diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java index 2ab23bda6..94e7f5221 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java @@ -63,7 +63,10 @@ public class Vocabulary implements Serializable { } public VocabularyTerm getTermBySynonym(final String syn) { - return getTerm(synonyms.get(syn.toLowerCase())); + return Optional + .ofNullable(syn) + .map(s -> getTerm(synonyms.get(s.toLowerCase()))) + .orElse(null); } public Qualifier getTermAsQualifier(final String termId) { diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index fc7175270..64b6f91af 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -135,6 +135,24 @@ public class VocabularyGroup implements Serializable { return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn); } + public Qualifier lookupTermBySynonym(final String vocId, final String syn) { + return find(vocId) + .map( + vocabulary -> Optional + .ofNullable(vocabulary.getTerm(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse( + Optional + .ofNullable(vocabulary.getTermBySynonym(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse(null))) + .orElse(null); + } + /** * getSynonymAsQualifierCaseSensitive * 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 aea046203..0461c9353 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 @@ -119,6 +119,131 @@ public class AuthorMerger { }); } + public static String normalizeFullName(final String fullname) { + return nfd(fullname) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + + .trim(); + } + + private static String authorFieldToBeCompared(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return author.getSurname(); + + } + if (StringUtils.isNotBlank(author.getFullname())) { + return author.getFullname(); + } + return null; + } + + /** + * This method tries to figure out when two author are the same in the contest + * of ORCID enrichment + * + * @param left Author in the OAF entity + * @param right Author ORCID + * @return based on a heuristic on the names of the authors if they are the same. + */ + public static boolean checkORCIDSimilarity(final Author left, final Author right) { + final Person pl = parse(left); + final Person pr = parse(right); + + // If one of them didn't have a surname we verify if they have the fullName not empty + // and verify if the normalized version is equal + if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && + pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) { + + if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null + && !pr.getFullname().isEmpty()) { + return pl + .getFullname() + .stream() + .anyMatch( + fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr)))); + } else { + return false; + } + } + // The Authors have one surname in common + if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { + + // If one of them has only a surname and is the same we can say that they are the same author + if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) || + (pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank))) + return true; + // The authors have the same initials of Name in common + if (pl + .getName() + .stream() + .anyMatch( + nl -> pr + .getName() + .stream() + .anyMatch(nr -> nr.equalsIgnoreCase(nl)))) + return true; + } + + // Sometimes we noticed that publication have author wrote in inverse order Surname, Name + // We verify if we have an exact match between name and surname + if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) && + pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl)))) + return true; + else + return false; + } + // + + /** + * Method to enrich ORCID information in one list of authors based on another list + * + * @param baseAuthor the Author List in the OAF Entity + * @param orcidAuthor The list of ORCID Author intersected + * @return The Author List of the OAF Entity enriched with the orcid Author + */ + public static List enrichOrcid(List baseAuthor, List orcidAuthor) { + + if (baseAuthor == null || baseAuthor.isEmpty()) + return orcidAuthor; + + if (orcidAuthor == null || orcidAuthor.isEmpty()) + return baseAuthor; + + if (baseAuthor.size() == 1 && orcidAuthor.size() > 10) + return baseAuthor; + + final List oAuthor = new ArrayList<>(); + oAuthor.addAll(orcidAuthor); + + baseAuthor.forEach(ba -> { + Optional aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst(); + if (aMatch.isPresent()) { + final Author sameAuthor = aMatch.get(); + addPid(ba, sameAuthor.getPid()); + oAuthor.remove(sameAuthor); + } + }); + return baseAuthor; + } + + private static void addPid(final Author a, final List pids) { + + if (a.getPid() == null) { + a.setPid(new ArrayList<>()); + } + + a.getPid().addAll(pids); + + } + public static String pidToComparableString(StructuredProperty pid) { final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""; @@ -171,7 +296,7 @@ public class AuthorMerger { } } - private static String normalize(final String s) { + public static String normalize(final String s) { String[] normalized = nfd(s) .toLowerCase() // do not compact the regexes in a single expression, would cause StackOverflowError diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index f5c8eea19..0225a5063 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -21,10 +21,15 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; /** @@ -35,6 +40,12 @@ public class GroupEntitiesSparkJob { private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private ArgumentApplicationParser parser; + + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -51,6 +62,17 @@ public class GroupEntitiesSparkJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { + String graphInputPath = parser.get("graphInputPath"); log.info("graphInputPath: {}", graphInputPath); @@ -60,19 +82,21 @@ public class GroupEntitiesSparkJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible")); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); log.info("filterInvisible: {}", filterInvisible); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + runWithSparkSession( conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); }); } @@ -81,7 +105,7 @@ public class GroupEntitiesSparkJob { String inputPath, String checkpointPath, String outputPath, - boolean filterInvisible) { + boolean filterInvisible, VocabularyGroup vocs) { Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); @@ -106,10 +130,14 @@ public class GroupEntitiesSparkJob { } Dataset groupedEntities = allEntities - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> OafMapperUtils.mergeEntities(b, a)) .map( - (MapFunction, Tuple2>) t -> new Tuple2( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( t._2().getClass().getName(), t._2()), Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index b4402a2fb..0124e96fc 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -1,8 +1,12 @@ package eu.dnetlib.dhp.schema.oaf.utils; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; +import java.net.MalformedURLException; +import java.net.URL; import java.time.LocalDate; import java.time.ZoneId; import java.time.format.DateTimeFormatter; @@ -19,6 +23,7 @@ import com.google.common.collect.Lists; import com.google.common.collect.Sets; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -26,6 +31,10 @@ import me.xuender.unidecode.Unidecode; public class GraphCleaningFunctions extends CleaningFunctions { + public static final String DNET_PUBLISHERS = "dnet:publishers"; + + public static final String DNET_LICENSES = "dnet:licenses"; + 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)"; @@ -36,6 +45,13 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+"; + + private static final Set INVALID_AUTHOR_NAMES = new HashSet<>(); + + private static final Set INVALID_URLS = new HashSet<>(); + + private static final Set INVALID_URL_HOSTS = new HashSet<>(); + private static final HashSet PEER_REVIEWED_TYPES = new HashSet<>(); static { @@ -48,6 +64,47 @@ public class GraphCleaningFunctions extends CleaningFunctions { PEER_REVIEWED_TYPES.add("Thesis"); PEER_REVIEWED_TYPES.add("Bachelor thesis"); PEER_REVIEWED_TYPES.add("Conference object"); + + INVALID_AUTHOR_NAMES.add("(:null)"); + INVALID_AUTHOR_NAMES.add("(:unap)"); + INVALID_AUTHOR_NAMES.add("(:tba)"); + INVALID_AUTHOR_NAMES.add("(:unas)"); + INVALID_AUTHOR_NAMES.add("(:unav)"); + INVALID_AUTHOR_NAMES.add("(:unkn)"); + INVALID_AUTHOR_NAMES.add("(:unkn) unknown"); + INVALID_AUTHOR_NAMES.add(":none"); + INVALID_AUTHOR_NAMES.add(":null"); + INVALID_AUTHOR_NAMES.add(":unas"); + INVALID_AUTHOR_NAMES.add(":unav"); + INVALID_AUTHOR_NAMES.add(":unkn"); + INVALID_AUTHOR_NAMES.add("[autor desconocido]"); + INVALID_AUTHOR_NAMES.add("[s. n.]"); + INVALID_AUTHOR_NAMES.add("[s.n]"); + INVALID_AUTHOR_NAMES.add("[unknown]"); + INVALID_AUTHOR_NAMES.add("anonymous"); + INVALID_AUTHOR_NAMES.add("n.n."); + INVALID_AUTHOR_NAMES.add("nn"); + INVALID_AUTHOR_NAMES.add("no name supplied"); + INVALID_AUTHOR_NAMES.add("none"); + INVALID_AUTHOR_NAMES.add("none available"); + INVALID_AUTHOR_NAMES.add("not available not available"); + INVALID_AUTHOR_NAMES.add("null &na;"); + INVALID_AUTHOR_NAMES.add("null anonymous"); + INVALID_AUTHOR_NAMES.add("unbekannt"); + INVALID_AUTHOR_NAMES.add("unknown"); + + INVALID_URL_HOSTS.add("creativecommons.org"); + INVALID_URL_HOSTS.add("www.academia.edu"); + INVALID_URL_HOSTS.add("academia.edu"); + INVALID_URL_HOSTS.add("researchgate.net"); + INVALID_URL_HOSTS.add("www.researchgate.net"); + + INVALID_URLS.add("http://repo.scoap3.org/api"); + INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:"); + INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf"); + INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf"); + INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/"); + INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten"); } public static T cleanContext(T value, String contextId, String verifyParam) { @@ -357,6 +414,14 @@ public class GraphCleaningFunctions extends CleaningFunctions { .getPublisher() .getValue() .replaceAll(NAME_CLEANING_REGEX, " ")); + + if (vocs.vocabularyExists(DNET_PUBLISHERS)) { + vocs + .find(DNET_PUBLISHERS) + .map(voc -> voc.getTermBySynonym(r.getPublisher().getValue())) + .map(VocabularyTerm::getName) + .ifPresent(publisher -> r.getPublisher().setValue(publisher)); + } } } if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) { @@ -517,6 +582,14 @@ public class GraphCleaningFunctions extends CleaningFunctions { i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS)); } + if (Objects.nonNull(i.getLicense()) && Objects.nonNull(i.getLicense().getValue())) { + vocs + .find(DNET_LICENSES) + .map(voc -> voc.getTermBySynonym(i.getLicense().getValue())) + .map(VocabularyTerm::getId) + .ifPresent(license -> i.getLicense().setValue(license)); + } + // from the script from Dimitris if ("0000".equals(i.getRefereed().getClassid())) { final boolean isFromCrossref = Optional @@ -558,6 +631,15 @@ public class GraphCleaningFunctions extends CleaningFunctions { ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) { i.setFulltext(null); } + if (Objects.nonNull(i.getUrl())) { + i + .setUrl( + i + .getUrl() + .stream() + .filter(GraphCleaningFunctions::urlFilter) + .collect(Collectors.toList())); + } } } if (Objects.isNull(r.getBestaccessright()) @@ -580,8 +662,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .getAuthor() .stream() .filter(Objects::nonNull) - .filter(a -> StringUtils.isNotBlank(a.getFullname())) - .filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", ""))) + .filter(GraphCleaningFunctions::isValidAuthorName) .map(GraphCleaningFunctions::cleanupAuthor) .collect(Collectors.toList())); @@ -608,6 +689,9 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(Objects::nonNull) .filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> StringUtils.isNotBlank(p.getValue())) + .filter( + p -> StringUtils + .contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID)) .map(p -> { // hack to distinguish orcid from orcid_pending String pidProvenance = getProvenance(p.getDataInfo()); @@ -617,7 +701,8 @@ public class GraphCleaningFunctions extends CleaningFunctions { .toLowerCase() .contains(ModelConstants.ORCID)) { if (pidProvenance - .equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { + .equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY) || + pidProvenance.equals("ORCID_ENRICHMENT")) { p.getQualifier().setClassid(ModelConstants.ORCID); } else { p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); @@ -739,12 +824,30 @@ public class GraphCleaningFunctions extends CleaningFunctions { // HELPERS private static boolean isValidAuthorName(Author a) { - return !Stream - .of(a.getFullname(), a.getName(), a.getSurname()) - .filter(s -> s != null && !s.isEmpty()) - .collect(Collectors.joining("")) - .toLowerCase() - .matches(INVALID_AUTHOR_REGEX); + return StringUtils.isNotBlank(a.getFullname()) && + StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) && + !INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) && + !Stream + .of(a.getFullname(), a.getName(), a.getSurname()) + .filter(StringUtils::isNotBlank) + .collect(Collectors.joining("")) + .toLowerCase() + .matches(INVALID_AUTHOR_REGEX); + } + + private static boolean urlFilter(String u) { + try { + final URL url = new URL(u); + if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) { + return false; + } + if (INVALID_URL_HOSTS.contains(url.getHost())) { + return false; + } + return !INVALID_URLS.contains(url.toString()); + } catch (MalformedURLException ex) { + return false; + } } private static List processPidCleaning(List pids) { @@ -794,4 +897,105 @@ public class GraphCleaningFunctions extends CleaningFunctions { return s; } + public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) { + + if (entity instanceof Result) { + final Result result = (Result) entity; + + Optional + .ofNullable(result.getInstance()) + .ifPresent( + instances -> instances + .forEach( + instance -> { + if (Objects.isNull(instance.getInstanceTypeMapping())) { + List mapping = Lists.newArrayList(); + mapping + .add( + OafMapperUtils + .instanceTypeMapping( + instance.getInstancetype().getClassname(), + OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + instance.setInstanceTypeMapping(mapping); + } + Optional optionalItm = instance + .getInstanceTypeMapping() + .stream() + .filter(GraphCleaningFunctions::originalResourceType) + .findFirst(); + if (optionalItm.isPresent()) { + InstanceTypeMapping coarItm = optionalItm.get(); + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType())) + .ifPresent(type -> { + coarItm.setTypeCode(type.getClassid()); + coarItm.setTypeLabel(type.getClassname()); + }); + final List mappings = Lists.newArrayList(); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode())) + .ifPresent( + type -> mappings + .add( + OafMapperUtils + .instanceTypeMapping(coarItm.getTypeCode(), type))); + } + if (!mappings.isEmpty()) { + instance.getInstanceTypeMapping().addAll(mappings); + } + } + })); + result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs)); + } + + return entity; + } + + private static boolean originalResourceType(InstanceTypeMapping itm) { + return StringUtils.isNotBlank(itm.getOriginalType()) && + OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) && + StringUtils.isBlank(itm.getTypeCode()) && + StringUtils.isBlank(itm.getTypeLabel()); + } + + private static Qualifier getMetaResourceType(final List instances, final VocabularyGroup vocs) { + return Optional + .ofNullable(instances) + .map(ii -> { + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional itm = ii + .stream() + .filter(Objects::nonNull) + .flatMap( + i -> Optional + .ofNullable(i.getInstanceTypeMapping()) + .map(Collection::stream) + .orElse(Stream.empty())) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!itm.isPresent() || Objects.isNull(itm.get().getTypeCode())) { + return null; + } else { + final String typeCode = itm.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + }) + .orElse(null); + } + } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index c58096d35..4cecd0895 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -14,7 +14,6 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -141,6 +140,28 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label, + String vocabularyName) { + final InstanceTypeMapping m = new InstanceTypeMapping(); + m.setVocabularyName(vocabularyName); + m.setOriginalType(originalType); + m.setTypeCode(code); + m.setTypeLabel(label); + return m; + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + return instanceTypeMapping(originalType, term.getClassid(), term.getClassname(), term.getSchemeid()); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType) { + return instanceTypeMapping(originalType, null, null, null); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType, String vocabularyName) { + return instanceTypeMapping(originalType, null, null, vocabularyName); + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json index 58e3ca711..512878457 100644 --- a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "filterInvisible", "paramDescription": "if true filters out invisible entities", "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java new file mode 100644 index 000000000..c0a8d6927 --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java @@ -0,0 +1,114 @@ + +package eu.dnetlib.oa.merge; + +import static org.junit.jupiter.api.Assertions.*; + +import java.io.BufferedReader; +import java.io.InputStreamReader; +import java.util.List; +import java.util.Objects; + +import org.junit.jupiter.api.Test; +import org.junit.platform.commons.util.StringUtils; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.merge.AuthorMerger; +import eu.dnetlib.dhp.schema.oaf.Author; + +public class AuthorMergerTest { + + @Test + public void testEnrcichAuthor() throws Exception { + final ObjectMapper mapper = new ObjectMapper(); + + BufferedReader pr = new BufferedReader(new InputStreamReader( + Objects + .requireNonNull( + AuthorMergerTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); + BufferedReader or = new BufferedReader(new InputStreamReader( + Objects + .requireNonNull( + AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); + + TypeReference> aclass = new TypeReference>() { + }; + String pubLine; + + int i = 0; + while ((pubLine = pr.readLine()) != null) { + final String pubId = pubLine; + final String MatchPidOrcid = or.readLine(); + final String pubOrcid = or.readLine(); + + final String data = pr.readLine(); + + if (StringUtils.isNotBlank(data)) { + List publicationAuthors = mapper.readValue(data, aclass); + List orcidAuthors = mapper.readValue(or.readLine(), aclass); + System.out.printf("OAF ID = %s \n", pubId); + System.out.printf("ORCID Intersected ID = %s \n", pubOrcid); + System.out.printf("OAF Author Size = %d \n", publicationAuthors.size()); + System.out.printf("Oricd Author Size = %d \n", orcidAuthors.size()); + System.out.printf("Oricd Matched PID = %s \n", MatchPidOrcid); + + long originalAuthorWithPiD = publicationAuthors + .stream() + .filter( + a -> a.getPid() != null && a + .getPid() + .stream() + .anyMatch( + p -> p.getQualifier() != null + && p.getQualifier().getClassid().toLowerCase().contains("orcid"))) + .count(); + long start = System.currentTimeMillis(); + +// final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + + long enrichedAuthorWithPid = enrichedList + .stream() + .filter( + a -> a.getPid() != null && a + .getPid() + .stream() + .anyMatch( + p -> p.getQualifier() != null + && p.getQualifier().getClassid().toLowerCase().contains("orcid"))) + .count(); + + long totalTime = (System.currentTimeMillis() - start) / 1000; + System.out + .printf( + "Enriched authors in %d seconds from %d pid to %d pid \n", totalTime, originalAuthorWithPiD, + enrichedAuthorWithPid); + + System.out.println("================="); + } + } + } + + @Test + public void checkSimilarityTest() { + final Author left = new Author(); + left.setName("Anand"); + left.setSurname("Rachna"); + left.setFullname("Anand, Rachna"); + + System.out.println(AuthorMerger.normalizeFullName(left.getFullname())); + + final Author right = new Author(); + right.setName("Rachna"); + right.setSurname("Anand"); + right.setFullname("Rachna, Anand"); +// System.out.println(AuthorMerger.normalize(right.getFullname())); + boolean same = AuthorMerger.checkORCIDSimilarity(left, right); + + assertTrue(same); + + } + +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json new file mode 100644 index 000000000..ec521b3b7 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json @@ -0,0 +1,3 @@ +WrappedArray(arXiv1507.08202) +50|arXiv_dedup_::34e03f2336b8b28286550425e65634ea +[{"fullname":"Liron Barak","name":"Liron","surname":"Barak","rank":null,"pid":[{"value":"0000-0002-3436-2726","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Giuseppe Avolio","name":"Giuseppe","surname":"Avolio","rank":null,"pid":[{"value":"0000-0003-2664-3437","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Tobias Golling","name":"Tobias","surname":"Golling","rank":null,"pid":[{"value":"0000-0001-8535-6687","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Ivan Sykora","name":"Ivan","surname":"Sykora","rank":null,"pid":[{"value":"0000-0003-3447-5621","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Joao Carvalho","name":"Joao","surname":"Carvalho","rank":null,"pid":[{"value":"0000-0002-3015-7821","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jonathan David 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Wu","name":"Xin","surname":"Wu","rank":null,"pid":[{"value":"0000-0001-7655-389X","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Luke Lambourne","name":"Luke","surname":"Lambourne","rank":null,"pid":[{"value":"0000-0002-7001-7575","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Kazunori Hanagaki","name":"Kazunori","surname":"Hanagaki","rank":null,"pid":[{"value":"0000-0003-0676-0441","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Krzysztof Sliwa","name":"Krzysztof","surname":"Sliwa","rank":null,"pid":[{"value":"0000-0002-1201-4771","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jiri 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Romano","name":"S. M. Romano","surname":"Saez","rank":115,"pid":[],"affiliation":null},{"fullname":"Santoni, C.","name":"C.","surname":"Santoni","rank":116,"pid":[],"affiliation":null},{"fullname":"Simon, D.","name":"D.","surname":"Simon","rank":117,"pid":[],"affiliation":null},{"fullname":"Theveneaux-Pelzer, Timothée","name":"Timothée","surname":"Theveneaux-Pelzer","rank":118,"pid":[],"affiliation":null},{"fullname":"Vazeille, F.","name":"F.","surname":"Vazeille","rank":119,"pid":[],"affiliation":null},{"fullname":"Yatsenko, E.","name":"E.","surname":"Yatsenko","rank":120,"pid":[],"affiliation":null}] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java new file mode 100644 index 000000000..69661bbf6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java @@ -0,0 +1,102 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.InputStream; +import java.net.URL; +import java.net.URLConnection; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.http.client.config.RequestConfig; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClientBuilder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class DownloadORCIDDumpApplication { + private static final Logger log = LoggerFactory.getLogger(DownloadORCIDDumpApplication.class); + + private final FileSystem fileSystem; + + public DownloadORCIDDumpApplication(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + DownloadORCIDDumpApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json")))); + argumentParser.parseArgument(args); + + final String hdfsuri = argumentParser.get("namenode"); + log.info("hdfsURI is {}", hdfsuri); + + final String targetPath = argumentParser.get("targetPath"); + log.info("targetPath is {}", targetPath); + + final String apiURL = argumentParser.get("apiURL"); + log.info("apiURL is {}", apiURL); + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsuri)); + + new DownloadORCIDDumpApplication(fileSystem).run(targetPath, apiURL); + + } + + private void downloadItem(final String name, final String itemURL, final String basePath) { + try { + final Path hdfsWritePath = new Path(String.format("%s/%s", basePath, name)); + final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); + final HttpGet request = new HttpGet(itemURL); + final int timeout = 60; // seconds + final RequestConfig config = RequestConfig + .custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000) + .build(); + log.info("Downloading url {} into {}", itemURL, hdfsWritePath.getName()); + try (CloseableHttpClient client = HttpClientBuilder.create().setDefaultRequestConfig(config).build(); + CloseableHttpResponse response = client.execute(request)) { + int responseCode = response.getStatusLine().getStatusCode(); + log.info("Response code is {}", responseCode); + if (responseCode >= 200 && responseCode < 400) { + IOUtils.copy(response.getEntity().getContent(), fsDataOutputStream); + } + } catch (Throwable eu) { + throw new RuntimeException(eu); + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + protected void run(final String targetPath, final String apiURL) throws Exception { + final ObjectMapper mapper = new ObjectMapper(); + final URL url = new URL(apiURL); + URLConnection conn = url.openConnection(); + InputStream is = conn.getInputStream(); + final String json = IOUtils.toString(is); + JsonNode jsonNode = mapper.readTree(json); + jsonNode + .get("files") + .forEach(i -> downloadItem(i.get("name").asText(), i.get("download_url").asText(), targetPath)); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java new file mode 100644 index 000000000..4aefdb5e9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java @@ -0,0 +1,71 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +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; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class ExtractORCIDDump { + private static final Logger log = LoggerFactory.getLogger(ExtractORCIDDump.class); + + private final FileSystem fileSystem; + + public ExtractORCIDDump(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + DownloadORCIDDumpApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json")))); + argumentParser.parseArgument(args); + + final String hdfsuri = argumentParser.get("namenode"); + log.info("hdfsURI is {}", hdfsuri); + + final String sourcePath = argumentParser.get("sourcePath"); + log.info("sourcePath is {}", sourcePath); + + final String targetPath = argumentParser.get("targetPath"); + log.info("targetPath is {}", targetPath); + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsuri)); + + new ExtractORCIDDump(fileSystem).run(sourcePath, targetPath); + + } + + public void run(final String sourcePath, final String targetPath) throws IOException, InterruptedException { + RemoteIterator ls = fileSystem.listFiles(new Path(sourcePath), false); + final List workers = new ArrayList<>(); + int i = 0; + while (ls.hasNext()) { + LocatedFileStatus current = ls.next(); + if (current.getPath().getName().endsWith("tar.gz")) { + workers.add(new ORCIDExtractor(fileSystem, "" + i++, current.getPath(), targetPath)); + } + } + workers.forEach(Thread::start); + for (ORCIDExtractor worker : workers) { + worker.join(); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java new file mode 100644 index 000000000..11f4c55d8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java @@ -0,0 +1,171 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.HashMap; +import java.util.Map; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/**\ + * The ORCIDExtractor class extracts ORCID data from a TAR archive. + * The class creates a map of SequenceFile.Writer objects, one for each type of data that is to be extracted (e.g., employments, works, summaries). + * Then, it iterates over the TAR archive and writes each entry to the appropriate SequenceFile.Writer object. + * Finally, it closes all the SequenceFile.Writer objects. + */ +public class ORCIDExtractor extends Thread { + + private static final Logger log = LoggerFactory.getLogger(ORCIDExtractor.class); + + private final FileSystem fileSystem; + + private final String id; + + private final Path sourcePath; + + private final String baseOutputPath; + + public ORCIDExtractor(FileSystem fileSystem, String id, Path sourcePath, String baseOutputPath) { + this.fileSystem = fileSystem; + this.id = id; + this.sourcePath = sourcePath; + this.baseOutputPath = baseOutputPath; + } + + /** + * creates a map of SequenceFile.Writer objects, + * one for each type of data that is to be extracted. The map is created based on the filename in the TAR archive. + * For example, if the filename is employments.json, the map will contain an entry for the SequenceFile.Writer + * object that writes employment data. + * @return the Map + */ + private Map createMap() { + try { + log.info("Thread {} Creating sequence files starting from this input Path {}", id, sourcePath.getName()); + Map res = new HashMap<>(); + if (sourcePath.getName().contains("summaries")) { + + final String summaryPath = String.format("%s/summaries_%s", baseOutputPath, id); + final SequenceFile.Writer summary_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(summaryPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + + log.info("Thread {} Creating only summary path here {}", id, summaryPath); + res.put("summary", summary_file); + return res; + } else { + String employmentsPath = String.format("%s/employments_%s", baseOutputPath, id); + final SequenceFile.Writer employments_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(employmentsPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + res.put("employments", employments_file); + log.info("Thread {} Creating employments path here {}", id, employmentsPath); + + final String worksPath = String.format("%s/works_%s", baseOutputPath, id); + final SequenceFile.Writer works_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(worksPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + res.put("works", works_file); + log.info("Thread {} Creating works path here {}", id, worksPath); + + return res; + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + @Override + public void run() { + + CompressionCodecFactory factory = new CompressionCodecFactory(fileSystem.getConf()); + CompressionCodec codec = factory.getCodec(sourcePath); + if (codec == null) { + System.err.println("No codec found for " + sourcePath.getName()); + System.exit(1); + } + + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fileSystem.open(sourcePath)); + final Map fileMap = createMap(); + iterateTar(fileMap, gzipInputStream); + + } catch (IOException e) { + throw new RuntimeException(e); + } finally { + log.info("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + + } + + private SequenceFile.Writer retrieveFile(Map fileMap, final String path) { + if (sourcePath.getName().contains("summaries")) { + return fileMap.get("summary"); + } + + if (path.contains("works")) { + return fileMap.get("works"); + } + if (path.contains("employments")) + return fileMap.get("employments"); + return null; + } + + private void iterateTar(Map fileMap, InputStream gzipInputStream) throws IOException { + + int extractedItem = 0; + try (final TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + + TarArchiveEntry entry; + while ((entry = tais.getNextTarEntry()) != null) { + + if (entry.isFile()) { + + final SequenceFile.Writer fl = retrieveFile(fileMap, entry.getName()); + if (fl != null) { + final Text key = new Text(entry.getName()); + final Text value = new Text( + org.apache.commons.io.IOUtils.toString(new BufferedReader(new InputStreamReader(tais)))); + fl.append(key, value); + extractedItem++; + if (extractedItem % 100000 == 0) { + log.info("Thread {}: Extracted {} items", id, extractedItem); + break; + } + } + } + } + } finally { + for (SequenceFile.Writer k : fileMap.values()) { + log.info("Thread {}: Completed processed {} items", id, extractedItem); + k.hflush(); + k.close(); + } + } + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java new file mode 100644 index 000000000..159b8a5fc --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java @@ -0,0 +1,251 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.ximpleware.*; + +import eu.dnetlib.dhp.collection.orcid.model.*; +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; + +public class OrcidParser { + + final Logger log = LoggerFactory.getLogger(OrcidParser.class); + private VTDNav vn; + + private AutoPilot ap; + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; + private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; + private static final String NS_PERSON = "person"; + private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; + private static final String NS_DETAILS = "personal-details"; + private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; + private static final String NS_OTHER = "other-name"; + private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; + private static final String NS_RECORD = "record"; + private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; + private static final String NS_ACTIVITIES = "activities"; + private static final String NS_ACTIVITIES_URL = "http://www.orcid.org/ns/activities"; + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + + private static final String NS_ERROR = "error"; + private static final String NS_HISTORY = "history"; + private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; + private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk"; + private static final String NS_BULK = "bulk"; + private static final String NS_EXTERNAL = "external-identifier"; + private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier"; + + private void generateParsedDocument(final String xml) throws ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(xml.getBytes()); + vg.parse(true); + this.vn = vg.getNav(); + this.ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); + ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); + ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); + ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + ap.declareXPathNameSpace(NS_HISTORY, NS_HISTORY_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL); + ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL); + } + + public Author parseSummary(final String xml) { + + try { + final Author author = new Author(); + generateParsedDocument(xml); + List recordNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, "//record:record", Arrays.asList("path")); + if (!recordNodes.isEmpty()) { + final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); + author.setOrcid(oid); + } else { + return null; + } + List personNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, "//person:name", Arrays.asList("visibility")); + final String visibility = (personNodes.get(0).getAttributes().get("visibility")); + author.setVisibility(visibility); + final String name = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:given-names"); + author.setGivenName(name); + + final String surnames = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:family-name"); + author.setFamilyName(surnames); + + final String creditNames = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:credit-name"); + author.setCreditName(creditNames); + + final String biography = VtdUtilityParser + .getSingleValue(ap, vn, "//person:biography/personal-details:content"); + author.setBiography(biography); + + final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); + if (!otherNames.isEmpty()) { + author.setOtherNames(otherNames); + } + + ap.selectXPath("//external-identifier:external-identifier"); + + while (ap.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + + ap1.selectXPath("./common:external-id-type"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:external-id-value"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + author.addOtherPid(pid); + } + + return author; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + } + + public Work parseWork(final String xml) { + + try { + final Work work = new Work(); + generateParsedDocument(xml); + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "visibility")); + if (!workNodes.isEmpty()) { + final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + work.setOrcid(oid); + } else { + return null; + } + + ap.selectXPath("//common:external-id"); + + while (ap.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + + ap1.selectXPath("./common:external-id-type"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:external-id-value"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + work.addPid(pid); + } + + work.setTitle(VtdUtilityParser.getSingleValue(ap, vn, "//work:title/common:title")); + + return work; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + + private String extractEmploymentDate(final String xpath) throws Exception { + + ap.selectXPath(xpath); + StringBuilder sb = new StringBuilder(); + while (ap.evalXPath() != -1) { + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + ap1.selectXPath("./common:year"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:month"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append("-"); + sb.append(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:day"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append("-"); + sb.append(vn.toNormalizedString(it)); + } + } + return sb.toString(); + + } + + public Employment parseEmployment(final String xml) { + try { + final Employment employment = new Employment(); + generateParsedDocument(xml); + final String oid = VtdUtilityParser + .getSingleValue(ap, vn, "//common:source-orcid/common:path"); + if (StringUtils.isNotBlank(oid)) { + employment.setOrcid(oid); + } else { + return null; + } + final String depName = VtdUtilityParser + .getSingleValue(ap, vn, "//common:department-name"); + final String rolTitle = VtdUtilityParser + .getSingleValue(ap, vn, "//common:role-title"); + if (StringUtils.isNotBlank(rolTitle)) + employment.setRoleTitle(rolTitle); + if (StringUtils.isNotBlank(depName)) + employment.setDepartmentName(depName); + else + employment + .setDepartmentName( + VtdUtilityParser + .getSingleValue(ap, vn, "//common:organization/common:name")); + + employment.setStartDate(extractEmploymentDate("//common:start-date")); + employment.setEndDate(extractEmploymentDate("//common:end-date")); + + final String affiliationId = VtdUtilityParser + .getSingleValue(ap, vn, "//common:disambiguated-organization-identifier"); + final String affiliationIdType = VtdUtilityParser + .getSingleValue(ap, vn, "//common:disambiguation-source"); + + if (StringUtils.isNotBlank(affiliationId) || StringUtils.isNotBlank(affiliationIdType)) + employment.setAffiliationId(new Pid(affiliationId, affiliationIdType)); + + return employment; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java new file mode 100644 index 000000000..32c321b41 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java @@ -0,0 +1,83 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +import java.util.ArrayList; +import java.util.List; + +public class Author extends ORCIDItem { + private String givenName; + private String familyName; + + private String visibility; + + private String creditName; + + private List otherNames; + + private List otherPids; + + private String biography; + + public String getBiography() { + return biography; + } + + public void setBiography(String biography) { + this.biography = biography; + } + + public String getGivenName() { + return givenName; + } + + public void setGivenName(String givenName) { + this.givenName = givenName; + } + + public String getFamilyName() { + return familyName; + } + + public void setFamilyName(String familyName) { + this.familyName = familyName; + } + + public String getCreditName() { + return creditName; + } + + public void setCreditName(String creditName) { + this.creditName = creditName; + } + + public List getOtherNames() { + return otherNames; + } + + public void setOtherNames(List otherNames) { + this.otherNames = otherNames; + } + + public String getVisibility() { + return visibility; + } + + public void setVisibility(String visibility) { + this.visibility = visibility; + } + + public List getOtherPids() { + return otherPids; + } + + public void setOtherPids(List otherPids) { + this.otherPids = otherPids; + } + + public void addOtherPid(final Pid pid) { + + if (otherPids == null) + otherPids = new ArrayList<>(); + otherPids.add(pid); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java new file mode 100644 index 000000000..baee67d46 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class Employment extends ORCIDItem { + + private String startDate; + private String EndDate; + + private Pid affiliationId; + + private String departmentName; + + private String roleTitle; + + public String getStartDate() { + return startDate; + } + + public void setStartDate(String startDate) { + this.startDate = startDate; + } + + public String getEndDate() { + return EndDate; + } + + public void setEndDate(String endDate) { + EndDate = endDate; + } + + public Pid getAffiliationId() { + return affiliationId; + } + + public void setAffiliationId(Pid affiliationId) { + this.affiliationId = affiliationId; + } + + public String getDepartmentName() { + return departmentName; + } + + public void setDepartmentName(String departmentName) { + this.departmentName = departmentName; + } + + public String getRoleTitle() { + return roleTitle; + } + + public void setRoleTitle(String roleTitle) { + this.roleTitle = roleTitle; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java new file mode 100644 index 000000000..6bc47bc26 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java @@ -0,0 +1,14 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class ORCIDItem { + private String orcid; + + public String getOrcid() { + return orcid; + } + + public void setOrcid(String orcid) { + this.orcid = orcid; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java new file mode 100644 index 000000000..077dc2550 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java @@ -0,0 +1,33 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class Pid { + + private String value; + + private String schema; + + public Pid() { + } + + public Pid(String value, String schema) { + this.value = value; + this.schema = schema; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getSchema() { + return schema; + } + + public void setSchema(String schema) { + this.schema = schema; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java new file mode 100644 index 000000000..670170323 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +import java.util.ArrayList; +import java.util.List; + +public class Work extends ORCIDItem { + + private String title; + + private List pids; + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public List getPids() { + return pids; + } + + public void setPids(List pids) { + this.pids = pids; + } + + public void addPid(Pid pid) { + if (pids == null) + pids = new ArrayList<>(); + pids.add(pid); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json new file mode 100644 index 000000000..4a84cbbb9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the FIGSHARE API id URL to retrieve all the dump files", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json new file mode 100644 index 000000000..4af371875 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH to extract files", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the PATH where the tar.gz files were downloaded", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json new file mode 100644 index 000000000..01d81ea97 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH of the DF tables", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the PATH of the ORCID sequence file", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml new file mode 100644 index 000000000..1a5f425e5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml @@ -0,0 +1,81 @@ + + + + targetPath + the path to store the original ORCID dump + + + apiURL + The figshare API URL to retrieve the list file to download + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.collection.orcid.DownloadORCIDDumpApplication + --namenode${nameNode} + --targetPath${targetPath} + --apiURL${apiURL} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + + eu.dnetlib.dhp.collection.orcid.ExtractORCIDDump + -Xmx6g + --namenode${nameNode} + --sourcePath${targetPath} + --targetPath${targetPath}/extracted + + + + + + + + yarn + cluster + Generate ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${targetPath}/extracted + --targetPath${targetPath}/tables + --masteryarn + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json new file mode 100644 index 000000000..4a84cbbb9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the FIGSHARE API id URL to retrieve all the dump files", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala new file mode 100644 index 000000000..f0c4cd214 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala @@ -0,0 +1,101 @@ +package eu.dnetlib.dhp.collection.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.collection.orcid.model.{Author, Employment, Pid, Work} +import org.apache.hadoop.io.Text +import org.apache.spark.SparkContext +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + val sourcePath: String = parser.get("sourcePath") + log.info("found parameters sourcePath: {}", sourcePath) + val targetPath: String = parser.get("targetPath") + log.info("found parameters targetPath: {}", targetPath) + extractORCIDTable(spark, sourcePath, targetPath) + extractORCIDEmploymentsTable(spark, sourcePath, targetPath) + extractORCIDWorksTable(spark, sourcePath, targetPath) + } + + def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author]) +// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("summaries")) + .map { r => + val p = new OrcidParser + p.parseSummary(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Authors") + } + + def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work]) + implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("works")) + .map { r => + val p = new OrcidParser + p.parseWork(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } + + def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment]) + implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("employments")) + .map { r => + val p = new OrcidParser + p.parseEmployment(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } +} + +object SparkGenerateORCIDTable { + + val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass) + + def main(args: Array[String]): Unit = { + + new SparkGenerateORCIDTable("/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json", args, log) + .initialize() + .run() + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 45f5f9729..7603715b9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -166,7 +166,7 @@ object DataciteToOAFTransformation { resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup - ): (Qualifier, Qualifier) = { + ): (Qualifier, Qualifier, String) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -176,7 +176,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), + resourceType ) } if (schemaOrg != null && schemaOrg.nonEmpty) { @@ -188,7 +189,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), + schemaOrg ) } @@ -203,7 +205,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), + resourceTypeGeneral ) } @@ -216,12 +219,18 @@ object DataciteToOAFTransformation { schemaOrg: String, vocabularies: VocabularyGroup ): Result = { - val typeQualifiers: (Qualifier, Qualifier) = + val typeQualifiers: (Qualifier, Qualifier, String) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) if (typeQualifiers == null) return null val i = new Instance i.setInstancetype(typeQualifiers._1) + // ADD ORIGINAL TYPE + val itm = new InstanceTypeMapping + itm.setOriginalType(typeQualifiers._3) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) + typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index a4ff41484..65c348062 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -176,7 +176,7 @@ object BioDBToOAF { i.setUrl(List(s"${resolvedURL(input.pidType)}${input.pid}").asJava) } - if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) + if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) { i.setInstancetype( OafMapperUtils.qualifier( "0037", @@ -185,7 +185,11 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) - else + val itm = new InstanceTypeMapping + itm.setOriginalType(input.pidType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) + } else { i.setInstancetype( OafMapperUtils.qualifier( "0046", @@ -194,6 +198,11 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) + } if (input.datasource == null || input.datasource.isEmpty) return null @@ -265,6 +274,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("uniprot")) d.setInstance(List(i).asJava) @@ -471,6 +484,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("pdb")) d.setInstance(List(i).asJava) @@ -571,6 +588,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("ebi")) d.setInstance(List(i).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 410686f97..d59d73bd0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -188,13 +188,24 @@ object PubMedToOaf { val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) pubmedInstance.setInstancetype(cojbCategory) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(ja.get.getValue) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala - .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) - .find(q => q != null) - if (i_type.isDefined) - pubmedInstance.setInstancetype(i_type.get) - else + .map(s => (s.getValue, getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))) + .find(q => q._2 != null) + + if (i_type.isDefined) { + pubmedInstance.setInstancetype(i_type.get._2) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(i_type.get._1) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) + } else return null } val result = createResult(pubmedInstance.getInstancetype, vocabularies) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java new file mode 100644 index 000000000..868f4e92d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java @@ -0,0 +1,119 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkContext; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; + +import eu.dnetlib.dhp.collection.orcid.model.Author; +import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem; +import eu.dnetlib.dhp.parser.utility.VtdException; + +public class DownloadORCIDTest { + private final Logger log = LoggerFactory.getLogger(DownloadORCIDTest.class); + + @Test + public void testSummary() throws Exception { + final String xml = IOUtils + .toString( + Objects.requireNonNull(getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/summary.xml"))); + + final OrcidParser parser = new OrcidParser(); + ORCIDItem orcidItem = parser.parseSummary(xml); + + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(orcidItem)); + + } + + @Test + public void testParsingWork() throws Exception { + + final List works_path = Arrays + .asList( + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml" + + ); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + works_path.stream().map(s -> { + try { + return IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream( + s))); + } catch (IOException e) { + throw new RuntimeException(e); + } + }).forEach(s -> { + try { + System.out.println(mapper.writeValueAsString(parser.parseWork(s))); + } catch (Exception e) { + throw new RuntimeException(e); + } + }); + } + + @Test + public void testParsingEmployments() throws Exception { + + final List works_path = Arrays + .asList( + "/eu/dnetlib/dhp/collection/orcid/employment.xml", + "/eu/dnetlib/dhp/collection/orcid/employment_2.xml", + "/eu/dnetlib/dhp/collection/orcid/employment_3.xml" + + ); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + works_path.stream().map(s -> { + try { + return IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream( + s))); + } catch (IOException e) { + throw new RuntimeException(e); + } + }).forEach(s -> { + try { + System.out.println(mapper.writeValueAsString(parser.parseEmployment(s))); + } catch (Exception e) { + throw new RuntimeException(e); + } + }); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml new file mode 100644 index 000000000..2c89b83f6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml @@ -0,0 +1,69 @@ + + + 2016-09-01T19:22:46.768Z + 2022-05-25T03:48:56.968Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + https://orcid.org/0000-0001-5010-5001 + 0000-0001-5010-5001 + orcid.org + + Quang Nguyen + + + Vision outcomes and major complications after endovascular coil embolization of ophthalmic segment aneurysms + + American Journal of Neuroradiology + + bibtex + @article{Nguyen2014,title = {Vision outcomes and major complications after endovascular coil embolization of ophthalmic segment aneurysms},journal = {American Journal of Neuroradiology},year = {2014},volume = {35},number = {11},pages = {2140-2145},author = {Durst, C. and Starke, R.M. and Gaughen, J. and Nguyen, Q. and Patrie, J. and Jensen, M.E. and Evans, A.J.}} + + journal-article + + 2014 + + + + doi + 10.3174/ajnr.A4032 + 10.3174/ajnr.a4032 + self + + + eid + 2-s2.0-84911865199 + 2-s2.0-84911865199 + self + + + http://www.scopus.com/inward/record.url?eid=2-s2.0-84911865199&partnerID=MN8TOARS + + + Durst, C. + + + Starke, R.M. + + + Gaughen, J. + + + Nguyen, Q. + + + Patrie, J. + + + Jensen, M.E. + + + Evans, A.J. + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml new file mode 100644 index 000000000..63b4405f1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml @@ -0,0 +1,79 @@ + + + 2018-11-01T19:49:45.562Z + 2018-11-01T19:49:45.562Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + + "Calling Out" in class: Degrees of candor in addressing social injustices in + racially homogenous and heterogeneous U.S. history classrooms + + Journal of Social Studies Research + + bibtex + @article{Massaro2018,title = {{"}Calling Out{"} in class: Degrees of + candor in addressing social injustices in racially homogenous and heterogeneous U.S. + history classrooms},journal = {Journal of Social Studies Research},year = {2018},author + = {Parkhouse, H. and Massaro, V.R.}} + + journal-article + + 2018 + + + + doi + 10.1016/j.jssr.2018.01.004 + 10.1016/j.jssr.2018.01.004 + self + + + eid + 2-s2.0-85041949043 + 2-s2.0-85041949043 + self + + + http://www.scopus.com/inward/record.url?eid=2-s2.0-85041949043&partnerID=MN8TOARS + + + Parkhouse, H. + + + Massaro, V.R. + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml new file mode 100644 index 000000000..650d5a4cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml @@ -0,0 +1,113 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Abdel-Dayem Fake + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 000000000..83752b145 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Khair Abde Daye + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml new file mode 100644 index 000000000..26e64aeda --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml @@ -0,0 +1,101 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + + seq0 + role0 + + + + creditname1 + + + creditname2 + + seq2 + + + + + creditname3 + + + role3 + + + + + + seq4 + role4 + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml new file mode 100644 index 000000000..89c7f7020 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml @@ -0,0 +1,50 @@ + + + 2016-09-01T19:21:05.791Z + 2016-09-01T19:21:05.791Z + + + https://orcid.org/0000-0001-5010-5001 + 0000-0001-5010-5001 + orcid.org + + Quang Nguyen + + + Beth Israel Deaconess Medical Center + + Boston + MA + US + + + 1859 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml new file mode 100644 index 000000000..c0e88e236 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml @@ -0,0 +1,55 @@ + + + 2018-09-03T01:46:19.474Z + 2018-09-03T01:46:19.474Z + + + https://orcid.org/0000-0001-5011-3001 + 0000-0001-5011-3001 + orcid.org + + zhengyan li + + + 2008 + 09 + 01 + + + Anhui Academy of Agricultural Sciences + + Hefei + Anhui + CN + + + 125385 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml new file mode 100644 index 000000000..8e7857fb8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml @@ -0,0 +1,62 @@ + + + 2021-03-11T14:48:29.603Z + 2021-03-11T14:48:29.603Z + + + https://orcid.org/0000-0001-5012-1001 + 0000-0001-5012-1001 + orcid.org + + Asma Bazzi + + Pathology and Laboratory Medicine + Medical Laboratory Technologist + + 1994 + 10 + 01 + + + 2000 + 06 + 30 + + + American University of Beirut + + Hamra + Beirut + LB + + + 11238 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml new file mode 100644 index 000000000..1f5a1bff1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml @@ -0,0 +1,581 @@ + + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + + es + + + Direct + 2023-01-17T23:50:40.215Z + 2023-09-04T17:51:57.749Z + true + true + true + + + + 2023-01-17T23:50:40.472Z + 2023-01-17T23:50:40.472Z + Patricio + Sánchez Quinchuela + + + + 2023-01-19T13:47:33.653Z + 2023-01-19T13:47:33.653Z + Especialista de vinculación con la sociedad y docente de la Universidad de las Artes. Magister en Economía Social y Solidaria por el IAEN; Magister en Proyectos Sociales y Productivos por la UNACH. Licenciado en Artes UCE. Licenciado en Castellano y Literatura por la UNACH. Doctorando del programa de Sociología de la UNED España. Larga trayectoria vinculado a las organizaciones sociales acompañando procesos de gestión cultural, formación de liderazgos y economía solidaria. + + + + + + + 2018-02-05T23:27:36.636Z + + 2013-03-08T03:20:39.347Z + 2018-02-05T23:27:36.636Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + https://orcid.org/0000-0001-7291-3210 + 0000-0001-7291-3210 + orcid.org + + Paolo Manghi + + Scopus Author ID + 6602255248 + http://www.scopus.com/inward/authorDetails.url?authorID=6602255248&partnerID=MN8TOARS + self + + + + + 2023-09-04T17:51:57.749Z + + 2023-01-19T13:49:48.482Z + + 2023-01-19T13:49:48.482Z + + + 2023-01-19T13:49:48.482Z + 2023-01-19T13:49:48.482Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Maestría + Becario del programa de Maestría en Economía Social y Solidaria + + 2014 + 10 + 20 + + + Instituto de Altos Estudios Nacionales + + Quito + Pichincha + EC + + + https://ror.org/011g3me54 + ROR + + + + + + + 2023-01-18T21:41:03.175Z + + 2023-01-18T21:41:03.175Z + + + 2023-01-18T21:41:03.175Z + 2023-01-18T21:41:03.175Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Doctorado en Sociología + Doctorando del Programa de Sociología + + 2020 + 11 + 06 + + + Universidad Nacional de Educación a Distancia Facultad de Ciencias Políticas y Sociología + + Madrid + Comunidad de Madrid + ES + + + 223339 + RINGGOLD + + + + + + + 2023-01-18T21:25:07.138Z + + 2023-01-18T21:22:21.513Z + + + 2023-01-17T23:57:08.246Z + 2023-01-18T21:22:21.513Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Dirección de Vinculación con la Sociedad + Especialista de Proyectos y docente + + 2021 + 11 + 01 + + + Universidad de las Artes + + Guayaquil + Guayas + EC + + + https://ror.org/016drwn73 + ROR + + + + + + 2023-01-18T21:25:07.138Z + + + 2023-01-18T21:25:07.138Z + 2023-01-18T21:25:07.138Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Dirección de Vinculación con la Sociedad + Director + + 2019 + 11 + 05 + + + 2021 + 10 + 31 + + + Universidad Regional Amazónica IKIAM + + Tena + Napo + EC + + + https://ror.org/05xedqd83 + ROR + + + http://ikiam.edu.ec + + + + + + + 2023-03-24T18:16:09.131Z + + 2023-03-24T18:16:09.131Z + + + 2023-03-24T18:16:09.131Z + 2023-03-24T18:16:09.131Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Artes Escénicas + Miembro + + 2000 + 07 + 15 + + + Casa de la Cultura Ecuatoriana + + Riobamba + Sierra Centro + EC + + + + + + + + 2023-01-18T21:45:07.379Z + + 2023-01-18T21:29:11.300Z + + + 2023-01-18T21:29:11.300Z + 2023-01-18T21:29:11.300Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Gobernabilidad + Magister en Economïa Social y Solidaria + + 2014 + 10 + 20 + + + 2017 + 01 + 26 + + + Instituto de Altos Estudios Nacionales + + Quito + Pichincha + EC + + + https://ror.org/011g3me54 + ROR + + + + + + 2023-01-18T21:34:32.093Z + + + 2023-01-18T21:34:32.093Z + 2023-01-18T21:34:32.093Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Posgrados + Magister en Proyectos Sociales y Productivos + + 2001 + 03 + 09 + + + 2003 + 02 + 27 + + + Universidad Nacional de Chimborazo + + Riobamba + Chimborazo + EC + + + https://ror.org/059wmd288 + ROR + + + + + + 2023-01-18T21:45:07.379Z + + + 2023-01-18T21:45:07.379Z + 2023-01-18T21:45:07.379Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Ciencias de la Educación + Licenciado en Ciencias de la Educación en Castellano y Literatura + + 1994 + 10 + 03 + + + 2000 + 01 + 31 + + + Universidad Nacional de Chimborazo + + Riobamba + Chimborazo + EC + + + https://ror.org/059wmd288 + ROR + + + + + + 2023-01-18T21:37:42.186Z + + + 2023-01-18T21:37:42.186Z + 2023-01-18T21:37:42.186Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Facultad de Artes + Licenciado en Artes + + 1989 + 09 + 05 + + + 1997 + 08 + 07 + + + Universidad Central del Ecuador + + Quito + Pichincha + EC + + + http://dx.doi.org/10.13039/100019134 + FUNDREF + + + + + + + + + 2023-09-04T17:51:57.749Z + + 2023-06-09T22:15:12.910Z + + + 2023-03-24T18:36:56.180Z + 2023-06-09T22:15:12.910Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Experience in a non-capitalist way: solidarity funds that do not tax interest on the use of money + + + + isbn + 978-9942-29-089-2 + 9789942290892 + part-of + + + book-chapter + + 2023 + 06 + 07 + + Finanzas éticas y solidarias en América Latina: diagnósticos, debates y propuestas + + + + 2023-03-24T19:05:36.384Z + + + 2023-03-24T19:05:36.384Z + 2023-03-24T19:05:36.384Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Incidence of artistic practices in the social transformation of the territory. study of case: Hilarte Association, Guayaquil-Ecuador + + + conference-abstract + + 2022 + 10 + 06 + + + + + 2023-09-04T17:40:30.215Z + + + other-id + 2018 + 2018 + self + + + + 2023-09-04T17:40:30.215Z + 2023-09-04T17:40:30.215Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Más allá de la transferencia de conocimientos, un espacio para el interaprendizaje y el diálogo de saberes + + + + other-id + 2018 + 2018 + self + + + https://drive.google.com/drive/folders/1Tclz6isxGzSjTq-hfTnxe6M1nux-88wF?usp=drive_link + conference-poster + + 2018 + 11 + 30 + + Más allá de la transferencia de conocimientos, un espacio para el interaprendizaje y el diálogo de saberes + + + + 2023-03-24T18:57:10.095Z + + + 2023-03-24T18:57:10.095Z + 2023-03-24T18:57:10.095Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Promotion of the popular and solidarity economy from the state: principles and challenges in the experience of Ecuador + + + dissertation-thesis + + 2017 + 01 + 26 + + + + + 2023-09-04T17:51:57.749Z + + + 2023-09-04T17:51:57.749Z + 2023-09-04T17:51:57.749Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + La Rebelión de los Dioses + + + https://drive.google.com/drive/folders/1Tclz6isxGzSjTq-hfTnxe6M1nux-88wF?usp=drive_link + registered-copyright + + 2001 + 08 + 28 + + Editorial pedagógica freire + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index 5e2fc0a01..306229e79 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -16,6 +16,10 @@ filterInvisible whether filter out invisible entities after merge + + isLookupUrl + the URL address of the lookUp service + sparkDriverMemory heap memory for driver process @@ -128,6 +132,7 @@ --graphInputPath${graphBasePath} --checkpointPath${workingPath}/grouped_entities --outputPath${graphOutputPath} + --isLookupUrl${isLookupUrl} --filterInvisible${filterInvisible} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index 40a17b486..ed6853229 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -133,32 +133,6 @@ --targetPath${inputPathMAG}/dataset --masteryarn-cluster - - - - - - - - yarn-cluster - cluster - Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkPreprocessORCID - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathOrcid} - --workingPath${workingPathOrcid} - --masteryarn-cluster - diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index 29a12f4df..84cbc5232 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -59,10 +59,10 @@ - - workingPathOrcid - the ORCID working path - + + + + @@ -84,7 +84,6 @@ ${wf:conf('resumeFrom') eq 'Skip'} ${wf:conf('resumeFrom') eq 'PreprocessMag'} ${wf:conf('resumeFrom') eq 'PreprocessUW'} - ${wf:conf('resumeFrom') eq 'ProcessORCID'} ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} ${wf:conf('resumeFrom') eq 'GenerateActionSet'} @@ -170,32 +169,6 @@ --targetPath${workingPath}/uwPublication --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 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --workingPath${workingPathOrcid} - --targetPath${workingPath}/orcidPublication - --masteryarn-cluster - diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 2cbd53097..9ffaeeeef 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -66,7 +66,7 @@ object SparkGenerateDoiBoost { Encoders.tuple(Encoders.STRING, mapEncoderPub) implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] - logger.info("Phase 2) Join Crossref with UnpayWall") + logger.info("Phase 1) Join Crossref with UnpayWall") val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p)) @@ -91,20 +91,10 @@ object SparkGenerateDoiBoost { .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/firstJoin") - logger.info("Phase 3) Join Result with ORCID") - val fj: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p)) - val orcidPublication: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p)) - fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left") - .map(applyMerge) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingDirPath/secondJoin") - logger.info("Phase 4) Join Result with MAG") + logger.info("Phase 2) Join Result with MAG") val sj: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) + spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p)) val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 565d34e62..ee857e2c4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -107,7 +107,7 @@ case object Crossref2Oaf { .map(f => f.id) } - def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { + def mappingResult(result: Result, json: JValue, cobjCategory: String, originalType: String): Result = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID @@ -283,6 +283,11 @@ case object Crossref2Oaf { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + //ADD ORIGINAL TYPE to the mapping + val itm = new InstanceTypeMapping + itm.setOriginalType(originalType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + instance.setInstanceTypeMapping(List(itm).asJava) result.setResourcetype( OafMapperUtils.qualifier( cobjCategory.substring(0, 4), @@ -367,7 +372,9 @@ case object Crossref2Oaf { objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type") ) - mappingResult(result, json, cOBJCategory) + + val originalType = if (mappingCrossrefSubType.contains(objectType)) objectType else objectSubType + mappingResult(result, json, cOBJCategory, originalType) if (result == null || result.getId == null) return List() diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index 262ca0290..cf33c6509 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -14,8 +14,6 @@ import org.jetbrains.annotations.NotNull; * @Date 06/10/23 */ public class QueryCommunityAPI { - private static final String PRODUCTION_BASE_URL = "https://services.openaire.eu/openaire/"; - private static final String BETA_BASE_URL = "https://beta.services.openaire.eu/openaire/"; private static String get(String geturl) throws IOException { URL url = new URL(geturl); @@ -32,35 +30,34 @@ public class QueryCommunityAPI { return body; } - public static String communities(boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/communities"); - return get(BETA_BASE_URL + "community/communities"); - } + public static String communities(String baseURL) throws IOException { - public static String community(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id); - return get(BETA_BASE_URL + "community/" + id); - } - - public static String communityDatasource(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/contentproviders"); - return (BETA_BASE_URL + "community/" + id + "/contentproviders"); + return get(baseURL + "communities"); } - public static String communityPropagationOrganization(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/propagationOrganizations"); - return get(BETA_BASE_URL + "community/" + id + "/propagationOrganizations"); + public static String community(String id, String baseURL) throws IOException { + + return get(baseURL + id); + } - public static String communityProjects(String id, String page, String size, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); - return get(BETA_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); + public static String communityDatasource(String id, String baseURL) throws IOException { + + return get(baseURL + id + "/contentproviders"); + + } + + public static String communityPropagationOrganization(String id, String baseURL) throws IOException { + + return get(baseURL + id + "/propagationOrganizations"); + + } + + public static String communityProjects(String id, String page, String size, String baseURL) throws IOException { + + return get(baseURL + id + "/projects/" + page + "/" + size); + } @NotNull diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index c1dda1ddc..d121b8b7e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -9,6 +9,8 @@ import java.util.Map; import java.util.Objects; import java.util.stream.Collectors; +import javax.management.Query; + import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -22,6 +24,7 @@ import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; import eu.dnetlib.dhp.bulktag.community.Provider; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory; +import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; /** * @author miriam.baglioni @@ -33,14 +36,14 @@ public class Utils implements Serializable { private static final Logger log = LoggerFactory.getLogger(Utils.class); - public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException { + public static CommunityConfiguration getCommunityConfiguration(String baseURL) throws IOException { final Map communities = Maps.newHashMap(); List validCommunities = new ArrayList<>(); - getValidCommunities(production) + getValidCommunities(baseURL) .forEach(community -> { try { CommunityModel cm = MAPPER - .readValue(QueryCommunityAPI.community(community.getId(), production), CommunityModel.class); + .readValue(QueryCommunityAPI.community(community.getId(), baseURL), CommunityModel.class); validCommunities.add(getCommunity(cm)); } catch (IOException e) { throw new RuntimeException(e); @@ -50,7 +53,7 @@ public class Utils implements Serializable { try { DatasourceList dl = MAPPER .readValue( - QueryCommunityAPI.communityDatasource(community.getId(), production), DatasourceList.class); + QueryCommunityAPI.communityDatasource(community.getId(), baseURL), DatasourceList.class); community.setProviders(dl.stream().map(d -> { if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) return null; @@ -95,9 +98,9 @@ public class Utils implements Serializable { return c; } - public static List getValidCommunities(boolean production) throws IOException { + public static List getValidCommunities(String baseURL) throws IOException { return MAPPER - .readValue(QueryCommunityAPI.communities(production), CommunitySummary.class) + .readValue(QueryCommunityAPI.communities(baseURL), CommunitySummary.class) .stream() .filter( community -> !community.getStatus().equals("hidden") && @@ -108,15 +111,15 @@ public class Utils implements Serializable { /** * it returns for each organization the list of associated communities */ - public static CommunityEntityMap getCommunityOrganization(boolean production) throws IOException { + public static CommunityEntityMap getCommunityOrganization(String baseURL) throws IOException { CommunityEntityMap organizationMap = new CommunityEntityMap(); - getValidCommunities(production) + getValidCommunities(baseURL) .forEach(community -> { String id = community.getId(); try { List associatedOrgs = MAPPER .readValue( - QueryCommunityAPI.communityPropagationOrganization(id, production), OrganizationList.class); + QueryCommunityAPI.communityPropagationOrganization(id, baseURL), OrganizationList.class); associatedOrgs.forEach(o -> { if (!organizationMap .keySet() @@ -133,9 +136,10 @@ public class Utils implements Serializable { return organizationMap; } - public static CommunityEntityMap getCommunityProjects(boolean production) throws IOException { + public static CommunityEntityMap getCommunityProjects(String baseURL) throws IOException { CommunityEntityMap projectMap = new CommunityEntityMap(); - getValidCommunities(production) + + getValidCommunities(baseURL) .forEach(community -> { int page = -1; int size = 100; @@ -147,7 +151,7 @@ public class Utils implements Serializable { .readValue( QueryCommunityAPI .communityProjects( - community.getId(), String.valueOf(page), String.valueOf(size), production), + community.getId(), String.valueOf(page), String.valueOf(size), baseURL), ContentModel.class); if (cm.getContent().size() > 0) { cm.getContent().forEach(p -> { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 15712ad66..5d1b2b38d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -62,8 +62,8 @@ public class SparkBulkTagJob { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("production")); - log.info("production: {}", production); + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class); log.info("pathMap: {}", new Gson().toJson(protoMappingParams)); @@ -79,7 +79,8 @@ public class SparkBulkTagJob { if (taggingConf != null) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { - cc = Utils.getCommunityConfiguration(production); + cc = Utils.getCommunityConfiguration(baseURL); + log.info(OBJECT_MAPPER.writeValueAsString(cc)); } runWithSparkSession( @@ -134,7 +135,7 @@ public class SparkBulkTagJob { ModelSupport.entityTypes .keySet() .parallelStream() - .filter(e -> ModelSupport.isResult(e)) + .filter(ModelSupport::isResult) .forEach(e -> { removeOutputDir(spark, outputPath + e.name()); ResultTagger resultTagger = new ResultTagger(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java index 13d29b940..82a6a3b85 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java @@ -13,7 +13,7 @@ public class Constraint implements Serializable { private String verb; private String field; private String value; - +// private String element; @JsonIgnore private Selection selection; @@ -41,6 +41,10 @@ public class Constraint implements Serializable { this.value = value; } +//@JsonIgnore + // public void setSelection(Selection sel) { +// selection = sel; +// } @JsonIgnore public void setSelection(VerbResolver resolver) throws InvocationTargetException, NoSuchMethodException, InstantiationException, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 3b231a52d..98c46cf00 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -82,11 +82,13 @@ public class ResultTagger implements Serializable { // communities contains all the communities to be not added to the context final Set removeCommunities = new HashSet<>(); + // if (conf.getRemoveConstraintsMap().keySet().size() > 0) conf .getRemoveConstraintsMap() .keySet() .forEach( communityId -> { + // log.info("Remove constraints for " + communityId); if (conf.getRemoveConstraintsMap().keySet().contains(communityId) && conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && conf diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java deleted file mode 100644 index 7d786058a..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java +++ /dev/null @@ -1,21 +0,0 @@ - -package eu.dnetlib.dhp.resulttocommunityfromorganization; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -public class OrganizationMap extends HashMap> { - - public OrganizationMap() { - super(); - } - - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } -} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 0fc8cb390..54fa60168 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -9,9 +9,7 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -20,6 +18,8 @@ import org.slf4j.LoggerFactory; import com.google.gson.Gson; +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -48,10 +48,10 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final OrganizationMap organizationMap = new Gson() - .fromJson( - parser.get("organizationtoresultcommunitymap"), - OrganizationMap.class); + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); + + final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(baseURL); log.info("organizationMap: {}", new Gson().toJson(organizationMap)); SparkConf conf = new SparkConf(); @@ -70,7 +70,7 @@ public class PrepareResultCommunitySet { SparkSession spark, String inputPath, String outputPath, - OrganizationMap organizationMap) { + CommunityEntityMap organizationMap) { Dataset relation = readPath(spark, inputPath, Relation.class); relation.createOrReplaceTempView("relation"); @@ -115,7 +115,7 @@ public class PrepareResultCommunitySet { } private static MapFunction mapResultCommunityFn( - OrganizationMap organizationMap) { + CommunityEntityMap organizationMap) { return value -> { String rId = value.getResultId(); Optional> orgs = Optional.ofNullable(value.getMerges()); 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 50df08f8c..df8ca3805 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 @@ -2,7 +2,7 @@ package eu.dnetlib.dhp.resulttocommunityfromorganization; import static eu.dnetlib.dhp.PropagationConstant.*; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; import java.util.Arrays; @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; @@ -53,29 +54,14 @@ public class SparkResultToCommunityFromOrganizationJob { final String possibleupdatespath = parser.get("preparedInfoPath"); log.info("preparedInfoPath: {}", possibleupdatespath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); - - @SuppressWarnings("unchecked") - Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + runWithSparkSession( conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, outputPath); - if (saveGraph) { - execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath); - } + execPropagation(spark, inputPath, outputPath, possibleupdatespath); + }); } @@ -83,22 +69,32 @@ public class SparkResultToCommunityFromOrganizationJob { SparkSession spark, String inputPath, String outputPath, - Class resultClazz, String possibleUpdatesPath) { Dataset possibleUpdates = readPath(spark, possibleUpdatesPath, ResultCommunityList.class); - Dataset result = readPath(spark, inputPath, resultClazz); - result - .joinWith( - possibleUpdates, - result.col("id").equalTo(possibleUpdates.col("resultId")), - "left_outer") - .map(resultCommunityFn(), Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + ModelSupport.entityTypes + .keySet() + .parallelStream() + .forEach(e -> { + if (ModelSupport.isResult(e)) { + Class resultClazz = ModelSupport.entityTypes.get(e); + removeOutputDir(spark, outputPath + e.name()); + Dataset result = readPath(spark, inputPath + e.name(), resultClazz); + + result + .joinWith( + possibleUpdates, + result.col("id").equalTo(possibleUpdates.col("resultId")), + "left_outer") + .map(resultCommunityFn(), Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + e.name()); + } + }); + } private static MapFunction, R> resultCommunityFn() { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index 7bee1ea0c..467e11a96 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -52,11 +52,10 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("production")); - log.info("production: {}", production); + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); - final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); - // log.info("projectsMap: {}", new Gson().toJson(projectsMap)); + final CommunityEntityMap projectsMap = Utils.getCommunityProjects(baseURL); SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json index dbe2d088f..ce1a8ecab 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json @@ -1,5 +1,4 @@ [ - { "paramName":"s", "paramLongName":"sourcePath", @@ -12,7 +11,6 @@ "paramDescription": "the json path associated to each selection field", "paramRequired": true }, - { "paramName": "out", "paramLongName": "outputPath", @@ -25,19 +23,16 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { "paramName": "tg", "paramLongName": "taggingConf", "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", "paramRequired": false }, - { - "paramName": "p", - "paramLongName": "production", - "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", - "paramRequired": true + "paramName": "bu", + "paramLongName": "baseURL", + "paramDescription": "this parameter is to specify the api to be queried (beta or production)", + "paramRequired": false } - ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index e3ca72493..03373eda0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -12,21 +12,10 @@ outputPath the output path - - - postgresURL - the url of the postgress server to query + baseURL + the community API base URL - - postgresUser - the username to access the postgres db - - - postgresPassword - the postgres password - - @@ -104,15 +93,13 @@ yarn-cluster cluster - bulkTagging-publication + bulkTagging-result eu.dnetlib.dhp.bulktag.SparkBulkTagJob dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} - --conf spark.executor.memoryOverhead=${memoryOverhead} - --conf spark.sql.shuffle.partitions=${partitions} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} @@ -122,14 +109,12 @@ --sourcePath${sourcePath}/ --outputPath${outputPath}/ --pathMap${pathMap} - --production${production} + --baseURL${baseURL} - - \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq deleted file mode 100644 index 052037efb..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq +++ /dev/null @@ -1,62 +0,0 @@ -for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') -let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() -let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept -let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept -let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept -let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() -let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() -let $zenodo := $x//param[./@name='zenodoCommunity']/text() -where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' -return - -{ $x//CONFIGURATION/context/@id} - -{$x//CONFIGURATION/context/param[./@name='removeConstraints']/text() } - - -{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() } - - - {for $y in tokenize($subj,',') - return - {$y}} - {for $y in tokenize($fos,',') - return - {$y}} - {for $y in tokenize($sdg,',') - return - {$y}} - - - {for $d in $datasources - where $d/param[./@name='enabled']/text()='true' - return - - - {$d//param[./@name='openaireId']/text()} - - - {$d/param[./@name='selcriteria']/text()} - - } - - -{for $zc in $zenodo -return - - -{$zc} - -} -{for $zc in $communities -return - - -{$zc/param[./@name='zenodoid']/text()} - - -{$zc/param[./@name='selcriteria']/text()} - -} - - \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json index eebc1a0ca..0db8085d1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json @@ -5,24 +5,7 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", - "paramRequired": true - }, - { - "paramName":"sg", - "paramLongName":"saveGraph", - "paramDescription": "true if the new version of the graph must be saved", - "paramRequired": false - }, - { - "paramName":"test", - "paramLongName":"isTest", - "paramDescription": "true if it is executing a test", - "paramRequired": false - }, + { "paramName": "out", "paramLongName": "outputPath", @@ -35,12 +18,6 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, { "paramName": "p", "paramLongName": "preparedInfoPath", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json index 8df509abf..3601db7ac 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json @@ -5,12 +5,6 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"ocm", - "paramLongName":"organizationtoresultcommunitymap", - "paramDescription": "the map for the association organization communities", - "paramRequired": true - }, { "paramName":"h", "paramLongName":"hive_metastore_uris", @@ -28,6 +22,12 @@ "paramLongName": "outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true + }, + { + "paramName": "bu", + "paramLongName": "baseURL", + "paramDescription": "the base URL to the community API to use", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index 6a329fdc4..e342bce23 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -4,14 +4,14 @@ sourcePath the source path - - organizationtoresultcommunitymap - organization community map - outputPath the output path + + baseURL + the community API base URL + @@ -93,149 +93,54 @@ eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet dhp-enrichment-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} + --executor-cores=6 + --executor-memory=5G + --conf spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 --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.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/relation --outputPath${workingDir}/preparedInfo/resultCommunityList --hive_metastore_uris${hive_metastore_uris} - --organizationtoresultcommunitymap${organizationtoresultcommunitymap} + --baseURL${baseURL} - + - - - - - - - - + yarn cluster - community2resultfromorganization-Publication + community2resultfromorganization eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob dhp-enrichment-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} + --executor-cores=6 + --executor-memory=5G + --conf spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/publication - --outputPath${outputPath}/publication - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --saveGraph${saveGraph} + --sourcePath${sourcePath}/ + --outputPath${outputPath}/ - + - - - yarn - cluster - community2resultfromorganization-Dataset - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --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.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/dataset - --outputPath${outputPath}/dataset - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --saveGraph${saveGraph} - - - - - - - yarn - cluster - community2resultfromorganization-ORP - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/otherresearchproduct - --outputPath${outputPath}/otherresearchproduct - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --saveGraph${saveGraph} - - - - - - - - yarn - cluster - community2resultfromorganization-Software - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --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.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/software - --outputPath${outputPath}/software - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --saveGraph${saveGraph} - - - - - - diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json index 9a50c79fa..cbc01c2d5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json @@ -19,10 +19,10 @@ "paramRequired": true }, { - "paramName": "p", - "paramLongName": "production", + "paramName": "bu", + "paramLongName": "baseURL", "paramDescription": "the path used to store temporary output files", - "paramRequired": true + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml index 21cc2d887..d0784c94d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml @@ -4,11 +4,14 @@ sourcePath the source path - outputPath the output path + + baseURL + the community API base URL + @@ -104,7 +107,7 @@ --sourcePath${sourcePath}/relation --outputPath${workingDir}/preparedInfo/resultCommunityList - --production${production} + --baseURL${baseURL} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 7cbbcaafb..743e62b5f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.HashMap; import java.util.List; import org.apache.commons.io.FileUtils; @@ -32,8 +31,6 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," + " \"title\" : \"$['title'][*]['value']\"," + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," @@ -43,7 +40,9 @@ public class BulkTagJobTest { "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} "; + "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + + "\"publisher\":\"$['publisher'].value\"," + + "\"publicationyear\":\"$['dateofacceptance'].value\"} "; private static SparkSession spark; @@ -534,6 +533,7 @@ public class BulkTagJobTest { + "where MyD.inferenceprovenance = 'bulktagging'"; org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(7, idExplodeCommunity.count()); Assertions @@ -1573,11 +1573,10 @@ public class BulkTagJobTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(), - "-taggingConf", taggingConf, - "-outputPath", workingDir.toString() + "/", - "-production", Boolean.TRUE.toString(), - "-pathMap", pathMap +// "-baseURL", "https://services.openaire.eu/openaire/community/", + "-pathMap", pathMap, + "-taggingConf", taggingConf }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java index 4dd8b976c..6440ded92 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java @@ -72,15 +72,13 @@ public class ResultToCommunityJobTest { SparkResultToCommunityFromOrganizationJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", getClass() - .getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample") + .getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample/") .getPath(), - "-hive_metastore_uris", "", - "-saveGraph", "true", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", + + "-outputPath", workingDir.toString() + "/", "-preparedInfoPath", preparedInfoPath }); diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml index edd6c7e0a..21c7d452f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml @@ -26,7 +26,7 @@ - re3data_____::a507cdacc5bbcc08761c92185dee5cab + 10|re3data_____::a507cdacc5bbcc08761c92185dee5cab @@ -140,39 +140,39 @@ - re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + 10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 - doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + 10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815 - doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + 10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b - doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + 10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 - doajarticles::0da84e9dfdc8419576169e027baa8028 + 10|doajarticles::0da84e9dfdc8419576169e027baa8028 - re3data_____::84e123776089ce3c7a33db98d9cd15a8 + 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 - openaire____::c5502a43e76feab55dd00cf50f519125 + 10|openaire____::c5502a43e76feab55dd00cf50f519125 - re3data_____::a48f09c562b247a9919acfe195549b47 + 10|re3data_____::a48f09c562b247a9919acfe195549b47 - opendoar____::97275a23ca44226c9964043c8462be96 + 10|opendoar____::97275a23ca44226c9964043c8462be96 @@ -287,55 +287,55 @@ - doajarticles::8cec81178926caaca531afbd8eb5d64c + 10|doajarticles::8cec81178926caaca531afbd8eb5d64c - doajarticles::0f7a7f30b5400615cae1829f3e743982 + 10|doajarticles::0f7a7f30b5400615cae1829f3e743982 - doajarticles::9740f7f5af3e506d2ad2c215cdccd51a + 10|doajarticles::9740f7f5af3e506d2ad2c215cdccd51a - doajarticles::9f3fbaae044fa33cb7069b72935a3254 + 10|doajarticles::9f3fbaae044fa33cb7069b72935a3254 - doajarticles::cb67f33eb9819f5c624ce0313957f6b3 + 10|doajarticles::cb67f33eb9819f5c624ce0313957f6b3 - doajarticles::e21c97cbb7a209afc75703681c462906 + 10|doajarticles::e21c97cbb7a209afc75703681c462906 - doajarticles::554cde3be9e5c4588b4c4f9f503120cb + 10|doajarticles::554cde3be9e5c4588b4c4f9f503120cb - tubitakulakb::11e22f49e65b9fd11d5b144b93861a1b + 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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+{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055422336,"id":"50|od______2017::0750a4d0782265873d669520f5e33c07","originalId":["od______2017::0750a4d0782265873d669520f5e33c07"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção integrada","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"O uso dos pesticidas em Portugal. Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das culturas.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2016-07-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Quercus","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/chicago-covid-19"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobretodo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que puede tener para el deportista. \"Lo que estamos investigando es cómo una sustancia, que te puede hacer rendir mejor, cómo puede afectar negativamente cuando termina una competición\".\n\nPero esta investigación no sólo puede extraer conclusiones interesantes y útiles para los deportistas profesionales, \"investigando el deporte de alto rendimiento podemos conocer los beneficios y perjuicios de la cafeína que también afectarían al deportista amateur y hacer un deporte en general más seguro\".\n\nPara el desarrollo de este proyecto de investigación están colaborando el Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela y la Agencia para la Protección de la Salud en el Deporte.\nPara el desarrollo de este proyecto de investigación están colaborando el Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela y la Agencia para la Protección de la Salud en el 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobretodo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this population.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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- protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance(); + protected static final UrlValidator URL_VALIDATOR = new UrlValidator(UrlValidator.ALLOW_2_SLASHES); private final boolean invisible; @@ -41,6 +41,7 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; + protected static final Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -169,7 +170,8 @@ public abstract class AbstractMdRecordToOafMapper { final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity( + doc, type, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -516,6 +518,19 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + protected abstract String findOriginalType(Document doc); + + protected List prepareInstanceTypeMapping(Document doc) { + return Optional + .ofNullable(findOriginalType(doc)) + .map(originalType -> { + final List mappings = Lists.newArrayList(); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + return mappings; + }) + .orElse(new ArrayList<>()); + } + private Journal prepareJournal(final Document doc, final DataInfo info) { final Node n = doc.selectSingleNode("//oaf:journal"); if (n != null) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index a9f9367af..a63296d18 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -139,6 +139,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -187,6 +189,29 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { return Lists.newArrayList(instance); } + /** + * The Dublin Core element dc:type can be repeated, but we need to base our mapping on a single value + * So this method tries to give precedence to the COAR resource type, when available. Otherwise, it looks for the + * openaire's info:eu-repo type, and as last resort picks the 1st type text available + * + * http://purl.org/coar/resource_type/c_5794 + * info:eu-repo/semantics/article + * Conference article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + return (String) doc + .selectNodes("//dc:type") + .stream() + .map(o -> "" + ((Node) o).getText().trim()) + .sorted(new OriginalTypeComparator()) + .findFirst() + .orElse(null); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return prepareListFields(doc, "//dc:source", info); 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 bbd1e7ab1..e63b01a00 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 @@ -9,6 +9,7 @@ import java.net.URLDecoder; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -139,6 +140,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -217,6 +220,30 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } } + /** + * The Datacite element + * + * journal article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + return Optional + .ofNullable( + (Element) doc + .selectSingleNode( + "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) + .map(element -> { + final String resourceTypeURI = element.attributeValue("anyURI"); + final String resourceTypeTxt = element.getText(); + + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + }) + .orElse(null); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return new ArrayList<>(); // Not present in ODF ??? diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java new file mode 100644 index 000000000..c3d8b4789 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -0,0 +1,33 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static org.apache.commons.lang3.StringUtils.contains; +import static org.apache.commons.lang3.StringUtils.startsWith; + +import java.util.Comparator; + +public class OriginalTypeComparator implements Comparator { + + @Override + public int compare(String t1, String t2) { + + if (t1.equals(t2)) { + return 0; + } + if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { + return -1; + } + if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { + return 1; + } + if (startsWith(t1, "info:eu-repo/semantics")) { + return -1; + } + if (startsWith(t2, "info:eu-repo/semantics")) { + return 1; + } + + return t1.compareTo(t2); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json new file mode 100644 index 000000000..765c0e8ff --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "orcidPath", + "paramDescription": "the path of the orcid Table generated by the dump", + "paramRequired": true + }, + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the path of the graph we want to apply enrichment", + "paramRequired": true + }, + { + "paramName": "tp", + "paramLongName": "targetPath", + "paramDescription": "the output path of the graph enriched", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml new file mode 100644 index 000000000..8a7bc8942 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + 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 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml new file mode 100644 index 000000000..ce117b5e9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml @@ -0,0 +1,84 @@ + + + + orcidPath + the path of the orcid Table generated by the dump + + + graphPath + the path of the graph we want to apply enrichment + + + targetPath + the output path of the graph enriched + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Enrich Graph with ORCID + eu.dnetlib.dhp.enrich.orcid.SparkEnrichGraphWithOrcidAuthors + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --orcidPath${orcidPath} + --targetPath${targetPath} + --graphPath${graphPath} + --masteryarn + + + + + + + + ${nameNode}/${graphPath}/datasource + ${nameNode}/${targetPath}/datasource + + + + + + + ${nameNode}/${graphPath}/organization + ${nameNode}/${targetPath}/organization + + + + + + + ${nameNode}/${graphPath}/project + ${nameNode}/${targetPath}/project + + + + + + + ${nameNode}/${graphPath}/relation + ${nameNode}/${targetPath}/relation + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml index 190788c9d..2f44bea9d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml @@ -12,6 +12,10 @@ graphOutputPath path of the output graph + + isLookupUrl + the URL address of the lookUp service + filterInvisible whether filter out invisible entities after merge @@ -98,6 +102,7 @@ --graphInputPath${graphBasePath} --checkpointPath${workingPath}/grouped_entities --outputPath${graphOutputPath} + --isLookupUrl${isLookupUrl} --filterInvisible${filterInvisible} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala new file mode 100644 index 000000000..15513c8af --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala @@ -0,0 +1,40 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import eu.dnetlib.dhp.schema.sx.OafUtils +import org.apache.spark.sql.Row + +import scala.collection.JavaConverters._ + +object AuthorEnricher extends Serializable { + + def createAuthor(givenName: String, familyName: String, orcid: String): Author = { + val a = new Author + a.setName(givenName) + a.setSurname(familyName) + a.setFullname(s"$givenName $familyName") + val pid = OafUtils.createSP(orcid, ModelConstants.ORCID, ModelConstants.ORCID) + pid.setDataInfo(OafUtils.generateDataInfo()) + pid.getDataInfo.setProvenanceaction(OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT")) + a.setPid(List(pid).asJava) + a + } + + def toOAFAuthor(r: Row): java.util.List[Author] = { + r.getList[Row](1) + .asScala + .map(s => createAuthor(s.getAs[String]("givenName"), s.getAs[String]("familyName"), s.getAs[String]("orcid"))) + .toList + .asJava + } + +// def enrichAuthor(p:Publication,r:Row): Unit = { +// val k:Map[String, OAuthor] =r.getList[Row](1).asScala.map(s => (s.getAs[String]("orcid"), OAuthor(s.getAs[String]("givenName") ,s.getAs[String]("familyName") ))).groupBy(_._1).mapValues(_.map(_._2).head) +// println(k) +// +// +// +// } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala new file mode 100644 index 000000000..4822059c6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -0,0 +1,138 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software} +import org.apache.spark.sql.functions._ +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ + +class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + val graphPath = parser.get("graphPath") + log.info(s"graphPath is '$graphPath'") + val orcidPath = parser.get("orcidPath") + log.info(s"orcidPath is '$orcidPath'") + val targetPath = parser.get("targetPath") + log.info(s"targetPath is '$targetPath'") + val orcidPublication: Dataset[Row] = generateOrcidTable(spark, orcidPath) +// ModelSupport.entityTypes.entrySet().asScala.filter(k => k.getKey.getClass isInstance(Result)) + + enrichResult( + spark, + s"$graphPath/publication", + orcidPublication, + s"$targetPath/publication", + Encoders.bean(classOf[Publication]) + ) + enrichResult( + spark, + s"$graphPath/dataset", + orcidPublication, + s"$targetPath/dataset", + Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset]) + ) + enrichResult( + spark, + s"$graphPath/software", + orcidPublication, + s"$targetPath/software", + Encoders.bean(classOf[Software]) + ) + enrichResult( + spark, + s"$graphPath/otherresearchproduct", + orcidPublication, + s"$targetPath/otherresearchproduct", + Encoders.bean(classOf[OtherResearchProduct]) + ) + } + + private def enrichResult[T <: Result]( + spark: SparkSession, + graphPath: String, + orcidPublication: Dataset[Row], + outputPath: String, + enc: Encoder[T] + ): Unit = { + + val entities = spark.read + .schema(enc.schema) + .json(graphPath) + .select(col("id"), col("datainfo"), col("instance")) + .where("datainfo.deletedbyinference != true") + .drop("datainfo") + .withColumn("instances", explode(col("instance"))) + .withColumn("pids", explode(col("instances.pid"))) + .select( + col("pids.qualifier.classid").alias("pid_schema"), + col("pids.value").alias("pid_value"), + col("id").alias("dnet_id") + ) + + val orcidDnet = orcidPublication + .join( + entities, + lower(col("schema")).equalTo(lower(col("pid_schema"))) && + lower(col("value")).equalTo(lower(col("pid_value"))), + "inner" + ) + .groupBy(col("dnet_id")) + .agg(collect_set(orcidPublication("author")).alias("orcid_authors")) + .select("dnet_id", "orcid_authors") + .cache() + orcidDnet.count() + val result = spark.read.schema(enc.schema).json(graphPath).as[T](enc) + + result + .joinWith(orcidDnet, result("id").equalTo(orcidDnet("dnet_id")), "left") + .map { + case (r: T, null) => + r + case (p: T, r: Row) => + p.setAuthor(AuthorMerger.enrichOrcid(p.getAuthor, AuthorEnricher.toOAFAuthor(r))) + p + }(enc) + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath) + } + + private def generateOrcidTable(spark: SparkSession, inputPath: String): Dataset[Row] = { + val orcidAuthors = + spark.read.load(s"$inputPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + val orcidWorks = spark.read + .load(s"$inputPath/Works") + .select(col("orcid"), explode(col("pids")).alias("identifier")) + .where( + "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" + ) + val orcidPublication = orcidAuthors + .join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) + .select( + col("identifier.schema").alias("schema"), + col("identifier.value").alias("value"), + struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") + ) + orcidPublication.cache() + } +} + +object SparkEnrichGraphWithOrcidAuthors { + + val log: Logger = LoggerFactory.getLogger(SparkEnrichGraphWithOrcidAuthors.getClass) + + def main(args: Array[String]): Unit = { + new SparkEnrichGraphWithOrcidAuthors("/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json", args, log) + .initialize() + .run() + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 65182108e..4ae3f82c2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -251,9 +251,19 @@ public class CleanGraphSparkJobTest { .filter(String.format("id = '%s'", id)) .first(); + final Set invalidURLs = new HashSet<>(); + invalidURLs.add("http://academia.edu/abcd"); + invalidURLs.add("http://repo.scoap3.org/api"); + invalidURLs.add("http://hdl.handle.net/"); + assertNull(p_in.getBestaccessright()); assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Publication); + assertNotNull(p_in.getAuthor()); + assertEquals(14, p_in.getAuthor().size()); + assertNotNull(p_in.getInstance()); + assertNotNull(p_in.getInstance().get(0)); + assertEquals(3, p_in.getInstance().get(0).getUrl().stream().filter(invalidURLs::contains).count()); new CleanGraphSparkJob( args( @@ -273,6 +283,9 @@ public class CleanGraphSparkJobTest { assertNull(p.getPublisher()); + assertNotNull(p.getAuthor()); + assertEquals(12, p.getAuthor().size()); + assertEquals("und", p.getLanguage().getClassid()); assertEquals("Undetermined", p.getLanguage().getClassname()); @@ -364,6 +377,8 @@ public class CleanGraphSparkJobTest { .stream() .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + assertTrue(p.getInstance().get(0).getUrl().stream().noneMatch(invalidURLs::contains)); + assertNotNull(p.getSubject()); List fos_subjects = p @@ -675,6 +690,38 @@ public class CleanGraphSparkJobTest { } + @Test + void testClean_ORP() throws Exception { + final String prefix = "gcube "; + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/orp", + "--outputPath", graphOutputPath + "/orp", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", OtherResearchProduct.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + Dataset orp = read(spark, graphOutputPath + "/orp", OtherResearchProduct.class); + + assertEquals(1, orp.count()); + + } + @Test void testCleanCfHbSparkJob() throws Exception { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index 0887adf45..242aed88e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -1,15 +1,23 @@ package eu.dnetlib.dhp.oa.graph.group; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; import java.io.IOException; import java.net.URISyntaxException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; @@ -17,20 +25,36 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +@ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class GroupEntitiesSparkJobTest { + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + private static SparkSession spark; private static ObjectMapper mapper = new ObjectMapper() @@ -45,10 +69,10 @@ public class GroupEntitiesSparkJobTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + workingDir = Files.createTempDirectory(GroupEntitiesSparkJobTest.class.getSimpleName()); SparkConf conf = new SparkConf(); - conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setAppName(GroupEntitiesSparkJobTest.class.getSimpleName()); conf.setMaster("local"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); @@ -56,10 +80,17 @@ public class GroupEntitiesSparkJobTest { } @BeforeEach - public void beforeEach() throws IOException, URISyntaxException { + public void beforeEach() throws IOException, URISyntaxException, ISLookUpException { dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); checkpointPath = workingDir.resolve("grouped_entity"); outputPath = workingDir.resolve("dispatched_entity"); + + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); } @AfterAll @@ -71,18 +102,17 @@ public class GroupEntitiesSparkJobTest { @Test @Order(1) void testGroupEntities() throws Exception { - GroupEntitiesSparkJob.main(new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-graphInputPath", - dataInputPath.toString(), - "-checkpointPath", - checkpointPath.toString(), - "-outputPath", - outputPath.toString(), - "-filterInvisible", - Boolean.FALSE.toString() - }); + new GroupEntitiesSparkJob( + args( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json", + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--graphInputPath", dataInputPath.toString(), + "--checkpointPath", checkpointPath.toString(), + "--outputPath", outputPath.toString(), + "--filterInvisible", Boolean.FALSE.toString(), + "--isLookupUrl", "lookupurl" + })).run(false, isLookUpService); Dataset checkpointTable = spark .read() @@ -109,6 +139,14 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); assertEquals(3, output.count()); + + List resultTypes = output + .map((MapFunction) value -> value.getResulttype().getClassid(), Encoders.STRING()) + .distinct() + .collectAsList(); + + assertEquals(2, resultTypes.size()); + assertEquals( 2, output @@ -121,5 +159,68 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) .filter((FilterFunction) s -> s.equals("dataset")) .count()); + + Result result = output + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + + result.getInstance().forEach(instance -> { + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "journal-article".equals(itm.getOriginalType())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_2df8fbb1", coarType.get().getTypeCode()); + assertEquals("research article", coarType.get().getTypeLabel()); + }); + + final Dataset filtered = output.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'"); + assertEquals(1, filtered.count()); + result = filtered.first(); + + result + .getInstance() + .stream() + .flatMap(instance -> instance.getInstanceTypeMapping().stream()) + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "Patent".equals(itm.getOriginalType())) + .forEach(itm -> { + assertEquals("http://purl.org/coar/resource_type/c_15cd", itm.getTypeCode()); + assertEquals("patent", itm.getTypeLabel()); + }); } + + private List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"))); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + GroupEntitiesSparkJobTest.class.getResourceAsStream(path))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 53b3f8432..6d6b2ffbd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -92,13 +92,14 @@ class GenerateEntitiesApplicationTest { private List vocs() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + GenerateEntitiesApplicationTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); } private List synonyms() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + GenerateEntitiesApplicationTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } } 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 b506d3a62..ac0435ce2 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 @@ -14,6 +14,8 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import org.dom4j.DocumentException; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -25,8 +27,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.CleaningRuleMap; +import eu.dnetlib.dhp.oa.graph.clean.OafCleaner; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -74,7 +79,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -97,14 +102,14 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); + assertFalse(p.getSubject().isEmpty()); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertTrue(p.getPid().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -116,6 +121,27 @@ class MappersTest { assertNotNull(instance.getPid()); assertTrue(instance.getPid().isEmpty()); + assertNotNull(instance.getInstanceTypeMapping()); + assertEquals(1, instance.getInstanceTypeMapping().size()); + + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); + + Optional userType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); + + assertFalse(userType.isPresent()); + assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue()); @@ -207,7 +233,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -230,13 +256,13 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getPid().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getPid().isEmpty()); assertEquals("PMC1517292", p.getPid().get(0).getValue()); assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -245,8 +271,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); assertNotNull(p.getInstance().get(0).getPid()); assertEquals(2, p.getInstance().get(0).getPid().size()); @@ -266,7 +292,7 @@ class MappersTest { final List list = new OafToOafMapper(vocs, true, true).processMdRecord(xml); - assertTrue(list.size() > 0); + assertFalse(list.isEmpty()); assertTrue(list.get(0) instanceof Publication); final Publication p = (Publication) list.get(0); @@ -322,7 +348,7 @@ class MappersTest { assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertTrue(d.getAuthor().size() > 0); + assertFalse(d.getAuthor().isEmpty()); final Optional author = d .getAuthor() @@ -356,13 +382,13 @@ class MappersTest { final Field affiliation = opAff.get(); assertEquals("ISTI-CNR", affiliation.getValue()); - assertTrue(d.getSubject().size() > 0); - assertTrue(d.getInstance().size() > 0); - assertTrue(d.getContext().size() > 0); - assertTrue(d.getContext().get(0).getId().length() > 0); + assertFalse(d.getSubject().isEmpty()); + assertFalse(d.getInstance().isEmpty()); + assertFalse(d.getContext().isEmpty()); + assertFalse(d.getContext().get(0).getId().isEmpty()); assertNotNull(d.getInstance()); - assertTrue(d.getInstance().size() > 0); + assertFalse(d.getInstance().isEmpty()); d .getInstance() .forEach(i -> { @@ -436,7 +462,7 @@ class MappersTest { // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -448,14 +474,14 @@ class MappersTest { assertEquals("Potwarka", author.get().getSurname()); assertEquals("Luke R.", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -464,8 +490,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -583,8 +609,129 @@ class MappersTest { assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059")); Dataset d_cleaned = cleanup(d, vocs); - assertEquals("0000", d_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", d_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + } + + @Test + void test_record_from_Crossref() throws IOException { + + final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); + + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_crossref.xml"))); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Publication); + + final Publication p = OafCleaner.apply(fixVocabularyNames((Publication) list.get(0)), mapping); + + assertNotNull(p.getDateofcollection()); + assertEquals("2020-08-06T07:04:09.62Z", p.getDateofcollection()); + + assertNotNull(p.getDateoftransformation()); + assertEquals("2020-08-06T07:20:57.911Z", p.getDateoftransformation()); + + assertNotNull(p.getDataInfo()); + assertFalse(p.getDataInfo().getInvisible()); + assertFalse(p.getDataInfo().getDeletedbyinference()); + assertEquals("0.9", p.getDataInfo().getTrust()); + + assertValidId(p.getId()); + assertEquals(2, p.getOriginalId().size()); + + assertEquals("50|doi_________::7f0f7807f17db50e5c2b5c452ccaf06d", p.getOriginalId().get(0)); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertEquals(1, p.getTitle().size()); + assertEquals( + "A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine", + p + .getTitle() + .get(0) + .getValue()); + + assertNotNull(p.getDescription()); + assertEquals(0, p.getDescription().size()); + + assertEquals(8, p.getAuthor().size()); + + assertNotNull(p.getInstance()); + assertEquals(1, p.getInstance().size()); + + final Instance i = p.getInstance().get(0); + + assertNotNull(i.getAccessright()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename()); + assertEquals("OPEN", i.getAccessright().getClassid()); + assertEquals("Open Access", i.getAccessright().getClassname()); + + assertNotNull(i.getCollectedfrom()); + assertEquals("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", i.getCollectedfrom().getKey()); + assertEquals("Crossref", i.getCollectedfrom().getValue()); + + assertNotNull(i.getHostedby()); + assertEquals("10|openaire____::55045bd2a65019fd8e6741a755395c8c", i.getHostedby().getKey()); + assertEquals("Unknown Repository", i.getHostedby().getValue()); + + assertNotNull(i.getInstancetype()); + assertEquals("0001", i.getInstancetype().getClassid()); + assertEquals("Article", i.getInstancetype().getClassname()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename()); + + assertNull(i.getLicense()); + assertNotNull(i.getDateofacceptance()); + assertEquals("2020-06-04", i.getDateofacceptance().getValue()); + + assertNull(i.getProcessingchargeamount()); + assertNull(i.getProcessingchargecurrency()); + + assertNotNull(i.getPid()); + assertEquals(1, i.getPid().size()); + + assertNotNull(i.getAlternateIdentifier()); + assertEquals(0, i.getAlternateIdentifier().size()); + + assertNotNull(i.getUrl()); + assertEquals(1, i.getUrl().size()); + assertTrue(i.getUrl().contains("http://dx.doi.org/10.1080/23744235.2020.1774644")); + + assertEquals("", p.getInstance().get(0).getRefereed().getClassid()); + assertEquals("", p.getInstance().get(0).getRefereed().getClassname()); + + Publication p_cleaned = cleanup(p, vocs); + + assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + + assertNull(p_cleaned.getMetaResourceType()); + + assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); + assertEquals(1, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .anyMatch( + t -> "journal-article".equals(t.getOriginalType()) && + ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && + Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel()))); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .noneMatch( + t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()))); } @Test @@ -603,9 +750,9 @@ class MappersTest { assertValidId(s.getId()); assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); - assertTrue(s.getAuthor().size() > 0); - assertTrue(s.getSubject().size() > 0); - assertTrue(s.getInstance().size() > 0); + assertFalse(s.getAuthor().isEmpty()); + assertFalse(s.getSubject().isEmpty()); + assertFalse(s.getInstance().isEmpty()); final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); @@ -797,6 +944,20 @@ class MappersTest { assertFalse(p_cleaned.getTitle().isEmpty()); } + @Test + void test_instance_url_validation() throws IOException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml"))); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + final Publication p = (Publication) list.get(0); + + assertNotNull(p.getInstance()); + assertFalse(p.getInstance().isEmpty()); + assertNotNull(p.getInstance().get(0).getUrl()); + assertFalse(p.getInstance().get(0).getUrl().isEmpty()); + assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0)); + } + @Test void testZenodo() throws IOException, DocumentException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); @@ -861,7 +1022,7 @@ class MappersTest { assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -871,14 +1032,14 @@ class MappersTest { assertEquals("Museum Sønderjylland", author.get().getFullname()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -887,8 +1048,8 @@ class MappersTest { }); Dataset p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -918,10 +1079,10 @@ class MappersTest { System.out.println("***************"); final Dataset p = (Dataset) list.get(0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); for (String url : p.getInstance().get(0).getUrl()) { System.out.println(url); - assertTrue(!url.contains("&")); + assertFalse(url.contains("&")); } } @@ -938,7 +1099,7 @@ class MappersTest { assertTrue(o.isPresent()); Publication p = (Publication) o.get(); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); assertEquals("https://doi.org/10.1155/2015/439379", p.getInstance().get(0).getUrl().get(0)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/orp/orp.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/orp/orp.json new file mode 100644 index 000000000..85045e361 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/orp/orp.json @@ -0,0 +1 @@ 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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml new file mode 100644 index 000000000..1bfa3c7c3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml @@ -0,0 +1,65 @@ + + +
+ od______3272::6a4d00217a024a46ce9697ce98b13c2a + oai:idus.us.es:11441/118940 + + + + + + 2021-08-20T12:32:32.826Z + 2023-07-04T15:47:55.397Z + od______3272 +
+ + El museo pictorico y escala optica : tomo I : theorica de la pintura en que se describe su origen ... y se aprueban con demonstraciomes mathematicas y filosoficas, sus mas radicales fundamentos + Palomino de Castro y Velasco, Antonio, 1653-1726 + Rovira y Brocandel, Hipólito, 1693-1765 + Palomino de Castro y Velasco, Antonio, 1653-1726 + 2021-08-12T08:59:53Z + 1715 + A 042(a)/063 + application/pdf + https://idus.us.es/handle//11441/118940 + spa + En Madrid : por Lucas Antonio de Bedmar ... : vendese en casa de Don Joseph de Villar y Villanueva, 1715 + info:eu-repo/semantics/book + info:eu-repo/semantics/publishedVersion + 0002 + 1715-01-01 + + opendoar____::3272 + OPEN + + + https://idus.us.es/handle//11441/118940 + + http://creativecommons.org/licenses/by-nc-nd/4.0/ + + + + + http%3A%2F%2Fidus.us.es%2Foai%2Fdriver + oai:idus.us.es:11441/118940 + 2021-08-12T08:59:54Z + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml new file mode 100644 index 000000000..182820a08 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml @@ -0,0 +1,68 @@ + + +
+ doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + 2020-08-06T07:04:09.62Z + + + + + + 2020-08-06T07:20:57.911Z + openaire____ +
+ + A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine + Maillart, E. + Leemans, S. + Van Noten, H. + Vandergraesen, T. + Mahadeb, B. + Salaouatchi, M. T. + De Bels, D. + Clevenbergh, P. + + http://dx.doi.org/10.1080/23744235.2020.1774644 + + Informa UK Limited + Crossref + Infectious Diseases + Microbiology (medical) + General Immunology and Microbiology + Infectious Diseases + General Medicine + journal-article + 0001 + 2020-06-04 + + OPEN + + + 10.1080/23744235.2020.1774644 + Infectious Diseases + + + + + file%3A%2F%2F%2Fsrv%2Fclaims%2Frecords%2Fpublication%2Fcrossref + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file 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 277578185..492fc9a7a 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 @@ -47,7 +47,9 @@ provisioning services regulating services supporting services - Research Article + conference paper + http://purl.org/coar/resource_type/c_5794 + info:eu-repo/semantics/article 0001 2017-01-01 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala new file mode 100644 index 000000000..cb05332b2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala @@ -0,0 +1,77 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import org.apache.spark.sql.{Column, Encoder, Encoders, Row, SparkSession} +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} +import org.apache.spark.sql.functions._ + +class EnrichOrcidTest { + + val log: Logger = LoggerFactory.getLogger(getClass) + + def test() = { + val spark = SparkSession.builder().master("local[*]").getOrCreate() +// spark.sparkContext.setLogLevel("ERROR") + +// new SparkEnrichGraphWithOrcidAuthors(null, null, null) +// .enrichResult( +// spark, +// "/Users/sandro/orcid_test/publication", +// "", +// "/tmp/graph/", +// Encoders.bean(classOf[Publication]) +// ) + + val schema = Encoders.bean(classOf[Publication]).schema +// +// val simplifyAuthor = udf((r: Seq[Row]) => { +// r +// .map(k => +// AuthorPid( +// k.getAs[String]("fullname"), +// k.getAs[Seq[Row]]("pid") +// .map(p => Pid(p.getAs[Row]("qualifier").getAs[String]("classid"), p.getAs[String]("value"))) +// .toList +// ) +// ) +// .filter(l => l.pids.nonEmpty) +// .toList +// }) +// +// val wrong_orcid_intersection = udf((a: Seq[Row]) => { +// a.map(author => { +// val pids_with_orcid: Seq[Row] = author +// .getAs[Seq[Row]]("pids") +// .filter(p => +// p.getAs[String]("pidScheme") != null && p.getAs[String]("pidScheme").toLowerCase.contains("orcid") +// ) +// if (pids_with_orcid.exists(p => p.getAs[String]("pidScheme").equals("ORCID"))) { +// if (pids_with_orcid.map(p => p.getAs[String]("pidValue").toLowerCase).distinct.size > 1) { +// AuthorPid( +// author.getAs[String]("fullName"), +// pids_with_orcid.map(p => Pid(p.getAs[String]("pidScheme"), p.getAs[String]("pidValue"))).toList +// ) +// +// } else +// null +// } else +// null +// }).filter(author => author != null) +// }) + + Encoders + import spark.implicits._ + +// val enriched = spark.read +// .schema(schema) +// .json("/Users/sandro/orcid_test/publication_enriched") +// .select(col("id"), explode(col("author")).as("authors")) +// .withColumn("ap", col("authors.pid.qualifier.classid")) +// .withColumn("dp", col("authors.pid.datainfo.provenanceAction.classid")) +// +// .show() + + } + +} 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 3b810ba8c..4d9d9c341 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 @@ -434,6 +434,24 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("processingchargecurrency", r.getProcessingchargecurrency().getValue())); } + if (r.getIsGreen() != null) { + metadata + .add(XmlSerializationUtils.asXmlElement("isgreen", Boolean.toString(r.getIsGreen()))); + } + if (r.getOpenAccessColor() != null) { + metadata + .add(XmlSerializationUtils.asXmlElement("openaccesscolor", r.getOpenAccessColor().toString())); + } + if (r.getIsInDiamondJournal() != null) { + metadata + .add( + XmlSerializationUtils + .asXmlElement("isindiamondjournal", Boolean.toString(r.getIsInDiamondJournal()))); + } + if (r.getPubliclyFunded() != null) { + metadata + .add(XmlSerializationUtils.asXmlElement("publiclyfunded", Boolean.toString(r.getPubliclyFunded()))); + } } switch (type) { diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index ce593cf07..e72883055 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -78,6 +78,22 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } + @Test + void testPeerReviewed() throws IOException, TransformerException { + + final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, + XmlConverterJob.schemaLocation); + + final Publication p = load("publication.json", Publication.class); + + final JoinedEntity je = new JoinedEntity<>(p); + final String record = xmlRecordFactory.build(je); + assertNotNull(record); + SolrInputDocument solrDoc = testRecordTransformation(record); + + assertEquals("true", solrDoc.get("peerreviewed").getValue()); + } + @Test public void testRiunet() throws IOException, TransformerException { @@ -184,7 +200,7 @@ public class IndexRecordTransformerTest { } } - private void testRecordTransformation(final String record) throws IOException, TransformerException { + private SolrInputDocument testRecordTransformation(final String record) throws IOException, TransformerException { final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")); @@ -200,6 +216,8 @@ public class IndexRecordTransformerTest { Assertions.assertNotNull(xmlDoc); System.out.println(xmlDoc); + + return solrDoc; } private T load(final String fileName, final Class clazz) throws IOException { diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java index 6f1956578..a3a140cf6 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java @@ -1,9 +1,12 @@ package eu.dnetlib.dhp.oa.provision; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.io.IOException; import java.io.StringReader; import java.net.URI; +import java.util.Map; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; @@ -11,6 +14,7 @@ import org.apache.solr.client.solrj.SolrQuery; import org.apache.solr.client.solrj.response.QueryResponse; import org.apache.solr.common.SolrInputField; import org.apache.solr.common.params.CommonParams; +import org.apache.solr.common.params.ModifiableSolrParams; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -101,14 +105,38 @@ public class XmlIndexingJobTest extends SolrTest { new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) .run(isLookupClient); - Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*")); - Assertions - .assertEquals( - nRecord, rsp.getResults().getNumFound(), - "the number of indexed records should be equal to the number of input records"); + assertEquals( + nRecord, rsp.getResults().getNumFound(), + "the number of indexed records should be equal to the number of input records"); + + rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isgreen:true")); + assertEquals( + 0, rsp.getResults().getNumFound(), + "the number of indexed records having isgreen = true"); + + rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze")); + assertEquals( + 0, rsp.getResults().getNumFound(), + "the number of indexed records having openaccesscolor = bronze"); + + rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true")); + assertEquals( + 0, rsp.getResults().getNumFound(), + "the number of indexed records having isindiamondjournal = true"); + + rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "publiclyfunded:true")); + assertEquals( + 0, rsp.getResults().getNumFound(), + "the number of indexed records having publiclyfunded = true"); + + rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "peerreviewed:true")); + assertEquals( + 0, rsp.getResults().getNumFound(), + "the number of indexed records having peerreviewed = true"); } @Test @@ -126,7 +154,7 @@ public class XmlIndexingJobTest extends SolrTest { .map(s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH)) .distinct() .count(); - Assertions.assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records"); + assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records"); final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString(); new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.HDFS, outputPath) @@ -142,7 +170,7 @@ public class XmlIndexingJobTest extends SolrTest { }, Encoders.STRING()) .distinct() .count(); - Assertions.assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output records"); + assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output records"); } 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 88bffd0e7..de69795f8 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 @@ -32,7 +32,7 @@ public class XmlRecordFactoryTest { .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); @Test - public void testXMLRecordFactory() throws IOException, DocumentException { + void testXMLRecordFactory() throws IOException, DocumentException { final ContextMapper contextMapper = new ContextMapper(); @@ -93,6 +93,10 @@ public class XmlRecordFactoryTest { "https://osf.io/preprints/socarxiv/7vgtu/download", doc.valueOf("//*[local-name() = 'result']/fulltext[1]")); + assertEquals("true", doc.valueOf("//*[local-name() = 'result']/isgreen/text()")); + assertEquals("bronze", doc.valueOf("//*[local-name() = 'result']/openaccesscolor/text()")); + assertEquals("true", doc.valueOf("//*[local-name() = 'result']/isindiamondjournal/text()")); + assertEquals("true", doc.valueOf("//*[local-name() = 'result']/publiclyfunded/text()")); } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml index 0bf588a57..ba3fa83df 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -1,116 +1,137 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file 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 index eec6c1493..d25c990a1 100644 --- 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 @@ -1067,8 +1067,8 @@ "schemename": "dnet:dataCite_resource" }, "refereed": { - "classid": "0001", - "classname": "peerReviewed", + "classid": "0002", + "classname": "nonPeerReviewed", "schemeid": "dnet:review_levels", "schemename": "dnet:review_levels" }, @@ -1968,5 +1968,9 @@ "schemename": "dnet:provenanceActions" } } - } + }, + "isGreen": true, + "openAccessColor": "bronze", + "isInDiamondJournal": true, + "publiclyFunded": true } \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema index 39c811f83..4e85ca3be 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema @@ -219,20 +219,6 @@ - - - - - - - - - - - - - - @@ -368,6 +354,11 @@ + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema index 977e0b2d7..e191c6223 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema @@ -365,7 +365,14 @@ + + + + + + + diff --git a/dhp-workflows/dhp-stats-actionsets/pom.xml b/dhp-workflows/dhp-stats-actionsets/pom.xml new file mode 100644 index 000000000..3daa8f995 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/pom.xml @@ -0,0 +1,75 @@ + + + 4.0.0 + + eu.dnetlib.dhp + dhp-workflows + 1.2.5-SNAPSHOT + + dhp-stats-actionsets + + + + org.apache.httpcomponents + httpclient + + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + + net.sf.saxon + Saxon-HE + + + dom4j + dom4j + + + + xml-apis + xml-apis + + + + jaxen + jaxen + + + + org.json + json + + + + + org.apache.poi + poi-ooxml + + + + + org.apache.commons + commons-compress + + + + org.mongodb + mongo-java-driver + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java b/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java new file mode 100644 index 000000000..0c3c2f3c0 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java @@ -0,0 +1,162 @@ + +package eu.dnetlib.dhp.actionmanager.stats_actionsets; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; + +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.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.DataTypes; +import org.apache.spark.sql.types.StructField; +import org.apache.spark.sql.types.StructType; +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.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import scala.Tuple2; + +/** + * created the Atomic Action for each type of results + */ +public class StatsAtomicActionsJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(StatsAtomicActionsJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + StatsAtomicActionsJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/stats_actionsets/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 outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + conf.set("spark.speculation", "false"); + conf.set("spark.hadoop.mapreduce.map.speculative", "false"); + conf.set("spark.hadoop.mapreduce.reduce.speculative", "false"); + + final String dbname = parser.get("statsDB"); + + final String workingPath = parser.get("workingPath"); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResultEnhancement(dbname, spark, workingPath + "/resultEnhancements", "id"); + writeActionSet(spark, workingPath, outputPath); + }); + } + + private static void prepareResultEnhancement(String dbname, SparkSession spark, String workingPath, + String resultAttributeName) { + spark + .sql( + String + .format( + "select r.%s as id, is_gold, is_bronze_oa, is_hybrid,green_oa, in_diamond_journal,f.publicly_funded as publicly_funded " + + + "from %s.publication r " + + "left outer join %s.indi_pub_bronze_oa b on r.id=b.id " + + "left outer join %s.indi_pub_gold_oa g on r.id=g.id " + + "left outer join %s.indi_pub_hybrid h on r.id=h.id " + + "left outer join %s.indi_pub_green_oa gr on r.id=gr.id " + + "left outer join %s.indi_pub_diamond d on b.id=d.id " + + "left outer join %s.indi_pub_publicly_funded f on r.id=f.id ", + resultAttributeName, dbname, dbname, dbname, dbname, dbname, dbname, dbname)) + .as(Encoders.bean(StatsResultEnhancementModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + } + + public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) { + + getResultEnhancements(spark, inputPath + "/resultEnhancements") + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile( + outputPath, + Text.class, + Text.class, + SequenceFileOutputFormat.class, + GzipCodec.class); + } + + private static Dataset getResultEnhancements(SparkSession spark, String inputPath) { + + return readPath(spark, inputPath, StatsResultEnhancementModel.class) + .map((MapFunction) usm -> { + Result r = new Result(); + r.setId("50|" + usm.getId()); + r.setIsInDiamondJournal(usm.isIn_diamond_journal()); + r.setIsGreen(usm.isGreen_oa()); + r.setPubliclyFunded(usm.isPublicly_funded()); + if (usm.isIs_gold()) + r.setOpenAccessColor(OpenAccessColor.gold); + else if (usm.isIs_hybrid()) + r.setOpenAccessColor(OpenAccessColor.hybrid); + else if (usm.isIs_bronze_oa()) + r.setOpenAccessColor(OpenAccessColor.bronze); + return r; + }, Encoders.bean(Result.class)); + } + + 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-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsResultEnhancementModel.java b/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsResultEnhancementModel.java new file mode 100644 index 000000000..f794c5591 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsResultEnhancementModel.java @@ -0,0 +1,76 @@ + +package eu.dnetlib.dhp.actionmanager.stats_actionsets; + +import java.io.Serializable; + +import eu.dnetlib.dhp.schema.oaf.*; + +/** + * @author dimitris.pierrakos + * @Date 30/10/23 + */ +public class StatsResultEnhancementModel implements Serializable { + private String id; + private Boolean is_gold; + private Boolean is_bronze_oa; + private Boolean is_hybrid; + private boolean in_diamond_journal; + private boolean green_oa; + private boolean publicly_funded; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public Boolean isIs_gold() { + return is_gold; + } + + public void setIs_gold(Boolean is_gold) { + this.is_gold = is_gold; + } + + public Boolean isIs_bronze_oa() { + return is_bronze_oa; + } + + public void setIs_bronze_oa(Boolean is_bronze_oa) { + this.is_bronze_oa = is_bronze_oa; + } + + public Boolean isIs_hybrid() { + return is_hybrid; + } + + public void setIs_hybrid(Boolean is_hybrid) { + this.is_hybrid = is_hybrid; + } + + public boolean isIn_diamond_journal() { + return in_diamond_journal; + } + + public void setIn_diamond_journal(boolean in_diamond_journal) { + this.in_diamond_journal = in_diamond_journal; + } + + public boolean isGreen_oa() { + return green_oa; + } + + public void setGreen_oa(boolean green_oa) { + this.green_oa = green_oa; + } + + public boolean isPublicly_funded() { + return publicly_funded; + } + + public void setPublicly_funded(boolean publicly_funded) { + this.publicly_funded = publicly_funded; + } +} diff --git a/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/input_actionset_parameter.json b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/input_actionset_parameter.json new file mode 100644 index 000000000..bb24d4c99 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/input_actionset_parameter.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "hmu", + "paramLongName": "hive_metastore_uris", + "paramDescription": "the URI for the hive metastore", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "sdb", + "paramLongName": "statsDB", + "paramDescription": "the name of the stats db to be used", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the workingPath where to save the content of the usage_stats table", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/workflow.xml new file mode 100644 index 000000000..79fd3f56e --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/workflow.xml @@ -0,0 +1,97 @@ + + + + outputPath + the path where to store the actionset + + + statsDB + the name of the stats db to be used + + + 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 + Produces the atomic action with the stats green_oa for results + eu.dnetlib.dhp.actionmanager.stats_actionsets.StatsAtomicActionsJob + dhp-stats-actionsets-${projectVersion}.jar + + --executor-memory=${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} + + --hive_metastore_uris${hiveMetastoreUris} + --outputPath${outputPath} + --statsDB${statsDB} + --workingPath${workingDir} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-actionsets/src/main/resources/log4j.properties b/dhp-workflows/dhp-stats-actionsets/src/main/resources/log4j.properties new file mode 100644 index 000000000..81458d1f7 --- /dev/null +++ b/dhp-workflows/dhp-stats-actionsets/src/main/resources/log4j.properties @@ -0,0 +1,12 @@ +# Set root logger level to DEBUG and its only appender to A1. +log4j.rootLogger=INFO, A1 + +# A1 is set to be a ConsoleAppender. +log4j.appender.A1=org.apache.log4j.ConsoleAppender + +# A1 uses PatternLayout. +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n + +log4j.logger.org.apache.spark=FATAL +log4j.logger.org.spark_project=FATAL diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh index 431978997..18ff6dca8 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh @@ -6,7 +6,6 @@ then ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} fi -#export HADOOP_USER_NAME="dimitris.pierrakos" export HADOOP_USER_NAME=$6 export PROD_USAGE_STATS_DB="openaire_prod_usage_stats" function copydb() { diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh new file mode 100644 index 000000000..46631a0c2 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh @@ -0,0 +1,42 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +function createPDFsAggregated() { + db=$1 + +impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop table if exists indi_is_result_accessible"; + +impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "create table indi_is_result_accessible stored as parquet as + select distinct p.id, coalesce(is_result_accessible, 0) as is_result_accessible from result p + left outer join + (select id, 1 as is_result_accessible from (select pl.* from result r + join pdfaggregation_i.publication p on r.id=p.id + join pdfaggregation_i.payload pl on pl.id=p.id + union all + select pl.* from result r + join pdfaggregation_i.publication p on r.id=p.dedupid + join pdfaggregation_i.payload pl on pl.id=p.id) foo) tmp on p.id=tmp.id"; +} + +STATS_DB=$1 +MONITOR_DB=$2 +HADOOP_USER_NAME=$3 + +createPDFsAggregated $STATS_DB +createPDFsAggregated $MONITOR_DB + +createPDFsAggregated $MONITOR_DB'_funded' +createPDFsAggregated $MONITOR_DB'_institutions' +createPDFsAggregated $MONITOR_DB'_ris_tail' + +contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other" +for i in ${contexts} +do + tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'` + createPDFsAggregated ${MONITOR_DB}'_'${tmp} +done \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index 92dedf243..bbd7b3bbc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -49,5 +49,7 @@ select * from openaire_prod_usage_stats.views_stats; -- Creation date of the database ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.creation_date purge; + create table ${stats_db_name}.creation_date STORED AS PARQUET as select date_format(current_date(), 'dd-MM-yyyy') as date; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index 41c3ed751..638fb0f7a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -20,6 +20,7 @@ WHERE project_tmp.id IN (SELECT pr.id ${stats_db_name}.result r WHERE pr.result = r.id AND r.type = 'publication'); +DROP TABLE IF EXISTS ${stats_db_name}.stored purge; CREATE TABLE ${stats_db_name}.project stored as parquet as SELECT p.id, diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql index 47d147f75..0a1904de7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql @@ -1,22 +1,32 @@ ------------------------------------------------------------------------------------------------------ -- Creating parquet tables from the updated temporary tables and removing unnecessary temporary tables ------------------------------------------------------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.datasource purge; + CREATE TABLE ${stats_db_name}.datasource stored AS parquet AS SELECT * FROM ${stats_db_name}.datasource_tmp; +DROP TABLE IF EXISTS ${stats_db_name}.publication purge; + CREATE TABLE ${stats_db_name}.publication stored AS parquet AS SELECT * FROM ${stats_db_name}.publication_tmp; +DROP TABLE IF EXISTS ${stats_db_name}.dataset purge; + CREATE TABLE ${stats_db_name}.dataset stored AS parquet AS SELECT * FROM ${stats_db_name}.dataset_tmp; +DROP TABLE IF EXISTS ${stats_db_name}.software purge; + CREATE TABLE ${stats_db_name}.software stored AS parquet AS SELECT * FROM ${stats_db_name}.software_tmp; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct stored AS parquet AS SELECT * FROM ${stats_db_name}.otherresearchproduct_tmp; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 24e1a1355..6493fa7d0 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -5,6 +5,8 @@ -- Sources related tables/views ------------------------------------------------------ ------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.publication_sources purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( @@ -16,6 +18,8 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_sources purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( @@ -27,6 +31,8 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.software_sources purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( @@ -38,6 +44,8 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_sources purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( @@ -48,7 +56,7 @@ LEFT OUTER JOIN SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; - + CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_sources AS SELECT * FROM ${stats_db_name}.publication_sources UNION ALL @@ -58,6 +66,7 @@ SELECT * FROM ${stats_db_name}.software_sources UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; +DROP TABLE IF EXISTS ${stats_db_name}.result_orcid purge; CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid @@ -69,6 +78,8 @@ from ( LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res; +DROP TABLE IF EXISTS ${stats_db_name}.result_result purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_result stored as parquet as select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype from ${openaire_db_name}.relation rel @@ -82,6 +93,8 @@ where reltype='resultResult' and r2.resulttype.classname != 'other' and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.result_citations_oc purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_citations_oc stored as parquet as select substr(target, 4) as id, count(distinct substr(source, 4)) as citations from ${openaire_db_name}.relation rel @@ -97,6 +110,8 @@ where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:cr and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE group by substr(target, 4); +DROP TABLE IF EXISTS ${stats_db_name}.result_references_oc purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_references_oc stored as parquet as select substr(source, 4) as id, count(distinct substr(target, 4)) as references from ${openaire_db_name}.relation rel diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index 39755d68e..f50c13521 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -5,21 +5,29 @@ -- Licences related tables/views ------------------------------------------------------ ------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.publication_licenses purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses STORED AS PARQUET AS -SELECT substr(p.id, 4) as id, licenses.value as type +SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_licenses purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.software_licenses purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_licenses purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses @@ -34,10 +42,14 @@ SELECT * FROM ${stats_db_name}.software_licenses UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; +DROP TABLE IF EXISTS ${stats_db_name}.organization_pids purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids STORED AS PARQUET AS select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid; +DROP TABLE IF EXISTS ${stats_db_name}.organization_sources purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources STORED AS PARQUET as SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource FROM ( @@ -48,6 +60,8 @@ FROM ( from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index 4a8f81943..066b197e6 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -6,21 +6,29 @@ ------------------------------------------------------ ------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.publication_refereed purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_refereed purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.software_refereed purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_refereed purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst @@ -35,12 +43,16 @@ select * from ${stats_db_name}.software_refereed union all select * from ${stats_db_name}.otherresearchproduct_refereed; +DROP TABLE IF EXISTS ${stats_db_name}.indi_impact_measures purge; + create table if not exists ${stats_db_name}.indi_impact_measures STORED AS PARQUET as select substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score, cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] impact_class from ${openaire_db_name}.result lateral view explode(measures) measures as measures_ids where measures_ids.id!='views' and measures_ids.id!='downloads'; +DROP TABLE IF EXISTS ${stats_db_name}.result_apc_affiliations purge; + create table if not exists ${stats_db_name}.result_apc_affiliations STORED AS PARQUET as select distinct substr(rel.target,4) id, substr(rel.source,4) organization, o.legalname.value name, cast(rel.properties[0].value as double) apc_amount, diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql index 615f523ce..2c606fb92 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql @@ -1,6 +1,8 @@ ------------------------------------------- --- Extra tables, mostly used by indicators +DROP TABLE IF EXISTS ${stats_db_name}.result_projectcount purge; + create table if not exists ${stats_db_name}.result_projectcount STORED AS PARQUET as select r.id, count(distinct p.id) as count from ${stats_db_name}.result r @@ -8,6 +10,8 @@ left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.project p on p.id=rp.project group by r.id; +DROP TABLE IF EXISTS ${stats_db_name}.result_fundercount purge; + create table if not exists ${stats_db_name}.result_fundercount STORED AS PARQUET as select r.id, count(distinct p.funder) as count from ${stats_db_name}.result r @@ -15,6 +19,8 @@ left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.project p on p.id=rp.project group by r.id; +DROP TABLE IF EXISTS ${stats_db_name}.project_resultcount purge; + create table if not exists ${stats_db_name}.project_resultcount STORED AS PARQUET as with rcount as ( select p.id as pid, count(distinct r.id) as `count`, r.type as type @@ -37,6 +43,8 @@ create or replace view ${stats_db_name}.totalresearchersft as select * from stat create or replace view ${stats_db_name}.hrrst as select * from stats_ext.hrrst; create or replace view ${stats_db_name}.graduatedoctorates as select * from stats_ext.graduatedoctorates; +DROP TABLE IF EXISTS ${stats_db_name}.result_instance purge; + create table if not exists ${stats_db_name}.result_instance stored as parquet as select distinct r.* from ( @@ -45,6 +53,8 @@ from ( from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r join ${stats_db_name}.result res on res.id=r.id; +DROP TABLE IF EXISTS ${stats_db_name}.result_apc purge; + create table if not exists ${stats_db_name}.result_apc STORED AS PARQUET as select r.id, r.amount, r.currency from ( diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 6af486340..5aa14e2c2 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -1,6 +1,18 @@ -- Sprint 1 ---- drop table if exists ${stats_db_name}.indi_pub_green_oa purge; +--create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as +--select distinct p.id, coalesce(green_oa, 0) as green_oa +--from ${stats_db_name}.publication p +-- left outer join ( +-- select p.id, 1 as green_oa +-- from ${stats_db_name}.publication p +-- join ${stats_db_name}.result_instance ri on ri.id = p.id +-- join ${stats_db_name}.datasource on datasource.id = ri.hostedby +-- where datasource.type like '%Repository%' +-- and (ri.accessright = 'Open Access' +-- or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp +-- on p.id= tmp.id; create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as select distinct p.id, coalesce(green_oa, 0) as green_oa from ${stats_db_name}.publication p @@ -11,7 +23,7 @@ from ${stats_db_name}.publication p join ${stats_db_name}.datasource on datasource.id = ri.hostedby where datasource.type like '%Repository%' and (ri.accessright = 'Open Access' - or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp + or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and datasource.name!='Other') tmp on p.id= tmp.id; drop table if exists ${stats_db_name}.indi_pub_grey_lit purge; @@ -104,7 +116,7 @@ from ${stats_db_name}.tmp as o1 join ${stats_db_name}.tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name group by o1.organization, o2.organization, o1.name, o2.name; -drop table ${stats_db_name}.tmp purge; +drop table if exists ${stats_db_name}.tmp purge; create TEMPORARY TABLE ${stats_db_name}.tmp AS select distinct ro.organization organization, ro.id, o.name, o.country from ${stats_db_name}.result_organization ro @@ -118,7 +130,7 @@ from ${stats_db_name}.tmp as o1 join ${stats_db_name}.tmp as o2 on o1.id=o2.id where o1.id=o2.id and o1.country!=o2.country group by o1.organization, o1.id, o1.name, o2.country; -drop table ${stats_db_name}.tmp purge; +drop table if exists ${stats_db_name}.tmp purge; create TEMPORARY TABLE ${stats_db_name}.tmp AS select o.id organization, o.name, ro.project as project from ${stats_db_name}.organization o @@ -133,7 +145,7 @@ from ${stats_db_name}.tmp as o1 where o1.organization<>o2.organization and o1.name<>o2.name group by o1.name,o2.name, o1.organization, o2.organization; -drop table ${stats_db_name}.tmp purge; +drop table if exists ${stats_db_name}.tmp purge; create TEMPORARY TABLE ${stats_db_name}.tmp AS select o.id organization, o.name, o.country , ro.project as project from ${stats_db_name}.organization o @@ -149,7 +161,7 @@ from ${stats_db_name}.tmp as o1 where o1.organization<>o2.organization and o1.country<>o2.country group by o1.organization, o2.country, o1.name; -drop table ${stats_db_name}.tmp purge; +drop table if exists ${stats_db_name}.tmp purge; drop table if exists ${stats_db_name}.indi_funder_country_collab purge; @@ -178,20 +190,29 @@ from ${stats_db_name}.tmp as o1 where o1.country<>o2.country group by o1.country, o2.country; -drop table ${stats_db_name}.tmp purge; +drop table if exists ${stats_db_name}.tmp purge; ---- Sprint 4 ---- drop table if exists ${stats_db_name}.indi_pub_diamond purge; +--create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as +--select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal +--from ${stats_db_name}.publication_datasources pd +-- left outer join ( +-- select pd.id, 1 as in_diamond_journal from ${stats_db_name}.publication_datasources pd +-- join ${stats_db_name}.datasource d on d.id=pd.datasource +-- join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) +-- and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp +-- on pd.id=tmp.id; + create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from ${stats_db_name}.publication_datasources pd - left outer join ( - select pd.id, 1 as in_diamond_journal from ${stats_db_name}.publication_datasources pd - join ${stats_db_name}.datasource d on d.id=pd.datasource - join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) - and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp - on pd.id=tmp.id; +left outer join (select pd.id, 1 as in_diamond_journal from ${stats_db_name}.publication_datasources pd +join ${stats_db_name}.datasource d on d.id=pd.datasource +join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) +and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp +on pd.id=tmp.id; drop table if exists ${stats_db_name}.indi_pub_in_transformative purge; @@ -312,28 +333,55 @@ drop table if exists ${stats_db_name}.indi_pub_gold_oa purge; -- JOIN gold_oa on issn.issn = gold_oa.issn) tmp -- on pd.id=tmp.id; +--create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as +--with gold_oa as ( +--SELECT issn,issn_l from stats_ext.issn_gold_oa_dataset_v5), +--issn AS (SELECT * FROM +--(SELECT id,issn_printed as issn FROM ${stats_db_name}.datasource +--WHERE issn_printed IS NOT NULL +--UNION ALL +--SELECT id, issn_online as issn FROM ${stats_db_name}.datasource +--WHERE issn_online IS NOT NULL or id like '%doajarticles%') as issn +--WHERE LENGTH(issn) > 7), +--alljournals AS(select issn, issn_l from stats_ext.alljournals +--where journal_is_in_doaj=true or journal_is_oa=true) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM ${stats_db_name}.publication_datasources pd +--left outer join ( +--select pd.id, 1 as is_gold FROM ${stats_db_name}.publication_datasources pd +--JOIN issn on issn.id=pd.datasource +--JOIN gold_oa on issn.issn = gold_oa.issn +--join alljournals on issn.issn=alljournals.issn +--left outer join ${stats_db_name}.result_instance ri on ri.id=pd.id +--and ri.accessright!='Closed Access' and ri.accessright_uw='gold') tmp +--on pd.id=tmp.id; create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as with gold_oa as ( -SELECT issn,issn_l from stats_ext.issn_gold_oa_dataset_v5), -issn AS (SELECT * FROM -(SELECT id,issn_printed as issn FROM ${stats_db_name}.datasource -WHERE issn_printed IS NOT NULL -UNION ALL -SELECT id, issn_online as issn FROM ${stats_db_name}.datasource -WHERE issn_online IS NOT NULL or id like '%doajarticles%') as issn -WHERE LENGTH(issn) > 7), -alljournals AS(select issn, issn_l from stats_ext.alljournals -where journal_is_in_doaj=true or journal_is_oa=true) +select distinct issn from ( + SELECT issn_l as issn from stats_ext.issn_gold_oa_dataset_v5 + UNION ALL + SELECT issn as issn from stats_ext.issn_gold_oa_dataset_v5 + UNION ALL + select issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true + UNION ALL + select issn_l as issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true) foo), +dd as ( +select distinct * from ( + select id, issn_printed as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%' + UNION ALL + select id, issn_online as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%' + UNION ALL + select id, issn_printed as issn from ${stats_db_name}.datasource d join gold_oa on gold_oa.issn=d.issn_printed + UNION ALL + select id, issn_online as issn from ${stats_db_name}.datasource d join gold_oa on gold_oa.issn=d.issn_online) foo +) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM ${stats_db_name}.publication_datasources pd left outer join ( -select pd.id, 1 as is_gold FROM ${stats_db_name}.publication_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn -join alljournals on issn.issn=alljournals.issn -left outer join ${stats_db_name}.result_instance ri on ri.id=pd.id -and ri.accessright!='Closed Access' and ri.accessright_uw='gold') tmp -on pd.id=tmp.id; + select pd.id, 1 as is_gold + FROM ${stats_db_name}.publication_datasources pd + join dd on dd.id=pd.datasource + left outer join ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; drop table if exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc purge; @@ -421,15 +469,26 @@ drop table if exists ${stats_db_name}.indi_pub_hybrid purge; -- where (gold_oa.journal_is_in_doaj=false or gold_oa.journal_is_oa=false))tmp -- on pd.id=tmp.id; +--create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as +--select distinct pd.id,coalesce(is_hybrid,0) is_hybrid from ${stats_db_name}.publication_datasources pd +--left outer join (select pd.id, 1 as is_hybrid from ${stats_db_name}.publication_datasources pd +--join ${stats_db_name}.datasource d on pd.datasource=d.id +--join ${stats_db_name}.result_instance ri on ri.id=pd.id +--join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id +--join ${stats_db_name}.result_accessroute ra on ra.id=pd.id +--where d.type like '%Journal%' and ri.accessright!='Closed Access' and (ri.accessright_uw!='gold' +--or indi_gold.is_gold=0) and (ra.accessroute='hybrid' or ri.license is not null)) tmp +--on pd.id=tmp.id; + create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as -select pd.id,coalesce(is_hybrid,0) is_hybrid from ${stats_db_name}.publication_datasources pd -left outer join (select pd.id, 1 as is_hybrid from ${stats_db_name}.publication_datasources pd -join ${stats_db_name}.datasource d on pd.datasource=d.id +select distinct pd.id,coalesce(is_hybrid,0) is_hybrid from ${stats_db_name}.publication pd +left outer join (select pd.id, 1 as is_hybrid from ${stats_db_name}.publication pd join ${stats_db_name}.result_instance ri on ri.id=pd.id join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id join ${stats_db_name}.result_accessroute ra on ra.id=pd.id -where d.type like '%Journal%' and ri.accessright!='Closed Access' and (ri.accessright_uw!='gold' -or indi_gold.is_gold=0) and (ra.accessroute='hybrid' or ri.license is not null)) tmp +join ${stats_db_name}.datasource d on d.id=ri.hostedby +where indi_gold.is_gold=0 and ((d.type like '%Journal%' and ri.accessright!='Closed Access' and ri.accessright!='Restricted' and ri.license is not null) or +ra.accessroute='hybrid'))tmp on pd.id=tmp.id; drop table if exists ${stats_db_name}.indi_org_fairness purge; @@ -492,7 +551,7 @@ CREATE TEMPORARY TABLE ${stats_db_name}.allresults as select year, ro.organizati drop table if exists ${stats_db_name}.indi_org_fairness_pub_year purge; create table if not exists ${stats_db_name}.indi_org_fairness_pub_year stored as parquet as -select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +select cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness from ${stats_db_name}.allresults join ${stats_db_name}.result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; @@ -813,15 +872,17 @@ drop table if exists ${stats_db_name}.indi_pub_bronze_oa purge; --and (d.type='Journal' or d.type='Journal Aggregator/Publisher') --and ri.accessright='Open Access') tmp on tmp.id=p.id; -create table ${stats_db_name}.indi_pub_bronze stored as parquet as -select pd.id,coalesce(is_bronze_oa,0) is_bronze_oa from ${stats_db_name}.publication_datasources pd -left outer join (select pd.id, 1 as is_bronze_oa from ${stats_db_name}.publication_datasources pd -join ${stats_db_name}.datasource d on pd.datasource=d.id +create table ${stats_db_name}.indi_pub_bronze_oa stored as parquet as +select distinct pd.id,coalesce(is_bronze_oa,0) is_bronze_oa from ${stats_db_name}.publication pd +left outer join (select pd.id, 1 as is_bronze_oa from ${stats_db_name}.publication pd join ${stats_db_name}.result_instance ri on ri.id=pd.id join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id +join ${stats_db_name}.indi_pub_hybrid indi_hybrid on indi_hybrid.id=pd.id join ${stats_db_name}.result_accessroute ra on ra.id=pd.id -where d.type like '%Journal%' and ri.accessright!='Closed Access' and (ri.accessright_uw!='gold' -or indi_gold.is_gold=0) and (ra.accessroute='bronze' or ri.license is null)) tmp +join ${stats_db_name}.datasource d on d.id=ri.hostedby +where indi_gold.is_gold=0 and indi_hybrid.is_hybrid=0 +and ((d.type like '%Journal%' and ri.accessright!='Closed Access' +and ri.accessright!='Restricted' and ri.license is null) or ra.accessroute='bronze')) tmp on pd.id=tmp.id; CREATE TEMPORARY TABLE ${stats_db_name}.project_year_result_year as @@ -1116,3 +1177,24 @@ select allresults.ri_initiative, result_findable.no_result_findable/allresults.n from allresults join result_findable on result_findable.ri_initiative=allresults.ri_initiative; +create table if not exists ${stats_db_name}.indi_pub_publicly_funded stored as parquet as +with org_names_pids as +(select org.id,name, pid from ${stats_db_name}.organization org +join ${stats_db_name}.organization_pids op on org.id=op.id), +publicly_funded_orgs as +(select distinct name from +(select pf.name from stats_ext.insitutions_for_publicly_funded pf +join ${stats_db_name}.fundref f on f.name=pf.name where f.type='government' +union all +select pf.name from stats_ext.insitutions_for_publicly_funded pf +join ${stats_db_name}.project p on p.funder=pf.name +union all +select pf.name from stats_ext.insitutions_for_publicly_funded pf +join org_names_pids op on (op.name=pf.name or op.pid=pf.ror) +and pf.publicly_funded='yes') foo) +select distinct p.id, coalesce(publicly_funded, 0) as publicly_funded +from ${stats_db_name}.publication p +left outer join ( +select distinct ro.id, 1 as publicly_funded from result_organization ro +join ${stats_db_name}.organization o on o.id=ro.organization +join publicly_funded_orgs pfo on o.name=pfo.name) tmp on p.id=tmp.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql index 41c95758c..b55af13d4 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql @@ -3,6 +3,8 @@ ---------------------------------------------------- -- Peer reviewed: +drop table if exists ${stats_db_name}.result_peerreviewed purge; + create table IF NOT EXISTS ${stats_db_name}.result_peerreviewed STORED AS PARQUET as select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed from ${stats_db_name}.result r @@ -10,12 +12,16 @@ left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; -- Green OA: +drop table if exists ${stats_db_name}.result_greenoa purge; + create table IF NOT EXISTS ${stats_db_name}.result_greenoa STORED AS PARQUET as select r.id, case when green.green_oa=1 then true else false end as green from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; -- GOLD OA: +drop table if exists ${stats_db_name}.result_gold purge; + create table IF NOT EXISTS ${stats_db_name}.result_gold STORED AS PARQUET as select r.id, case when gold.is_gold=1 then true else false end as gold from ${stats_db_name}.result r diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql index f737c1ea6..7faa91697 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql @@ -1,6 +1,7 @@ -- replace the creation of the result view to include the boolean fields from the previous tables (green, gold, -- peer reviewed) drop table if exists ${stats_db_name}.result_tmp; + CREATE TABLE ${stats_db_name}.result_tmp ( id STRING, title STRING, diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index 4ffbd384b..8e56f98fc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -5,6 +5,7 @@ -------------------------------------------------------------- -- Publication temporary table +DROP TABLE IF EXISTS ${stats_db_name}.publication_tmp purge; CREATE TABLE ${stats_db_name}.publication_tmp ( id STRING, @@ -40,12 +41,16 @@ SELECT substr(p.id, 4) as id, from ${openaire_db_name}.publication p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_classifications purge; + CREATE TABLE ${stats_db_name}.publication_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) as id, instancetype.classname as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.instancetype) instances as instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_concepts purge; + CREATE TABLE ${stats_db_name}.publication_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id @@ -55,6 +60,8 @@ from ${openaire_db_name}.publication p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_datasources purge; + CREATE TABLE ${stats_db_name}.publication_datasources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( @@ -66,29 +73,39 @@ FROM ( from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.publication_languages purge; + CREATE TABLE ${stats_db_name}.publication_languages STORED AS PARQUET AS select substr(p.id, 4) as id, p.language.classname as language FROM ${openaire_db_name}.publication p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_oids purge; + CREATE TABLE ${stats_db_name}.publication_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_pids purge; + CREATE TABLE ${stats_db_name}.publication_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_topics purge; + CREATE TABLE ${stats_db_name}.publication_topics STORED AS PARQUET as select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.publication_citations purge; + CREATE TABLE ${stats_db_name}.publication_citations STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.publication p diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index d5d242230..cc8348f26 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -1,79 +1,3 @@ ---drop database if exists TARGET cascade; ---create database if not exists TARGET; --- ---create view if not exists TARGET.category as select * from SOURCE.category; ---create view if not exists TARGET.concept as select * from SOURCE.concept; ---create view if not exists TARGET.context as select * from SOURCE.context; ---create view if not exists TARGET.country as select * from SOURCE.country; ---create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp; ---create view if not exists TARGET.creation_date as select * from SOURCE.creation_date; ---create view if not exists TARGET.funder as select * from SOURCE.funder; ---create view if not exists TARGET.fundref as select * from SOURCE.fundref; ---create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture; ---create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure; ---create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents; ---create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers; ---create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft; ---create view if not exists TARGET.hrrst as select * from SOURCE.hrrst; --- ---create table TARGET.result stored as parquet as --- select distinct * from ( --- select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id) --- union all --- select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) --- union all --- select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( --- 'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" --- 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council --- 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ?? --- 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University --- 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade --- 'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki --- 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho --- 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid --- 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen --- 'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens --- -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot --- 'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University --- 'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark --- 'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin --- 'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt --- 'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven --- 'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape --- 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute --- 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University --- 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg --- 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) --- 'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr --- 'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw --- 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly --- 'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete --- 'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus --- 'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras --- 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki --- 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank --- 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech --- 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University --- 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona --- 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University --- 'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia --- 'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University --- 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje --- 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan --- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork --- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University --- 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech --- 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town --- 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin --- 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology --- 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba --- 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili --- 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University --- 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique --- ) )) foo; --- ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; - create view if not exists TARGET.category as select * from SOURCE.category; create view if not exists TARGET.concept as select * from SOURCE.concept; create view if not exists TARGET.context as select * from SOURCE.context; @@ -91,85 +15,63 @@ create view if not exists TARGET.hrrst as select * from SOURCE.hrrst; create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS; create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS; create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS; create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS; create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS; create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS; create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS; create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS; create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS; create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS; create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS; create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS; create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; ---ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS; create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS; create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS; create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS; create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS; create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS; create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS; create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS; create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS; create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_publicly_funded stored as parquet as select * from SOURCE.indi_pub_publicly_funded orig where exists (select 1 from TARGET.result r where r.id=orig.id); + +create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id); create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; drop view TARGET.foo1; drop view TARGET.foo2; ---ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS; -- datasources create view if not exists TARGET.datasource as select * from SOURCE.datasource; @@ -178,7 +80,6 @@ create view if not exists TARGET.datasource_organizations as select * from SOURC create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources; ---ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS; -- organizations create view if not exists TARGET.organization as select * from SOURCE.organization; @@ -196,28 +97,27 @@ create view if not exists TARGET.project_classification as select * from SOURCE. create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; ---ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS; -- indicators -- Sprint 1 ---- create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS; + create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS; + -- Sprint 2 ---- create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS; + create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS; + create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS; + create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS; + ---- Sprint 3 ---- create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS; + create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; @@ -226,32 +126,32 @@ create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funde create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; ---- Sprint 4 ---- create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS; + create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS; + create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS; + ---- Sprint 5 ---- create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; + ---- Sprint 6 ---- create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; + create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS; + ---- Sprint 7 ---- create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS; + create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; @@ -262,17 +162,17 @@ create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS; + create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS; + create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS; + create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS; + create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS; + create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS; + create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id); create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql index df4795e3e..42812d159 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql @@ -78,10 +78,11 @@ create table TARGET.result stored as parquet as 'openorgs____::4d4051b56708688235252f1d8fddb8c1', -- Iscte - Instituto Universitário de Lisboa 'openorgs____::5d55fb216b14691cf68218daf5d78cd9', -- Munster Technological University 'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University - 'openorgs____::8839b55dae0c84d56fd533f52d5d483a' -- Leibniz Institute of Ecological Urban and Regional Development - ) )) foo; + 'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development + 'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology + 'openorgs____::b5ca9d4340e26454e367e2908ef3872f' -- Alma Mater Studiorum University of Bologna ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; + ) )) foo; create view if not exists TARGET.category as select * from SOURCE.category; create view if not exists TARGET.concept as select * from SOURCE.concept; @@ -97,86 +98,63 @@ create view if not exists TARGET.doctoratestudents as select * from SOURCE.docto create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers; create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft; create view if not exists TARGET.hrrst as select * from SOURCE.hrrst; ---create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates; +create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS; create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS; create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS; create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS; create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS; create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS; create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS; create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS; create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS; create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS; create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS; create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS; create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; ---ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS; create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS; create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS; create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS; create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS; create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS; create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS; create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS; create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS; + +create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; drop view TARGET.foo1; drop view TARGET.foo2; ---ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS; -- datasources create view if not exists TARGET.datasource as select * from SOURCE.datasource; @@ -185,7 +163,6 @@ create view if not exists TARGET.datasource_organizations as select * from SOURC create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources; ---ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS; -- organizations create view if not exists TARGET.organization as select * from SOURCE.organization; @@ -203,28 +180,26 @@ create view if not exists TARGET.project_classification as select * from SOURCE. create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; ---ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS; -- indicators -- Sprint 1 ---- create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS; + create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS; + -- Sprint 2 ---- create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS; + create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS; + create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS; + create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS; + ---- Sprint 3 ---- create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS; create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; @@ -233,32 +208,29 @@ create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funde create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; ---- Sprint 4 ---- create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS; + create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS; + create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS; ---- Sprint 5 ---- create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; ---- Sprint 6 ---- create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; + create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS; + create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); ---ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS; + ---- Sprint 7 ---- create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS; + create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS; create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; @@ -269,19 +241,22 @@ create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS; + create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS; + create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS; + create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS; + create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS; + create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS; -create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.id); -create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_publicly_funded stored as parquet as select * from SOURCE.indi_pub_publicly_funded orig where exists (select 1 from TARGET.result r where r.id=orig.id); + +create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +create view TARGET.indi_is_funder_plan_s as select * from SOURCE.indi_is_funder_plan_s; create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness; create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_openess; create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql index 9a9407c2d..4469782f0 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql @@ -11,5 +11,4 @@ create table TARGET.result stored as parquet as join SOURCE.context cont on cont.id=cat.context -- join SOURCE.result where rc.id=r.id and conc.category like CONTEXT) -) foo; ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file +) foo; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql index bad18efde..a28206d56 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql @@ -11,5 +11,4 @@ create table TARGET.result stored as parquet as join SOURCE.context cont on cont.id=cat.context -- join SOURCE.result where rc.id=r.id and conc.category not in (CONTEXTS)) -) foo; ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file +) foo; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql index b8d3c0242..ce6475c22 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql @@ -4,6 +4,4 @@ create database if not exists TARGET; create table TARGET.result stored as parquet as select distinct * from ( select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id) - ) foo; - ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file + ) foo; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql index 7bfba92a8..2c0ac337c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql @@ -58,7 +58,7 @@ create table TARGET.result stored as parquet as 'openorgs____::4d4051b56708688235252f1d8fddb8c1', -- Iscte - Instituto Universitário de Lisboa 'openorgs____::5d55fb216b14691cf68218daf5d78cd9', -- Munster Technological University 'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University - 'openorgs____::8839b55dae0c84d56fd533f52d5d483a' -- Leibniz Institute of Ecological Urban and Regional Development - ))) foo; - ---ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file + 'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development + 'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology + 'openorgs____::b5ca9d4340e26454e367e2908ef3872f' -- Alma Mater Studiorum University of Bologna + ))) foo; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql index b7e421813..2e6f0711c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql @@ -8,7 +8,6 @@ from ${stats_db_name}.result r group by rl.id ) rln on rln.id=r.id; ---ANALYZE TABLE ${observatory_db_name}.result_cc_licence COMPUTE STATISTICS; create table ${observatory_db_name}.result_affiliated_country stored as parquet as select @@ -39,7 +38,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_country COMPUTE STATISTICS; create table ${observatory_db_name}.result_affiliated_year stored as parquet as select @@ -70,7 +68,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_year COMPUTE STATISTICS; create table ${observatory_db_name}.result_affiliated_year_country stored as parquet as select @@ -101,7 +98,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_year_country COMPUTE STATISTICS; create table ${observatory_db_name}.result_affiliated_datasource stored as parquet as select @@ -134,8 +130,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource COMPUTE STATISTICS; - create table ${observatory_db_name}.result_affiliated_datasource_country stored as parquet as select count(distinct r.id) as total, @@ -167,8 +161,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_affiliated_organization stored as parquet as select count(distinct r.id) as total, @@ -198,8 +190,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization COMPUTE STATISTICS; - create table ${observatory_db_name}.result_affiliated_organization_country stored as parquet as select count(distinct r.id) as total, @@ -229,8 +219,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_affiliated_funder stored as parquet as select count(distinct r.id) as total, @@ -262,8 +250,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder COMPUTE STATISTICS; - create table ${observatory_db_name}.result_affiliated_funder_country stored as parquet as select count(distinct r.id) as total, @@ -295,8 +281,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_country stored as parquet as select count(distinct r.id) as total, @@ -328,8 +312,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_year stored as parquet as select count(distinct r.id) as total, @@ -361,7 +343,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_year COMPUTE STATISTICS; create table ${observatory_db_name}.result_deposited_year_country stored as parquet as select @@ -394,8 +375,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_year_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_datasource stored as parquet as select count(distinct r.id) as total, @@ -427,8 +406,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_datasource_country stored as parquet as select count(distinct r.id) as total, @@ -460,8 +437,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_organization stored as parquet as select count(distinct r.id) as total, @@ -493,8 +468,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_organization COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_organization_country stored as parquet as select count(distinct r.id) as total, @@ -526,8 +499,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_organization_country COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_funder stored as parquet as select count(distinct r.id) as total, @@ -561,8 +532,6 @@ group by r.green, r.gold, case when rl.type is not null then true else false end case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; ---ANALYZE TABLE ${observatory_db_name}.result_deposited_funder COMPUTE STATISTICS; - create table ${observatory_db_name}.result_deposited_funder_country stored as parquet as select count(distinct r.id) as total, @@ -595,5 +564,3 @@ from ${stats_db_name}.result r group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end, case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract, cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name; - ---ANALYZE TABLE ${observatory_db_name}.result_deposited_funder_country COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index eb97263a7..0384de4ec 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -5,6 +5,8 @@ ------------------------------------------------------ -- Dataset temporary table supporting updates +DROP TABLE IF EXISTS ${stats_db_name}.dataset_tmp purge; + CREATE TABLE ${stats_db_name}.dataset_tmp ( id STRING, @@ -40,6 +42,8 @@ SELECT substr(d.id, 4) AS id, FROM ${openaire_db_name}.dataset d WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_citations purge; + CREATE TABLE ${stats_db_name}.dataset_citations STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.dataset d @@ -47,12 +51,16 @@ FROM ${openaire_db_name}.dataset d WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_classifications purge; + CREATE TABLE ${stats_db_name}.dataset_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_concepts purge; + CREATE TABLE ${stats_db_name}.dataset_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id @@ -62,6 +70,8 @@ from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_datasources purge; + CREATE TABLE ${stats_db_name}.dataset_datasources STORED AS PARQUET AS SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM ( @@ -74,23 +84,31 @@ FROM ( FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_languages purge; + CREATE TABLE ${stats_db_name}.dataset_languages STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.dataset p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_oids purge; + CREATE TABLE ${stats_db_name}.dataset_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_pids purge; + CREATE TABLE ${stats_db_name}.dataset_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.dataset_topics purge; + CREATE TABLE ${stats_db_name}.dataset_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index 0d1f6323e..d8f4d65e4 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -5,6 +5,7 @@ -------------------------------------------------------- -- Software temporary table supporting updates +DROP TABLE IF EXISTS ${stats_db_name}.software_tmp purge; CREATE TABLE ${stats_db_name}.software_tmp ( id STRING, @@ -40,6 +41,8 @@ SELECT substr(s.id, 4) as id, from ${openaire_db_name}.software s where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_citations purge; + CREATE TABLE ${stats_db_name}.software_citations STORED AS PARQUET AS SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.software s @@ -47,6 +50,8 @@ FROM ${openaire_db_name}.software s where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_classifications purge; + CREATE TABLE ${stats_db_name}.software_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.software p @@ -62,6 +67,8 @@ FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_datasources purge; + CREATE TABLE ${stats_db_name}.software_datasources STORED AS PARQUET AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource FROM ( @@ -74,23 +81,31 @@ FROM ( FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.software_languages purge; + CREATE TABLE ${stats_db_name}.software_languages STORED AS PARQUET AS select substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.software p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_oids purge; + CREATE TABLE ${stats_db_name}.software_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_pids purge; + CREATE TABLE ${stats_db_name}.software_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.software_topics purge; + CREATE TABLE ${stats_db_name}.software_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index 06b616d6a..fae0fbb63 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -5,6 +5,8 @@ -------------------------------------------------------------------------------- -- Otherresearchproduct temporary table supporting updates +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_tmp purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp ( id STRING, @@ -40,6 +42,8 @@ FROM ${openaire_db_name}.otherresearchproduct o WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; -- Otherresearchproduct_citations +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_citations purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_citations STORED AS PARQUET AS SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation @@ -51,6 +55,8 @@ SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_concepts purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id @@ -59,6 +65,8 @@ SELECT substr(p.id, 4) as id, case FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_datasources purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources STORED AS PARQUET AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource @@ -68,21 +76,29 @@ FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) A from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_languages purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_languages STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.otherresearchproduct p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_oids purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_pids purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_topics purge; + CREATE TABLE ${stats_db_name}.otherresearchproduct_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index e0522e149..e5b3f504e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -3,29 +3,39 @@ -- Project table/view and Project related tables/views ------------------------------------------------------ ------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.project_oids purge; + CREATE TABLE ${stats_db_name}.project_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.project_organizations purge; + CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype = 'projectOrganization' and r.source like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.project_results purge; + CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultProject' and r.target like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.project_classification purge; + create table ${stats_db_name}.project_classification STORED AS PARQUET as select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3 from ${openaire_db_name}.project p lateral view explode(p.h2020classification) classifs as class where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null; +DROP TABLE IF EXISTS ${stats_db_name}.project_tmp purge; + CREATE TABLE ${stats_db_name}.project_tmp ( id STRING, @@ -80,12 +90,16 @@ SELECT substr(p.id, 4) AS id, FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.funder purge; + create table ${stats_db_name}.funder STORED AS PARQUET as select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/shortname') as shortname from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund; +DROP TABLE IF EXISTS ${stats_db_name}.project_organization_contribution purge; + CREATE TABLE ${stats_db_name}.project_organization_contribution STORED AS PARQUET AS SELECT distinct substr(r.source, 4) AS project, substr(r.target, 4) AS organization, properties[0].value contribution, properties[1].value currency diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index 1514ecf52..eb16a161e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -123,6 +123,8 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; +DROP TABLE IF EXISTS ${stats_db_name}.result_fos purge; + create table ${stats_db_name}.result_fos stored as parquet as with lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'), @@ -133,6 +135,8 @@ from lvl1 join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2) join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4); +DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge; + CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r @@ -140,6 +144,8 @@ WHERE r.reltype = 'resultOrganization' and r.target like '50|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.result_projects purge; + CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance FROM ${stats_db_name}.result r diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 248716b36..07204db0c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -5,6 +5,8 @@ -- Datasource table/view and Datasource related tables/views ------------------------------------------------------------ ------------------------------------------------------------ +DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge; + CREATE TABLE ${stats_db_name}.datasource_tmp ( `id` string, @@ -48,6 +50,7 @@ WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table. -- Creating a temporary dual table that will be removed after the following insert + CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); INSERT INTO ${stats_db_name}.dual VALUES ('X'); @@ -74,16 +77,22 @@ DROP TABLE ${stats_db_name}.dual; UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository'; UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; +DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; + CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, langs.languages AS language FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; + CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; +DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; + CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r @@ -91,6 +100,8 @@ WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = f -- datasource sources: -- where the datasource info have been collected from. +DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; + create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS select substr(d.id, 4) as id, substr(cf.key, 4) as datasource from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index 3da36dfe5..19d301e27 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -3,6 +3,8 @@ -- Organization table/view and Organization related tables/views ---------------------------------------------------------------- ---------------------------------------------------------------- +DROP TABLE IF EXISTS ${stats_db_name}.organization purge; + CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization STORED AS PARQUET AS SELECT substr(o.id, 4) as id, o.legalname.value as name, 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 aa991730b..cbf97944d 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 @@ -114,6 +114,7 @@ ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'} ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'} ${wf:conf('resumeFrom') eq 'step22-copyDataToImpalaCluster'} + ${wf:conf('resumeFrom') eq 'step22a-createPDFsAggregated'} ${wf:conf('resumeFrom') eq 'step23-finalizeImpalaCluster'} ${wf:conf('resumeFrom') eq 'Step24-updateCache'} @@ -448,6 +449,22 @@ ${hadoop_user_name} copyDataToImpalaCluster.sh + + + + + + + ${jobTracker} + ${nameNode} + createPDFsAggregated.sh + + + ${stats_db_name} + ${monitor_db_name} + ${hadoop_user_name} + createPDFsAggregated.sh + diff --git a/pom.xml b/pom.xml index f361a266c..3fd351c1d 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.17.2] + [4.17.2] [4.0.3] [6.0.5] [3.1.6]