 index 0000000000..8517f35ee0 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml @@ -0,0 +1,68 @@ + + + + workingPath + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2020_10_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/25032905 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_summaries.tar.gz /data/orcid_activities_2020/ORCID_2020_10_summaries.tar.gz ; rm -f /tmp/ORCID_2020_10_summaries.tar.gz + + the shell command that downloads and puts to hdfs orcid summaries + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_summaries.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDSManager + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_summaries.tar.gz + -oauthors/ + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml new file mode 100644 index 0000000000..b9383558cc --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -0,0 +1,168 @@ + + + + workingPath + the working dir base path + + + token + access token + + + shell_cmd + wget -O /tmp/last_modified.csv.tar http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar ; hdfs dfs -copyFromLocal /tmp/last_modified.csv.tar /data/orcid_activities_2020/last_modified.csv.tar ; rm -f /tmp/last_modified.csv.tar + + the shell command that downloads the lambda file from orcid containing last orcid update informations + + + sparkDriverMemory + 7G + memory for driver process + + + sparkExecutorMemory + 2G + memory for individual executor + + + sparkExecutorCores + 1 + number of cores used by single executor + + + spark2MaxExecutors + 10 + + + 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 + + + + + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDownloader + -w${workingPath}/ + -n${nameNode} + -flast_modified.csv.tar + -odownloads/ + -t${token} + + + + + + + + yarn-cluster + cluster + GenLastModifiedSeq + eu.dnetlib.doiboost.orcid.SparkGenLastModifiedSeq + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -flast_modified.csv.tar + -olast_modified.seq + -t- + + + + + + + + yarn-cluster + cluster + DownloadOrcidAuthors + eu.dnetlib.doiboost.orcid.SparkDownloadOrcidAuthors + dhp-doiboost-${projectVersion}.jar + + --conf spark.dynamicAllocation.enabled=true + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -flast_modified.seq + -odownloads/updated_authors + -t${token} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json new file mode 100644 index 0000000000..cb696f2793 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json @@ -0,0 +1,41 @@ +{ + "reference-entry": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "report": {"cobj":"0017", "value": "Report"}, + "dataset": {"cobj":"0021", "value": "Dataset"}, + "journal-article": {"cobj":"0001", "value": "Article"}, + "reference-book": {"cobj":"0002", "value": "Book"}, + "other": {"cobj":"0020", "value": "Other ORP type"}, + "proceedings-article": {"cobj":"0004", "value": "Conference object"}, + "standard": {"cobj":"0038", "value": "Other literature type"}, + "book-part": {"cobj":"0002", "value": "Book"}, + "monograph": {"cobj":"0002", "value": "Book"}, + "report-series": {"cobj":"0017", "value": "Report"}, + "book": {"cobj":"0002", "value": "Book"}, + "book-chapter": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "peer-review": {"cobj":"0015", "value": "Review"}, + "book-section": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "book-review": {"cobj":"0015", "value": "Review"}, + "conference-abstract": {"cobj":"0004", "value": "Conference object"}, + "conference-paper": {"cobj":"0004", "value": "Conference object"}, + "conference-poster": {"cobj":"0004", "value": "Conference object"}, + "data-set": {"cobj":"0021", "value": "Dataset"}, + "dictionary-entry": {"cobj":"0038", "value": "Other literature type"}, + "disclosure": {"cobj":"0038", "value": "Other literature type"}, + "dissertation": {"cobj":"0006", "value": "Doctoral thesis"}, + "edited-book": {"cobj":"0002", "value": "Book"}, + "encyclopedia-entry": {"cobj":"0038", "value": "Other literature type"}, + "lecture-speech": {"cobj":"0010", "value": "Lecture"}, + "license": {"cobj":"0038", "value": "Other literature type"}, + "magazine-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"}, + "manual": {"cobj":"0038", "value": "Other literature type"}, + "newsletter-article": {"cobj":"0012", "value": "Newsletter"}, + "newspaper-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"}, + "patent": {"cobj":"0019", "value": "Patent"}, + "research-technique": {"cobj":"0020", "value": "Other ORP type"}, + "research-tool": {"cobj":"0020", "value": "Other ORP type"}, + "standards-and-policy": {"cobj":"0038", "value": "Other literature type"}, + "supervised-student-publication": {"cobj":"0001", "value": "Article"}, + "technical-standard": {"cobj":"0038", "value": "Other literature type"}, + "website": {"cobj":"0020", "value": "Other ORP type"}, + "working-paper": {"cobj":"0014", "value": "Research"} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml new file mode 100644 index 0000000000..6cec48a6d3 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -0,0 +1,95 @@ + + + + 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 + + + workingPath + the working dir base path + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + yarn-cluster + cluster + GenOrcidNoDoiDataset + eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -f- + -owno_doi_works/ + -oewno_doi_dataset + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala index a3bb2a4f48..4568e23a57 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -158,7 +158,7 @@ class CrossrefMappingTest { rels.foreach(s => logger.info(s.getTarget)) - assertEquals(rels.size, 3 ) + assertEquals(rels.size, 6 ) } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index 5b82409421..0222b393da 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -1,5 +1,8 @@ package eu.dnetlib.doiboost.orcid +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.codehaus.jackson.map.ObjectMapper import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Test @@ -21,6 +24,30 @@ class MappingORCIDToOAFTest { }) } +// @Test +// def testOAFConvert():Unit ={ +// +// val spark: SparkSession = +// SparkSession +// .builder() +// .appName(getClass.getSimpleName) +// .master("local[*]").getOrCreate() +// +// +// SparkConvertORCIDToOAF.run( spark,"/Users/sandro/Downloads/orcid", "/Users/sandro/Downloads/orcid_oaf") +// implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] +// +// val df = spark.read.load("/Users/sandro/Downloads/orcid_oaf").as[Publication] +// println(df.first.getId) +// println(mapper.writeValueAsString(df.first())) +// +// +// +// +// } + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index 75f857ca44..66a7badb7b 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -3,23 +3,34 @@ package eu.dnetlib.doiboost.orcid; import static org.junit.jupiter.api.Assertions.assertTrue; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.nio.file.StandardOpenOption; import java.text.ParseException; import java.text.SimpleDateFormat; +import java.time.Duration; +import java.time.LocalDateTime; +import java.time.temporal.TemporalUnit; import java.util.Arrays; import java.util.Date; import java.util.List; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; +import org.apache.spark.sql.catalyst.expressions.objects.AssertNotNull; import org.junit.jupiter.api.Test; +import org.mortbay.log.Log; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import jdk.nashorn.internal.ir.annotations.Ignore; public class OrcidClientTest { final String orcidId = "0000-0001-7291-3210"; @@ -32,16 +43,64 @@ public class OrcidClientTest { String lastUpdate = "2019-09-30 00:00:00"; String shortDate = "2020-05-06 16:06:11"; -// curl -i -H "Accept: application/vnd.orcid+xml" +// curl -i -H "Accept: application/vnd.orcid+xml" // -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d' // 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record' - public String testDownloadRecord(String orcidId) throws Exception { + @Test + private void multipleDownloadTest() throws Exception { + int toDownload = 10; + long start = System.currentTimeMillis(); + OrcidDownloader downloader = new OrcidDownloader(); + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + int modified = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + if (downloader.isModified(orcidId, recordInfo.get(3))) { + slowedDownDownload(orcidId); + modified++; + } + rowNum++; + if (modified > toDownload) { + break; + } + } + entryNum++; + entry = input.getNextTarEntry(); + } + long end = System.currentTimeMillis(); + logToFile("start test: " + new Date(start).toString()); + logToFile("end test: " + new Date(end).toString()); + } + + @Test + private void downloadTest(String orcid) throws Exception { + String record = testDownloadRecord(orcid); + String filename = "/tmp/downloaded_".concat(orcid).concat(".xml"); + File f = new File(filename); + OutputStream outStream = new FileOutputStream(f); + IOUtils.write(record.getBytes(), outStream); + } + + private String testDownloadRecord(String orcidId) throws Exception { try (CloseableHttpClient client = HttpClients.createDefault()) { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d"); + logToFile("start connection: " + new Date(System.currentTimeMillis()).toString()); CloseableHttpResponse response = client.execute(httpGet); + logToFile("end connection: " + new Date(System.currentTimeMillis()).toString()); if (response.getStatusLine().getStatusCode() != 200) { System.out .println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); @@ -53,8 +112,8 @@ public class OrcidClientTest { return new String(""); } -// @Test - public void testLambdaFileParser() throws Exception { + // @Test + private void testLambdaFileParser() throws Exception { try (BufferedReader br = new BufferedReader( new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) { String line; @@ -99,8 +158,8 @@ public class OrcidClientTest { } } -// @Test - public void getRecordDatestamp() throws ParseException { + // @Test + private void getRecordDatestamp() throws ParseException { Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate); Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate); Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); @@ -108,7 +167,7 @@ public class OrcidClientTest { assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt)); } - public void testDate(String value) throws ParseException { + private void testDate(String value) throws ParseException { System.out.println(value.toString()); if (value.length() != 19) { value = value.substring(0, 19); @@ -117,20 +176,126 @@ public class OrcidClientTest { System.out.println(valueDt.toString()); } -// @Test - public void testModifiedDate() throws ParseException { + // @Test + @Ignore + private void testModifiedDate() throws ParseException { testDate(toRetrieveDate); testDate(toNotRetrieveDate); testDate(shortDate); } -// @Test - public void testReadBase64CompressedRecord() throws Exception { + @Test + private void testReadBase64CompressedRecord() throws Exception { final String base64CompressedRecord = IOUtils - .toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64")); + .toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64")); final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); - System.out.println(recordFromSeqFile); - final String downloadedRecord = testDownloadRecord("0000-0001-6645-509X"); + logToFile("\n\ndownloaded \n\n" + recordFromSeqFile); + final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161"); assertTrue(recordFromSeqFile.equals(downloadedRecord)); } + + @Test + private void lambdaFileReaderTest() throws Exception { + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/develop/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + assertTrue(recordInfo.size() == 4); + + rowNum++; + if (rowNum == 1) { + assertTrue(recordInfo.get(3).equals("last_modified")); + } else if (rowNum == 2) { + assertTrue(recordInfo.get(0).equals("0000-0002-0499-7333")); + } + } + entryNum++; + assertTrue(entryNum == 1); + entry = input.getNextTarEntry(); + } + } + + @Test + private void lambdaFileCounterTest() throws Exception { + final String lastUpdate = "2020-09-29 00:00:00"; + OrcidDownloader downloader = new OrcidDownloader(); + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + int modified = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + if (downloader.isModified(orcidId, recordInfo.get(3))) { + modified++; + } + rowNum++; + } + entryNum++; + entry = input.getNextTarEntry(); + } + logToFile("rowNum: " + rowNum); + logToFile("modified: " + modified); + } + + private void logToFile(String log) + throws IOException { + log = log.concat("\n"); + Path path = Paths.get("/tmp/orcid_log.txt"); + Files.write(path, log.getBytes(), StandardOpenOption.APPEND); + } + + @Test + private void slowedDownDownloadTest() throws Exception { + String orcid = "0000-0001-5496-1243"; + String record = slowedDownDownload(orcid); + String filename = "/tmp/downloaded_".concat(orcid).concat(".xml"); + File f = new File(filename); + OutputStream outStream = new FileOutputStream(f); + IOUtils.write(record.getBytes(), outStream); + } + + private String slowedDownDownload(String orcidId) throws Exception { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d"); + long start = System.currentTimeMillis(); + CloseableHttpResponse response = client.execute(httpGet); + long endReq = System.currentTimeMillis(); + long reqSessionDuration = endReq - start; + logToFile("req time (millisec): " + reqSessionDuration); + if (reqSessionDuration < 1000) { + logToFile("wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } + long end = System.currentTimeMillis(); + long total = end - start; + logToFile("total time (millisec): " + total); + if (response.getStatusLine().getStatusCode() != 200) { + logToFile("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); + } + return IOUtils.toString(response.getEntity().getContent()); + } catch (Throwable e) { + e.printStackTrace(); + } + return new String(""); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index d5da4eec02..b7be5e5cd2 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -2,17 +2,19 @@ package eu.dnetlib.doiboost.orcid.xml; import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.Test; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class XMLRecordParserTest { @Test - public void testOrcidAuthorDataXMLParser() throws Exception { + private void testOrcidAuthorDataXMLParser() throws Exception { String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml")); @@ -27,7 +29,7 @@ public class XMLRecordParserTest { } @Test - public void testOrcidXMLErrorRecordParser() throws Exception { + private void testOrcidXMLErrorRecordParser() throws Exception { String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml")); @@ -40,11 +42,11 @@ public class XMLRecordParserTest { } @Test - public void testOrcidWorkDataXMLParser() throws Exception { + private void testOrcidWorkDataXMLParser() throws Exception { String xml = IOUtils .toString( - this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml")); + this.getClass().getResourceAsStream("activity_work_0000-0003-2760-1191.xml")); XMLRecordParser p = new XMLRecordParser(); @@ -55,4 +57,21 @@ public class XMLRecordParserTest { assertNotNull(workData.getDoi()); System.out.println("doi: " + workData.getDoi()); } + + @Test + public void testOrcidOtherNamesXMLParser() throws Exception { + + String xml = IOUtils + .toString( + this.getClass().getResourceAsStream("summary_0000-0001-5109-1000_othername.xml")); + + XMLRecordParser p = new XMLRecordParser(); + + AuthorData authorData = XMLRecordParser.VTDParseAuthorData(xml.getBytes()); + assertNotNull(authorData); + assertNotNull(authorData.getOtherNames()); + assertTrue(authorData.getOtherNames().get(0).equals("Andrew C. Porteus")); + String jsonData = JsonWriter.create(authorData); + assertNotNull(jsonData); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java new file mode 100644 index 0000000000..01e26dcb4d --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java @@ -0,0 +1,78 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import static org.junit.jupiter.api.Assertions.*; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; +import jdk.nashorn.internal.ir.annotations.Ignore; + +public class PublicationToOafTest { + + private static final Logger logger = LoggerFactory.getLogger(PublicationToOafTest.class); + + @Test + @Ignore + private void convertOafPublicationTest() throws Exception { + String jsonPublication = IOUtils + .toString( + PublicationToOafTest.class.getResourceAsStream("publication.json")); + JsonElement j = new JsonParser().parse(jsonPublication); + logger.info("json publication loaded: " + j.toString()); + PublicationToOaf publicationToOaf = new PublicationToOaf(); + Publication oafPublication = (Publication) publicationToOaf + .generatePublicationActionsFromDump(j.getAsJsonObject()); + assertNotNull(oafPublication.getId()); + assertNotNull(oafPublication.getOriginalId()); + assertEquals(oafPublication.getOriginalId().get(0), "60153327"); + logger.info("oafPublication.getId(): " + oafPublication.getId()); + assertEquals( + oafPublication.getTitle().get(0).getValue(), + "Evaluation of a percutaneous optical fibre glucose sensor (FiberSense) across the glycemic range with rapid glucoseexcursions using the glucose clamp"); + assertNotNull(oafPublication.getLastupdatetimestamp()); + assertNotNull(oafPublication.getDateofcollection()); + assertNotNull(oafPublication.getDateoftransformation()); + assertTrue(oafPublication.getAuthor().size() == 7); + oafPublication.getAuthor().forEach(a -> { + assertNotNull(a.getFullname()); + assertNotNull(a.getRank()); + logger.info("a.getFullname(): " + a.getFullname()); + if (a.getName() != null) { + logger.info("a.getName(): " + a.getName()); + } + if (a.getSurname() != null) { + logger.info("a.getSurname(): " + a.getSurname()); + } + logger.info("a.getRank(): " + a.getRank()); + if (a.getPid() != null) { + logger.info("a.getPid(): " + a.getPid().get(0).getValue()); + } + + }); + assertNotNull(oafPublication.getCollectedfrom()); + if (oafPublication.getSource() != null) { + logger.info((oafPublication.getSource().get(0).getValue())); + } + if (oafPublication.getExternalReference() != null) { + oafPublication.getExternalReference().forEach(e -> { + assertNotNull(e.getRefidentifier()); + assertEquals(e.getQualifier().getSchemeid(), "dnet:pid_types"); + }); + } + assertNotNull(oafPublication.getInstance()); + oafPublication.getInstance().forEach(i -> { + assertNotNull(i.getInstancetype().getClassid()); + logger.info("i.getInstancetype().getClassid(): " + i.getInstancetype().getClassid()); + assertNotNull(i.getInstancetype().getClassname()); + logger.info("i.getInstancetype().getClassname(): " + i.getInstancetype().getClassname()); + }); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java new file mode 100644 index 0000000000..1f77197ab5 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -0,0 +1,348 @@ + +package eu.dnetlib.doiboost.orcidnodoi.xml; + +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.IOException; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.collect.Lists; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.schema.orcid.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; + +public class OrcidNoDoiTest { + + private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class); + + static String nameA = "Khairy"; + static String surnameA = "Abdel Dayem"; + static String orcidIdA = "0000-0003-2760-1191"; + + @Test + public void readPublicationFieldsTest() + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + logger.info("running loadPublicationFieldsTest ...."); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0002-2536-4498.xml")); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + assertNotNull(workData.getOid()); + logger.info("oid: " + workData.getOid()); + assertNotNull(workData.getTitles()); + logger.info("titles: "); + workData.getTitles().forEach(t -> { + logger.info(t); + }); + logger.info("source: " + workData.getSourceName()); + logger.info("type: " + workData.getType()); + logger.info("urls: "); + workData.getUrls().forEach(u -> { + logger.info(u); + }); + logger.info("publication date: "); + workData.getPublicationDates().forEach(d -> { + logger.info(d.getYear() + " - " + d.getMonth() + " - " + d.getDay()); + }); + logger.info("external id: "); + workData.getExtIds().removeIf(e -> e.getRelationShip() != null && !e.getRelationShip().equals("self")); + workData.getExtIds().forEach(e -> { + logger.info(e.getType() + " - " + e.getValue() + " - " + e.getRelationShip()); + }); + logger.info("contributors: "); + workData.getContributors().forEach(c -> { + logger + .info( + c.getName() + " - " + c.getRole() + " - " + c.getSequence()); + }); + + } + + @Test + public void authorDoubleMatchTest() throws Exception { + logger.info("running authorSimpleMatchTest ...."); + String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; + AuthorData author = new AuthorData(); + author.setName(nameA); + author.setSurname(surnameA); + author.setOid(orcidIdA); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + + Contributor a = workData.getContributors().get(0); + assertTrue(a.getCreditName().equals("Abdel-Dayem K")); + + AuthorMatcher.match(author, workData.getContributors()); + + assertTrue(workData.getContributors().size() == 6); + } + + @Test + public void readContributorsTest() + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + logger.info("running loadPublicationFieldsTest ...."); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191_contributors.xml")); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData.getContributors()); + assertTrue(workData.getContributors().size() == 5); + assertTrue(StringUtils.isBlank(workData.getContributors().get(0).getCreditName())); + assertTrue(workData.getContributors().get(0).getSequence().equals("seq0")); + assertTrue(workData.getContributors().get(0).getRole().equals("role0")); + assertTrue(workData.getContributors().get(1).getCreditName().equals("creditname1")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getSequence())); + assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getRole())); + assertTrue(workData.getContributors().get(2).getCreditName().equals("creditname2")); + assertTrue(workData.getContributors().get(2).getSequence().equals("seq2")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(2).getRole())); + assertTrue(workData.getContributors().get(3).getCreditName().equals("creditname3")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(3).getSequence())); + assertTrue(workData.getContributors().get(3).getRole().equals("role3")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(4).getCreditName())); + assertTrue(workData.getContributors().get(4).getSequence().equals("seq4")); + assertTrue(workData.getContributors().get(4).getRole().equals("role4")); + } + + @Test + public void authorSimpleMatchTest() throws Exception { + String orcidWork = "activity_work_0000-0002-5982-8983.xml"; + AuthorData author = new AuthorData(); + author.setName("Parkhouse"); + author.setSurname("H."); + author.setOid("0000-0002-5982-8983"); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + + Contributor a = workData.getContributors().get(0); + assertTrue(a.getCreditName().equals("Parkhouse, H.")); + + AuthorMatcher.match(author, workData.getContributors()); + + assertTrue(workData.getContributors().size() == 2); + Contributor c = workData.getContributors().get(0); + assertTrue(c.getOid().equals("0000-0002-5982-8983")); + assertTrue(c.getName().equals("Parkhouse")); + assertTrue(c.getSurname().equals("H.")); + assertTrue(c.getCreditName().equals("Parkhouse, H.")); + } + + @Test + public void match() { + + AuthorData author = new AuthorData(); + author.setName("Joe"); + author.setSurname("Dodge"); + author.setOid("0000-1111-2222-3333"); + Contributor contributor = new Contributor(); + contributor.setCreditName("Joe Dodge"); + List contributors = Arrays.asList(contributor); + AuthorMatcher am = new AuthorMatcher(); + int matchCounter = 0; + List matchCounters = Arrays.asList(matchCounter); + contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (am.simpleMatch(c.getCreditName(), author.getName()) || + am.simpleMatch(c.getCreditName(), author.getSurname()) || + am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); + + assertTrue(matchCounters.get(0) == 1); + am.updateAuthorsSimpleMatch(contributors, author); + assertTrue(contributors.get(0).getName().equals("Joe")); + assertTrue(contributors.get(0).getSurname().equals("Dodge")); + assertTrue(contributors.get(0).getCreditName().equals("Joe Dodge")); + assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333")); + + AuthorData authorX = new AuthorData(); + authorX.setName(nameA); + authorX.setSurname(surnameA); + authorX.setOid(orcidIdA); + Contributor contributorA = new Contributor(); + contributorA.setCreditName("Abdel-Dayem Khai"); + Contributor contributorB = new Contributor(); + contributorB.setCreditName("Abdel-Dayem Fake"); + List contributorList = new ArrayList<>(); + contributorList.add(contributorA); + contributorList.add(contributorB); + int matchCounter2 = 0; + List matchCounters2 = Arrays.asList(matchCounter2); + contributorList + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (am.simpleMatch(c.getCreditName(), authorX.getName()) || + am.simpleMatch(c.getCreditName(), authorX.getSurname()) || + am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { + int currentCounter = matchCounters2.get(0); + currentCounter += 1; + matchCounters2.set(0, currentCounter); + c.setSimpleMatch(true); + } + }); + + assertTrue(matchCounters2.get(0) == 2); + assertTrue(contributorList.get(0).isSimpleMatch()); + assertTrue(contributorList.get(1).isSimpleMatch()); + + Optional optCon = contributorList + .stream() + .filter(c -> c.isSimpleMatch()) + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .map(c -> { + c.setScore(am.bestMatch(authorX.getName(), authorX.getSurname(), c.getCreditName())); + return c; + }) + .filter(c -> c.getScore() >= AuthorMatcher.threshold) + .max(Comparator.comparing(c -> c.getScore())); + assertTrue(optCon.isPresent()); + + final Contributor bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + assertTrue(bestMatchContributor.getCreditName().equals("Abdel-Dayem Khai")); + assertTrue(contributorList.get(0).isBestMatch()); + assertTrue(!contributorList.get(1).isBestMatch()); + am.updateAuthorsSimilarityMatch(contributorList, authorX); + assertTrue(contributorList.get(0).getName().equals(nameA)); + assertTrue(contributorList.get(0).getSurname().equals(surnameA)); + assertTrue(contributorList.get(0).getCreditName().equals("Abdel-Dayem Khai")); + assertTrue(contributorList.get(0).getOid().equals(orcidIdA)); + assertTrue(StringUtils.isBlank(contributorList.get(1).getOid())); + } + + @Test + public void authorBestMatchTest() throws Exception { + String name = "Khairy"; + String surname = "Abdel Dayem"; + String orcidWork = "activity_work_0000-0003-2760-1191.xml"; + AuthorData author = new AuthorData(); + author.setName(name); + author.setSurname(surname); + author.setOid(orcidIdA); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + AuthorMatcher.match(author, workData.getContributors()); + assertTrue(workData.getContributors().size() == 5); + List c = workData.getContributors(); + assertTrue(c.get(0).getName().equals(name)); + assertTrue(c.get(0).getSurname().equals(surname)); + assertTrue(c.get(0).getCreditName().equals("Khair Abde Daye")); + assertTrue(c.get(0).getOid().equals(orcidIdA)); + } + + @Test + public void otherNamesMatchTest() + throws VtdException, ParseException, IOException, XPathEvalException, NavException, XPathParseException { + + AuthorData author = new AuthorData(); + author.setName("Joe"); + author.setSurname("Dodge"); + author.setOid("0000-1111-2222-3333"); + String otherName1 = new String("Joe Dr. Dodge"); + String otherName2 = new String("XY"); + List others = Lists.newArrayList(); + others.add(otherName1); + others.add(otherName2); + author.setOtherNames(others); + Contributor contributor = new Contributor(); + contributor.setCreditName("XY"); + List contributors = Arrays.asList(contributor); + AuthorMatcher.match(author, contributors); + assertTrue(contributors.get(0).getName().equals("Joe")); + assertTrue(contributors.get(0).getSurname().equals("Dodge")); + assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333")); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 deleted file mode 100644 index 1b088e061c..0000000000 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 new file mode 100644 index 0000000000..8dc3d32ad8 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 @@ -0,0 +1 @@ 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 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 0000000000..485f4f8e8c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml new file mode 100644 index 0000000000..7abc2f35ae --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml @@ -0,0 +1,770 @@ + + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + zh_CN + + + API + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + true + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + 2001-12-31T12:00:00 + true + true + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + give-names + family-name + credit-name + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + other-name-1 + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + biography + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + url-name-1 + http://url.com/ + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + user1@email.com + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + US + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + keyword1 + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + type-1 + value-1 + http://url.com/1 + self + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + distinction:department-name + distinction:role-title + + 1948 + 02 + 02 + + + 1948 + 02 + 02 + + + distinction-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-distinction + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + education:department-name + education:role-title + + 1948 + 02 + 02 + + + 2019 + 01 + 01 + + + education-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-education + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + employment:department-name + employment:role-title + + 1948 + 02 + 02 + + + 2025 + + + employment-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-employment + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + grant_number + external-id-value-1 + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + + common:title + common:translated-title + + + + grant_number + external-id-value-1 + http://tempuri.org + self + + + grant + + 1948 + 02 + 02 + + + 1948 + 02 + 02 + + + common:name + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-funding + FUNDREF + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + invited-position:department-name + invited-position:role-title + + 2019 + 01 + 01 + + + 2025 + 01 + 01 + + + invited-position-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-invited-position + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + membership:department-name + membership:role-title + + 1948 + 02 + 02 + + + membership-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-membership + RINGGOLD + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + something + external-id-value + http://orcid.org + self + + + + 2001-12-31T12:00:00 + + + something + external-id-value + + http://orcid.org + self + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/client/APP-9999999999999901 + APP-9999999999999901 + orcid.org + + + + reviewer + + + something + external-id-value + http://orcid.org + self + + + http://orcid.org + review + + 1948 + 02 + 02 + + orcid-generated:12345 + + common:name + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-peer-review + RINGGOLD + + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + qualification:department-name + qualification:role-title + + 1948 + 02 + 02 + + + 2025 + 12 + + + qualification-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-qualification + RINGGOLD + + + + + + + 2017-01-18T15:06:05.147-06:00 + + 2017-01-18T15:03:56.856-06:00 + + + proposal_id + 123456 + self + + + + + 2015-06-25T16:01:12.718Z + 2017-09-08T13:31:19.987Z + + + + https://orcid.org/0000-0000-0000-0000 + 0000-0000-0000-0000 + orcid.org + + XSEDE ORCID integration + + + + + Giant Laser Award + + + + XSEDE + + city + region + US + + + XX + grid + + + + + + proposal_id + 123456 + self + + + + 1999 + 02 + 02 + + + 2012 + 02 + 02 + + http://xsede.org/GiantLaserAward + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + service:department-name + service:role-title + + 1948 + 02 + 02 + + + service-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-service + RINGGOLD + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + agr + external-id-value + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/client/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + + common:title + + common:translated-title + + + + agr + external-id-value + http://tempuri.org + self + + + artistic-performance + + 1948 + 02 + 02 + + Procedia Computer Science + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml new file mode 100644 index 0000000000..43bc96b8cd --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml @@ -0,0 +1,196 @@ + + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + + en + + + Member-referred + 2019-05-01T13:04:57.507Z + 2019-05-01T13:59:54.268Z + true + true + true + + + 2019-05-01T13:45:47.727Z + + 2019-05-01T13:04:57.507Z + 2019-05-01T13:04:57.740Z + Andrew + Porteus + + + 2019-05-01T13:44:57.072Z + + 2019-05-01T13:44:57.072Z + 2019-05-01T13:44:57.072Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Andrew C. Porteus + + + + 2019-05-01T13:59:54.263Z + 2019-05-01T13:59:54.263Z + Retired Librarian + + + 2019-05-01T13:45:47.727Z + + 2019-05-01T13:45:47.727Z + 2019-05-01T13:45:47.727Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Niagara Falls Poetry Project + http://niagarapoetry.ca + + + + + 2019-05-01T13:45:09.764Z + + 2019-05-01T13:45:09.764Z + 2019-05-01T13:45:09.764Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + CA + + + + + + + 2019-05-01T13:57:45.787Z + + + 2019-05-01T13:15:26.102Z + + 2019-05-01T13:15:26.102Z + + + 2019-05-01T13:15:26.102Z + 2019-05-01T13:15:26.102Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Library Technician Diploma + + 1976 + 09 + + + 1978 + 05 + + + Niagara College + + Welland + ON + CA + + + 125147 + RINGGOLD + + + + + + + + + + + + 2019-05-01T13:19:49.021Z + + 2019-05-01T13:19:49.021Z + + + 2019-05-01T13:19:49.021Z + 2019-05-01T13:19:49.021Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Communication, Film & Popular Culture + Master's Candidate + + 2018 + 09 + + + Brock University + + Saint Catharines + ON + CA + + + 7497 + RINGGOLD + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json new file mode 100644 index 0000000000..579e12f2eb --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json @@ -0,0 +1 @@ +{"oid":"0000-0002-4147-3387","id":"60153327","sourceName":"The Chinese University of Hong Kong","type":"conference-paper","titles":["Evaluation of a percutaneous optical fibre glucose sensor (FiberSense) across the glycemic range with rapid glucoseexcursions using the glucose clamp"],"extIds":[{"type":"wosuid","value":"000425015800225","relationShip":"self"},{"type":"other-id","value":"441f521e-ab19-448d-ba32-83157b348ada","relationShip":"self"}],"publicationDates":[],"contributors":[{"sequence":"1","oid":"0000-0002-4147-3387","name":"Elaine","surname":"Chow","creditName":"Elaine Chow"},{"sequence":"2","creditName":"Victor Tsui"},{"sequence":"3","creditName":"Achim Müller"},{"sequence":"4","creditName":"Vincy Lee"},{"sequence":"5","creditName":"Lucia Krivánekova"},{"sequence":"6","creditName":"Roland Krivánek"},{"sequence":"7","creditName":"Juliana CN Chan"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml new file mode 100644 index 0000000000..43d3b23515 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml @@ -0,0 +1,72 @@ + + + 2019-10-22T03:18:13.755Z + 2020-06-17T11:07:13.703Z + + + https://orcid.org/client/0000-0001-8607-8906 + 0000-0001-8607-8906 + orcid.org + + INSPIRE-HEP + + + Measurement of the $t\bar{t}$ production cross-section and lepton differential distributions in $e\mu$ dilepton events from $pp$ collisions at $\sqrt{s}=13$ TeV with the ATLAS detector + + + + other-id + 1759875 + 1759875 + http://inspirehep.net/record/1759875 + self + + + doi + 10.1140/epjc/s10052-020-7907-9 + 10.1140/epjc/s10052-020-7907-9 + http://dx.doi.org/10.1140/epjc/s10052-020-7907-9 + self + + + arxiv + 1910.08819 + arXiv:1910.08819 + http://arxiv.org/abs/1910.08819 + self + + + http://inspirehep.net/record/1759875 + journal-article + + 2020 + 06 + 12 + + Eur.Phys.J.C + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0002-5982-8983.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-5982-8983.xml similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0002-5982-8983.xml rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-5982-8983.xml diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml new file mode 100644 index 0000000000..650d5a4cb4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml @@ -0,0 +1,113 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Abdel-Dayem Fake + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 0000000000..83752b1457 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Khair Abde Daye + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml new file mode 100644 index 0000000000..26e64aedae --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml @@ -0,0 +1,101 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + + seq0 + role0 + + + + creditname1 + + + creditname2 + + seq2 + + + + + creditname3 + + + role3 + + + + + + seq4 + role4 + + + + diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 1cc41c395e..692605b035 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -44,8 +44,6 @@ public class PropagationConstant { public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result"; public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations"; - public static final String PROPAGATION_AUTHOR_PID = "ORCID"; - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String cfHbforResultQuery = "select distinct r.id, inst.collectedfrom.key cf, inst.hostedby.key hb " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index 869831ba2b..dd8342980d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -22,6 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; @@ -102,7 +103,8 @@ public class PrepareResultOrcidAssociationStep1 { + " FROM result " + " LATERAL VIEW EXPLODE (author) a AS MyT " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " - + " WHERE lower(MyP.qualifier.classid) = 'orcid') tmp " + + " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or " + + " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + " GROUP BY id) r_t " + " JOIN (" + " SELECT source, target " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 3fc1270645..9f08fe580b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -23,6 +23,7 @@ import com.google.common.collect.Lists; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; @@ -176,7 +177,7 @@ public class SparkOrcidToResultFromSemRelJob { if (toaddpid) { StructuredProperty p = new StructuredProperty(); p.setValue(autoritative_author.getOrcid()); - p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID)); + p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME)); p .setDataInfo( getDataInfo( @@ -201,7 +202,8 @@ public class SparkOrcidToResultFromSemRelJob { return false; } for (StructuredProperty pid : pids.get()) { - if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) { + if (ModelConstants.ORCID_PENDING.equals(pid.getQualifier().getClassid().toLowerCase()) || + ModelConstants.ORCID.equals(pid.getQualifier().getClassid().toLowerCase())) { return true; } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index edd2e7ba73..238375197f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -19,8 +19,11 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.cloudera.org.codehaus.jackson.map.jsontype.impl.ClassNameIdResolver; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.PropagationConstant; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Dataset; public class OrcidPropagationJobTest { @@ -166,7 +169,9 @@ public class OrcidPropagationJobTest { propagatedAuthors .filter( "id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' " - + "and name = 'Vajinder' and surname = 'Kumar' and pidType = 'ORCID'") + + "and name = 'Vajinder' and surname = 'Kumar' and pidType = '" + + + ModelConstants.ORCID_PENDING + "'") .count()); Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 5155d0242b..fbb20f1433 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -189,6 +189,7 @@ public class CleaningFunctions { author.setRank(i++); } } + for (Author a : r.getAuthor()) { if (Objects.isNull(a.getPid())) { a.setPid(Lists.newArrayList()); @@ -201,13 +202,29 @@ public class CleaningFunctions { .filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> StringUtils.isNotBlank(p.getValue())) .map(p -> { + // hack to distinguish orcid from orcid_pending + String pidProvenance = Optional + .ofNullable(p.getDataInfo()) + .map( + d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse("")) + .orElse(""); + if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { + p.getQualifier().setClassid(ModelConstants.ORCID); + } else { + p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + } p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, "")); return p; }) .collect( Collectors .toMap( - StructuredProperty::getValue, Function.identity(), (p1, p2) -> p1, + p -> p.getQualifier().getClassid() + p.getValue(), + Function.identity(), + (p1, p2) -> p1, LinkedHashMap::new)) .values() .stream() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index a466cf0742..86a275ae22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -40,4 +40,18 @@ public class Constants { coarCodeLabelMap.put("c_14cb", "CLOSED"); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } + + public enum DUMPTYPE { + COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder"); + + private String type; + + DUMPTYPE(String type) { + this.type = type; + } + + public String getType() { + return type; + } + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index 1279ede533..d20a3036e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,17 +11,12 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -33,7 +28,7 @@ public class DumpProducts implements Serializable { public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { SparkConf conf = new SparkConf(); @@ -42,7 +37,7 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph); + execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } @@ -53,13 +48,13 @@ public class DumpProducts implements Serializable { String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); Utils .readPath(spark, inputPath, inputClazz) - .map((MapFunction) value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz)) + .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) @@ -70,18 +65,18 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - boolean graph) { + String dumpType) { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { - if (odInfo.get().getDeletedbyinference()) { + if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) { return null; } } else { return null; } - if (!graph) { + if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) { Set communities = communityMap.keySet(); Optional> inputContext = Optional @@ -102,7 +97,8 @@ public class DumpProducts implements Serializable { return null; } } - return (O) ResultMapper.map(value, communityMap, graph); + + return (O) ResultMapper.map(value, communityMap, dumpType); } } 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 4c3bc0dd52..cb052ebaa8 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 @@ -21,10 +21,10 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, boolean graph) { + E in, Map communityMap, String dumpType) { Result out; - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { out = new GraphResult(); } else { out = new CommunityResult(); @@ -217,7 +217,7 @@ public class ResultMapper implements Serializable { .ofNullable(input.getInstance()); if (oInst.isPresent()) { - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((GraphResult) out) .setInstance(oInst.get().stream().map(i -> getGraphInstance(i)).collect(Collectors.toList())); } else { @@ -296,7 +296,7 @@ public class ResultMapper implements Serializable { out.setType(input.getResulttype().getClassid()); } - if (!graph) { + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((CommunityResult) out) .setCollectedfrom( input diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 6be1befce1..55f075e954 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -9,6 +9,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -54,7 +55,7 @@ public class CommunitySplit implements Serializable { private static void printResult(String c, Dataset result, String outputPath) { Dataset community_products = result - .filter(r -> containsCommunity(r, c)); + .filter((FilterFunction) r -> containsCommunity(r, c)); try { community_products.first(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java index c4b89936ff..63970d14bc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java @@ -4,12 +4,15 @@ package eu.dnetlib.dhp.oa.graph.dump.community; import java.io.Serializable; import java.util.*; +import javax.swing.text.html.Option; + import org.apache.commons.io.IOUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Result; @@ -48,6 +51,11 @@ public class SparkDumpCommunityProducts implements Serializable { String communityMapPath = parser.get("communityMapPath"); + final String dumpType = Optional + .ofNullable(parser.get("dumpType")) + .map(String::valueOf) + .orElse("community"); + Class inputClazz = (Class) Class.forName(resultClassName); DumpProducts dump = new DumpProducts(); @@ -55,7 +63,7 @@ public class SparkDumpCommunityProducts implements Serializable { dump .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, - false); + dumpType); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 39850b5b8e..2d43888b46 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -34,7 +34,7 @@ import scala.Tuple2; /** * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to */ public class SparkPrepareResultProject implements Serializable { @@ -76,16 +76,16 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); projects - .joinWith(relation, projects.col("id").equalTo(relation.col("source"))) + .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") .groupByKey( (MapFunction, String>) value -> value ._2() - .getTarget(), + .getSource(), Encoders.STRING()) .mapGroups( (MapGroupsFunction, ResultProject>) (s, @@ -93,7 +93,7 @@ public class SparkPrepareResultProject implements Serializable { Set projectSet = new HashSet<>(); Tuple2 first = it.next(); ResultProject rp = new ResultProject(); - rp.setResultId(first._2().getTarget()); + rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); Project ps = getProject(p); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java index 1276d8495e..2b80b1d861 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java @@ -8,6 +8,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -20,6 +21,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import scala.Tuple2; public class SparkUpdateProjectInfo implements Serializable { @@ -73,7 +75,7 @@ public class SparkUpdateProjectInfo implements Serializable { .joinWith( resultProject, result.col("id").equalTo(resultProject.col("resultId")), "left") - .map(value -> { + .map((MapFunction, CommunityResult>) value -> { CommunityResult r = value._1(); Optional.ofNullable(value._2()).ifPresent(rp -> { r.setProjects(rp.getProjectsList()); 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 23224f8dba..ccb84c7138 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 @@ -1,22 +1,25 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; +import java.io.*; import java.nio.charset.StandardCharsets; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.crypto.utils.IoUtils; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.CompressionOutputStream; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; @@ -76,8 +79,11 @@ public class CreateContextEntities implements Serializable { } else { fsDataOutputStream = fileSystem.create(hdfsWritePath); } + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); } 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 773068dfb2..36ced3a4ab 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 @@ -49,7 +49,7 @@ public class DumpGraphEntities implements Serializable { d .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class, - true); + eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType()); break; case "40": runWithSparkSession( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java new file mode 100644 index 0000000000..00f604b14b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -0,0 +1,130 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.api.zenodo.Community; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +/** + * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC + * for the EC it specifies also the fundingStream (FP7 or H2020) + */ +public class SparkDumpFunderResults implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath, relationPath); + }); + } + + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, + String relationPath) { + + Dataset relation = Utils + .readPath(spark, relationPath + "/relation", Relation.class) + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + + List funderList = relation + .select("target") + .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) + .distinct() + .collectAsList(); + + funderList.forEach(funder -> { + String fundernsp = funder.substring(3); + String funderdump; + if (fundernsp.startsWith("corda")) { + funderdump = "EC_"; + if (fundernsp.endsWith("h2020")) { + funderdump += "H2020"; + } else { + funderdump += "FP7"; + } + } else { + funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); + } + writeFunderResult(funder, result, outputPath + "/" + funderdump); + }); + + } + + private static void writeFunderResult(String funder, Dataset results, String outputPath) { + + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + if (p.getId().startsWith(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java new file mode 100644 index 0000000000..1a28a21f43 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -0,0 +1,106 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; + +/** + * Selects the results linked to projects. Only for these results the dump will be performed. + * The code to perform the dump and to expend the dumped results with the informaiton related to projects + * is the one used for the dump of the community products + */ +public class SparkResultLinkedToProject implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); + + Class inputClazz = (Class) Class.forName(resultClassName); + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + }); + } + + private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, + String inputPath, String outputPath, String relationPath) { + + Dataset results = Utils + .readPath(spark, inputPath, inputClazz) + .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); + Dataset relations = Utils + .readPath(spark, relationPath, Relation.class) + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + + relations + .joinWith( + results, relations.col("source").equalTo(results.col("id")), + "inner") + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getId(), + Encoders.STRING()) + .mapGroups((MapGroupsFunction, R>) (k, it) -> { + return it.next()._2(); + }, Encoders.bean(inputClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 95dd1e1cad..cccf15398f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -75,6 +75,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final Qualifier MAG_PID_TYPE = qualifier( "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; + protected static final Map nsContext = new HashMap<>(); static { @@ -244,25 +246,54 @@ public abstract class AbstractMdRecordToOafMapper { final String originalId = ((Node) o).getText(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + if (StringUtils.isNotBlank(originalId)) { final String projectId = createOpenaireId(40, originalId, true); res .add( - getRelation( + getRelationWithValidationDate( docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + lastUpdateTimestamp, validationdDate)); res .add( - getRelation( + getRelationWithValidationDate( projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + lastUpdateTimestamp, validationdDate)); } } return res; } + protected Relation getRelationWithValidationDate(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp, + final String validationDate) { + + final Relation r = getRelation( + source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); + r.setValidated(StringUtils.isNotBlank(validationDate)); + r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + + if (StringUtils.isNotBlank(validationDate)) { + r.setValidated(true); + r.setValidationDate(validationDate); + r.getDataInfo().setTrust(DEFAULT_TRUST_FOR_VALIDATED_RELS); + } else { + r.setValidated(false); + r.setValidationDate(null); + } + + return r; + } + protected Relation getRelation(final String source, final String target, final String relType, 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 index 161fd2dec1..fcef2547ac 100644 --- 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 @@ -26,8 +26,8 @@ the metadata associated to the deposition - newDeposition - true if it is a brand new depositon. false for new version of an old deposition + depositionType + one among {new, update, version} conceptRecordId @@ -419,6 +419,7 @@ --metadata${metadata} --communityMapPath${workingDir}/communityMap --conceptRecordId${conceptRecordId} + --depositionId${depositionId} --depositionType${depositionType} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml index 4c286e4a24..8189e25945 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + @@ -368,7 +368,7 @@ eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${workingDir}/collect/communities_infrastructures + --hdfsPath${workingDir}/collect/communities_infrastructures/communities_infrastructure.json.gz --nameNode${nameNode} --isLookUpUrl${isLookUpUrl} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json new file mode 100644 index 0000000000..9a5a553b1f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, +{ + "paramName": "rp", + "paramLongName": "relationPath", + "paramDescription": "the relationPath", + "paramRequired": true +} +] \ 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/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/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 new file mode 100644 index 0000000000..650b972fa3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -0,0 +1,563 @@ + + + + + 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/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index b1f4c026ae..1d986fc261 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -29,6 +29,12 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true + }, + { + "paramName":"dt", + "paramLongName":"dumpType", + "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", + "paramRequired": false } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json new file mode 100644 index 0000000000..fdd9492fe7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -0,0 +1,35 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName":"rp", + "paramLongName":"relationPath", + "paramDescription": "the path to the relations", + "paramRequired": true + } +] + + + 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 54a610b9c4..271ae8fc1f 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 @@ -8,7 +8,6 @@ import java.util.Arrays; import java.util.List; import org.apache.commons.io.FileUtils; -import org.apache.hadoop.yarn.webapp.hamlet.Hamlet; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -23,7 +22,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -155,7 +153,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -220,7 +218,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, true); + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -253,7 +251,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -285,7 +283,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -321,7 +319,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -357,7 +355,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -392,7 +390,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 411e6f4b01..3ecbd18943 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -3,15 +3,24 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; import static org.mockito.Mockito.lenient; +import java.io.BufferedWriter; import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.function.Consumer; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; @@ -60,6 +69,8 @@ public class CreateEntityTest { private QueryInformationSystem queryInformationSystem; + private static String workingDir; + @BeforeEach public void setUp() throws ISLookUpException { lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); @@ -67,6 +78,13 @@ public class CreateEntityTest { queryInformationSystem.setIsLookUp(isLookUpService); } + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName()) + .toString(); + } + @Test public void test1() throws ISLookUpException, IOException { List cInfoList = new ArrayList<>(); @@ -123,4 +141,33 @@ public class CreateEntityTest { riList.forEach(c -> System.out.println(new Gson().toJson(c))); } + + @Test + @Disabled + public void test2() throws IOException, ISLookUpException { + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + Path hdfsWritePath = new Path(workingDir + "/prova"); + FSDataOutputStream fsDataOutputStream = null; + if (fs.exists(hdfsWritePath)) { + fsDataOutputStream = fs.append(hdfsWritePath); + } else { + fsDataOutputStream = fs.create(hdfsWritePath); + } + CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); + + BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + for (ContextInfo cInfo : cInfoList) { + writer.write(new Gson().toJson(Process.getEntity(cInfo))); + } + writer.close(); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java new file mode 100644 index 0000000000..dbe3db6fe2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -0,0 +1,137 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class ResultLinkedToProjectTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testNoMatch() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); + + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Result.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + } + + @Test + public void testMatchOne() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); + + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java new file mode 100644 index 0000000000..71bf5d9421 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -0,0 +1,141 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + +public class SplitPerFunderTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SplitPerFunderTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getPath(); + + SparkDumpFunderResults.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath, + "-relationPath", sourcePath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + // FP7 3 + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(3, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + + // CIHR 2 + tmp = sc + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); + + // NWO 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // NIH 3 + tmp = sc + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); + + // NSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // SNSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // NHMRC 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // H2020 3 + tmp = sc + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(3, tmp.count()); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 2d4cccdfbb..2a62e25b2a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -141,7 +141,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); - + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); // System.out.println(new ObjectMapper().writeValueAsString(p)); // System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r2)); @@ -246,6 +249,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); } @Test @@ -355,6 +362,37 @@ public class MappersTest { assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(1, p.getAuthor().size()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue())); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid())); + assertEquals("dataset", p.getResulttype().getClassname()); + assertEquals(1, p.getInstance().size()); + assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); + assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); + assertValidId(p.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); + assertEquals(1, p.getInstance().get(0).getUrl().size()); +// System.out.println(p.getInstance().get(0).getUrl().get(0)); +// System.out.println(p.getInstance().get(0).getHostedby().getValue()); + System.out.println(p.getPid().get(0).getValue()); + } + + @Test + void testBologna() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml")); + final List list = new OafToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + System.out.println(p.getTitle().get(0).getValue()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); System.out.println(p.getTitle().get(0).getValue()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 5c903cd0e6..e746d236e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -49,6 +49,28 @@ "schemename": "dnet:pid_types" }, "value": "https://orcid.org/0000-0001-9613-6639" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "orcid", + "classname": "ORCID12", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" } ], "rank": 1, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 93cc00eca4..67c070d1dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1031,6 +1031,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ jprn @=@ JPRN Identifier dnet:pid_types @=@ dnet:pid_types @=@ mag_id @=@ Microsoft Academic Graph Identifier dnet:pid_types @=@ dnet:pid_types @=@ oai @=@ Open Archives Initiative dnet:pid_types @=@ dnet:pid_types @=@ orcid @=@ Open Researcher and Contributor ID +dnet:pid_types @=@ dnet:pid_types @=@ orcid_pending @=@ Open Researcher and Contributor ID dnet:pid_types @=@ dnet:pid_types @=@ PANGAEA @=@ PANGAEA dnet:pid_types @=@ dnet:pid_types @=@ epo_nr_epodoc @=@ Patent application number in EPODOC format dnet:pid_types @=@ dnet:pid_types @=@ UNKNOWN @=@ UNKNOWN diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication new file mode 100644 index 0000000000..901b34abc0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication @@ -0,0 +1,12 @@ +{"author":[{"fullname":"Eric A. Wright","name":"Eric A.","pid":{"id":{"scheme":"orcid","value":"0000-0001-8604-7026"}},"rank":1,"surname":"Wright"},{"fullname":"Christopher D. d’Esterre","name":"Christopher D.","rank":2,"surname":"d’Esterre"},{"fullname":"Laura B. Morrison","name":"Laura B.","rank":3,"surname":"Morrison"},{"fullname":"Neil Cockburn","name":"Neil","rank":4,"surname":"Cockburn"},{"fullname":"Michael Kovacs","name":"Michael","rank":5,"surname":"Kovacs"},{"fullname":"Ting-Yim Lee","name":"Ting-Yim","rank":6,"surname":"Lee"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"}],"context":[{"code":"ni","label":"Neuroinformatics","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Jiang, Quan"],"country":[],"coverage":[],"dateofcollection":"","description":["CT Perfusion (CTP) derived cerebral blood flow (CBF) thresholds have been proposed as the optimal parameter for distinguishing the infarct core prior to reperfusion. Previous threshold-derivation studies have been limited by uncertainties introduced by infarct expansion between the acute phase of stroke and follow-up imaging, or DWI lesion reversibility. In this study a model is proposed for determining infarction CBF thresholds at 3hr ischemia time by comparing contemporaneously acquired CTP derived CBF maps to 18F-FFMZ-PET imaging, with the objective of deriving a CBF threshold for infarction after 3 hours of ischemia. Endothelin-1 (ET-1) was injected into the brain of Duroc-Cross pigs (n = 11) through a burr hole in the skull. CTP images were acquired 10 and 30 minutes post ET-1 injection and then every 30 minutes for 150 minutes. 370 MBq of 18F-FFMZ was injected ~120 minutes post ET-1 injection and PET images were acquired for 25 minutes starting ~155-180 minutes post ET-1 injection. CBF maps from each CTP acquisition were co-registered and converted into a median CBF map. The median CBF map was co-registered to blood volume maps for vessel exclusion, an average CT image for grey/white matter segmentation, and 18F-FFMZ-PET images for infarct delineation. Logistic regression and ROC analysis were performed on infarcted and non-infarcted pixel CBF values for each animal that developed infarct. Six of the eleven animals developed infarction. The mean CBF value corresponding to the optimal operating point of the ROC curves for the 6 animals was 12.6 ± 2.8 mL·min-1·100g-1 for infarction after 3 hours of ischemia. The porcine ET-1 model of cerebral ischemia is easier to implement then other large animal models of stroke, and performs similarly as long as CBF is monitored using CTP to prevent reperfusion."],"format":[],"id":"50|dedup_wf_001::0017bb7bb6a0e2f5624db2721a1bc1a5","instance":[{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"http://creativecommons.org/licenses/by/4.0","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1371/journal.pone.0158157"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},"hostedby":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"publicationdate":"2016-06-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Article","url":["http://dx.plos.org/10.1371/journal.pone.0158157","http://dx.doi.org/10.1371/journal.pone.0158157"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0158157&type=printable"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"refereed":"UNKNOWN","type":"Article","url":["https://www.ncbi.nlm.nih.gov/pubmed/27347877","http://ui.adsabs.harvard.edu/abs/2016PLoSO..1158157W/abstract","https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158157","https://paperity.org/p/80470187/absolute-cerebral-blood-flow-infarction-threshold-for-3-hour-ischemia-time-determined","https://dx.plos.org/10.1371/journal.pone.0158157","https://academic.microsoft.com/#/detail/2460634846"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566?pdf=render","https://doaj.org/toc/1932-6203"]},{"collectedfrom":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2016-06-27T17:32:46Z","refereed":"UNKNOWN","type":"UNKNOWN","url":["https://dx.doi.org/10.1371/journal.pone.0158157"]}],"language":{"code":"UNKNOWN","label":"UNKNOWN"},"lastupdatetimestamp":1603727328518,"maintitle":"Absolute Cerebral Blood Flow Infarction Threshold for 3-Hour Ischemia Time Determined with CT Perfusion and 18F-FFMZ-PET Imaging in a Porcine Model of Cerebral Ischemia","originalId":["10.1371/journal.pone.0158157","oai:pubmedcentral.nih.gov:4922566","2460634846","oai:doaj.org/article:a0a0f971217e4277aae02c2ddb0243ed","27347877"],"pid":[{"scheme":"doi","value":"10.1371/journal.pone.0158157"},{"scheme":"pmc","value":"PMC4922566"},{"scheme":"pmid","value":"27347877"}],"projects":[{"code":"unidentified","funder":{"jurisdiction":"CA","name":"Canadian Institutes of Health Research","shortName":"CIHR"},"id":"40|cihr________::1e5e62235d094afd01cd56e65112fc63","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"unidentified"}],"publicationdate":"2016-06-27","publisher":"Public Library of Science (PLoS)","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research Article"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine and Health Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Signs and Symptoms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Infarction"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pathology and Laboratory Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Critical Care and Emergency Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Reperfusion"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research and Analysis Methods"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Imaging Techniques"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroimaging"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Positron Emission Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Biology and Life Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroscience"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Radiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Radiology and Imaging"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neurology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Cerebral Ischemia"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Vascular Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Ischemia"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Cerebrovascular Diseases"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Stroke"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Ischemic Stroke"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Computed Axial Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Model Organisms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Animal Models"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pig Models"}},{"subject":{"scheme":"keywords","value":"General Biochemistry, Genetics and Molecular Biology"}},{"subject":{"scheme":"keywords","value":"General Agricultural and Biological Sciences"}},{"subject":{"scheme":"keywords","value":"General Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8487"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular system"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.7884"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular diseases"}}],"type":"publication"} +{"author":[{"fullname":"NIOO-KNAW KNAW","name":"NIOO-KNAW","pid":{"id":{"scheme":"orcid","value":"0000-0002-3835-159X"}},"rank":1,"surname":"KNAW"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de","value":"NARCIS"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Universidad de Alicante. Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. 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In this paper the first results from the proton–lead collision data taken in early 2013 are presented. The Z boson production cross section is measured in the muon decay channel in bins of transverse momentum and rapidity together with the forward–backward ratio. The W production is studied in the muon and electron decay channels and the differential cross sections, lepton-charge and forward–backward asymmetries are computed as a function of the lepton pseudorapidity. 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prognostic accuracy in patients with disorders of consciousness. Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. We also show that more liberal analyses may further increase the detection-rate, but at the potential cost of increased false alarms.","Highlights • The N400 is a candidate marker of linguistic function after severe brain injury. • The probability of detecting N400s is dependent on task demands. • Passive listening is less sensitive than command-following. • The probability of detecting N400s is dependent on stimuli choices. • Word-pairs generated from association norms provide the highest sensitivity."],"format":["application/pdf"],"id":"50|dedup_wf_001::03d1b1b04480058e646b34c174e61082","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a","value":"NeuroImage: 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). F.C.P. is the recipient of a SEGAI-ULL fellowship.","Peer Reviewed"],"format":["application/pdf"],"id":"50|dedup_wf_001::06496bbae2934f9443037f3df7293791","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::4e99a7004945b3f6298b66c2b8dd4fc6","value":"SESAM Publication Database - FP7 KBBE"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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bias"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Article"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Child abuse"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Mental health"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Adolescence"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Early adulthood"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Assessment"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Recall bias"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.72"},"subject":{"scheme":"mesheuropmc","value":"humanities"}}],"type":"publication"} +{"author":[{"fullname":"Mara Novero","name":"Mara","pid":{"id":{"scheme":"orcid","value":"0000-0001-7412-8750"}},"rank":1,"surname":"Novero"},{"fullname":"Paola Bonfante","name":"Paola","pid":{"id":{"scheme":"orcid","value":"0000-0003-3576-8530"}},"rank":2,"surname":"Bonfante"},{"fullname":"Matteo Chialva","name":"Matteo","pid":{"id":{"scheme":"orcid","value":"0000-0002-6996-6642"}},"rank":3,"surname":"Chialva"},{"fullname":"Silvia PEROTTO","name":"Silvia","pid":{"id":{"scheme":"orcid","value":"0000-0003-0121-1806"}},"rank":4,"surname":"PEROTTO"},{"fullname":"Marco Chiapello","name":"Marco","pid":{"id":{"scheme":"orcid","value":"0000-0001-7768-3047"}},"rank":5,"surname":"Chiapello"},{"fullname":"Stefano Ghignone","name":"Stefano","pid":{"id":{"scheme":"orcid","value":"0000-0002-2033-2286"}},"rank":6,"surname":"Ghignone"},{"fullname":"Stefania DAGHINO","name":"Stefania","pid":{"id":{"scheme":"orcid","value":"0000-0001-5722-1558"}},"rank":7,"surname":"DAGHINO"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"}],"container":{"ep":"1308","issnPrinted":"0028-646X","name":"New Phytologist","sp":"1296","vol":"220"},"context":[{"code":"sdsn-gr","label":"SDSN - Greece","provenance":[{"provenance":"Inferred by 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Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.\r\nUsing transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).\r\nNative soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} +{"author":[{"fullname":"K.P. Moustris","name":"K. P.","rank":1,"surname":"Moustris"},{"fullname":"D. Zafirakis","name":"D.","rank":2,"surname":"Zafirakis"},{"fullname":"K.A. Kavvadias","name":"K. A.","rank":3,"surname":"Kavvadias"},{"fullname":"J.K. Kaldellis","name":"J. 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To this end, the main objective of this work is the prognosis of the mean, maximum and minimum hourly wind power (WP) 8hours ahead. For this purpose, Artificial Neural Networks (ANN) modeling is applied. For the appropriate training of the developed ANN models hourly meteorological data are used. These data have been recorded by a meteorological mast in Tilos Island, Greece.\n\nFor the evaluation of the developed ANN forecasting models proper statistical evaluation indices are used. According to the results, the coefficient of the determination ranges from 0.285 up to 0.768 (mean hourly WP), from 0.227 up to 0.798 (maximum hourly WP) and from 0.025 up to 0.398 (minimum hourly WP). Furthermore, the proposed forecasting methodology shows that is able to give sufficient and adequate prognosis of WP by a wind turbine in a specific location 8 hours ahead. This will be a useful tool for the operator of a RES system in order to achieve a better monitoring and a better management of the whole system."],"format":[],"id":"50|dedup_wf_001::0a6525f420fd1f922125c3a1a280c8df","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2017-02-23T20:11:53Z","refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094?crawler=true","http://dx.doi.org/10.1049/cp.2016.1094"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"cc-by","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339/files/Wind%20power%20forecasting%20using%20historical%20data%20and%20artificial%20neural%20networks%20modeling.pdf"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094","https://core.ac.uk/display/144851191","http://jglobal.jst.go.jp/public/20090422/201702260673071390","https://academic.microsoft.com/#/detail/2590295725"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"hostedby":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"license":"http://creativecommons.org/licenses/by/4.0/legalcode","publicationdate":"2016-11-07","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Wind power forecasting using historical data and artificial neural networks modeling","originalId":["10.1049/cp.2016.1094","2590295725","oai:zenodo.org:887339"],"pid":[{"scheme":"doi","value":"10.1049/cp.2016.1094"}],"projects":[{"acronym":"TILOS","code":"646529","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::64c901e621f90b9a38badb1d78902205","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Technology Innovation for the Local Scale, Optimum Integration of Battery Energy Storage"}],"publicationdate":"2016-11-07","publisher":"Institution of Engineering and Technology","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Wind Power, Forecasting, Artificial Neural Networks"}}],"type":"publication"} +{"author":[{"fullname":"Juan M. 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The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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+ + CONSOLE Project - Deliverable 5.1 - "Guidelines for Community of Practice (CoP) + management at local level" + Blanco-Velázquez, Francisco José + Runge, Tania + Anaya-Romero, María + 2020-05-11 + The Community of Practice (CoP) is foreseen to play a key role in boosting + innovation in the effective and long-lasting delivery of agri-environmental-climate + public goods (AECPGs). The CONSOLE CoP will be organized around practitioners + experienced in the provision of AECPGs and those interested in it and will be nourished + throughout the project lifetime. In line with the definition of Wenger1 the CoP is + defined as a group of people (the community) who share a common interest and who learn + how to perform better through regular interaction and exchange of experiences. The idea + is to set up a pan-European CoP with national and/or local (regional) sub-groups managed + by the CONSOLE partners with the aim of developing improved and novel contract solutions + in collaboration with its members. This document sets out: (a) the purpose and + objectives of the CoP in CONSOLE, (b) the setting up and management of the CoP at + European, national and local level, (c) the process for motivating individuals to + participate. The CONSOLE CoP is intended to facilitate knowledge exchange and mutual + learning, mainly through virtual contacts. Participation in the CoP is based on sharing + and reciprocity principle. A core objective of these guidelines is to ensure a sound + management and facilitation of the CoP by all CONSOLE partners in view of optimizing the + input from CoP members in the project activities. Members within a national or local + CONSOLE CoP are: 1) CONSOLE partners; 2) practitioners, mainly farmers and foresters, + who test and implement practically the contractual models, and 3) experts, that may have + punctual interventions in the CoP. A vibrant CoP with active involvement of its members + is crucial for the assessment and testing of improved and novel voluntary measures for + the delivery of AECPGs. For each of the CONSOLE countries one national contact person is + nominated to take over the role as national focal point for the CoP activities in his + country and to serve as facilitator of the CoP. These facilitators are responsible to + ensure participation along the various project tasks foreseen within several WPs and to + overcome potential language barriers. The national contact person may be supported by + other CONSOLE partners from his country for local activities. At local level the CoP + benefits from existing contacts of CONSOLE partners to practitioners, including the + experts interviewed for the case studies analysis within WP2. The forming/development of + a CoP requires promoting exchanges taking on board the interests and needs of the actors + involved and to animate them to share their expertise. Collaborative learning within the + CoP supported by dedicated training activities will be crucial to ensure the intended + major transition towards smarter AECPGs-related practices in Europe. These guidelines + focus on the identification of the various tasks where CoP participation is foreseen at + local (regional) level and to provide support for the identification of potential + members. In the deliverable D5.2 “Guidelines for testing the solutions catalogue by CoP + and partners” further details about the involvement of the CoP will be + provided. + application/pdf + http://amsacta.unibo.it/6382/ + eng + info:eu-repo/grantAgreement/EC/H2020/817949/EU/CONtract SOLutions for Effective + and lasting delivery of agri-environmental-climate public goods by EU agriculture and + forestry/CONSOLE + info:eu-repo/semantics/altIdentifier/doi/10.6092/unibo/amsacta/6382 + info:eu-repo/semantics/reference/url/https://console-project.eu/ + Blanco-Velázquez, Francisco José ; Runge, Tania ; Anaya-Romero, María (2020) + CONSOLE Project - Deliverable 5.1 - "Guidelines for Community of Practice (CoP) + management at local level". p. 21. DOI 10.6092/unibo/amsacta/6382 + <http://doi.org/10.6092/unibo/amsacta/6382>. + AGR/01 Economia ed estimo rurale + SECS-S/01 Statistica + info:eu-repo/semantics/book + info:eu-repo/semantics/publishedVersion + 0002 + 2020-05-11 + corda__h2020::817949 + + opendoar____::3 + OPEN + + + 10.6092/unibo/amsacta/6382 + + + + + + http%3A%2F%2Famsacta.unibo.it%2Fcgi%2Fopenaire3 + oai:amsacta.unibo.it:6382 + 2020-05-13T09:27:00Z + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 2c6c98ebb3..f4b0c477fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -51,7 +51,7 @@ 0001 2017-01-01 - corda_______::226852 + corda_______::226852 OPEN und - 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null, + "validationDate": null, + "properties": [] + } + diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml new file mode 100644 index 0000000000..c64c2f58e0 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -0,0 +1,32 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.4-SNAPSHOT + + 4.0.0 + dhp-stats-promote + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + + + + pl.project13.maven + git-commit-id-plugin + 2.1.11 + + false + + + + + diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml new file mode 100644 index 0000000000..9331d4ac59 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hive_jdbc_url + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + stats_tool_api_url + ${stats_tool_api_url} + + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh new file mode 100644 index 0000000000..70112dc7be --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh @@ -0,0 +1,18 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +echo "Getting file from " $3 +hdfs dfs -copyToLocal $3 + +echo "Running impala shell make the new database visible" +impala-shell -q "INVALIDATE METADATA;" + +echo "Running impala shell to compute new table stats" +impala-shell -d $1 -f $2 +echo "Impala shell finished" +rm $2 diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/promoteCache.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/promoteCache.sh new file mode 100644 index 0000000000..2d28377fb8 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/promoteCache.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +curl --request GET $1/cache/promoteCache + diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql new file mode 100644 index 0000000000..34e48a18a3 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql @@ -0,0 +1,8 @@ +------------------------------------------------------ +------------------------------------------------------ +-- Impala table statistics - Needed to make the tables +-- visible for impala +------------------------------------------------------ +------------------------------------------------------ + +INVALIDATE METADATA ${stats_db_name}; diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql new file mode 100644 index 0000000000..48f8d58fd2 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql @@ -0,0 +1,207 @@ +------------------------------------------------------ +------------------------------------------------------ +-- Shadow schema table exchange +------------------------------------------------------ +------------------------------------------------------ + +-- Dropping old views +DROP VIEW IF EXISTS ${stats_db_production_name}.category; +DROP VIEW IF EXISTS ${stats_db_production_name}.concept; +DROP VIEW IF EXISTS ${stats_db_production_name}.context; +DROP VIEW IF EXISTS ${stats_db_production_name}.country; +DROP VIEW IF EXISTS ${stats_db_production_name}.countrygdp; +DROP VIEW IF EXISTS ${stats_db_production_name}.creation_date; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_citations; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_classifications; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_concepts; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_licenses; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_refereed; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_topics; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_organizations; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_results; +DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.funder; +DROP VIEW IF EXISTS ${stats_db_production_name}.fundref; +DROP VIEW IF EXISTS ${stats_db_production_name}.numbers_country; +DROP VIEW IF EXISTS ${stats_db_production_name}.organization; +DROP VIEW IF EXISTS ${stats_db_production_name}.organization_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.organization_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.organization_projects; +DROP VIEW IF EXISTS ${stats_db_production_name}.organization_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_citations; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_classifications; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_concepts; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_licenses; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_refereed; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_topics; +DROP VIEW IF EXISTS ${stats_db_production_name}.project; +DROP VIEW IF EXISTS ${stats_db_production_name}.project_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.project_organizations; +DROP VIEW IF EXISTS ${stats_db_production_name}.project_results; +DROP VIEW IF EXISTS ${stats_db_production_name}.project_resultcount; +DROP VIEW IF EXISTS ${stats_db_production_name}.project_results_publication; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_citations; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_classifications; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_concepts; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_licenses; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_refereed; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.publication_topics; +DROP VIEW IF EXISTS ${stats_db_production_name}.result; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_affiliated_country; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_citations; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_classifications; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_concepts; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_deposited_country; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_fundercount; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_gold; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_greenoa; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_licenses; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_organization; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_peerreviewed; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_projectcount; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_projects; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_refereed; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.result_topics; +DROP VIEW IF EXISTS ${stats_db_production_name}.rndexpediture; +DROP VIEW IF EXISTS ${stats_db_production_name}.roarmap; +DROP VIEW IF EXISTS ${stats_db_production_name}.software; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_citations; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_classifications; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_concepts; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_datasources; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_languages; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_licenses; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_oids; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_pids; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_refereed; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_sources; +DROP VIEW IF EXISTS ${stats_db_production_name}.software_topics; + + +-- Creating the shadow database, in case it doesn't exist +CREATE database IF NOT EXISTS ${stats_db_production_name}; + +-- Creating new views +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.category AS SELECT * FROM ${stats_db_name}.category; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.concept AS SELECT * FROM ${stats_db_name}.concept; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.context AS SELECT * FROM ${stats_db_name}.context; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.country AS SELECT * FROM ${stats_db_name}.country; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.countrygdp AS SELECT * FROM ${stats_db_name}.countrygdp; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.creation_date AS SELECT * FROM ${stats_db_name}.creation_date; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset AS SELECT * FROM ${stats_db_name}.dataset; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_citations AS SELECT * FROM ${stats_db_name}.dataset_citations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_classifications AS SELECT * FROM ${stats_db_name}.dataset_classifications; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_concepts AS SELECT * FROM ${stats_db_name}.dataset_concepts; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_datasources AS SELECT * FROM ${stats_db_name}.dataset_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_languages AS SELECT * FROM ${stats_db_name}.dataset_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_licenses AS SELECT * FROM ${stats_db_name}.dataset_licenses; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_oids AS SELECT * FROM ${stats_db_name}.dataset_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_pids AS SELECT * FROM ${stats_db_name}.dataset_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_refereed AS SELECT * FROM ${stats_db_name}.dataset_refereed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_sources AS SELECT * FROM ${stats_db_name}.dataset_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_topics AS SELECT * FROM ${stats_db_name}.dataset_topics; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource AS SELECT * FROM ${stats_db_name}.datasource; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_languages AS SELECT * FROM ${stats_db_name}.datasource_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_oids AS SELECT * FROM ${stats_db_name}.datasource_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_organizations AS SELECT * FROM ${stats_db_name}.datasource_organizations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_results AS SELECT * FROM ${stats_db_name}.datasource_results; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_sources AS SELECT * FROM ${stats_db_name}.datasource_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.funder AS SELECT * FROM ${stats_db_name}.funder; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.fundref AS SELECT * FROM ${stats_db_name}.fundref; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.numbers_country AS SELECT * FROM ${stats_db_name}.numbers_country; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization AS SELECT * FROM ${stats_db_name}.organization; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_datasources AS SELECT * FROM ${stats_db_name}.organization_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_pids AS SELECT * FROM ${stats_db_name}.organization_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_projects AS SELECT * FROM ${stats_db_name}.organization_projects; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_sources AS SELECT * FROM ${stats_db_name}.organization_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct AS SELECT * FROM ${stats_db_name}.otherresearchproduct; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_citations AS SELECT * FROM ${stats_db_name}.otherresearchproduct_citations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_classifications AS SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_concepts AS SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_datasources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_languages AS SELECT * FROM ${stats_db_name}.otherresearchproduct_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_licenses AS SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_oids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_pids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_refereed AS SELECT * FROM ${stats_db_name}.otherresearchproduct_refereed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_sources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_topics AS SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project AS SELECT * FROM ${stats_db_name}.project; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_oids AS SELECT * FROM ${stats_db_name}.project_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_organizations AS SELECT * FROM ${stats_db_name}.project_organizations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results AS SELECT * FROM ${stats_db_name}.project_results; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_resultcount AS SELECT * FROM ${stats_db_name}.project_resultcount; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results_publication AS SELECT * FROM ${stats_db_name}.project_results_publication; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication AS SELECT * FROM ${stats_db_name}.publication; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_citations AS SELECT * FROM ${stats_db_name}.publication_citations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_languages AS SELECT * FROM ${stats_db_name}.publication_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_oids AS SELECT * FROM ${stats_db_name}.publication_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_pids AS SELECT * FROM ${stats_db_name}.publication_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_refereed AS SELECT * FROM ${stats_db_name}.publication_refereed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_sources AS SELECT * FROM ${stats_db_name}.publication_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_topics AS SELECT * FROM ${stats_db_name}.publication_topics; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result AS SELECT * FROM ${stats_db_name}.result; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_affiliated_country AS SELECT * FROM ${stats_db_name}.result_affiliated_country; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_citations AS SELECT * FROM ${stats_db_name}.result_citations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_classifications AS SELECT * FROM ${stats_db_name}.result_classifications; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_concepts AS SELECT * FROM ${stats_db_name}.result_concepts; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_datasources AS SELECT * FROM ${stats_db_name}.result_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_deposited_country AS SELECT * FROM ${stats_db_name}.result_deposited_country; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_fundercount AS SELECT * FROM ${stats_db_name}.result_fundercount; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_gold AS SELECT * FROM ${stats_db_name}.result_gold; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_greenoa AS SELECT * FROM ${stats_db_name}.result_greenoa; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_languages AS SELECT * FROM ${stats_db_name}.result_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_licenses AS SELECT * FROM ${stats_db_name}.result_licenses; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_oids AS SELECT * FROM ${stats_db_name}.result_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_organization AS SELECT * FROM ${stats_db_name}.result_organization; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_peerreviewed AS SELECT * FROM ${stats_db_name}.result_peerreviewed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_pids AS SELECT * FROM ${stats_db_name}.result_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projectcount AS SELECT * FROM ${stats_db_name}.result_projectcount; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projects AS SELECT * FROM ${stats_db_name}.result_projects; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_refereed AS SELECT * FROM ${stats_db_name}.result_refereed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_sources AS SELECT * FROM ${stats_db_name}.result_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_topics AS SELECT * FROM ${stats_db_name}.result_topics; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.rndexpediture AS SELECT * FROM ${stats_db_name}.rndexpediture; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.roarmap AS SELECT * FROM ${stats_db_name}.roarmap; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software AS SELECT * FROM ${stats_db_name}.software; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_citations AS SELECT * FROM ${stats_db_name}.software_citations; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_classifications AS SELECT * FROM ${stats_db_name}.software_classifications; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_concepts AS SELECT * FROM ${stats_db_name}.software_concepts; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_datasources AS SELECT * FROM ${stats_db_name}.software_datasources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_languages AS SELECT * FROM ${stats_db_name}.software_languages; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_licenses AS SELECT * FROM ${stats_db_name}.software_licenses; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_oids AS SELECT * FROM ${stats_db_name}.software_oids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_pids AS SELECT * FROM ${stats_db_name}.software_pids; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_refereed AS SELECT * FROM ${stats_db_name}.software_refereed; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_sources AS SELECT * FROM ${stats_db_name}.software_sources; +CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_topics AS SELECT * FROM ${stats_db_name}.software_topics; diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml new file mode 100644 index 0000000000..d744f18da0 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -0,0 +1,87 @@ + + + + stats_db_name + the target stats database name + + + stats_db_production_name + the name of the production schema + + + stats_tool_api_url + The url of the API of the stats tool. Is used to trigger the cache promote. + + + hive_metastore_uris + hive server metastore URIs + + + hive_jdbc_url + hive server jdbc url + + + hive_timeout + the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds. + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hive_metastore_uris} + + + hive.txn.timeout + ${hive_timeout} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${hive_jdbc_url} + + stats_db_name=${stats_db_name} + stats_db_production_name=${stats_db_production_name} + + + + + + + + ${jobTracker} + ${nameNode} + impala-shell.sh + ${stats_db_production_name} + computeProductionStats.sql + ${wf:appPath()}/scripts/computeProductionStats.sql + impala-shell.sh + + + + + + + + ${jobTracker} + ${nameNode} + promoteCache.sh + ${stats_tool_api_url} + promoteCache.sh + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index 2cd53a37bc..9331d4ac59 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -27,4 +27,8 @@ oozie.wf.workflow.notification.url {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + stats_tool_api_url + ${stats_tool_api_url} + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 21a944164e..b4745535df 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -11,7 +11,7 @@ CREATE TABLE ${stats_db_name}.project_oids AS SELECT substr(p.id, 4) AS id, oids -- Project_organizations Table DROP TABLE IF EXISTS ${stats_db_name}.project_organizations; -CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization'; +CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization' and r.datainfo.deletedbyinference=false; -- Project_results Table DROP TABLE IF EXISTS ${stats_db_name}.project_results; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index 7acabf1dda..36a4a8a49f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -25,7 +25,7 @@ CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS SELECT * FROM ${stats_db_ CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS SELECT * FROM ${stats_db_name}.publication_topics UNION ALL SELECT * FROM ${stats_db_name}.software_topics UNION ALL SELECT * FROM ${stats_db_name}.dataset_topics UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; DROP TABLE IF EXISTS ${stats_db_name}.result_organization; -CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization'; +CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization' and r.datainfo.deletedbyinference=false; DROP TABLE IF EXISTS ${stats_db_name}.result_projects; CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id=pr.result JOIN ${stats_db_name}.project_tmp p ON p.id=pr.id; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 4e13b3dd8c..197047c8b9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -47,7 +47,7 @@ DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids; CREATE TABLE ${stats_db_name}.datasource_oids AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids; DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations; -CREATE TABLE ${stats_db_name}.datasource_organizations AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='datasourceOrganization'; +CREATE TABLE ${stats_db_name}.datasource_organizations AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='datasourceOrganization' and r.datainfo.deletedbyinference=false; -- datasource sources: -- where the datasource info have been collected from. diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh new file mode 100644 index 0000000000..36e74a5561 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +curl --request GET $1/cache/updateCache + diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index d6cc14e255..dcd034166f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -17,6 +17,10 @@ stats_db_shadow_name the name of the shadow schema + + stats_tool_api_url + The url of the API of the stats tool. Is used to trigger the cache update. + hive_metastore_uris hive server metastore URIs @@ -255,7 +259,7 @@ ${hive_jdbc_url} - + stats_db_name=${stats_db_name} stats_db_shadow_name=${stats_db_shadow_name} @@ -283,10 +287,22 @@ ${nameNode} impala-shell.sh ${stats_db_shadow_name} - step19.sql - ${wf:appPath()}/scripts/step19.sql + computeProductionStats.sql + ${wf:appPath()}/scripts/computeProductionStats.sql impala-shell.sh + + + + + + + ${jobTracker} + ${nameNode} + updateCache.sh + ${stats_tool_api_url} + updateCache.sh + diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index f1167b1849..190c9847e3 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -7,7 +7,7 @@ eu.dnetlib.dhp dhp 1.2.4-SNAPSHOT - ../ + ../pom.xml dhp-workflows diff --git a/pom.xml b/pom.xml index d0757f145a..a2e2587b31 100644 --- a/pom.xml +++ b/pom.xml @@ -278,12 +278,12 @@ org.apache.httpcomponents httpclient - 4.5.3 + ${org.apache.httpcomponents.version} org.apache.httpcomponents httpmime - 4.5.3 + ${org.apache.httpcomponents.version} org.noggit @@ -478,6 +478,12 @@ ${jsonschemagenerator.version} + + org.apache.commons + commons-text + ${common.text.version} + + @@ -706,5 +712,8 @@ 4.13.0 1.8 4.1.2 + 1.8 + 4.5.3 + 4.0.1