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 index 6a986e145d..2b8ef4e300 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.common; -import com.google.common.collect.Maps; - import java.util.Map; +import com.google.common.collect.Maps; + public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); 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 index 3956410d57..44599eb83f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -1,6 +1,10 @@ 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; @@ -10,406 +14,399 @@ import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Journal; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - public class GraphResultMapper implements Serializable { - public static Result map( - E in) { + public static Result map( + E in) { - CommunityResult out = new CommunityResult(); + 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())); + 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 + .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": + 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()))); + 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())); + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": + 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)); + 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 + .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()); + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - break; - } + break; + } - Optional - .ofNullable(input.getAuthor()) - .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + 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 + // 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)); - } - } + 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); + 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()))); + 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); + 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()); + 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 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()); + 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()); + Optional> oInst = Optional + .ofNullable(input.getInstance()); - if (oInst.isPresent()) { - out - .setInstance( - oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); + 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()); - } + 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()); - } + 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 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)))); + 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.setSubjects(subjectList); - out.setType(input.getResulttype().getClassid()); - } + out.setType(input.getResulttype().getClassid()); + } - out - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); + out + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + return out; - return out; + } - } + private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { + CommunityInstance instance = new CommunityInstance(); + setCommonValue(i, instance); - private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - setCommonValue(i, instance); + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - instance - .setCollectedfrom( - KeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + return instance; - 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 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()); - 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); - } + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } - return subject; - } + return a; + } - 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()); + 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()) - 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; - } + } + } + return null; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 17482c0198..0b602b7746 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge; import java.text.Normalizer; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; @@ -32,27 +33,33 @@ public class AuthorMerger { } - public static List mergeAuthor(final List a, final List b) { + public static List mergeAuthor(final List a, final List b, Double threshold) { int pa = countAuthorsPids(a); int pb = countAuthorsPids(b); List base, enrich; int sa = authorsSize(a); int sb = authorsSize(b); - if (pa == pb) { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } else { + if (sa == sb) { base = pa > pb ? a : b; enrich = pa > pb ? b : a; + } else { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; } - enrichPidFromList(base, enrich); + enrichPidFromList(base, enrich, threshold); return base; } - private static void enrichPidFromList(List base, List enrich) { + public static List mergeAuthor(final List a, final List b) { + return mergeAuthor(a, b, THRESHOLD); + } + + private static void enrichPidFromList(List base, List enrich, Double threshold) { if (base == null || enrich == null) return; + + // (if an Author has more than 1 pid, it appears 2 times in the list) final Map basePidAuthorMap = base .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -63,6 +70,7 @@ public class AuthorMerger { .map(p -> new Tuple2<>(pidToComparableString(p), a))) .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + // (list of pid that are missing in the other list) final List> pidToEnrich = enrich .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -83,10 +91,10 @@ public class AuthorMerger { .max(Comparator.comparing(Tuple2::_1)); if (simAuthor.isPresent()) { - double th = THRESHOLD; + double th = threshold; // increase the threshold if the surname is too short if (simAuthor.get()._2().getSurname() != null - && simAuthor.get()._2().getSurname().length() <= 3) + && simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0) th = 0.99; if (simAuthor.get()._1() > th) { @@ -156,7 +164,7 @@ public class AuthorMerger { } private static String normalize(final String s) { - return nfd(s) + String[] normalized = nfd(s) .toLowerCase() // do not compact the regexes in a single expression, would cause StackOverflowError // in case @@ -166,7 +174,12 @@ public class AuthorMerger { .replaceAll("(\\p{Punct})+", " ") .replaceAll("(\\d)+", " ") .replaceAll("(\\n)+", " ") - .trim(); + .trim() + .split(" "); + + Arrays.sort(normalized); + + return String.join(" ", normalized); } private static String nfd(final String s) { diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java new file mode 100644 index 0000000000..9c4e622148 --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java @@ -0,0 +1,100 @@ + +package eu.dnetlib.dhp.oa.merge; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.util.MapDocumentUtil; +import scala.Tuple2; + +public class AuthorMergerTest { + + private String publicationsBasePath; + + private List> authors; + + @BeforeEach + public void setUp() throws Exception { + + publicationsBasePath = Paths + .get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI()) + .toFile() + .getAbsolutePath(); + + authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + } + + @Test + public void mergeTest() { // used in the dedup: threshold set to 0.95 + + for (List authors1 : authors) { + System.out.println("List " + (authors.indexOf(authors1) + 1)); + for (Author author : authors1) { + System.out.println(authorToString(author)); + } + } + + List merge = AuthorMerger.merge(authors); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(7, merge.size()); + + } + + public List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res + .add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } + + return res; + } + + public String authorToString(Author a) { + + String print = "Fullname = "; + print += a.getFullname() + " pid = ["; + if (a.getPid() != null) + for (StructuredProperty sp : a.getPid()) { + print += sp.toComparableString() + " "; + } + print += "]"; + return print; + } +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json new file mode 100644 index 0000000000..600181ba56 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json @@ -0,0 +1,3 @@ +{ "journal":{ "dataInfo":null, "conferenceplace":null, "issnPrinted":"0009-9260", "issnOnline":null, "issnLinking":null, "ep":"636", "iss":null, "sp":"632", "vol":"55", "edition":null, "conferencedate":null, "name":"Clinical Radiology" }, "measures":null, "author":[ { "rank":null, "fullname":"KARL TURETSCHEK", "affiliation":null, "pid":null, "surname":"TURETSCHEK", "name":"KARL" }, { "rank":null, "fullname":"WOLFGANG EBNER", "affiliation":null, "pid":null, "surname":"EBNER", "name":"WOLFGANG" }, { "rank":null, "fullname":"DOMINIK FLEISCHMANN", "affiliation":null, "pid":null, "surname":"FLEISCHMANN", "name":"DOMINIK" }, { "rank":null, "fullname":"PATRICK WUNDERBALDINGER", "affiliation":null, "pid":null, "surname":"WUNDERBALDINGER", "name":"PATRICK" }, { "rank":null, "fullname":"LUDWIG ERLACHER", "affiliation":null, "pid":null, "surname":"ERLACHER", "name":"LUDWIG" }, { "rank":null, "fullname":"THOMAS ZONTSICH", "affiliation":null, "pid":null, "surname":"ZONTSICH", "name":"THOMAS" }, { "rank":null, "fullname":"ALEXANDER A. 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Bankier", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/1107971609" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Patrick Wunderbaldinger", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2422340537" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Wolfgang Ebner", "affiliation":null, "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2186462571" } ], "surname":null, "name":null }, { "rank":null, "fullname":"K. Turetschek", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/321765676" } ], "surname":null, "name":null } ], "resulttype":{ "classid":"publication", "schemeid":"dnet:result_typologies", "schemename":"dnet:result_typologies", "classname":"publication" }, "title":[ { "qualifier":{ "classid":"main title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"main title" }, "dataInfo":null, "value":"early pulmonary involvement in ankylosing spondylitis assessment with thin section ct" }, { "qualifier":{ "classid":"alternative title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"alternative title" }, "dataInfo":null, "value":"Early pulmonary involvement in ankylosing spondylitis: assessment with thin-section CT." } ], "relevantdate":null, "dateofacceptance":{ "dataInfo":null, "value":"2000-08-01" }, "publisher":{ "dataInfo":null, "value":"Elsevier" }, "embargoenddate":null, "fulltext":null, "contributor":null, "resourcetype":null, "coverage":null, "bestaccessright":null, "externalReference":null, "format":null, "description":[ { "dataInfo":null, "value":"Abstract AIM: To determine the frequency and the distribution of early pulmonary lesions in patients with ankylosing spondylitis (AS) and a normal chest X-ray on thin-section CT and to correlate the CT findings with the results of pulmonary function tests and clinical data. MATERIALS AND METHODS: Twenty-five patients with clinically proven AS and no history of smoking underwent clinical examinations, pulmonary function tests (PFT), chest radiography, and thin-section CT. Four of 25 patients (16%), who had obvious signs on plain films suggestive of pre-existing disorders unrelated to AS were excluded. RESULTS: Fifteen of 21 patients (71%) had abnormalities on thin-section CT. The most frequent abnormalities were thickening of the interlobular septa in seven of 21 patients (33%), mild bronchial wall thickening in (6/21, 29%), pleural thickening and pleuropulmonary irregularities (both 29%) and linear septal thickening (6/21, 29%). In six patients there were no signs of pleuropulmonary involvement. Eight of 15 patients (53%) with abnormal and four of six patients (67%) with normal CT findings revealed mild restrictive lung function impairment. CONCLUSION: Patients with AS but a normal chest radiograph frequently have abnormalities on thin-section CT. As these abnormalities are usually subtle and their extent does not correlate with functional and clinical data, the overall routine impact of thin-section CT in the diagnosis of AS is limited. 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"schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Radiology" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.medical_specialty" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.40295774", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business.industry" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.40295774", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Pulmonary function testing" } ], "language":null, "instance":[ { "processingchargecurrency":null, "refereed":null, "instancetype":null, "hostedby":null, "distributionlocation":null, "processingchargeamount":null, "license":null, "accessright":null, "dateofacceptance":null, "collectedfrom":{ "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" }, "url":[ "https://www.ncbi.nlm.nih.gov/pubmed/10964736", "https://www.sciencedirect.com/science/article/pii/S0009926000904987", "https://academic.microsoft.com/#/detail/1990704599" ] } ], "context":null, "country":null, "originalId":[ "1990704599", "10.1053/crad.2000.0498" ], "pid":[ { "qualifier":{ "classid":"doi", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"doi" }, "dataInfo":null, "value":"10.1053/crad.2000.0498" } ], "dateofcollection":null, "dateoftransformation":null, "oaiprovenance":null, "extraInfo":null, "id":"50|doiboost____::994b7e47b9e225ab6d5e14841cb45a7f", "collectedfrom":[ { "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset"} }, "lastupdatetimestamp":null } \ No newline at end of file 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 1efa865862..bff92ecf98 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 @@ -105,6 +105,8 @@ public class ModelConstants { public static final KeyValue UNKNOWN_REPOSITORY = keyValue( "10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository"); + public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE); + private static Qualifier qualifier( final String classid, final String classname, 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 fef32c0c6b..494123fdf5 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 @@ -49,23 +49,22 @@ public abstract class Oaf implements Serializable { 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); + 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())); setLastupdatetimestamp( - Math.max( + Math + .max( Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java index b698c957d0..4be4d5d30c 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java @@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable { ? p.getFundedamount() : fundedamount; - // programme = mergeLists(programme, p.getProgramme()); - h2020classification = mergeLists(h2020classification, p.getH2020classification()); mergeOAFDataInfo(e); diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 443c182308..845c4c9825 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -243,7 +243,7 @@ public class Result extends OafEntity implements Serializable { Result r = (Result) e; - // TODO consider merging also Measures + measures = mergeLists(measures, r.getMeasures()); instance = mergeLists(instance, r.getInstance()); @@ -323,13 +323,13 @@ public class Result extends OafEntity implements Serializable { if (a.size() == b.size()) { int msa = a .stream() - .filter(i -> i.getValue() != null) + .filter(i -> i != null && i.getValue() != null) .map(i -> i.getValue().length()) .max(Comparator.naturalOrder()) .orElse(0); int msb = b .stream() - .filter(i -> i.getValue() != null) + .filter(i -> i != null && i.getValue() != null) .map(i -> i.getValue().length()) .max(Comparator.naturalOrder()) .orElse(0); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java new file mode 100644 index 0000000000..d5b2ced7cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + +/** + * Class that maps the model of the bipFinder! input data. + * Only needed for deserialization purposes + */ + +public class BipDeserialize extends HashMap> implements Serializable { + + public BipDeserialize() { + super(); + } + + public List get(String key) { + + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java new file mode 100644 index 0000000000..2475466949 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.List; + +/** + * Rewriting of the bipFinder input data by extracting the identifier of the result (doi) + */ + +public class BipScore implements Serializable { + private String id; // doi + private List scoreList; // unit as given in the inputfile + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getScoreList() { + return scoreList; + } + + public void setScoreList(List scoreList) { + this.scoreList = scoreList; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java new file mode 100644 index 0000000000..0bebe2fb0e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java @@ -0,0 +1,85 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +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.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Result; + +/** + * Just collects all the atomic actions produced for the different results and saves them in + * outputpath for the ActionSet + */ +public class CollectAndSave implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CollectAndSave.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.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("inputPath"); + log.info("inputPath {}: ", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + collectAndSave(spark, inputPath, outputPath); + }); + } + + private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + sc + .sequenceFile(inputPath + "/publication", Text.class, Text.class) + .union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + ; + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java new file mode 100644 index 0000000000..6909a96344 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +public class KeyValue implements Serializable { + + private String key; + private String value; + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java new file mode 100644 index 0000000000..493e944177 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +/** + * Subset of the information of the generic results that are needed to create the atomic action + */ +public class PreparedResult implements Serializable { + private String id; // openaire id + private String value; // doi + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java new file mode 100644 index 0000000000..7cc21b44da --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.List; + +/** + * represents the score in the input file + */ +public class Score implements Serializable { + + private String id; + private List unit; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getUnit() { + return unit; + } + + public void setUnit(List unit) { + this.unit = unit; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java new file mode 100644 index 0000000000..2cd37d9ea0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -0,0 +1,200 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +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.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.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import scala.Tuple2; + +/** + * created the Atomic Action for each tipe of results + */ +public class SparkAtomicActionScoreJob implements Serializable { + + private static String DOI = "doi"; + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionScoreJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_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("inputPath"); + log.info("inputPath {}: ", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + final String bipScorePath = parser.get("bipScorePath"); + log.info("bipScorePath: {}", bipScorePath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class inputClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz); + }); + } + + private static void prepareResults(SparkSession spark, String inputPath, String outputPath, + String bipScorePath, Class inputClazz) { + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD bipDeserializeJavaRDD = sc + .textFile(bipScorePath) + .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + + Dataset bipScores = spark + .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(entry.get(key)); + return bs; + }).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class)); + + System.out.println(bipScores.count()); + + Dataset results = readPath(spark, inputPath, inputClazz); + + results.createOrReplaceTempView("result"); + + Dataset preparedResult = spark + .sql( + "select pIde.value value, id " + + "from result " + + "lateral view explode (pid) p as pIde " + + "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") + .as(Encoders.bean(PreparedResult.class)); + + bipScores + .joinWith( + preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), + "inner") + .map((MapFunction, BipScore>) value -> { + BipScore ret = value._1(); + ret.setId(value._2().getId()); + return ret; + }, Encoders.bean(BipScore.class)) + .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + Result ret = new Result(); + ret.setDataInfo(getDataInfo()); + BipScore first = it.next(); + ret.setId(first.getId()); + + ret.setMeasures(getMeasure(first)); + it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); + + return ret; + }, Encoders.bean(Result.class)) + .toJavaRDD() + .map(p -> new AtomicAction(inputClazz, p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + + } + + private static List getMeasure(BipScore value) { + return value + .getScoreList() + .stream() + .map(score -> { + Measure m = new Measure(); + m.setId(score.getId()); + m + .setUnit( + score + .getUnit() + .stream() + .map(unit -> { + KeyValue kv = new KeyValue(); + kv.setValue(unit.getValue()); + kv.setKey(unit.getKey()); + kv.setDataInfo(getDataInfo()); + return kv; + }) + .collect(Collectors.toList())); + return m; + }) + .collect(Collectors.toList()); + } + + private static DataInfo getDataInfo() { + DataInfo di = new DataInfo(); + di.setInferred(false); + di.setInvisible(false); + di.setDeletedbyinference(false); + di.setTrust(""); + Qualifier qualifier = new Qualifier(); + qualifier.setClassid("sysimport:actionset"); + qualifier.setClassname("Harvested"); + qualifier.setSchemename("dnet:provenanceActions"); + qualifier.setSchemeid("dnet:provenanceActions"); + di.setProvenanceaction(qualifier); + return di; + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json new file mode 100644 index 0000000000..7663a454b9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json new file mode 100644 index 0000000000..31771a40ad --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "rtn", + "paramLongName": "resultTableName", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "bsp", + "paramLongName": "bipScorePath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml new file mode 100644 index 0000000000..5311a6614a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + inputPath + the input path of the resources to be extended + + + + bipScorePath + the path where to find the bipFinder scores + + + outputPath + the path where to store the actionset + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for publications + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${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} + + --inputPath${inputPath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/publication + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for datasets + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${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=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dataset + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for orp + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${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} + + --inputPath${inputPath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/otherresearchproduct + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for software + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${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=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/software + --bipScorePath${bipScorePath} + + + + + + + + + + yarn + cluster + saves all the aa produced for the several types of results in the as output path + eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${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} + + --inputPath${workingDir} + --outputPath${outputPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java new file mode 100644 index 0000000000..7200d2896d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java @@ -0,0 +1,323 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Publication; + +public class SparkAtomicActionScoreJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionScoreJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionScoreJobTest.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(SparkAtomicActionScoreJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void matchOne() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(2, execVerification.count()); + + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + "0.227515392", + execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + + } + + @Test + public void matchOneWithTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); + + List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); + String tmp_influence = tmp_ds.get(0).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); + + tmp_influence = tmp_ds.get(1).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); + + Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); + + } + + @Test + public void matchTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 2); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); + + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "1.98956540239e-08", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "0.282046161584", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "0.227515392", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json new file mode 100644 index 0000000000..a4f3fa8b82 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json @@ -0,0 +1,1101 @@ +{"10.1001/10-v4n2-hsf10003": [{"id": "influence", "unit": [{"value": "1.62759106106e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.22519296", "key": "score"}]}]} +{"10.1001/2012.jama.10456": [{"id": "influence", "unit": [{"value": "1.66083991022e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.8690688", "key": "score"}]}]} +{"10.1001/2013.jamadermatol.729": [{"id": "influence", "unit": [{"value": "2.0769133069e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.0279936", "key": "score"}]}]} +{"10.1001/archderm.107.6.853": [{"id": "influence", "unit": [{"value": "1.95361113607e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.600657255944", "key": "score"}]}]} +{"10.1001/archderm.1926.02370130020002": [{"id": "influence", "unit": [{"value": "1.48611319422e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.20903253662e-16", "key": "score"}]}]} +{"10.1001/archpediatrics.2012.157": [{"id": "influence", "unit": [{"value": "1.42089114725e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.1575936", "key": "score"}]}]} +{"10.1002/bjs.1800830139": [{"id": "influence", "unit": [{"value": "3.73834652128e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.73174997252", "key": "score"}]}]} +{"10.1016/j.buildenv.2007.01.013": [{"id": "influence", "unit": [{"value": "1.54849335991e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.4885963776", "key": "score"}]}]} +{"10.1016/j.bulcan.2015.02.014": [{"id": "influence", "unit": [{"value": "1.43539656097e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.3456", "key": "score"}]}]} +{"10.1016/j.buildenv.2007.01.014": [{"id": "influence", "unit": [{"value": "1.65673923548e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.61188397056", "key": "score"}]}]} +{"10.1016/j.buildenv.2007.01.015": [{"id": "influence", "unit": [{"value": "1.4250528394e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.05028397056", "key": "score"}]}]} +{"10.1016/j.bulcan.2015.02.016": [{"id": "influence", "unit": [{"value": "1.41753303696e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.42336", "key": "score"}]}]} +{"10.1016/j.buildenv.2009.08.004": [{"id": "influence", "unit": [{"value": "2.40827378083e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.3699383296", "key": "score"}]}]} +{"10.1016/j.buildenv.2007.01.016": [{"id": "influence", "unit": [{"value": "2.54472083616e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.12517350811", "key": "score"}]}]} +{"10.1016/j.bulcan.2015.03.005": [{"id": "influence", "unit": [{"value": "1.40543881698e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.216", "key": "score"}]}]} +{"10.1016/j.buildenv.2009.08.005": [{"id": "influence", "unit": [{"value": "4.98246170342e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "13.4951290928", "key": "score"}]}]} +{"10.1016/j.buildenv.2007.01.017": [{"id": "influence", "unit": [{"value": "2.8107768688e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.99055570262", "key": "score"}]}]} +{"10.1002/bjs.1800770731": [{"id": "influence", "unit": [{"value": 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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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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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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. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. 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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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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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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. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. 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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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travail de thèse est consacré à l'extension de l'Inversion Dynamique non-linéaire (NDI-Nonlinear Dynamic Inversion) pour un ensemble plus grand de systèmes non-linéaires, tout en garantissant des conditions de stabilité suffisantes. La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. However, this method is inherently non-robust to modelling errors and input saturations. Moreover, obtaining a quantifiable guarantee of the attained stability domain in a nonlinear control context is not a very straightforward task. Unlike standard NDI approaches, our methodology can be viewed as a generalized nonlinear compensation framework which allows to incorporate uncertainties and input saturations in the design process. Paralleling anti-windup strategies, the controller can be computed through a single multichannel optimization problem or through a simple two-step process. Within this framework, linear fractional transformations of the nonlinear closed-loop can be easily derived for robust stability analysis using standard tools for linear systems. The proposed method is tested for the flight control of a delta wing type reentry vehicle at hypersonic, transonic and subsonic phases of the atmospheric reentry. For this thesis work, a Flight Mechanics simulator including diverse external factors and modelling errors was developed in Simulink."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|artemis___fr::630e47d8b572e3df0e91327d6d8f036d","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE (ArTeMIS)"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2012-09-21"},"distributionlocation":"","hostedby":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE 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atmosphérique"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"A generalized framework for robust nonlinear compensation : application to an atmospheric reentry control problem"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 5ca865e8fc..d42c692f7b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -32,15 +32,15 @@ public class CheckDuplictedIdsJob { IOUtils .toString( CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String countPath = parser.get("workingPath") + "/counts"; + final String countPath = parser.get("outputDir") + "/counts"; log.info("countPath: {}", countPath); final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); @@ -59,6 +59,7 @@ public class CheckDuplictedIdsJob { .map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG())) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(countPath); ; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index cfee360c57..1ae241e340 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -44,10 +44,10 @@ public class GenerateEventsJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String eventsPath = workingPath + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final Set dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist"); @@ -59,6 +59,9 @@ public class GenerateEventsJob { final Set dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist"); log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ",")); + final Set topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist"); + log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ",")); + final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { @@ -70,12 +73,12 @@ public class GenerateEventsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_events"); final Dataset groups = ClusterUtils - .readPath(spark, workingPath + "/duplicates", ResultGroup.class); + .readPath(spark, workingDir + "/duplicates", ResultGroup.class); final Dataset dataset = groups .map( g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators), Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index d5c53ea360..2772f8fd16 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -46,7 +46,7 @@ public class GenerateStatsJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String dbUrl = parser.get("dbUrl"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index d3cbe0034f..e18a7ef560 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -46,7 +46,7 @@ public class IndexEventSubsetJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); @@ -55,6 +55,18 @@ public class IndexEventSubsetJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic")); log.info("maxEventsForTopic: {}", maxEventsForTopic); @@ -86,10 +98,10 @@ public class IndexEventSubsetJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 792a2354a4..75f4eb066d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -54,7 +54,7 @@ public class IndexNotificationsJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); @@ -63,6 +63,18 @@ public class IndexNotificationsJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); @@ -92,10 +104,10 @@ public class IndexNotificationsJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 762bfbb903..380a689e4d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -36,7 +36,7 @@ public class IndexOnESJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); @@ -45,6 +45,18 @@ public class IndexOnESJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); final JavaRDD inputRdd = ClusterUtils @@ -53,15 +65,13 @@ public class IndexOnESJob { .javaRDD(); final Map esCfg = new HashMap<>(); - // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); - esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java index 39fa76e43d..01778ad74f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java @@ -42,10 +42,10 @@ public class JoinStep0Job { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step0"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step0"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class JoinStep0Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class); + .readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java index 8e502f7366..82c3619e10 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java @@ -40,10 +40,10 @@ public class JoinStep1Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step1"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step1"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep1Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedProjects", RelatedProject.class); + .readPath(spark, workingDir + "/relatedProjects", RelatedProject.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedProjectAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java index 55ab497f07..bd6135d413 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java @@ -39,10 +39,10 @@ public class JoinStep2Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step2"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step2"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class JoinStep2Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class); + .readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java index 4d06f6f133..18e8c00b2a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java @@ -40,10 +40,10 @@ public class JoinStep3Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step3"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step3"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep3Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class); + .readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java index b53d7e39b9..9655303620 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java @@ -40,10 +40,10 @@ public class JoinStep4Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step4"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step4"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep4Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class); + .readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator() .toColumn(); 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 e9644122f3..e061c0d3b7 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 @@ -36,7 +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 = "10|opendoar____::"; + private static final String OPENDOAR_NSPREFIX = "opendoar____::"; public static void main(final String[] args) throws Exception { @@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; + final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId"; log.info("partitionPath: {}", partitionPath); final String opendoarIds = parser.get("opendoarIds"); @@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob { .write() .partitionBy("group") .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(partitionPath); }); @@ -122,6 +123,7 @@ public class PartitionEventsByDsIdJob { final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId(); + res.setEventId(e.getEventId()); res.setOriginalId(payload.getResult().getOriginalId()); res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null)); res.setTopic(e.getTopic()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index eb9add00de..dc156cbcf9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -45,10 +45,10 @@ public class PrepareGroupsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String groupsPath = workingPath + "/duplicates"; + final String groupsPath = workingDir + "/duplicates"; log.info("groupsPath: {}", groupsPath); final SparkConf conf = new SparkConf(); @@ -60,10 +60,10 @@ public class PrepareGroupsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups"); final Dataset results = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); final TypedColumn, ResultGroup> aggr = new ResultAggregator() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 0cfc1adcbb..9bdf32a642 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasets"; + final String relsPath = workingDir + "/relatedDatasets"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); @@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob { .map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob { final Dataset dataset = rels .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2); + final RelatedDataset rel = new RelatedDataset(t._1.getSource(), + t._2); rel.getRelDataset().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedDataset.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java index 166372a7f4..0c23181274 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java @@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasources"; + final String relsPath = workingDir + "/relatedDatasources"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index e988366c8c..9498c0f337 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedProjects"; + final String relsPath = workingDir + "/relatedProjects"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); @@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob { .map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 724acc4dce..8270500fd4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedPublications"; + final String relsPath = workingDir + "/relatedPublications"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); @@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob { Encoders.bean(OaBrokerRelatedPublication.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob { final Dataset dataset = rels .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2); + final RelatedPublication rel = new RelatedPublication( + t._1.getSource(), t._2); rel.getRelPublication().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedPublication.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index d15565d0d7..16b4507338 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedSoftwares"; + final String relsPath = workingDir + "/relatedSoftwares"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); @@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob { .map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java index d3c7113ec0..cf44506038 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java @@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String simpleEntitiesPath = workingPath + "/simpleEntities"; + final String simpleEntitiesPath = workingDir + "/simpleEntities"; log.info("simpleEntitiesPath: {}", simpleEntitiesPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index 26ebbb7c03..cb3ea54645 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher { public EnrichMissingSubject() { super(20, - s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MISSING_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MISSING_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MISSING_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MISSING_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MISSING_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index bbe6609d75..1f6edf96e7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher { public EnrichMoreSubject() { super(20, - s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MORE_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MORE_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MORE_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MORE_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MORE_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index d8b8dd8079..9ce64f6bde 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Relation; public class ClusterUtils { @@ -30,6 +31,16 @@ public class ClusterUtils { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } + public static Dataset loadRelations(final String graphPath, final SparkSession spark) { + return ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .map(r -> { + r.setSource(ConversionUtils.cleanOpenaireId(r.getSource())); + r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget())); + return r; + }, Encoders.bean(Relation.class)); + } + public static Dataset readPath( final SparkSession spark, final String inputPath, @@ -67,6 +78,7 @@ public class ClusterUtils { .map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz)) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(path); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 053627a5fb..ecbfd821ea 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -74,7 +74,7 @@ public class ConversionUtils { } final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset(); - res.setOpenaireId(d.getId()); + res.setOpenaireId(cleanOpenaireId(d.getId())); res.setOriginalId(first(d.getOriginalId())); res.setTitle(structPropValue(d.getTitle())); res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -89,7 +89,7 @@ public class ConversionUtils { } final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setOriginalId(first(p.getOriginalId())); res.setTitle(structPropValue(p.getTitle())); res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -106,7 +106,7 @@ public class ConversionUtils { final OaBrokerMainEntity res = new OaBrokerMainEntity(); - res.setOpenaireId(result.getId()); + res.setOpenaireId(cleanOpenaireId(result.getId())); res.setOriginalId(first(result.getOriginalId())); res.setTypology(classId(result.getResulttype())); res.setTitles(structPropList(result.getTitle())); @@ -129,6 +129,10 @@ public class ConversionUtils { return res; } + public static String cleanOpenaireId(final String id) { + return id.contains("|") ? StringUtils.substringAfter(id, "|") : id; + } + private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) { if (author == null) { return null; @@ -188,7 +192,7 @@ public class ConversionUtils { } final OaBrokerProject res = new OaBrokerProject(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setTitle(fieldValue(p.getTitle())); res.setAcronym(fieldValue(p.getAcronym())); res.setCode(fieldValue(p.getCode())); @@ -214,7 +218,7 @@ public class ConversionUtils { } final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware(); - res.setOpenaireId(sw.getId()); + res.setOpenaireId(cleanOpenaireId(sw.getId())); res.setName(structPropValue(sw.getTitle())); res.setDescription(fieldValue(sw.getDescription())); res.setRepository(fieldValue(sw.getCodeRepositoryUrl())); @@ -230,7 +234,7 @@ public class ConversionUtils { final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource(); res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname()))); - res.setOpenaireId(ds.getId()); + res.setOpenaireId(cleanOpenaireId(ds.getId())); res.setType(classId(ds.getDatasourcetype())); return res; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java index 75c4625ce4..c693be93c5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java @@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable { final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator(); collectedFromSet .stream() - .map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL)) + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.COLLECTED_FROM_REL)) .forEach(res::addTuple); - hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple); + + hostedBySet + .stream() + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.HOSTED_BY_REL)) + .forEach(res::addTuple); + return res; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java index 1ab56cc346..103751f954 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java @@ -76,6 +76,7 @@ public class EventFinder { final Set dsIdWhitelist, final Set dsIdBlacklist, final Set dsTypeWhitelist, + final Set topicWhitelist, final Map accumulators) { final List> list = new ArrayList<>(); @@ -84,7 +85,13 @@ public class EventFinder { for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) { if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) { for (final UpdateMatcher matcher : matchers) { - list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)); + for (final UpdateInfo info : matcher + .searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) { + if (topicWhitelist == null || topicWhitelist.isEmpty() + || topicWhitelist.contains(info.getTopic().getPath())) { + list.add(info); + } + } } } } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json new file mode 100644 index 0000000000..2584b78fcc --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json @@ -0,0 +1,9 @@ +[ + + { + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where the data are stored", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json index adee1888a1..0d942cd59f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json @@ -7,7 +7,7 @@ }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "workingDir", "paramDescription": "the path where the temporary data will be stored", "paramRequired": true } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 14e33b0916..d06eec87e3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the path where the graph is stored - workingPath + outputDir the path where the the generated data will be stored @@ -24,6 +24,11 @@ - a black list (comma separeted, - for empty list) of datasource ids + + topicWhitelist + * + a white list (comma separeted, * for all) of topics + esEventIndexName the elasticsearch index name for events @@ -36,6 +41,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -111,15 +136,15 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - + @@ -152,7 +177,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -176,7 +201,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -201,7 +226,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -225,7 +250,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -249,7 +274,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -273,7 +298,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -299,7 +324,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -323,7 +348,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -347,7 +372,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -371,7 +396,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -395,7 +420,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -419,7 +444,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -442,10 +467,12 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --workingDir${workingDir} + --outputDir${outputDir} --datasourceIdWhitelist${datasourceIdWhitelist} --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} + --topicWhitelist${topicWhitelist} @@ -468,9 +495,13 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -495,9 +526,13 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -521,7 +556,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --dbUrl${brokerDbUrl} --dbUser${brokerDbUser} --dbPassword${brokerDbPassword} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index bab8081932..e803bb5b90 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -1,7 +1,13 @@ [ + { + "paramName": "wp", + "paramLongName": "workingDir", + "paramDescription": "the path where the temporary data are stored", + "paramRequired": true + }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "outputDir", "paramDescription": "the path where the generated events will be stored", "paramRequired": true }, @@ -22,5 +28,11 @@ "paramLongName": "datasourceIdBlacklist", "paramDescription": "a black list (comma separeted, - for empty list) of datasource ids", "paramRequired": true + }, + { + "paramName": "topicWhitelist", + "paramLongName": "topicWhitelist", + "paramDescription": "a white list (comma separeted, * for all) of topics", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json index ac1dbf7867..f7e072d0fb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the data path", "paramRequired": true }, { @@ -16,5 +16,29 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json index 4921bc03e2..0046490bbb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the path where the generated data are stored", "paramRequired": true }, { @@ -16,7 +16,31 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "n", "paramLongName": "maxEventsForTopic", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json index 5eea894c8e..370b484115 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the dir that contains the events folder", "paramRequired": true }, { @@ -17,6 +17,30 @@ "paramDescription": "the ES host", "paramRequired": true }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "broker", "paramLongName": "brokerApiBaseUrl", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 879c0d3490..248326d57e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -6,8 +6,8 @@ the path where the graph is stored - workingPath - the path where the the generated data will be stored + outputDir + the path where the the generated data are stored datasourceIdWhitelist @@ -36,6 +36,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -122,9 +142,13 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json index 10ba926abf..12cd6a391c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the path where the temporary data will be stored", + "paramLongName": "outputDir", + "paramDescription": "the path where the data will be stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index dba3c9f73b..7c5b722d21 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --opendoarIds${opendoarIds} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml new file mode 100644 index 0000000000..2e0ed9aeea --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + 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-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml new file mode 100644 index 0000000000..9095004ad5 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -0,0 +1,140 @@ + + + + + outputDir + the path where the the generated data will be stored + + + esEventIndexName + the elasticsearch index name for events + + + esIndexHost + the elasticsearch host + + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + + + maxIndexedEventsForDsAndTopic + the max number of events for each couple (ds/topic) + + + brokerApiBaseUrl + the url of the broker service api + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + IndexEventSubsetOnESJob + eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob + dhp-broker-events-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --index${esEventIndexName} + --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} + --maxEventsForTopic${maxIndexedEventsForDsAndTopic} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json index 15d7d251f6..2388b1c1f4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json @@ -1,8 +1,8 @@ [ { - "paramName": "wp", - "paramLongName": "workingPath", - "paramDescription": "the working path", + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where generated data are stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 30cfebe799..c35bbf424d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -10,10 +10,11 @@ import java.io.Serializable; import java.nio.file.Paths; import java.util.*; -import org.codehaus.jackson.map.ObjectMapper; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.util.MapDocumentUtil; @@ -100,8 +101,8 @@ public class EntityMergerTest implements Serializable { assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); // verify authors - assertEquals(pub_merged.getAuthor().size(), 9); - assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + assertEquals(13, pub_merged.getAuthor().size()); + assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor())); // verify title int count = 0; diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java index 8646ac7422..9bc90d51da 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java @@ -7,7 +7,6 @@ import java.util.List; import org.apache.commons.io.IOUtils; 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.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; @@ -16,8 +15,8 @@ import org.apache.spark.rdd.RDD; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.codehaus.jackson.map.ObjectMapper; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.hash.Hashing; import eu.dnetlib.dedup.graph.ConnectedComponent; diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java index 572824e3db..7adf992cd2 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java @@ -10,7 +10,8 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Oaf; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 9c9221b272..683986de24 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.utils.DHPUtils import org.apache.commons.lang3.StringUtils -import org.codehaus.jackson.map.ObjectMapper +import com.fasterxml.jackson.databind.ObjectMapper import org.json4s import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ -import scala.io.Source case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} @@ -19,23 +18,18 @@ case class HostedByItemType(id: String, officialname: String, issn: String, eiss case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){} object DoiBoostMappingUtil { - def getUnknownCountry(): Qualifier = { - createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries") - } - - def generateMAGAffiliationId(affId: String): String = { s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}" } - val logger: Logger = LoggerFactory.getLogger(getClass) //STATIC STRING val MAG = "microsoft" val MAG_NAME = "Microsoft Academic Graph" - val ORCID = "ORCID" + val ORCID = "orcid" + val ORCID_PENDING = "orcid_pending" val CROSSREF = "Crossref" val UNPAYWALL = "UnpayWall" val GRID_AC = "grid.ac" diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala index 7a6cd3faaa..78477ae4d9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -39,33 +39,38 @@ object SparkGenerateDOIBoostActionSet { val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath") val dbOrganizationPath = parser.get("dbOrganizationPath") val workingDirPath = parser.get("targetPath") + val sequenceFilePath = parser.get("sFilePath") - spark.read.load(dbDatasetPath).as[OafDataset] + val asDataset = spark.read.load(dbDatasetPath).as[OafDataset] .map(d =>DoiBoostMappingUtil.fixResult(d)) .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet") - spark.read.load(dbPublicationPath).as[Publication] + val asPublication =spark.read.load(dbPublicationPath).as[Publication] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(dbOrganizationPath).as[Organization] + val asOrganization = spark.read.load(dbOrganizationPath).as[Organization] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(crossRefRelation).as[Relation] + val asCRelation = spark.read.load(crossRefRelation).as[Relation] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(dbaffiliationRelationPath).as[Relation] + val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] - d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) + + val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation) + +// spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] + + d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) 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 860254527a..11f9828db4 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 @@ -2,6 +2,7 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils @@ -30,7 +31,7 @@ object SparkGenerateDoiBoost { import spark.implicits._ val hostedByMapPath = parser.get("hostedByMapPath") - val workingDirPath = parser.get("workingDirPath") + val workingDirPath = parser.get("workingPath") implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] @@ -132,7 +133,7 @@ object SparkGenerateDoiBoost { o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get)) if (affiliation.OfficialPage.isDefined) o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get)) - o.setCountry(DoiBoostMappingUtil.getUnknownCountry()) + o.setCountry(ModelConstants.UNKNOWN_COUNTRY) o } else 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 5ba01357e7..d1ceb9a072 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, generateDataInfo())).asJava) + a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava) a } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java index f69a05da1c..cda4983b72 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java @@ -2,18 +2,16 @@ package eu.dnetlib.doiboost.crossref; import java.io.ByteArrayOutputStream; +import java.util.Optional; import java.util.zip.Inflater; import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -30,34 +28,45 @@ public class CrossrefImporter { parser.parseArgument(args); - final String hdfsuri = parser.get("namenode"); - System.out.println("HDFS URI" + hdfsuri); - Path hdfswritepath = new Path(parser.get("targetPath")); - System.out.println("TargetPath: " + hdfsuri); + final String namenode = parser.get("namenode"); + System.out.println("namenode: " + namenode); - final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp")) - ? Long.parseLong(parser.get("timestamp")) - : -1; + Path targetPath = new Path(parser.get("targetPath")); + System.out.println("targetPath: " + targetPath); - if (timestamp > 0) - System.out.println("Timestamp added " + timestamp); + final Long timestamp = Optional + .ofNullable(parser.get("timestamp")) + .map(s -> { + try { + return Long.parseLong(s); + } catch (NumberFormatException e) { + return -1L; + } + }) + .orElse(-1L); + System.out.println("timestamp: " + timestamp); + + final String esServer = parser.get("esServer"); + System.out.println("esServer: " + esServer); + + final String esIndex = parser.get("esIndex"); + System.out.println("esIndex: " + esIndex); // ====== Init HDFS File System Object Configuration conf = new Configuration(); // Set FileSystem URI - conf.set("fs.defaultFS", hdfsuri); + conf.set("fs.defaultFS", namenode); // 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()); - ESClient client = timestamp > 0 - ? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp) - : new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref"); + // "ip-90-147-167-25.ct1.garrservices.it", "crossref" + final ESClient client = new ESClient(esServer, esIndex, timestamp); try (SequenceFile.Writer writer = SequenceFile .createWriter( conf, - SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.file(targetPath), SequenceFile.Writer.keyClass(IntWritable.class), SequenceFile.Writer.valueClass(Text.class))) { @@ -74,8 +83,7 @@ public class CrossrefImporter { end = System.currentTimeMillis(); final float time = (end - start) / 1000.0F; System.out - .println( - String.format("Imported %d records last 100000 imported in %f seconds", i, time)); + .println(String.format("Imported %s records last 100000 imported in %s seconds", i, time)); start = System.currentTimeMillis(); } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java index e31ccf399b..dcebbbcac8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java @@ -1,11 +1,11 @@ package eu.dnetlib.doiboost.crossref; -import java.io.IOException; import java.util.Iterator; import java.util.List; import org.apache.commons.io.IOUtils; +import org.apache.http.HttpHeaders; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpPost; import org.apache.http.entity.StringEntity; @@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory; import com.jayway.jsonpath.JsonPath; public class ESClient implements Iterator { - private static final Logger logger = LoggerFactory.getLogger(ESClient.class); - static final String blobPath = "$.hits[*].hits[*]._source.blob"; - static final String scrollIdPath = "$._scroll_id"; - static final String JSON_NO_TS = "{\"size\":1000}"; - static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; - static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}"; + private static final String BLOB_PATH = "$.hits.hits[*]._source.blob"; + private static final String SCROLL_ID_PATH = "$._scroll_id"; + private static final String JSON_NO_TS = "{\"size\":1000}"; + private static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; + private static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}"; + + public static final String APPLICATION_JSON = "application/json"; + + public static final String ES_SEARCH_URL = "http://%s:9200/%s/_search?scroll=1m"; + public static final String ES_SCROLL_URL = "http://%s:9200/_search/scroll"; private final String scrollId; @@ -31,47 +35,30 @@ public class ESClient implements Iterator { private final String esHost; - public ESClient(final String esHost, final String esIndex) throws IOException { - + public ESClient(final String esHost, final String esIndex, final long timestamp) { this.esHost = esHost; - final String body = getResponse( - String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS); - scrollId = getJPathString(scrollIdPath, body); - buffer = getBlobs(body); - } - public ESClient(final String esHost, final String esIndex, final long timestamp) - throws IOException { - this.esHost = esHost; - final String body = getResponse( - String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), - String.format(JSON_WITH_TS, timestamp)); - scrollId = getJPathString(scrollIdPath, body); + final String body = timestamp > 0 + ? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp)) + : getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS); + scrollId = getJPathString(SCROLL_ID_PATH, body); buffer = getBlobs(body); } private String getResponse(final String url, final String json) { - CloseableHttpClient client = HttpClients.createDefault(); - try { - + try (CloseableHttpClient client = HttpClients.createDefault()) { HttpPost httpPost = new HttpPost(url); if (json != null) { StringEntity entity = new StringEntity(json); httpPost.setEntity(entity); - httpPost.setHeader("Accept", "application/json"); - httpPost.setHeader("Content-type", "application/json"); + httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON); + httpPost.setHeader(HttpHeaders.CONTENT_TYPE, APPLICATION_JSON); + } + try (CloseableHttpResponse response = client.execute(httpPost)) { + return IOUtils.toString(response.getEntity().getContent()); } - CloseableHttpResponse response = client.execute(httpPost); - - return IOUtils.toString(response.getEntity().getContent()); } catch (Throwable e) { throw new RuntimeException("Error on executing request ", e); - } finally { - try { - client.close(); - } catch (IOException e) { - throw new RuntimeException("Unable to close client ", e); - } } } @@ -87,7 +74,7 @@ public class ESClient implements Iterator { } private List getBlobs(final String body) { - final List res = JsonPath.read(body, "$.hits.hits[*]._source.blob"); + final List res = JsonPath.read(body, BLOB_PATH); return res; } @@ -102,11 +89,11 @@ public class ESClient implements Iterator { if (buffer.isEmpty()) { final String json_param = String.format(JSON_SCROLL, scrollId); - final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param); + final String body = getResponse(String.format(ES_SCROLL_URL, esHost), json_param); try { buffer = getBlobs(body); } catch (Throwable e) { - logger.error("Error on get next page: body:" + body); + System.out.println("Error on get next page: body:" + body); } } return nextItem; 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/SparkProcessMAG.scala similarity index 99% rename from dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala rename to dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala index 02dc4979af..780e65c1e9 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/SparkProcessMAG.scala @@ -11,7 +11,7 @@ import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ -object SparkPreProcessMAG { +object SparkProcessMAG { def main(args: Array[String]): Unit = { val logger: Logger = LoggerFactory.getLogger(getClass) 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 f7255e5591..e9773dbbb9 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 @@ -1,11 +1,11 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.ObjectMapper 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 -import org.codehaus.jackson.map.ObjectMapper import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ @@ -18,7 +18,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {} object ORCIDToOAF { val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass) - val mapper = new ObjectMapper + val mapper = new ObjectMapper() def isJsonValid(inputStr: String): Boolean = { import java.io.IOException 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 index 598835a000..1422a08407 100644 --- 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 @@ -3,10 +3,8 @@ 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; @@ -18,11 +16,9 @@ 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; @@ -36,7 +32,7 @@ public class SparkDownloadOrcidAuthors { 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 { + public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors { .orElse(Boolean.TRUE); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); - logger.info("workingPath: ", workingPath); + logger.info("workingPath: {}", workingPath); final String outputPath = parser.get("outputPath"); - logger.info("outputPath: ", outputPath); + logger.info("outputPath: {}", outputPath); final String token = parser.get("token"); final String lambdaFileName = parser.get("lambdaFileName"); - logger.info("lambdaFileName: ", lambdaFileName); + logger.info("lambdaFileName: {}", lambdaFileName); SparkConf conf = new SparkConf(); runWithSparkSession( @@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors { } private static boolean isModified(String orcidId, String modifiedDate) { - Date modifiedDateDt = null; - Date lastUpdateDt = null; + Date modifiedDateDt; + Date lastUpdateDt; try { if (modifiedDate.length() != 19) { modifiedDate = modifiedDate.substring(0, 19); diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json index 6eb1ec6f16..93d24a8910 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json @@ -5,5 +5,6 @@ {"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true}, {"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, {"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, - {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true} + {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}, + {"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true} ] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json index ea08f47d43..1ff63dd0ec 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json @@ -3,5 +3,5 @@ {"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true}, {"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, {"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true}, - {"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true} + {"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true} ] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json index 87a138d525..0920d516a4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json @@ -1,5 +1,7 @@ [ - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true}, - {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true}, - {"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true}, + {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true}, + {"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false}, + {"paramName":"ess", "paramLongName":"esServer", "paramDescription": "elasticsearch server url", "paramRequired": true}, + {"paramName":"esi", "paramLongName":"esIndex", "paramDescription": "elasticsearch index name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml new file mode 100644 index 0000000000..508202e301 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl: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/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml new file mode 100644 index 0000000000..3f5805b629 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -0,0 +1,335 @@ + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorIntersectionMemory + memory for individual executor + + + + sparkExecutorCores + number of cores used by single executor + + + + + + workingPath + the working Path + + + + hostedByMapPath + the hostedByMap Path + + + outputPath + the Path of the sequence file action set + + + + + + inputPathCrossref + the Crossref input path + + + crossrefTimestamp + Timestamp for the Crossref incremental Harvesting + + + esServer + elasticsearch server url for the Crossref Harvesting + + + esIndex + elasticsearch index name for the Crossref Harvesting + + + + + inputPathMAG + the MAG working path + + + + + + inputPathUnpayWall + the UnpayWall working path + + + + + inputPathOrcid + the ORCID working path + + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + ${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'} + ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} + ${wf:conf('resumeFrom') eq 'PreprocessMag'} + ${wf:conf('resumeFrom') eq 'PreprocessUW'} + ${wf:conf('resumeFrom') eq 'PreprocessORCID'} + ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} + ${wf:conf('resumeFrom') eq 'GenerateActionSet'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.doiboost.crossref.CrossrefImporter + --targetPath${inputPathCrossref}/index_update + --namenode${nameNode} + --esServer${esServer} + --esIndex${esIndex} + --timestamp${crossrefTimestamp} + + + + + + + + + + + yarn-cluster + cluster + GenerateCrossrefDataset + eu.dnetlib.doiboost.crossref.CrossrefDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --workingPath${inputPathCrossref} + --masteryarn-cluster + + + + + + + + + + + + + + + + + + yarn-cluster + cluster + 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 + ${sparkExtraOPT} + + --sourcePath${inputPathCrossref}/crossref_ds + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + + + + + + + + + + + + yarn-cluster + cluster + Convert Mag to Dataset + eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + ${sparkExtraOPT} + + --sourcePath${inputPathMAG}/input + --targetPath${inputPathMAG}/dataset + --masteryarn-cluster + + + + + + + + yarn-cluster + cluster + Convert Mag to OAF Dataset + eu.dnetlib.doiboost.mag.SparkProcessMAG + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathMAG}/dataset + --workingPath${inputPathMAG}/process + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + yarn-cluster + cluster + Convert UnpayWall to Dataset + eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathUnpayWall}/uw_extracted + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathOrcid} + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Create DOIBoost Infospace + eu.dnetlib.doiboost.SparkGenerateDoiBoost + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorIntersectionMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --hostedByMapPath${hostedByMapPath} + --affiliationPath${inputPathMAG}/process/Affiliations + --paperAffiliationPath${inputPathMAG}/process/PaperAuthorAffiliations + --workingPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Generate DOIBoost ActionSet + eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --dbPublicationPath${workingPath}/doiBoostPublicationFiltered + --dbDatasetPath${workingPath}/crossrefDataset + --crossRefRelation${workingPath}/crossrefRelation + --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation + --dbOrganizationPath${workingPath}/doiBoostOrganization + --targetPath${workingPath}/actionDataSet + --sFilePath${outputPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file 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 0222b393da..a1b3d06b7c 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 @@ -1,9 +1,9 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.ObjectMapper 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 import org.slf4j.{Logger, LoggerFactory} 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 dd8342980d..b3ef3a1121 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 @@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 { + " LATERAL VIEW EXPLODE (author) a AS MyT " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " + " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or " - + " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + + " lower(MyP.qualifier.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/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 66297e1779..60ad438598 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -108,7 +108,7 @@ public class SparkResultToCommunityFromOrganizationJob { .stream() .map(con -> con.getId()) .collect(Collectors.toList()); - Result res = new Result(); + R res = (R) ret.getClass().newInstance(); res.setId(ret.getId()); List propagatedContexts = new ArrayList<>(); for (String cId : communitySet) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 0c613d1b4a..5ac1176931 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -130,7 +130,7 @@ public class SparkResultToCommunityThroughSemRelJob { }) .filter(Objects::nonNull) .collect(Collectors.toList()); - Result r = new Result(); + R r = (R) ret.getClass().newInstance(); r.setId(ret.getId()); r.setContext(contextList); ret.mergeFrom(r); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index a8e1ab8414..7709e00a85 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -24,7 +24,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest; import eu.dnetlib.dhp.schema.oaf.Dataset; public class ResultToCommunityJobTest { @@ -66,7 +65,7 @@ public class ResultToCommunityJobTest { } @Test - public void test1() throws Exception { + public void testSparkResultToCommunityThroughSemRelJob() throws Exception { SparkResultToCommunityThroughSemRelJob .main( new String[] { 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 fbb20f1433..db7d34ec96 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 @@ -15,8 +15,11 @@ import eu.dnetlib.dhp.schema.oaf.*; public class CleaningFunctions { - public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; - public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/"; + public static final String DOI_PREFIX_REGEX = "^10\\."; + + public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})"; + public static final int ORCID_LEN = 19; + public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)"; public static final Set PID_BLACKLIST = new HashSet<>(); @@ -56,13 +59,19 @@ public class CleaningFunctions { } } if (Objects.nonNull(r.getAuthor())) { - r.getAuthor().forEach(a -> { - if (Objects.nonNull(a.getPid())) { - a.getPid().forEach(p -> { - fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES); - }); - } - }); + r + .getAuthor() + .stream() + .filter(Objects::nonNull) + .forEach(a -> { + if (Objects.nonNull(a.getPid())) { + a + .getPid() + .stream() + .filter(Objects::nonNull) + .forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)); + } + }); } if (value instanceof Publication) { @@ -86,7 +95,7 @@ public class CleaningFunctions { } else if (value instanceof Organization) { Organization o = (Organization) value; if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) { - o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE)); + o.setCountry(ModelConstants.UNKNOWN_COUNTRY); } } else if (value instanceof Relation) { // nothing to clean here @@ -101,6 +110,16 @@ public class CleaningFunctions { .setLanguage( qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES)); } + if (Objects.nonNull(r.getCountry())) { + r + .setCountry( + r + .getCountry() + .stream() + .filter(Objects::nonNull) + .filter(c -> StringUtils.isNotBlank(c.getClassid())) + .collect(Collectors.toList())); + } if (Objects.nonNull(r.getSubject())) { r .setSubject( @@ -153,12 +172,14 @@ public class CleaningFunctions { if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { r .setResourcetype( - qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE)); + qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE)); } if (Objects.nonNull(r.getInstance())) { for (Instance i : r.getInstance()) { if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) { - i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); + i + .setAccessright( + qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES)); } if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) { i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY); @@ -173,12 +194,22 @@ public class CleaningFunctions { if (Objects.isNull(bestaccessrights)) { r .setBestaccessright( - qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); + qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES)); } else { r.setBestaccessright(bestaccessrights); } } if (Objects.nonNull(r.getAuthor())) { + r + .setAuthor( + r + .getAuthor() + .stream() + .filter(a -> Objects.nonNull(a)) + .filter(a -> StringUtils.isNotBlank(a.getFullname())) + .filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", ""))) + .collect(Collectors.toList())); + boolean nullRank = r .getAuthor() .stream() @@ -199,6 +230,7 @@ public class CleaningFunctions { a .getPid() .stream() + .filter(Objects::nonNull) .filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> StringUtils.isNotBlank(p.getValue())) .map(p -> { @@ -211,14 +243,31 @@ public class CleaningFunctions { .map(Qualifier::getClassid) .orElse("")) .orElse(""); - if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { - p.getQualifier().setClassid(ModelConstants.ORCID); - } else { - p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + if (p + .getQualifier() + .getClassid() + .toLowerCase() + .contains(ModelConstants.ORCID)) { + if (pidProvenance + .equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { + p.getQualifier().setClassid(ModelConstants.ORCID); + } else { + p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + } + final String orcid = p + .getValue() + .trim() + .toLowerCase() + .replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4"); + if (orcid.length() == ORCID_LEN) { + p.setValue(orcid); + } else { + p.setValue(""); + } } - p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, "")); return p; }) + .filter(p -> StringUtils.isNotBlank(p.getValue())) .collect( Collectors .toMap( @@ -286,7 +335,7 @@ public class CleaningFunctions { // TODO add cleaning for more PID types as needed case "doi": - pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, "")); + pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10.")); break; } return pid; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java index 9c80528e34..3186f828ce 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java @@ -21,6 +21,7 @@ import org.apache.spark.sql.expressions.Aggregator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.jayway.jsonpath.Configuration; import com.jayway.jsonpath.DocumentContext; @@ -44,7 +45,8 @@ public class GroupEntitiesAndRelationsSparkJob { private final static String SOURCE_JPATH = "$.source"; - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static void main(String[] args) throws Exception { 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/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b6210013cb..3adbd244c6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; -import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty; import java.io.Closeable; import java.io.IOException; @@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i return Arrays.asList(r); } else { + final String validationDate = rs.getString("curation_date"); + final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false); final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false); final Relation r1 = new Relation(); final Relation r2 = new Relation(); - if (rs.getString(SOURCE_TYPE).equals("project")) { - r1.setCollectedfrom(collectedFrom); - r1.setRelType(RESULT_PROJECT); - r1.setSubRelType(OUTCOME); - r1.setRelClass(PRODUCES); - - r2.setCollectedfrom(collectedFrom); - r2.setRelType(RESULT_PROJECT); - r2.setSubRelType(OUTCOME); - r2.setRelClass(IS_PRODUCED_BY); - } else { - r1.setCollectedfrom(collectedFrom); - r1.setRelType(RESULT_RESULT); - r1.setSubRelType(RELATIONSHIP); - r1.setRelClass(IS_RELATED_TO); - - r2.setCollectedfrom(collectedFrom); - r2.setRelType(RESULT_RESULT); - r2.setSubRelType(RELATIONSHIP); - r2.setRelClass(IS_RELATED_TO); - } - + r1.setValidated(true); + r1.setValidationDate(validationDate); + r1.setCollectedfrom(collectedFrom); r1.setSource(sourceId); r1.setTarget(targetId); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); + r2.setValidationDate(validationDate); + r2.setValidated(true); + r2.setCollectedfrom(collectedFrom); r2.setSource(targetId); r2.setTarget(sourceId); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); + if (rs.getString(SOURCE_TYPE).equals("project")) { + r1.setRelType(RESULT_PROJECT); + r1.setSubRelType(OUTCOME); + r1.setRelClass(PRODUCES); + + r2.setRelType(RESULT_PROJECT); + r2.setSubRelType(OUTCOME); + r2.setRelClass(IS_PRODUCED_BY); + } else { + r1.setRelType(RESULT_RESULT); + r1.setSubRelType(RELATIONSHIP); + r1.setRelClass(IS_RELATED_TO); + + r2.setRelType(RESULT_RESULT); + r2.setSubRelType(RELATIONSHIP); + r2.setRelClass(IS_RELATED_TO); + } + return Arrays.asList(r1, r2); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 6d2e28ba8c..683b376309 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -51,31 +51,34 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final Node n = (Node) o; final Author author = new Author(); final String fullname = n.valueOf("./datacite:creatorName"); - author.setFullname(fullname); - - final PacePerson pp = new PacePerson(fullname, false); final String name = n.valueOf("./datacite:givenName"); - if (StringUtils.isBlank(name) & pp.isAccurate()) { - author.setName(pp.getNormalisedFirstName()); - } else { - author.setName(name); - } - final String surname = n.valueOf("./datacite:familyName"); - if (StringUtils.isBlank(surname) & pp.isAccurate()) { - author.setSurname(pp.getNormalisedSurname()); - } else { - author.setSurname(surname); - } + if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) { + author.setFullname(fullname); - if (StringUtils.isBlank(author.getFullname())) { - author.setFullname(String.format("%s, %s", author.getSurname(), author.getName())); - } + final PacePerson pp = new PacePerson(fullname, false); - author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); - author.setPid(preparePids(n, info)); - author.setRank(pos++); - res.add(author); + if (StringUtils.isBlank(name) & pp.isAccurate()) { + author.setName(pp.getNormalisedFirstName()); + } else { + author.setName(name); + } + + if (StringUtils.isBlank(surname) & pp.isAccurate()) { + author.setSurname(pp.getNormalisedSurname()); + } else { + author.setSurname(surname); + } + + if (StringUtils.isBlank(author.getFullname())) { + author.setFullname(String.format("%s, %s", author.getSurname(), author.getName())); + } + + author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); + author.setPid(preparePids(n, info)); + author.setRank(pos++); + res.add(author); + } } return res; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index f7579c0a08..a0ce4f5a69 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -11,7 +11,8 @@ import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Oaf; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql index 0390c11aa3..f912d3ce92 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql @@ -1 +1 @@ -SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE; \ No newline at end of file +SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE; \ No newline at end of file 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 46cb1a5359..9827dcc991 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 @@ -355,7 +362,31 @@ public class MappersTest { assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - System.out.println(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 testTextGridNoAuthor() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("textgrid-noauthor.xml")); + final List list = new OdfToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9cf75f2080..0d1ec1ad1a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -35,7 +35,7 @@ public class MigrateDbEntitiesApplicationTest { private MigrateDbEntitiesApplication app; - @Mock + @Mock(lenient = true) private ResultSet rs; @Mock 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 - corda_______::226852 + corda_______::226852 0001s diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml new file mode 100644 index 0000000000..53256bed01 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml @@ -0,0 +1,117 @@ + + + + r3f52792889d::00002412cb25f2f3047712d00ab2c8eb + hdl:11858/00-1734-0000-0003-EE73-2 + 2020-12-16T10:04:03.148Z + r3f52792889d + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + 2020-12-16T16:02:37.562Z + + + + hdl:11858/00-1734-0000-0003-EE73-2 + + + + + + + + Auf dem Trocknen + Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster & Loeffler, 1909. + + TextGrid + 2012 + + + tvitt@textgrid.de + + + Digitale Bibliothek + TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c + + + + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + + + + textgrid:rn8z.0 + http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2 + + + hdl:11858/00-1734-0000-0003-EE72-4 + + + 527 Bytes + + + text/tg.edition+tg.aggregation+xml + + 0 + + Der annotierte Datenbestand der Digitalen Bibliothek inklusive + Metadaten sowie davon einzeln zugängliche Teile sind eine Abwandlung + des Datenbestandes von www.editura.de durch TextGrid und werden + unter der Lizenz Creative Commons Namensnennung 3.0 Deutschland + Lizenz (by-Nennung TextGrid) veröffentlicht. Die Lizenz bezieht sich + nicht auf die der Annotation zu Grunde liegenden allgemeinfreien + Texte (Siehe auch Punkt 2 der Lizenzbestimmungen). + + + + + + + + Berlin + + + + hdl:11858/00-1734-0000-0003-EE73-2 + 0021 + 0002 + 2012-01-29 + OPEN + http://creativecommons.org/licenses/by/3.0/de/legalcode + und + DE + + + + + + + https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + + + + + false + false + 0.9 + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml index eddbc1ec43..7ad7c4d6bd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml @@ -6,29 +6,29 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - r3f52792889d::000051aa1f61d77d2c0b340091f8024e - textgrid:q9cv.0 - 2020-11-17T09:34:11.128+01:00 + r3f52792889d::00002412cb25f2f3047712d00ab2c8eb + hdl:11858/00-1734-0000-0003-EE73-2 + 2020-12-16T10:04:03.148Z r3f52792889d - textgrid:q9cv.0 - 2012-01-21T13:35:20Z - 2020-11-17T19:08:56.703+01:00 + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + 2020-12-16T16:02:37.562Z - hdl:11858/00-1734-0000-0003-7664-F + hdl:11858/00-1734-0000-0003-EE73-2 - Hoffmann von Fallersleben, August Heinrich - 118552589 + Liliencron, Detlev von + 118572954 - Mailied - August Heinrich Hoffmann von Fallersleben: Unpolitische Lieder von Hoffmann von Fallersleben, 1. + 2. Theil, 1. Theil, Hamburg: Hoffmann und Campe, 1841. + Auf dem Trocknen + Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster & Loeffler, 1909. TextGrid 2012 @@ -38,21 +38,21 @@ Digitale Bibliothek - TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c + TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c - 2012-01-21T13:35:20Z - 2012-01-21T13:35:20Z - 2012-01-21T13:35:20Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z - textgrid:q9cv.0 - http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F + textgrid:rn8z.0 + http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2 - hdl:11858/00-1734-0000-0003-7666-B + hdl:11858/00-1734-0000-0003-EE72-4 527 Bytes @@ -77,17 +77,18 @@ Hamburg + xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin - hdl:11858/00-1734-0000-0003-7664-F + hdl:11858/00-1734-0000-0003-EE73-2 0021 0002 - 2012-01-21 + 2012-01-29 OPEN http://creativecommons.org/licenses/by/3.0/de/legalcode und + DE @@ -95,11 +96,11 @@ xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - + https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai - textgrid:q9cv.0 - 2012-01-21T13:35:20Z - http://schema.datacite.org/oai/oai-1.0/ + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + @@ -107,9 +108,10 @@ false 0.9 - - \ No newline at end of file + + diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala index 705160a2bb..8043236e01 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala @@ -1,15 +1,15 @@ package eu.dnetlib.dhp.export +import com.fasterxml.jackson.databind.ObjectMapper + import java.time.LocalDateTime import java.time.format.DateTimeFormatter - import eu.dnetlib.dhp.common.PacePerson import eu.dnetlib.dhp.schema.action.AtomicAction -import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import eu.dnetlib.dhp.utils.DHPUtils import org.apache.commons.lang3.StringUtils -import org.codehaus.jackson.map.ObjectMapper import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._ import scala.collection.JavaConverters._ diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala index f1e374f954..3f632af226 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala @@ -1,27 +1,21 @@ package eu.dnetlib.dhp.`export` import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import org.apache.commons.io.IOUtils import org.apache.hadoop.io.Text import org.apache.hadoop.io.compress.GzipCodec import org.apache.hadoop.mapred.SequenceFileOutputFormat -import org.apache.spark.rdd.RDD import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql.functions._ import org.apache.spark.sql.expressions.Window -import org.apache.spark.{SparkConf, SparkContext} -import org.codehaus.jackson.map.ObjectMapper +import org.apache.spark.SparkConf import scala.collection.mutable.ArrayBuffer -import scala.collection.JavaConverters._ object SparkExportContentForOpenAire { - - - def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json"))) @@ -178,11 +172,4 @@ object SparkExportContentForOpenAire { fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) } - - - - - - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java index 1b5849f356..7598fd9573 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java @@ -10,7 +10,8 @@ import org.apache.http.client.methods.HttpPut; import org.apache.http.entity.StringEntity; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala index 81bdb29418..8133666a67 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.provision +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.provision.scholix.Scholix import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary @@ -7,7 +8,6 @@ import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SparkSession} -import org.codehaus.jackson.map.ObjectMapper object SparkConvertDatasetToJson { diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 1547056b94..0d44d8e5eb 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -54,6 +54,13 @@ spark-solr + + + junit + junit + 4.12 + test + org.apache.solr solr-test-framework @@ -140,6 +147,12 @@ org.apache.zookeeper zookeeper + + + junit + junit + + diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java new file mode 100644 index 0000000000..7391569ed9 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.provision.utils; + +import java.util.Comparator; +import java.util.Optional; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class AuthorPidTypeComparator implements Comparator { + + @Override + public int compare(StructuredProperty left, StructuredProperty right) { + + String lClass = Optional + .ofNullable(left) + .map(StructuredProperty::getQualifier) + .map(Qualifier::getClassid) + .orElse(null); + + String rClass = Optional + .ofNullable(right) + .map(StructuredProperty::getQualifier) + .map(Qualifier::getClassid) + .orElse(null); + + if (lClass == null && rClass == null) + return 0; + if (lClass == null) + return 1; + if (rClass == null) + return -1; + + if (lClass.equals(rClass)) + return 0; + + if (lClass.equals(ModelConstants.ORCID)) + return -1; + if (rClass.equals(ModelConstants.ORCID)) + return 1; + + if (lClass.equals(ModelConstants.ORCID_PENDING)) + return -1; + if (rClass.equals(ModelConstants.ORCID_PENDING)) + return 1; + + return 0; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index eba7362287..9f16e99d8a 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -254,6 +254,18 @@ public class XmlRecordFactory implements Serializable { p -> p, (p1, p2) -> p1)) .values() + .stream() + .collect( + Collectors + .groupingBy( + p -> p.getValue(), + Collectors + .mapping( + p -> p, + Collectors.minBy(new AuthorPidTypeComparator())))) + .values() + .stream() + .map(op -> op.get()) .forEach( sp -> { String pidType = getAuthorPidType(sp.getQualifier().getClassid()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java index 33def91b39..f57b8dcafd 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java @@ -6,15 +6,13 @@ import org.apache.solr.client.solrj.response.UpdateResponse; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; -import junit.framework.Assert; - public class SolrAdminApplicationTest extends SolrTest { @Test public void testPing() throws Exception { SolrPingResponse pingResponse = miniCluster.getSolrClient().ping(); log.info("pingResponse: '{}'", pingResponse.getStatus()); - Assert.assertTrue(pingResponse.getStatus() == 0); + Assertions.assertTrue(pingResponse.getStatus() == 0); } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 992ab26e81..8ae8a55c39 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -14,33 +14,33 @@ import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Publication; -//TODO to enable it we need to update the joined_entity.json test file -@Disabled public class XmlRecordFactoryTest { private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; + private static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + @Test public void testXMLRecordFactory() throws IOException, DocumentException { - String json = IOUtils.toString(getClass().getResourceAsStream("joined_entity.json")); - - assertNotNull(json); - JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class); - assertNotNull(je); - ContextMapper contextMapper = new ContextMapper(); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, otherDsTypeId); - String xml = xmlRecordFactory.build(je); + Publication p = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); + + String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); assertNotNull(xml); @@ -48,6 +48,14 @@ public class XmlRecordFactoryTest { assertNotNull(doc); + System.out.println(doc.asXML()); + + Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid")); + Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending")); + + Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid")); + Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending")); + // TODO add assertions based of values extracted from the XML record } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json new file mode 100644 index 0000000000..ea7a300513 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -0,0 +1,820 @@ +{ + "author": [ + { + "affiliation": [], + "fullname": "Lee, Jaehyun", + "name": "Jaehyun", + "pid": [ + { + "qualifier": { + "classid": "orcid", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6638" + }, + { + "qualifier": { + "classid": "orcid_pending", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" + } + ], + "rank": 1, + "surname": "Lee" + }, + { + "affiliation": [], + "fullname": "Berrada, Salim", + "name": "Salim", + "pid": [ + { + "qualifier": { + "classid": "orcid", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-9956" + }, + { + "qualifier": { + "classid": "orcid_pending", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-9956" + } + ], + "rank": 2, + "surname": "Berrada" + }, + { + "affiliation": [], + "fullname": "Adamu-Lema, Fikru", + "name": "Fikru", + "pid": [], + "rank": 3, + "surname": "Adamu-Lema" + }, + { + "affiliation": [], + "fullname": "Nagy, Nicole", + "name": "Nicole", + "pid": [], + "rank": 4, + "surname": "Nagy" + }, + { + "affiliation": [], + "fullname": "Georgiev, Vihar P.", + "name": "Vihar P.", + "pid": [], + "rank": 5, + "surname": "Georgiev" + }, + { + "affiliation": [], + "fullname": "Sadi, Toufik", + "name": "Toufik", + "pid": [], + "rank": 6, + "surname": "Sadi" + }, + { + "affiliation": [], + "fullname": "Liang, Jie", + "name": "Jie", + "pid": [], + "rank": 7, + "surname": "Liang" + }, + { + "affiliation": [], + "fullname": "Ramos, Raphael", + "name": "Raphael", + "pid": [], + "rank": 8, + "surname": "Ramos" + }, + { + "affiliation": [], + "fullname": "Carrillo-Nunez, Hamilton", + "name": "Hamilton", + "pid": [], + "rank": 9, + "surname": "Carrillo-Nunez" + }, + { + "affiliation": [], + "fullname": "Kalita, Dipankar", + "name": "Dipankar", + "pid": [], + "rank": 10, + "surname": "Kalita" + }, + { + "affiliation": [], + "fullname": "Lilienthal, Katharina", + "name": "Katharina", + "pid": [], + "rank": 11, + "surname": "Lilienthal" + }, + { + "affiliation": [], + "fullname": "Wislicenus, Marcus", + "name": "Marcus", + "pid": [], + "rank": 12, + "surname": "Wislicenus" + }, + { + "affiliation": [], + "fullname": "Pandey, Reeturaj", + "name": "Reeturaj", + "pid": [], + "rank": 13, + "surname": "Pandey" + }, + { + "affiliation": [], + "fullname": "Chen, Bingan", + "name": "Bingan", + "pid": [], + "rank": 14, + "surname": "Chen" + }, + { + "affiliation": [], + "fullname": "Teo, Kenneth B.K.", + "name": "Kenneth B. 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+ "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Contacts" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Cu-carbon nanotubes (CNT) composites" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "density functional theory (DFT)" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Discrete Fourier transforms" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Electromigration" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "electromigration (EM)" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "electrothermal" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "interconnects" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Lattices" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "multiscale simulation" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Resistance" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "self-heating." + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "Thermal conductivity" + } + ], + "title": [ + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "value": "Understanding Electromigration in Cu-CNT Composite Interconnects A Multiscale Electrothermal Simulation Study" + } + ] +} \ 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/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index dcd034166f..ceaa47794c 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 @@ -259,7 +259,7 @@ ${hive_jdbc_url} - + stats_db_name=${stats_db_name} stats_db_shadow_name=${stats_db_shadow_name} @@ -287,8 +287,8 @@ ${nameNode} impala-shell.sh ${stats_db_shadow_name} - computeProductionStats.sql - ${wf:appPath()}/scripts/computeProductionStats.sql + step19.sql + ${wf:appPath()}/scripts/step19.sql impala-shell.sh diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml new file mode 100644 index 0000000000..a78f92d410 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -0,0 +1,91 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.4-SNAPSHOT + + 4.0.0 + dhp-usage-raw-data-update + + + + pl.project13.maven + git-commit-id-plugin + 2.1.15 + + + + revision + + + + + ${project.basedir}/../.git + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.6.1 + + 1.8 + 1.8 + + + + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + dhp-usage-raw-data-update + diff --git a/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh b/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh new file mode 100755 index 0000000000..4465dae217 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh @@ -0,0 +1 @@ +mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/usagerawdata \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java new file mode 100644 index 0000000000..5b2e6804b9 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java @@ -0,0 +1,125 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageStatsDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getUsageStatsDBSchema() { + return ConnectDB.usageStatsDBSchema; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + return cpds.getConnection(); + + } + +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java new file mode 100644 index 0000000000..e0e0d3687a --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java @@ -0,0 +1,211 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + + static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; + static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; + static String lareferenciaBaseURL; + static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + + static boolean piwikEmptyDirs; + static boolean downloadPiwikLogs; + static boolean processPiwikLogs; + + static Calendar startingLogPeriod; + static Calendar endingLogPeriod; + static int numberOfPiwikIdsToDownload; + static int numberOfSiteIdsToDownload; + + static boolean laReferenciaEmptyDirs; + static boolean downloadLaReferenciaLogs; + static boolean processLaReferenciaLogs; + + static boolean irusCreateTablesEmptyDirs; + static boolean irusDownloadReports; + static boolean irusProcessStats; + static int irusNumberOfOpendoarsToDownload; + + static boolean sarcCreateTablesEmptyDirs; + static boolean sarcDownloadReports; + static boolean sarcProcessStats; + static int sarcNumberOfIssnToDownload; + + static boolean finalizeStats; + + static int numberOfDownloadThreads; + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters + matomoAuthToken = parser.get("matomoAuthToken"); + matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); + irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); + lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); + lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { + recreateDbAndTables = true; + } else { + recreateDbAndTables = false; + } + + if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) { + piwikEmptyDirs = true; + } else { + piwikEmptyDirs = false; + } + + if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) { + downloadPiwikLogs = true; + } else { + downloadPiwikLogs = false; + } + + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { + processPiwikLogs = true; + } else { + processPiwikLogs = false; + } + + String startingLogPeriodStr = parser.get("startingLogPeriod"); + Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); + startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); + +// String endingLogPeriodStr = parser.get("endingLogPeriod"); +// Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); +// endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + + numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); + numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); + + if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) { + laReferenciaEmptyDirs = true; + } else { + laReferenciaEmptyDirs = false; + } + + if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) { + downloadLaReferenciaLogs = true; + } else { + downloadLaReferenciaLogs = false; + } + + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { + processLaReferenciaLogs = true; + } else { + processLaReferenciaLogs = false; + } + + if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) { + irusCreateTablesEmptyDirs = true; + } else { + irusCreateTablesEmptyDirs = false; + } + + if (parser.get("irusDownloadReports").toLowerCase().equals("true")) { + irusDownloadReports = true; + } else { + irusDownloadReports = false; + } + + if (parser.get("irusProcessStats").toLowerCase().equals("true")) { + irusProcessStats = true; + } else { + irusProcessStats = false; + } + irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); + + if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) { + sarcCreateTablesEmptyDirs = true; + } else { + sarcCreateTablesEmptyDirs = false; + } + + if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) { + sarcDownloadReports = true; + } else { + sarcDownloadReports = false; + } + + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { + sarcProcessStats = true; + } else { + sarcProcessStats = false; + } + sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); + + if (parser.get("finalizeStats").toLowerCase().equals("true")) { + finalizeStats = true; + } else { + finalizeStats = false; + } + + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + // usagestatsExport.createdDBWithTablesOnly(); + } + + private static Calendar startingLogPeriodStr(Date date) { + + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; + + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java new file mode 100644 index 0000000000..7ec5b0fca2 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java @@ -0,0 +1,358 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class IrusStats { + + private String irusUKURL; + + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + + public IrusStats(String irusUKURL) throws Exception { + this.irusUKURL = irusUKURL; + // The following may not be needed - It will be created when JSON tables are created +// createTmpTables(); + } + + public void reCreateLogDirs() throws Exception { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); + + logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); + } + + public void createTables() throws Exception { + try { + logger.info("Creating sushilog"); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sushilogtmp_json table"); + String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sushilogtmp_json"; + stmt.executeUpdate(dropSushilogtmpJson); + logger.info("Dropped sushilogtmp_json table"); + + logger.info("Creating irus_sushilogtmp_json table"); + String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " Type: STRING,\n" + + " Value: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` ARRAY<\n" + + " struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(createSushilogtmpJson); + logger.info("Created irus_sushilogtmp_json table"); + + logger.info("Dropping irus_sushilogtmp table"); + String dropSushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(dropSushilogtmp); + logger.info("Dropped irus_sushilogtmp table"); + + logger.info("Creating irus_sushilogtmp table"); + String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(createSushilogtmp); + logger.info("Created irus_sushilogtmp table"); + + logger.info("Inserting to irus_sushilogtmp table"); + String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + + "WHERE `ItemIdent`.`Type`= 'OAI'"; + stmt.executeUpdate(insertSushilogtmp); + logger.info("Inserted to irus_sushilogtmp table"); + + logger.info("Inserting to sushilog table"); + String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(insertToShushilog); + logger.info("Inserted to sushilog table"); + + ConnectDB.getHiveConnection().close(); + } + + public void getIrusRRReport(String irusUKReportPath) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + + logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); + + String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; + + logger.info("(getIrusRRReport) Getting report: " + reportUrl); + + String text = getJson(reportUrl, "", ""); + + List opendoarsToVisit = new ArrayList(); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray != null) { + int i = 0; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); + for (Object identifier : itemIdentifier) { + JSONObject opendoar = (JSONObject) identifier; + if (opendoar.get("Type").toString().equals("OpenDOAR")) { + i++; + opendoarsToVisit.add(opendoar.get("Value").toString()); + break; + } + } + // break; + } + + logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); + + if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 + && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + } + + logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); + + for (String opendoar : opendoarsToVisit) { + logger.info("Now working on openDoar: " + opendoar); + this.getIrusIRReport(opendoar, irusUKReportPath); + } + logger.info("(getIrusRRReport) Finished with report: " + reportUrl); + } else { + logger.info("IRUS Reports not found for day"); + } + + } + + private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { + + logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); + + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, "opendoar____::" + opendoar); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + int batch_size = 0; + + if (dateMax != null && end.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); + } else { + start.add(Calendar.MONTH, 1); + while (start.before(end)) { + logger.info("Downloading for date: " + simpleDateFormat.format(start.getTime())); + String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) + + "&RepositoryIdentifier=opendoar%3A" + opendoar + + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; + start.add(Calendar.MONTH, 1); + + logger.info("Downloading file: " + reportUrl); + String text = getJson(reportUrl, "", ""); + if (text == null) { + continue; + } + + FileSystem fs = FileSystem.get(new Configuration()); + String filePath = irusUKReportPath + "/" + "IrusIRReport_" + + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePath); + FSDataOutputStream fin = fs.create(new Path(filePath), true); + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray == null) { + continue; + } + String oai = ""; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + fin.write(jsonObjectRow.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + fin.close(); + } + + } + // ConnectDB.getHiveConnection().close(); + + logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); + } + + private String getJson(String url) throws Exception { + try { + System.out.println("===> Connecting to: " + url); + URL website = new URL(url); + System.out.println("Connection url -----> " + url); + URLConnection connection = website.openConnection(); + + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + System.out.println("response ====> " + response.toString()); + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + private String getJson(String url, String username, String password) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL", e); + return null; + } + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java new file mode 100644 index 0000000000..904290af8d --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java @@ -0,0 +1,273 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); + + public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + this.createTables(); +// this.createTmpTables(); + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); +// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialog " +// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," +// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " +// + "FROM lareferencialog " +// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; +// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); +// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + +// private void createTmpTables() throws Exception { +// +// try { +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; +// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialogtmp " +// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," +// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " +// + "FROM lareferencialogtmp " +// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); +// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); +// +// stmt.close(); +// log.info("Lareferencia Tmp Tables Created"); +// +// } catch (Exception e) { +// log.error("Failed to create tmptables: " + e); +// throw new Exception("Failed to create tmp tables: " + e.toString(), e); +// // System.exit(0); +// } +// } + private String getPiwikLogUrl() { + return piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { + + String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; + String content = ""; + + List siteIdsToVisit = new ArrayList(); + + // Getting all the siteIds in a list for logging reasons & limiting the list + // to the max number of siteIds + content = getJson(baseApiUrl); + JSONParser parser = new JSONParser(); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); + } + logger.info("Found the following siteIds for download: " + siteIdsToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); + + for (int siteId : siteIdsToVisit) { + logger.info("Now working on LaReferencia MatomoId: " + siteId); + this.GetLaReFerenciaLogs(repoLogsPath, siteId); + } + } + + public void GetLaReFerenciaLogs(String repoLogsPath, + int laReferencialMatomoID) throws Exception { + + logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog WHERE matomoid=?"); + st.setInt(1, laReferencialMatomoID); + Date dateMax = null; + + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + Date date = currDay.getTime(); + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger + .info( + "Date found in logs " + dateMax + " and not downloanding Matomo logs for " + + laReferencialMatomoID); + } else { + logger + .info( + "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " + + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + outFolder = repoLogsPath; + + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path( + outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), + true); + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + int i = 0; + + JSONParser parser = new JSONParser(); + do { + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + fin.write(jsonObjectRaw.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + logger + .info( + "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID + + " and for " + + sdf.format(date)); + i++; + } while (true); + fin.close(); + } + } + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java new file mode 100644 index 0000000000..bcf1711cb3 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java @@ -0,0 +1,291 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaStats { + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); + + private String logRepoPath; + + private Statement stmt = null; + + private String CounterRobotsURL; + private ArrayList robotsList; + + public LaReferenciaStats(String logRepoPath) throws Exception { + this.logRepoPath = logRepoPath; + this.createTables(); +// this.createTmpTables(); + } + + /* + * private void connectDB() throws Exception { try { ConnectDB connectDB = new ConnectDB(); } catch (Exception e) { + * log.error("Connect to db failed: " + e); throw new Exception("Failed to connect to db: " + e.toString(), e); } } + */ + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + + public void processLogs() throws Exception { + try { + logger.info("Processing LaReferencia repository logs"); + processlaReferenciaLog(); + logger.info("LaReferencia repository logs process done"); + + logger.info("LaReferencia removing double clicks"); + removeDoubleClicks(); + logger.info("LaReferencia removed double clicks"); + + logger.info("LaReferencia updating Production Tables"); + updateProdTables(); + logger.info("LaReferencia updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processlaReferenciaLog() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping lareferencialogtmp_json table"); + String drop_lareferencialogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json"; + stmt.executeUpdate(drop_lareferencialogtmp_json); + logger.info("Dropped lareferencialogtmp_json table"); + + logger.info("Creating lareferencialogtmp_json"); + String create_lareferencialogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `repItem` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " timestamp: STRING,\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >,\n" + + " `2`: struct<\n" + + " `customVariablePageValue2`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + " >" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.lareferenciaLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_lareferencialogtmp_json); + logger.info("Created lareferencialogtmp_json"); + + logger.info("Dropping lareferencialogtmp table"); + String drop_lareferencialogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp"; + stmt.executeUpdate(drop_lareferencialogtmp); + logger.info("Dropped lareferencialogtmp table"); + + logger.info("Creating lareferencialogtmp"); + String create_lareferencialogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_lareferencialogtmp); + logger.info("Created lareferencialogtmp"); + + logger.info("Inserting into lareferencialogtmp"); + String insert_lareferencialogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp " + + "SELECT DISTINCT cast(idSite as INT) as matomoid, CONCAT('opendoar____::', " + + "actiondetail.customVariables.`2`.customVariablePageValue2) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_lareferencialogtmp); + logger.info("Inserted into lareferencialogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp WHERE EXISTS (" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p2 " + + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id " + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp " + + "AND p1.timestamp listHdfsDir(String dir) throws Exception { + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + // log.info("Found hdfs file " + fileName); + fileNames.add(fileName); + } + // hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logRepoPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logRepoPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java new file mode 100644 index 0000000000..a84d6743f6 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java @@ -0,0 +1,331 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.Authenticator; +import java.net.URL; +import java.net.URLConnection; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + + private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); + + public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + + } + + private String getPiwikLogUrl() { + return "https://" + piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + logger.debug("Connecting to download the JSON: " + url); + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + url + " Exception: " + e); + throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); + } + } + + class WorkerThread implements Runnable { + + private Calendar currDay; + private int siteId; + private String repoLogsPath; + private String portalLogPath; + private String portalMatomoID; + + public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws IOException { + this.currDay = (Calendar) currDay.clone(); + this.siteId = new Integer(siteId); + this.repoLogsPath = new String(repoLogsPath); + this.portalLogPath = new String(portalLogPath); + this.portalMatomoID = new String(portalMatomoID); + } + + public void run() { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + System.out + .println( + Thread.currentThread().getName() + " (Start) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + try { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out + .println( + Thread.currentThread().getName() + " (End) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } + } + + public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { + + Statement statement = ConnectDB.getHiveConnection().createStatement(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + ResultSet rs = statement + .executeQuery( + "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() + + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + + // Getting all the piwikids in a list for logging reasons & limitting the list + // to the max number of piwikids + List piwikIdToVisit = new ArrayList(); + while (rs.next()) { + piwikIdToVisit.add(rs.getInt(1)); + } + logger.info("Found the following piwikIds for download: " + piwikIdToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { + logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + + // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + // Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + // end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + logger.info("Now working on piwikId: " + siteId); + + PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog WHERE source=?"); + st.setInt(1, siteId); + Date dateMax = null; + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); + + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + // logger.info("Date used " + currDay.toString()); + // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // executor.execute(worker);// calling execute method of ExecutorService + logger.info("Date used " + currDay.getTime().toString()); + + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); + } else { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } + + } + } + // executor.shutdown(); + // while (!executor.isTerminated()) { + // } + // System.out.println("Finished all threads"); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java new file mode 100644 index 0000000000..9144620b75 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java @@ -0,0 +1,835 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.*; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikStatsDB { + + private String logPath; + private String logRepoPath; + private String logPortalPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + private String CounterRobotsURL; + private ArrayList robotsList; + + public PiwikStatsDB(String logRepoPath, String logPortalPath) throws Exception { + this.logRepoPath = logRepoPath; + this.logPortalPath = logPortalPath; + + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + } + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + this.createTables(); + // The piwiklog table is not needed since it is built + // on top of JSON files + //////////// this.createTmpTables(); + } + + public ArrayList getRobotsList() { + return robotsList; + } + + public void setRobotsList(ArrayList robotsList) { + this.robotsList = robotsList; + } + + public String getCounterRobotsURL() { + return CounterRobotsURL; + } + + public void setCounterRobotsURL(String CounterRobotsURL) { + this.CounterRobotsURL = CounterRobotsURL; + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Piwiklog table - This table should exist + String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) " + + "into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePiwikLog); + +// String dropT = "TRUNCATE TABLE " +// + ConnectDB.getUsageStatsDBSchema() +// + ".piwiklog "; +// stmt.executeUpdate(dropT); +// logger.info("truncated piwiklog"); + + ///////////////////////////////////////// + // Rule for duplicate inserts @ piwiklog + ///////////////////////////////////////// + String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log + ////////////////////////////////////////////////// + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void processLogs() throws Exception { + try { + ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); + this.robotsList = counterRobots.getRobotsPatterns(); + + logger.info("Processing repository logs"); + processRepositoryLog(); + logger.info("Repository logs process done"); + + logger.info("Removing double clicks"); + removeDoubleClicks(); + logger.info("Removing double clicks done"); + + logger.info("Cleaning oai"); + cleanOAI(); + logger.info("Cleaning oai done"); + + logger.info("Processing portal logs"); + processPortalLog(); + logger.info("Portal logs process done"); + + logger.info("Processing portal usagestats"); + portalLogs(); + logger.info("Portal usagestats process done"); + + logger.info("Updating Production Tables"); + updateProdTables(); + logger.info("Updated Production Tables"); + + logger.info("Create Pedocs Tables"); + createPedocsOldUsageData(); + logger.info("Pedocs Tables Created"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processRepositoryLog() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping piwiklogtmp_json table"); + String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json"; + stmt.executeUpdate(drop_piwiklogtmp_json); + logger.info("Dropped piwiklogtmp_json table"); + + logger.info("Creating piwiklogtmp_json"); + String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >\n" + + " >,\n" + + " timestamp: String\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_piwiklogtmp_json); + logger.info("Created piwiklogtmp_json"); + + logger.info("Dropping piwiklogtmp table"); + String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp"; + stmt.executeUpdate(drop_piwiklogtmp); + logger.info("Dropped piwiklogtmp"); + + logger.info("Creating piwiklogtmp"); + String create_piwiklogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_piwiklogtmp); + logger.info("Created piwiklogtmp"); + + logger.info("Inserting into piwiklogtmp"); + String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent\n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_piwiklogtmp); + logger.info("Inserted into piwiklogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "WHERE EXISTS (\n" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + + "AND p1.timestamp\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_process_portal_log_tmp_json); + logger.info("Created process_portal_log_tmp_json"); + + logger.info("Droping process_portal_log_tmp table"); + String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp"; + stmt.executeUpdate(drop_process_portal_log_tmp); + logger.info("Dropped process_portal_log_tmp"); + + logger.info("Creating process_portal_log_tmp"); + String create_process_portal_log_tmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_process_portal_log_tmp); + logger.info("Created process_portal_log_tmp"); + + logger.info("Inserting into process_portal_log_tmp"); + String insert_process_portal_log_tmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " + + "actiondetail.url as url, " + + "CASE\n" + + " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + + " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " + + " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + + " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + + " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + + " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + + " ELSE '' " + + "END AS entity_id, " + + "CASE " + + " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + + " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + + " ELSE '' " + + "END AS source_item_type, " + + "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + + "browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_process_portal_log_tmp); + logger.info("Inserted into process_portal_log_tmp"); + + stmt.close(); + } + + public void portalLogs() throws SQLException { + Connection con = ConnectDB.getHiveConnection(); + Statement stmt = con.createStatement(); + con.setAutoCommit(false); + + logger.info("PortalStats - Step 1"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".result_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("PortalStats - Step 2"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".datasource_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + /* + * logger.info("PortalStats - Step 3"); stmt = con.createStatement(); sql = "INSERT INTO " + + * ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + * "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'organization', `timestamp`, referrer_name, agent " + * + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + * "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + * "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + * ".organization_oids roid WHERE roid.id IS NOT NULL)"; // stmt.executeUpdate(sql); stmt.close(); + */ + logger.info("PortalStats - Step 3"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".project_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + con.close(); + } + + private void cleanOAI() throws Exception { + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning oai - Step 1"); + stmt = ConnectDB.getHiveConnection().createStatement(); + String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + + "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 2"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + + "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 3"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + + "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 4"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + + "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 5"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + + "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 6"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + + "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 7"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + + "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 8"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + + "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 9"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + + "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 10"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + + "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 11"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + + "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 12"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + + "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 13"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + + "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 14"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + + "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 15"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + + "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 16"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + + "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 17"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + + "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 18"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + + "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 19"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + + "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 20"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + + "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 21"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + + "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 22"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + + "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 23"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + + "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 24"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + + "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 25"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + + "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 26"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + + "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 27"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + + "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 28"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + + "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 29"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + + "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Done, closing connection"); + ConnectDB.getHiveConnection().close(); + } + + private void updateProdTables() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Inserting data to piwiklog"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping piwiklogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp"); + + logger.info("Dropping process_portal_log_tmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } + + public void finalizeStats() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping piwiklogtmp"); + String sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp"); + + logger.info("Dropping process_portal_log_tmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp"); + + logger.info("Dropping irus_sushilogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped irus_sushilogtmp"); + + logger.info("Dropping irus_sushilogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped irus_sushilogtmp_json"); + + logger.info("Dropping lareferencialogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped lareferencialogtmp_json"); + + logger.info("Dropping piwiklogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp_json"); + + logger.info("Dropping process_portal_log_tmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp_json"); + + logger.info("Dropping sarc_sushilogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp"); + + logger.info("Dropping sarc_sushilogtmp_json_array"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp_json_array"); + + logger.info("Dropping sarc_sushilogtmp_json_non_array"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp_json_non_array"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } + + private ArrayList listHdfsDir(String dir) throws Exception { + + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + fileNames.add(fileName); + } + + hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } + + public void createPedocsOldUsageData() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating PeDocs Old Views Table"); + String sql = "Create TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pedocsoldviews as select * from default.pedocsviews"; + stmt.executeUpdate(sql); + logger.info("PeDocs Old Views Table created"); + + logger.info("Creating PeDocs Old Downloads Table"); + sql = "Create TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pedocsolddownloads as select * from default.pedocsdownloads"; + stmt.executeUpdate(sql); + logger.info("PeDocs Old Downloads Table created"); + + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java new file mode 100644 index 0000000000..6f020daa08 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java @@ -0,0 +1,54 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.nio.charset.Charset; +import java.util.ArrayList; + +import org.json.JSONException; +import org.json.simple.JSONArray; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + +public class ReadCounterRobotsList { + + private ArrayList robotsPatterns = new ArrayList(); + private String COUNTER_ROBOTS_URL; + + public ReadCounterRobotsList(String url) throws IOException, JSONException, ParseException { + COUNTER_ROBOTS_URL = url; + robotsPatterns = readRobotsPartners(COUNTER_ROBOTS_URL); + } + + private ArrayList readRobotsPartners(String url) throws MalformedURLException, IOException, ParseException { + InputStream is = new URL(url).openStream(); + JSONParser parser = new JSONParser(); + BufferedReader reader = new BufferedReader(new InputStreamReader(is, Charset.forName("ISO-8859-1"))); + JSONArray jsonArray = (JSONArray) parser.parse(reader); + for (Object aJsonArray : jsonArray) { + org.json.simple.JSONObject jsonObjectRow = (org.json.simple.JSONObject) aJsonArray; + robotsPatterns.add(jsonObjectRow.get("pattern").toString().replace("\\", "\\\\")); + } + return robotsPatterns; + } + + public ArrayList getRobotsPatterns() { + return robotsPatterns; + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java new file mode 100644 index 0000000000..e85c972f54 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java @@ -0,0 +1,500 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +// import java.io.BufferedReader; +// import java.io.InputStreamReader; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class SarcStats { + + private Statement stmtHive = null; + private Statement stmtImpala = null; + + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + + public SarcStats() throws Exception { +// createTables(); + } + + private void createTables() throws Exception { + try { + + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); + + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void reCreateLogDirs() throws IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); + + logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); + + logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); + + logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); + } + + public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sarc_sushilogtmp_json_array table"); + String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); + logger.info("Dropped sarc_sushilogtmp_json_array table"); + + logger.info("Creating sarc_sushilogtmp_json_array table"); + String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_array); + logger.info("Created sarc_sushilogtmp_json_array table"); + + logger.info("Dropping sarc_sushilogtmp_json_non_array table"); + String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); + logger.info("Dropped sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp_json_non_array table"); + String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + + " `ItemIdentifier` struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathNonArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); + logger.info("Created sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp table"); + String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(create_sarc_sushilogtmp); + logger.info("Created sarc_sushilogtmp table"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "WHERE `ItemIdent`.`Type`='DOI'"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + + ConnectDB.getHiveConnection().close(); + } + + public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + logger.info("Dropping sarc_sushilogtmp table"); + String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp"; + stmt.executeUpdate(drop_sarc_sushilogtmp); + logger.info("Dropped sarc_sushilogtmp table"); + ConnectDB.getHiveConnection().close(); + + List issnAndUrls = new ArrayList(); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" + }); + issnAndUrls.add(new String[] { + "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" + }); + + if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 + && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); + issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); + } + + logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); + + for (String[] issnAndUrl : issnAndUrls) { + logger.info("Now working on ISSN: " + issnAndUrl[1]); + getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); + } + + } + + public void updateSarcLogs() throws Exception { + stmtHive = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + stmtImpala = ConnectDB.getImpalaConnection().createStatement(); + + // Insert into sushilog + logger.info("Inserting into sushilog"); + String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(insertSushiLog); + logger.info("Inserted into sushilog"); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + } + + public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, + String url, String issn) throws Exception { + logger.info("Processing SARC! issn: " + issn + " with url: " + url); + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + + logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, issn); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + // Creating the needed configuration for the correct storing of data + Configuration config = new Configuration(); + config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); + config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); + config + .set( + "fs.hdfs.impl", + org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + config + .set( + "fs.file.impl", + org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem dfs = FileSystem.get(config); + + if (dateMax != null && end.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); + } else { + start.add(Calendar.MONTH, 1); + while (start.before(end)) { + String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); + start.add(Calendar.MONTH, 1); + + logger.info("(getARReport) Getting report: " + reportUrl); + String text = getJson(reportUrl); + if (text == null) { + continue; + } + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = null; + try { + jsonObject = (JSONObject) parser.parse(text); + } // if there is a parsing error continue with the next url + catch (ParseException pe) { + continue; + } + + jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("sc:Report"); + if (jsonObject == null) { + continue; + } + jsonObject = (JSONObject) jsonObject.get("c:Report"); + jsonObject = (JSONObject) jsonObject.get("c:Customer"); + Object obj = jsonObject.get("c:ReportItems"); + JSONArray jsonArray = new JSONArray(); + if (obj instanceof JSONObject) { + jsonArray.add(obj); + } else { + jsonArray = (JSONArray) obj; + // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); + } + if (jsonArray == null) { + continue; + } + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathArray); + FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathNonArray); + FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); + + for (Object aJsonArray : jsonArray) { + + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + renameKeysRecursively(":", jsonObjectRow); + + if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { + finNonArray.write(jsonObjectRow.toJSONString().getBytes()); + finNonArray.writeChar('\n'); + } else { + finArray.write(jsonObjectRow.toJSONString().getBytes()); + finArray.writeChar('\n'); + } + } + + finArray.close(); + finNonArray.close(); + + // Check the file size and if it is too big, delete it + File fileArray = new File(filePathArray); + if (fileArray.length() == 0) { + fileArray.delete(); + } + File fileNonArray = new File(filePathNonArray); + if (fileNonArray.length() == 0) { + fileNonArray.delete(); + } + + } + + dfs.close(); + } + // ConnectDB.getHiveConnection().close(); + } + + private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { + for (Object jjval : givenJsonObj) { + if (jjval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jjval); + } else if (jjval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jjval); + } // All other types of vals + else + ; + } + } + + private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { + Set jkeys = new HashSet(givenJsonObj.keySet()); + for (String jkey : jkeys) { + + String[] splitArray = jkey.split(delimiter); + String newJkey = splitArray[splitArray.length - 1]; + + Object jval = givenJsonObj.get(jkey); + givenJsonObj.remove(jkey); + givenJsonObj.put(newJkey, jval); + + if (jval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jval); + } + + if (jval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jval); + } + } + } + + private String getJson(String url) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + + // Logging error and silently continuing + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); +// return null; +// throw new Exception("Failed to get URL: " + e.toString(), e); + } + return ""; + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java new file mode 100644 index 0000000000..07e15605fd --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java @@ -0,0 +1,206 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + private void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) { + piwikstatsdb.recreateDBAndTables(); + logger.info("DB-Tables-TmpTables are created "); + } + + logger.info("Initializing the download logs module"); + PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); + + if (ExecuteWorkflow.piwikEmptyDirs) { + logger.info("Recreating Piwik log directories"); + piwikstatsdb.reCreateLogDirs(); + } + + // Downloading piwik logs (also managing directory creation) + if (ExecuteWorkflow.downloadPiwikLogs) { + logger.info("Downloading piwik logs"); + piwd + .GetOpenAIRELogs( + ExecuteWorkflow.repoLogPath, + ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); + } + logger.info("Downloaded piwik logs"); + + // Create DB tables, insert/update statistics + String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; + piwikstatsdb.setCounterRobotsURL(cRobotsUrl); + + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing logs"); + piwikstatsdb.processLogs(); + } + + logger.info("Creating LaReferencia tables"); + LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, + ExecuteWorkflow.lareferenciaAuthToken); + + if (ExecuteWorkflow.laReferenciaEmptyDirs) { + logger.info("Recreating LaReferencia log directories"); + lrf.reCreateLogDirs(); + } + + if (ExecuteWorkflow.downloadLaReferenciaLogs) { + logger.info("Downloading LaReferencia logs"); + lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); + logger.info("Downloaded LaReferencia logs"); + } + + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } + + IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); + if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { + logger.info("Creating Irus Stats tables"); + irusstats.createTables(); + logger.info("Created Irus Stats tables"); + + logger.info("Re-create log dirs"); + irusstats.reCreateLogDirs(); + logger.info("Re-created log dirs"); + } + + if (ExecuteWorkflow.irusDownloadReports) { + irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); + } + + if (ExecuteWorkflow.irusProcessStats) { + irusstats.processIrusStats(); + logger.info("Irus done"); + } + + SarcStats sarcStats = new SarcStats(); + if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { + sarcStats.reCreateLogDirs(); + } + if (ExecuteWorkflow.sarcDownloadReports) { + sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + } + + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + sarcStats.updateSarcLogs(); + } + logger.info("Sarc done"); + // finalize usagestats + + logger.info("Dropping tmp tables"); + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Dropped tmp tables"); + } + + logger.info("Raw Data Download End"); + } + + public void createdDBWithTablesOnly() throws Exception { + logger.info("Initialising DB properties"); + ConnectDB.init(); + + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + piwikstatsdb.recreateDBAndTables(); + + piwikstatsdb.createPedocsOldUsageData(); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); + + logger.info("Creating sushilog"); + + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); + + logger.info("Updating piwiklog"); + String sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog select * from openaire_prod_usage_raw.piwiklog"; + stmt.executeUpdate(sql); + + logger.info("Updating lareferencialog"); + sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog select * from openaire_prod_usage_raw.lareferencialog"; + stmt.executeUpdate(sql); + + logger.info("Updating sushilog"); + sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog select * from openaire_prod_usage_raw.sushilog"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + + } + +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json new file mode 100644 index 0000000000..1aa5ad6f80 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json @@ -0,0 +1,219 @@ +[ + { + "paramName": "mat", + "paramLongName": "matomoAuthToken", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "mbu", + "paramLongName": "matomoBaseURL", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukbuw", + "paramLongName": "irusUKBaseURL", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lbu", + "paramLongName": "lareferenciaBaseURL", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lat", + "paramLongName": "lareferenciaAuthToken", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "pwed", + "paramLongName": "piwikEmptyDirs", + "paramDescription": "Empty piwik directories?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dpwl", + "paramLongName": "downloadPiwikLogs", + "paramDescription": "download piwik logs?", + "paramRequired": true + }, + { + "paramName": "slp", + "paramLongName": "startingLogPeriod", + "paramDescription": "Starting log period", + "paramRequired": true + }, + { + "paramName": "npidd", + "paramLongName": "numberOfPiwikIdsToDownload", + "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", + "paramRequired": true + }, + { + "paramName": "nsidd", + "paramLongName": "numberOfSiteIdsToDownload", + "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", + "paramRequired": true + }, + { + "paramName": "lerd", + "paramLongName": "laReferenciaEmptyDirs", + "paramDescription": "Empty LaReferencia directories?", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dlrl", + "paramLongName": "downloadLaReferenciaLogs", + "paramDescription": "download La Referencia logs?", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "irusCreateTablesEmptyDirs", + "paramDescription": "Irus section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "irusDownloadReports", + "paramDescription": "Irus section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "irusNumberOfOpendoarsToDownload", + "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "sarcCreateTablesEmptyDirs", + "paramDescription": "Sarc section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "sarcDownloadReports", + "paramDescription": "Sarc section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "sarcNumberOfIssnToDownload", + "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", + "paramRequired": true + }, + + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml new file mode 100644 index 0000000000..b5c8073787 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml new file mode 100644 index 0000000000..022a107abe --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml @@ -0,0 +1,88 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.usagerawdata.export.ExecuteWorkflow + --matomoAuthToken${matomoAuthToken} + --matomoBaseURL${matomoBaseURL} + --repoLogPath${repoLogPath} + --portalLogPath${portalLogPath} + --portalMatomoID${portalMatomoID} + --irusUKBaseURL${irusUKBaseURL} + --irusUKReportPath${irusUKReportPath} + --sarcsReportPathArray${sarcsReportPathArray} + --sarcsReportPathNonArray${sarcsReportPathNonArray} + --lareferenciaLogPath${lareferenciaLogPath} + --lareferenciaBaseURL${lareferenciaBaseURL} + --lareferenciaAuthToken${lareferenciaAuthToken} + --dbHiveUrl${hiveJdbcUrl} + --dbImpalaUrl${impalaJdbcUrl} + --usageStatsDBSchema${usageStatsDBSchema} + --statsDBSchema${statsDBSchema} + --recreateDbAndTables${recreateDbAndTables} + --piwikEmptyDirs${piwikEmptyDirs} + --downloadPiwikLogs${downloadPiwikLogs} + --processPiwikLogs${processPiwikLogs} + --startingLogPeriod${startingLogPeriod} + --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} + --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} + --laReferenciaEmptyDirs${laReferenciaEmptyDirs} + --downloadLaReferenciaLogs${downloadLaReferenciaLogs} + --processLaReferenciaLogs${processLaReferenciaLogs} + --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} + --irusDownloadReports${irusDownloadReports} + --irusProcessStats${irusProcessStats} + --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} + --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} + --sarcDownloadReports${sarcDownloadReports} + --sarcProcessStats${sarcProcessStats} + --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} + --finalizeStats${finalizeStats} + --numberOfDownloadThreads${numberOfDownloadThreads} + + + + + + + + diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml new file mode 100644 index 0000000000..20d2f5b76f --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -0,0 +1,91 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.4-SNAPSHOT + + 4.0.0 + dhp-usage-stats-build + + + + pl.project13.maven + git-commit-id-plugin + 2.1.15 + + + + revision + + + + + ${project.basedir}/../.git + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.6.1 + + 1.8 + 1.8 + + + + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + dhp-usage-stats-build + diff --git a/dhp-workflows/dhp-usage-stats-build/runworkflow.sh b/dhp-workflows/dhp-usage-stats-build/runworkflow.sh new file mode 100755 index 0000000000..191fb24c61 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/runworkflow.sh @@ -0,0 +1 @@ +mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/usagestatsbuild \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java new file mode 100644 index 0000000000..e53709f1a5 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java @@ -0,0 +1,147 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageRawDataDBSchema; + private static String usageStatsDBSchema; + private static String usagestatsPermanentDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + usageRawDataDBSchema = ExecuteWorkflow.usageRawDataDBSchema; + usagestatsPermanentDBSchema = ExecuteWorkflow.usagestatsPermanentDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getUsageRawDataDBSchema() { + return ConnectDB.usageRawDataDBSchema; + } + + public static String getUsageStatsDBSchema() { + String datePattern = "YYYYMMdd"; + DateFormat df = new SimpleDateFormat(datePattern); +// Get the today date using Calendar object. + Date today = Calendar.getInstance().getTime(); + String todayAsString = df.format(today); + + return ConnectDB.usageStatsDBSchema + "_" + todayAsString; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + public static String getUsagestatsPermanentDBSchema() { + return ConnectDB.usagestatsPermanentDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + return cpds.getConnection(); + + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java new file mode 100644 index 0000000000..26e44b1f6f --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java @@ -0,0 +1,153 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + +// static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; +// static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; +// static String lareferenciaBaseURL; +// static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageRawDataDBSchema; + static String usageStatsDBSchema; + static String usagestatsPermanentDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + + static boolean processPiwikLogs; + static boolean processLaReferenciaLogs; + + static boolean irusProcessStats; + + static boolean sarcProcessStats; + + static boolean finalizeStats; + static boolean finalTablesVisibleToImpala; + + static int numberOfDownloadThreads; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters +// matomoAuthToken = parser.get("matomoAuthToken"); +// matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); +// irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); +// lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); +// lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageRawDataDBSchema = parser.get("usageRawDataDBSchema"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + usagestatsPermanentDBSchema = parser.get("usagestatsPermanentDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { + processPiwikLogs = true; + } else { + processPiwikLogs = false; + } + +// String startingLogPeriodStr = parser.get("startingLogPeriod"); +// Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); +// startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); +// +// String endingLogPeriodStr = parser.get("endingLogPeriod"); +// Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); +// endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { + recreateDbAndTables = true; + } else { + recreateDbAndTables = false; + } + + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { + processLaReferenciaLogs = true; + } else { + processLaReferenciaLogs = false; + } + + if (parser.get("irusProcessStats").toLowerCase().equals("true")) { + irusProcessStats = true; + } else { + irusProcessStats = false; + } + + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { + sarcProcessStats = true; + } else { + sarcProcessStats = false; + } + + if (parser.get("finalizeStats").toLowerCase().equals("true")) { + finalizeStats = true; + } else { + finalizeStats = false; + } + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) { + finalTablesVisibleToImpala = true; + } else { + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + } + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } + + private static Calendar startingLogPeriodStr(Date date) { + + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; + + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java new file mode 100644 index 0000000000..4439f848ed --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class IrusStats { + + private String irusUKURL; + + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + + public IrusStats() throws Exception { + } + + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating irus_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".irus_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created irus_downloads_stats_tmp table"); + + logger.info("Inserting into irus_downloads_stats_tmp"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into irus_downloads_stats_tmp"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java new file mode 100644 index 0000000000..0d34ebef38 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java @@ -0,0 +1,145 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaStats { + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); + + private String logRepoPath; + + private Statement stmt = null; + + private String CounterRobotsURL; + private ArrayList robotsList; + + public LaReferenciaStats() throws Exception { + } + + public void processLogs() throws Exception { + try { + logger.info("LaReferencia creating viewsStats"); + viewsStats(); + logger.info("LaReferencia created viewsStats"); + logger.info("LaReferencia creating downloadsStats"); + downloadsStats(); + logger.info("LaReferencia created downloadsStats"); + +// logger.info("LaReferencia updating Production Tables"); +// updateProdTables(); +// logger.info("LaReferencia updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void viewsStats() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating la_result_views_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp AS " + + + "SELECT entity_id AS id, COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + + "THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".lareferencialog where action='action' and " + + "(source_item_type='oaItem' or source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created la_result_views_monthly_tmp view"); + + logger.info("Dropping la_views_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".la_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped la_views_stats_tmp table"); + + logger.info("Creating la_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp " + + "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.oid AND p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month"; + stmt.executeUpdate(sql); + logger.info("Created la_views_stats_tmp table"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + + private void downloadsStats() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating la_result_downloads_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".la_result_downloads_monthly_tmp AS " + + "SELECT entity_id AS id, COUNT(entity_id) as downloads, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + + "THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".lareferencialog where action='download' and " + + "(source_item_type='oaItem' or source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created la_result_downloads_monthly_tmp view"); + + logger.info("Dropping la_downloads_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".la_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped la_downloads_stats_tmp table"); + + logger.info("Creating la_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp " + + "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(downloads) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.oid AND p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month"; + stmt.executeUpdate(sql); + logger.info("Created la_downloads_stats_tmp table"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java new file mode 100644 index 0000000000..253dc03b54 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java @@ -0,0 +1,559 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikStatsDB { + + private String logPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + public PiwikStatsDB() throws Exception { + + } + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + // The piwiklog table is not needed since it is built + // on top of JSON files + //////////// this.createTmpTables(); + } + + private void createDatabase() throws Exception { + +// try { +// +// stmt = ConnectDB.getHiveConnection().createStatement(); +// +// logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); +// String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; +// stmt.executeUpdate(dropDatabase); +// } catch (Exception e) { +// logger.error("Failed to drop database: " + e); +// throw new Exception("Failed to drop database: " + e.toString(), e); +// } +// + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + logger.info("Usagestats DB created: " + ConnectDB.getUsageStatsDBSchema()); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating permanent usagestats DB: " + ConnectDB.getUsagestatsPermanentDBSchema()); + String createPermanentDatabase = "CREATE DATABASE IF NOT EXISTS " + + ConnectDB.getUsagestatsPermanentDBSchema(); + stmt.executeUpdate(createPermanentDatabase); + logger.info("Created permanent usagestats DB: " + ConnectDB.getUsagestatsPermanentDBSchema()); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + public void processLogs() throws Exception { + try { + + logger.info("ViewsStats processing starts at: " + new Timestamp(System.currentTimeMillis())); + viewsStats(); + logger.info("ViewsStats processing ends at: " + new Timestamp(System.currentTimeMillis())); + + logger.info("DownloadsStats processing starts at: " + new Timestamp(System.currentTimeMillis())); + downloadsStats(); + logger.info("DownloadsStats processing ends at: " + new Timestamp(System.currentTimeMillis())); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void viewsStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping openaire_result_views_monthly_tmp view"); + String drop_result_views_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_piwikresult_views_monthly_tmp"; + stmt.executeUpdate(drop_result_views_monthly); + logger.info("Dropped openaire_result_views_monthly_tmp view"); + + logger.info("Creating openaire_result_views_monthly_tmp view"); + String create_result_views_monthly = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_views_monthly_tmp " + + "AS SELECT entity_id, " + + "reflect('java.net.URLDecoder', 'decode', entity_id) AS id," + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) " + + "AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + + ".piwiklog where action='action' and (source_item_type='oaItem' or " + + "source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(create_result_views_monthly); + logger.info("Created openaire_result_views_monthly_tmp table"); + + logger.info("Dropping openaire_views_stats_tmp table"); + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_views_stats_tmp"; + stmt.executeUpdate(drop_views_stats); + logger.info("Dropped openaire_views_stats_tmp table"); + + logger.info("Creating openaire_views_stats_tmp table"); + String create_views_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_views_stats_tmp " + + "AS SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id AND p.id=ro.oid AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(create_views_stats); + logger.info("Created openaire_views_stats_tmp table"); + + logger.info("Creating openaire_pageviews_stats_tmp table"); + String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_pageviews_stats_tmp AS SELECT " + + "'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, max(views) AS count " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=" + ExecuteWorkflow.portalMatomoID + + " AND p.source=d.piwik_id and p.id=ro.id AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(create_pageviews_stats); + logger.info("Created pageviews_stats table"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + + private void downloadsStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping openaire_result_downloads_monthly_tmp view"); + String drop_result_downloads_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_downloads_monthly_tmp"; + stmt.executeUpdate(drop_result_downloads_monthly); + logger.info("Dropped openaire_result_downloads_monthly_tmp view"); + + logger.info("Creating openaire_result_downloads_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_downloads_monthly_tmp " + + "AS SELECT entity_id, " + + "reflect('java.net.URLDecoder', 'decode', entity_id) AS id," + + "COUNT(entity_id) as downloads, " + + "SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog where action='download' " + + "AND (source_item_type='oaItem' OR source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) , source " + + "ORDER BY source, entity_id, month"; + stmt.executeUpdate(sql); + logger.info("Created openaire_result_downloads_monthly_tmp view"); + + logger.info("Dropping openaire_downloads_stats_tmp table"); + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_downloads_stats_tmp"; + stmt.executeUpdate(drop_views_stats); + logger.info("Dropped openaire_downloads_stats_tmp table"); + + logger.info("Creating openaire_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(downloads) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id and p.id=ro.oid AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(sql); + logger.info("Created downloads_stats table"); + + logger.info("Dropping openaire_result_downloads_monthly_tmp view"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp"; + logger.info("Dropped openaire_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + + public void uploadOldPedocs() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + // Dropping Pedocs pedocs_views_stats_tmp table + logger.info("Dropping Pedocs pedocs_views_stats_tmp table"); + String sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp"; + logger.info("Dropped pedocs_views_stats_tmp table "); + stmt.executeUpdate(sql); + + // Dropping Pedocs pedocs_downloads_stats table + logger.info("Dropping pedocs_downloads_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats"; + logger.info("Dropped pedocs_downloads_stats table "); + stmt.executeUpdate(sql); + + // Creating Pedocs pedocs_views_stats_tmp table + logger.info("Creating Pedocs pedocs_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, 'opendoar____::ab1a4d0dd4d48a2ba1077c4494791306' as repository_id," + + "r.id as result_id,date,counter_abstract as count, 0 as openaire " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".pedocsoldviews p, " + ConnectDB.getStatsDBSchema() + + ".result_oids r where r.oid=p.identifier"; + stmt.executeUpdate(sql); + logger.info("Created pedocs_views_stats_tmp table "); + + // Creating Pedocs pedocs_downloads_stats_tmp table + logger.info("Creating Pedocs pedocs_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, 'opendoar____::ab1a4d0dd4d48a2ba1077c4494791306' as repository_id," + + "r.id as result_id, date, counter as count, 0 as openaire " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".pedocsolddownloads p, " + ConnectDB.getStatsDBSchema() + + ".result_oids r where r.oid=p.identifier"; + stmt.executeUpdate(sql); + logger.info("Created pedocs_downloads_stats_tmp table "); + + } + + public void uploadTUDELFTStats() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_views_monthly_tmp view"); + String sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp"; + logger.info("Dropped tudelft_result_views_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp"; + logger.info("Dropped tudelft_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_views_stats_tmp table + logger.info("Dropping TUDELFT tudelft_views_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp"; + logger.info("Dropped tudelft_views_stats_tmp table "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_downloads_stats_tmp table + logger.info("Dropping TUDELFT tudelft_downloads_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp"; + logger.info("Dropped tudelft_downloads_stats_tmp table "); + stmt.executeUpdate(sql); + + // Creating TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Creating TUDELFT tudelft_result_views_monthly_tmp view"); + sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp " + + "AS SELECT entity_id, reflect('java.net.URLDecoder', 'decode', entity_id) AS id, " + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog " + + "WHERE action='action' and (source_item_type='oaItem' or source_item_type='repItem') and source=252 " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created tudelft_result_views_monthly_tmp view "); + + // Creating TUDELFT tudelft_views_stats_tmp table + logger.info("Creating TUDELFT tudelft_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire FROM " + ConnectDB.getUsageStatsDBSchema() + + ".tudelft_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE concat('tud:',p.id)=ro.oid and d.id='opendoar____::c9892a989183de32e976c6f04e700201' " + + "GROUP BY d.id, ro.id, month ORDER BY d.id, ro.id"; + stmt.executeUpdate(sql); + logger.info("Created TUDELFT tudelft_views_stats_tmp table"); + + // Creating TUDELFT tudelft_result_downloads_monthly_tmp view + logger.info("Creating TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp " + + "AS SELECT entity_id, reflect('java.net.URLDecoder', 'decode', entity_id) AS id, " + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog " + + "WHERE action='download' and (source_item_type='oaItem' or source_item_type='repItem') and source=252 " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created tudelft_result_downloads_monthly_tmp view "); + + // Creating TUDELFT tudelft_downloads_stats_tmp table + logger.info("Creating TUDELFT tudelft_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire FROM " + ConnectDB.getUsageStatsDBSchema() + + ".tudelft_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE concat('tud:',p.id)=ro.oid and d.id='opendoar____::c9892a989183de32e976c6f04e700201' " + + "GROUP BY d.id, ro.id, month ORDER BY d.id, ro.id"; + stmt.executeUpdate(sql); + logger.info("Created TUDELFT tudelft_downloads_stats_tmp table"); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_views_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp"; + logger.info("Dropped tudelft_result_views_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp"; + logger.info("Dropped tudelft_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + + } + + public void finalizeStats() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + // Dropping views_stats table + logger.info("Dropping views_stats table"); + String sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + logger.info("Dropped views_stats table "); + stmt.executeUpdate(sql); + + // Dropping downloads_stats table + logger.info("Dropping downloads_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + logger.info("Dropped downloads_stats table "); + stmt.executeUpdate(sql); + + // Dropping page_views_stats table + logger.info("Dropping pageviews_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + logger.info("Dropped pageviews_stats table "); + stmt.executeUpdate(sql); + + // Dropping usage_stats table + logger.info("Dropping usage_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + logger.info("Dropped usage_stats table "); + stmt.executeUpdate(sql); + + // Creating views_stats table + logger.info("Creating views_stats table"); + String createViewsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".views_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(createViewsStats); + logger.info("Created views_stats table"); + + // Inserting OpenAIRE views stats + logger.info("Inserting Openaire data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Openaire views updated to views_stats"); + + // Inserting Pedocs old views stats + logger.info("Inserting Pedocs old data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Pedocs views updated to views_stats"); + + // Inserting TUDELFT views stats + logger.info("Inserting TUDELFT data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("TUDELFT views updated to views_stats"); + + // Inserting Lareferencia views stats + logger.info("Inserting LaReferencia data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("LaReferencia views updated to views_stats"); + + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); + + // Inserting OpenAIRE downloads stats + logger.info("Inserting OpenAIRE data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Inserted OpenAIRE data to downloads_stats"); + + // Inserting Pedocs old downloads stats + logger.info("Inserting PeDocs old data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Inserted Pedocs data to downloads_stats"); + + // Inserting TUDELFT downloads stats + logger.info("Inserting TUDELFT old data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Inserted TUDELFT data to downloads_stats"); + + // Inserting Lareferencia downloads stats + logger.info("Inserting LaReferencia data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Lareferencia downloads updated to downloads_stats"); + + // Inserting IRUS downloads stats + logger.info("Inserting IRUS data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("IRUS downloads updated to downloads_stats"); + + // Inserting SARC-OJS downloads stats + logger.info("Inserting SARC data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("SARC-OJS downloads updated to downloads_stats"); + + logger.info("Creating pageviews_stats table"); + String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pageviews_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(create_pageviews_stats); + logger.info("Created pageviews_stats table"); + + // Inserting OpenAIRE views stats from Portal + logger.info("Inserting data to page_views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping full_dates table"); + String dropFullDates = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".full_dates"; + stmt.executeUpdate(dropFullDates); + logger.info("Dropped full_dates table"); + + Calendar startCalendar = Calendar.getInstance(); + startCalendar.setTime(new SimpleDateFormat("yyyy-MM-dd").parse("2016-01-01")); + Calendar endCalendar = Calendar.getInstance(); + int diffYear = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR); + int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); + + logger.info("Creating full_dates table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".full_dates AS " + + "SELECT from_unixtime(unix_timestamp(cast(add_months(from_date,i) AS DATE)), 'yyyy/MM') AS txn_date " + + "FROM (SELECT DATE '2016-01-01' AS from_date) p " + + "LATERAL VIEW " + + "posexplode(split(space(" + diffMonth + "),' ')) pe AS i,x"; + stmt.executeUpdate(sql); + logger.info("Created full_dates table"); + + logger.info("Inserting data to usage_stats"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats AS " + + "SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(sql); + logger.info("Inserted data to usage_stats"); + + logger.info("Building views at permanent DB starts at: " + new Timestamp(System.currentTimeMillis())); + + logger.info("Dropping view views_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view views_stats on permanent usagestats DB"); + + logger.info("Create view views_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + logger.info("Created view views_stats on permanent usagestats DB"); + + logger.info("Dropping view pageviews_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view pageviews_stats on permanent usagestats DB"); + + logger.info("Create view pageviews_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + logger.info("Created view pageviews_stats on permanent usagestats DB"); + + logger.info("Dropping view downloads_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view on downloads_stats on permanent usagestats DB"); + + logger.info("Create view on downloads_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + logger.info("Created view on downloads_stats on permanent usagestats DB"); + + logger.info("Dropping view usage_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view on usage_stats on permanent usagestats DB"); + + logger.info("Create view on usage_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + logger.info("Created view on usage_stats on permanent usagestats DB"); + + logger.info("Building views at permanent DB ends at: " + new Timestamp(System.currentTimeMillis())); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java new file mode 100644 index 0000000000..880233f00c --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java @@ -0,0 +1,107 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +// import java.io.BufferedReader; +// import java.io.InputStreamReader; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +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.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class SarcStats { + + private Statement stmtHive = null; + private Statement stmtImpala = null; + + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + + public SarcStats() throws Exception { +// createTables(); + } + + private void createTables() throws Exception { + try { + + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); + + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void processSarc() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating sarc_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created sarc_downloads_stats_tmp table"); + + logger.info("Inserting into sarc_downloads_stats_tmp"); + String insertSarcStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " + + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; + stmt.executeUpdate(insertSarcStats); + logger.info("Inserted into sarc_downloads_stats_tmp"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java new file mode 100644 index 0000000000..47986f52aa --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java @@ -0,0 +1,127 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + +// runImpalaQuery(); + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(); + + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) { + piwikstatsdb.recreateDBAndTables(); + logger.info("DB-Tables are created "); + } +// else { +// piwikstatsdb.createTmpTables(); +// logger.info("TmpTables are created "); +// } + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing Piwik logs"); + piwikstatsdb.processLogs(); + logger.info("Piwik logs Done"); + logger.info("Processing Pedocs Old Stats"); + piwikstatsdb.uploadOldPedocs(); + logger.info("Processing Pedocs Old Stats Done"); + logger.info("Processing TUDELFT Stats"); + piwikstatsdb.uploadTUDELFTStats(); + logger.info("Processing TUDELFT Stats Done"); + + } + + LaReferenciaStats lastats = new LaReferenciaStats(); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } + + IrusStats irusstats = new IrusStats(); + + if (ExecuteWorkflow.irusProcessStats) { + logger.info("Processing IRUS"); + irusstats.processIrusStats(); + logger.info("Irus done"); + } + + SarcStats sarcStats = new SarcStats(); + + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(); + } + logger.info("Sarc done"); + + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } + + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } + + logger.info("End"); + } + + private void invalidateMetadata() throws SQLException { + Statement stmt = null; + + stmt = ConnectDB.getImpalaConnection().createStatement(); + + String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json new file mode 100644 index 0000000000..407370ada7 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json @@ -0,0 +1,128 @@ +[ + { + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "urdbs", + "paramLongName": "usageRawDataDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "uspdbs", + "paramLongName": "usagestatsPermanentDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml new file mode 100644 index 0000000000..b5c8073787 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml new file mode 100644 index 0000000000..71e8a50d61 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml @@ -0,0 +1,73 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.usagestatsbuild.export.ExecuteWorkflow + --repoLogPath${repoLogPath} + --portalLogPath${portalLogPath} + --portalMatomoID${portalMatomoID} + --irusUKReportPath${irusUKReportPath} + --sarcsReportPathArray${sarcsReportPathArray} + --sarcsReportPathNonArray${sarcsReportPathNonArray} + --lareferenciaLogPath${lareferenciaLogPath} + --dbHiveUrl${hiveJdbcUrl} + --dbImpalaUrl${impalaJdbcUrl} + --usageRawDataDBSchema${usageRawDataDBSchema} + --usageStatsDBSchema${usageStatsDBSchema} + --usagestatsPermanentDBSchema${usagestatsPermanentDBSchema} + --statsDBSchema${statsDBSchema} + --recreateDbAndTables${recreateDbAndTables} + --processPiwikLogs${processPiwikLogs} + --processLaReferenciaLogs${processLaReferenciaLogs} + --irusProcessStats${irusProcessStats} + --sarcProcessStats${sarcProcessStats} + --finalizeStats${finalizeStats} + --finalTablesVisibleToImpala${finalTablesVisibleToImpala} + --numberOfDownloadThreads${numberOfDownloadThreads} + + + + + + + + diff --git a/pom.xml b/pom.xml index a2e2587b31..3e0626aed2 100644 --- a/pom.xml +++ b/pom.xml @@ -704,7 +704,7 @@ 3.3.3 3.4.2 [2.12,3.0) - 3.1.1 + 3.1.6 7.5.0 4.7.2 1.20