diff --git a/.gitignore b/.gitignore index 6fafc7055..ef9144ae3 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,4 @@ spark-warehouse /**/.scalafmt.conf /.java-version /dhp-shade-package/dependency-reduced-pom.xml +/**/job.properties diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index 0477d6399..6a4bb34d3 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -10,6 +10,11 @@ public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); public static final Map coarCodeLabelMap = Maps.newHashMap(); + public static final String RAID_NS_PREFIX = "raid________"; + + public static final String END_DATE = "endDate"; + public static final String START_DATE = "startDate"; + public static final String ROR_NS_PREFIX = "ror_________"; public static final String ROR_OPENAIRE_ID = "10|openaire____::993a7ae7a863813cf95028b50708e222"; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/enrichment/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/enrichment/Constants.java index df433dddb..becadb82b 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/enrichment/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/enrichment/Constants.java @@ -1,5 +1,6 @@ + package eu.dnetlib.dhp.common.enrichment; public class Constants { - public static final String PROPAGATION_DATA_INFO_TYPE = "propagation"; + public static final String PROPAGATION_DATA_INFO_TYPE = "propagation"; } 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 24de1a787..98ec09277 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 @@ -2,8 +2,7 @@ package eu.dnetlib.dhp.oa.merge; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.spark.sql.functions.col; -import static org.apache.spark.sql.functions.when; +import static org.apache.spark.sql.functions.*; import java.util.Map; import java.util.Optional; @@ -135,7 +134,9 @@ public class GroupEntitiesSparkJob { .applyCoarVocabularies(entity, vocs), OAFENTITY_KRYO_ENC) .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .mapGroups((MapGroupsFunction) MergeUtils::mergeById, OAFENTITY_KRYO_ENC) + .mapGroups( + (MapGroupsFunction) (key, group) -> MergeUtils.mergeById(group, vocs), + OAFENTITY_KRYO_ENC) .map( (MapFunction>) t -> new Tuple2<>( t.getClass().getName(), t), 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 fdfd63a15..9153a6476 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 @@ -2,7 +2,6 @@ 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; @@ -696,6 +695,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { } } + // set ORCID_PENDING to all orcid values that are not coming from ORCID provenance for (Author a : r.getAuthor()) { if (Objects.isNull(a.getPid())) { a.setPid(Lists.newArrayList()); @@ -752,6 +752,40 @@ public class GraphCleaningFunctions extends CleaningFunctions { .collect(Collectors.toList())); } } + + // Identify clashing ORCIDS:that is same ORCID associated to multiple authors in this result + Map clashing_orcid = new HashMap<>(); + + for (Author a : r.getAuthor()) { + a + .getPid() + .stream() + .filter( + p -> StringUtils + .contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID_PENDING)) + .map(StructuredProperty::getValue) + .distinct() + .forEach(orcid -> clashing_orcid.compute(orcid, (k, v) -> (v == null) ? 1 : v + 1)); + } + + Set clashing = clashing_orcid + .entrySet() + .stream() + .filter(ee -> ee.getValue() > 1) + .map(Map.Entry::getKey) + .collect(Collectors.toSet()); + + // filter out clashing orcids + for (Author a : r.getAuthor()) { + a + .setPid( + a + .getPid() + .stream() + .filter(p -> !clashing.contains(p.getValue())) + .collect(Collectors.toList())); + } + } if (value instanceof Publication) { @@ -810,7 +844,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { return author; } - private static Optional cleanDateField(Field dateofacceptance) { + public static Optional cleanDateField(Field dateofacceptance) { return Optional .ofNullable(dateofacceptance) .map(Field::getValue) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java index 79a12d630..c092f6035 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -23,24 +23,30 @@ import org.apache.commons.lang3.tuple.Pair; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.base.Joiner; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.AccessRightComparator; +import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; public class MergeUtils { - public static T mergeById(String s, Iterator oafEntityIterator) { - return mergeGroup(s, oafEntityIterator, true); + public static T mergeById(Iterator oafEntityIterator, VocabularyGroup vocs) { + return mergeGroup(oafEntityIterator, true, vocs); } - public static T mergeGroup(String s, Iterator oafEntityIterator) { - return mergeGroup(s, oafEntityIterator, false); + public static T mergeGroup(Iterator oafEntityIterator) { + return mergeGroup(oafEntityIterator, false); } - public static T mergeGroup(String s, Iterator oafEntityIterator, - boolean checkDelegateAuthority) { + public static T mergeGroup(Iterator oafEntityIterator, boolean checkDelegateAuthority) { + return mergeGroup(oafEntityIterator, checkDelegateAuthority, null); + } + + public static T mergeGroup(Iterator oafEntityIterator, + boolean checkDelegateAuthority, VocabularyGroup vocs) { ArrayList sortedEntities = new ArrayList<>(); oafEntityIterator.forEachRemaining(sortedEntities::add); @@ -49,13 +55,55 @@ public class MergeUtils { Iterator it = sortedEntities.iterator(); T merged = it.next(); - while (it.hasNext()) { - merged = checkedMerge(merged, it.next(), checkDelegateAuthority); + if (!it.hasNext() && merged instanceof Result && vocs != null) { + return enforceResultType(vocs, (Result) merged); + } else { + while (it.hasNext()) { + merged = checkedMerge(merged, it.next(), checkDelegateAuthority); + } } - return merged; } + private static T enforceResultType(VocabularyGroup vocs, Result mergedResult) { + if (Optional.ofNullable(mergedResult.getInstance()).map(List::isEmpty).orElse(true)) { + return (T) mergedResult; + } else { + final Instance i = mergedResult.getInstance().get(0); + + if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { + return (T) mergedResult; + } else { + final String expectedResultType = Optional + .ofNullable( + vocs + .lookupTermBySynonym( + ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid())) + .orElse(ModelConstants.ORP_DEFAULT_RESULTTYPE) + .getClassid(); + + // there is a clash among the result types + if (!expectedResultType.equals(mergedResult.getResulttype().getClassid())) { + + Result result = (Result) Optional + .ofNullable(ModelSupport.oafTypes.get(expectedResultType)) + .map(r -> { + try { + return r.newInstance(); + } catch (InstantiationException | IllegalAccessException e) { + throw new IllegalStateException(e); + } + }) + .orElse(new OtherResearchProduct()); + result.setId(mergedResult.getId()); + return (T) mergeResultFields(result, mergedResult); + } else { + return (T) mergedResult; + } + } + } + } + public static T checkedMerge(final T left, final T right, boolean checkDelegateAuthority) { return (T) merge(left, right, checkDelegateAuthority); } @@ -106,7 +154,7 @@ public class MergeUtils { return mergeSoftware((Software) left, (Software) right); } - return mergeResultFields((Result) left, (Result) right); + return left; } else if (sameClass(left, right, Datasource.class)) { // TODO final int trust = compareTrust(left, right); @@ -654,16 +702,9 @@ public class MergeUtils { } private static Field selectOldestDate(Field d1, Field d2) { - if (d1 == null || StringUtils.isBlank(d1.getValue())) { + if (!GraphCleaningFunctions.cleanDateField(d1).isPresent()) { return d2; - } else if (d2 == null || StringUtils.isBlank(d2.getValue())) { - return d1; - } - - if (StringUtils.contains(d1.getValue(), "null")) { - return d2; - } - if (StringUtils.contains(d2.getValue(), "null")) { + } else if (!GraphCleaningFunctions.cleanDateField(d2).isPresent()) { return d1; } @@ -715,7 +756,9 @@ public class MergeUtils { private static String spKeyExtractor(StructuredProperty sp) { return Optional .ofNullable(sp) - .map(s -> Joiner.on("||") + .map( + s -> Joiner + .on("||") .useForNull("") .join(qualifierKeyExtractor(s.getQualifier()), s.getValue())) .orElse(null); diff --git a/dhp-common/src/main/scala/eu/dnetlib/dhp/common/author/SparkEnrichWithOrcidAuthors.scala b/dhp-common/src/main/scala/eu/dnetlib/dhp/common/author/SparkEnrichWithOrcidAuthors.scala index 47d563649..ad8ebd681 100644 --- a/dhp-common/src/main/scala/eu/dnetlib/dhp/common/author/SparkEnrichWithOrcidAuthors.scala +++ b/dhp-common/src/main/scala/eu/dnetlib/dhp/common/author/SparkEnrichWithOrcidAuthors.scala @@ -25,14 +25,16 @@ abstract class SparkEnrichWithOrcidAuthors(propertyPath: String, args: Array[Str log.info(s"targetPath is '$targetPath'") val workingDir = parser.get("workingDir") log.info(s"targetPath is '$workingDir'") - val classid = Option(parser.get("matchingSource")).map(_=>ModelConstants.ORCID_PENDING).getOrElse(ModelConstants.ORCID) + val classid = + Option(parser.get("matchingSource")).map(_ => ModelConstants.ORCID_PENDING).getOrElse(ModelConstants.ORCID) log.info(s"classid is '$classid'") - val provenance = Option(parser.get("matchingSource")).map(_=>PROPAGATION_DATA_INFO_TYPE).getOrElse("ORCID_ENRICHMENT") + val provenance = + Option(parser.get("matchingSource")).map(_ => PROPAGATION_DATA_INFO_TYPE).getOrElse("ORCID_ENRICHMENT") log.info(s"targetPath is '$workingDir'") createTemporaryData(spark, graphPath, orcidPath, workingDir) - analisys(workingDir,classid,provenance) + analisys(workingDir, classid, provenance) generateGraph(spark, graphPath, workingDir, targetPath) } @@ -70,18 +72,20 @@ abstract class SparkEnrichWithOrcidAuthors(propertyPath: String, args: Array[Str def createTemporaryData(spark: SparkSession, graphPath: String, orcidPath: String, targetPath: String): Unit - private def analisys(targetPath: String, classid:String, provenance:String): Unit = { + private def analisys(targetPath: String, classid: String, provenance: String): Unit = { ModelSupport.entityTypes.asScala .filter(e => ModelSupport.isResult(e._1)) .foreach(e => { val resultType = e._1.name() + val c = classid + val p = provenance spark.read .parquet(s"$targetPath/${resultType}_unmatched") .where("size(graph_authors) > 0") .as[MatchData](Encoders.bean(classOf[MatchData])) .map(md => { - ORCIDAuthorEnricher.enrichOrcid(md.id, md.graph_authors, md.orcid_authors, classid, provenance) + ORCIDAuthorEnricher.enrichOrcid(md.id, md.graph_authors, md.orcid_authors, c, p) })(Encoders.bean(classOf[ORCIDAuthorEnricherResult])) .write .option("compression", "gzip") @@ -90,4 +94,3 @@ abstract class SparkEnrichWithOrcidAuthors(propertyPath: String, args: Array[Str }) } } - diff --git a/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/AuthorMatchers.scala b/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/AuthorMatchers.scala index 5f842726f..a75fec592 100644 --- a/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/AuthorMatchers.scala +++ b/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/AuthorMatchers.scala @@ -1,11 +1,12 @@ package eu.dnetlib.dhp.utils +import java.text.Normalizer import java.util.Locale import java.util.regex.Pattern import scala.util.control.Breaks.{break, breakable} object AuthorMatchers { - val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+") + val SPLIT_REGEX = Pattern.compile("[\\s\\p{Punct}\\p{Pd}]+") val WORD_DIFF = 2 @@ -24,9 +25,16 @@ object AuthorMatchers { } } + def normalize(s: String): Array[String] = { + SPLIT_REGEX + .split(Normalizer.normalize(s, Normalizer.Form.NFC).toLowerCase(Locale.ROOT)) + .filter(_.nonEmpty) + .sorted + } + def matchOrderedTokenAndAbbreviations(a1: String, a2: String): Boolean = { - val p1: Array[String] = SPLIT_REGEX.split(a1.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted - val p2: Array[String] = SPLIT_REGEX.split(a2.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted + val p1: Array[String] = normalize(a1) + val p2: Array[String] = normalize(a2) if (p1.length < 2 || p2.length < 2) return false if (Math.abs(p1.length - p2.length) > WORD_DIFF) return false // use alternative comparison algo diff --git a/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/ORCIDAuthorEnricher.scala b/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/ORCIDAuthorEnricher.scala index ff9715c07..81d7bf81a 100644 --- a/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/ORCIDAuthorEnricher.scala +++ b/dhp-common/src/main/scala/eu/dnetlib/dhp/utils/ORCIDAuthorEnricher.scala @@ -7,6 +7,7 @@ import eu.dnetlib.dhp.schema.sx.OafUtils import java.util import scala.beans.BeanProperty import scala.collection.JavaConverters._ +import scala.collection.mutable.ArrayBuffer import scala.util.control.Breaks.{break, breakable} case class OrcidAuthor( @@ -20,9 +21,9 @@ case class OrcidAuthor( } case class MatchedAuthors( - @BeanProperty var author: Author, - @BeanProperty var orcid: OrcidAuthor, - @BeanProperty var `type`: String + @BeanProperty var author: Author, + @BeanProperty var orcid: OrcidAuthor, + @BeanProperty var `type`: String ) case class MatchData( @@ -47,13 +48,14 @@ object ORCIDAuthorEnricher extends Serializable { id: String, graph_authors: java.util.List[Author], orcid_authors: java.util.List[OrcidAuthor], - classid:String, - provenance:String + classid: String, + provenance: String ): ORCIDAuthorEnricherResult = { // Author enriching strategy: // 1) create a copy of graph author list in unmatched_authors // 2) find best match in unmatched_authors, remove it from unmatched_authors and enrich it so - // that the enrichment is reflected in graph_authors (they share author instances) + // that the enrichment is reflected in graph_authors (they share author instances). + // Do not match in case of ambiguity: two authors match and at least one of them has affiliation string // 3) repeat (2) till the end of the list and then with different matching algorithms that have decreasing // trust in their output // At the end unmatched_authors will contain authors not matched with any of the matching algos @@ -87,7 +89,19 @@ object ORCIDAuthorEnricher extends Serializable { (author, orcid) => AuthorMatchers .matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName), - "orderedTokens", + "orderedTokens-1", + classid, + provenance, + skipAmbiguities = true + ) ++ + // split author names in tokens, order the tokens, then check for matches of full tokens or abbreviations + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + AuthorMatchers + .matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName), + "orderedTokens-2", classid, provenance ) ++ @@ -116,50 +130,54 @@ object ORCIDAuthorEnricher extends Serializable { } private def extractAndEnrichMatches( - graph_authors: java.util.List[Author], - orcid_authors: java.util.List[OrcidAuthor], - matchingFunc: (Author, OrcidAuthor) => Boolean, - matchName: String, - classid:String, - provenance : String - ) = { - val matched = scala.collection.mutable.ArrayBuffer.empty[MatchedAuthors] + unmatched_authors: java.util.List[Author], + orcid_authors: java.util.List[OrcidAuthor], + matchingFunc: (Author, OrcidAuthor) => Boolean, + matchName: String, + classid: String, + provenance: String, + skipAmbiguities: Boolean = false + ): ArrayBuffer[MatchedAuthors] = { + val matched = ArrayBuffer.empty[MatchedAuthors] - if (graph_authors != null && !graph_authors.isEmpty) { - val ait = graph_authors.iterator + if (unmatched_authors == null || unmatched_authors.isEmpty) { + return matched + } - while (ait.hasNext) { - val author = ait.next() - val oit = orcid_authors.iterator - - breakable { - while (oit.hasNext) { - val orcid = oit.next() - - if (matchingFunc(author, orcid)) { - ait.remove() - oit.remove() - matched += MatchedAuthors(author, orcid, matchName) - - if (author.getPid == null) { - author.setPid(new util.ArrayList[StructuredProperty]()) - } - - val orcidPID = OafUtils.createSP(orcid.orcid, classid, classid) - //val orcidPID = OafUtils.createSP(orcid.orcid, ModelConstants.ORCID, ModelConstants.ORCID) - orcidPID.setDataInfo(OafUtils.generateDataInfo()) - orcidPID.getDataInfo.setProvenanceaction( - //OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT") - OafUtils.createQualifier(provenance, provenance) - ) - - author.getPid.add(orcidPID) - - break() - } - } + val oit = orcid_authors.iterator + while (oit.hasNext) { + val orcid = oit.next() + val candidates = unmatched_authors.asScala.foldLeft(ArrayBuffer[Author]())((res, author) => { + if (matchingFunc(author, orcid)) { + res += author } + + res + }) + + if ( + candidates.size == 1 || + (candidates.size > 1 && !skipAmbiguities && !candidates + .exists(a => a.getRawAffiliationString != null && !a.getRawAffiliationString.isEmpty)) + ) { + val author = candidates(0) + unmatched_authors.remove(author) + oit.remove() + matched += MatchedAuthors(author, orcid, matchName) + + if (author.getPid == null) { + author.setPid(new util.ArrayList[StructuredProperty]()) + } + + val orcidPID = OafUtils.createSP(orcid.orcid, classid, classid) + orcidPID.setDataInfo(OafUtils.generateDataInfo()) + orcidPID.getDataInfo.setProvenanceaction( + OafUtils.createQualifier(provenance, provenance) + ) + + author.getPid.add(orcidPID) } + } matched diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java index 25a12bcdf..5cd21adcd 100644 --- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java @@ -21,7 +21,7 @@ public class CodeMatch extends AbstractStringComparator { public CodeMatch(Map params) { super(params); this.params = params; - this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]::\\d+")); + this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]+::\\d+")); } public Set getRegexList(String input) { diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java new file mode 100644 index 000000000..6349c944b --- /dev/null +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java @@ -0,0 +1,67 @@ + +package eu.dnetlib.pace.tree; + +import java.time.DateTimeException; +import java.time.LocalDate; +import java.time.Period; +import java.time.format.DateTimeFormatter; +import java.util.Locale; +import java.util.Map; + +import com.wcohen.ss.AbstractStringDistance; + +import eu.dnetlib.pace.config.Config; +import eu.dnetlib.pace.tree.support.AbstractStringComparator; +import eu.dnetlib.pace.tree.support.ComparatorClass; + +@ComparatorClass("dateRange") +public class DateRange extends AbstractStringComparator { + + int YEAR_RANGE; + + public DateRange(Map params) { + super(params, new com.wcohen.ss.JaroWinkler()); + YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3")); + } + + public DateRange(final double weight) { + super(weight, new com.wcohen.ss.JaroWinkler()); + } + + protected DateRange(final double weight, final AbstractStringDistance ssalgo) { + super(weight, ssalgo); + } + + public static boolean isNumeric(String str) { + return str.matches("\\d+"); // match a number with optional '-' and decimal. + } + + @Override + public double distance(final String a, final String b, final Config conf) { + if (a.isEmpty() || b.isEmpty()) { + return -1.0; // return -1 if a field is missing + } + + try { + DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH); + LocalDate d1 = LocalDate.parse(a, formatter); + LocalDate d2 = LocalDate.parse(b, formatter); + Period period = Period.between(d1, d2); + + return period.getYears() <= YEAR_RANGE ? 1.0 : 0.0; + } catch (DateTimeException e) { + return -1.0; + } + + } + + @Override + public double getWeight() { + return super.weight; + } + + @Override + protected double normalize(final double d) { + return d; + } +} diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java index 3897e37f8..2f845b067 100644 --- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java @@ -41,21 +41,38 @@ public class JsonListMatch extends AbstractListComparator { return -1; } - final Set ca = sa.stream().map(this::toComparableString).collect(Collectors.toSet()); - final Set cb = sb.stream().map(this::toComparableString).collect(Collectors.toSet()); + Set ca = sa.stream().map(this::toComparableString).collect(Collectors.toSet()); + Set cb = sb.stream().map(this::toComparableString).collect(Collectors.toSet()); - int incommon = Sets.intersection(ca, cb).size(); - int simDiff = Sets.symmetricDifference(ca, cb).size(); + switch (MODE) { + case "count": + return Sets.intersection(ca, cb).size(); - if (incommon + simDiff == 0) { - return 0.0; + case "percentage": + int incommon = Sets.intersection(ca, cb).size(); + int simDiff = Sets.symmetricDifference(ca, cb).size(); + if (incommon + simDiff == 0) { + return 0.0; + } + return (double) incommon / (incommon + simDiff); + + case "type": + Set typesA = ca.stream().map(s -> s.split("::")[0]).collect(Collectors.toSet()); + Set typesB = cb.stream().map(s -> s.split("::")[0]).collect(Collectors.toSet()); + + Set types = Sets.intersection(typesA, typesB); + + if (types.isEmpty()) // if no common type, it is impossible to compare + return -1; + + ca = ca.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet()); + cb = cb.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet()); + + return (double) Sets.intersection(ca, cb).size() / types.size(); + + default: + return -1; } - - if (MODE.equals("percentage")) - return (double) incommon / (incommon + simDiff); - else - return incommon; - } // converts every json into a comparable string basing on parameters diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java index d2e83e695..0abde84bc 100644 --- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java +++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java @@ -65,6 +65,43 @@ public class ComparatorTest extends AbstractPaceTest { } + @Test + public void datasetVersionCodeMatchTest() { + + params.put("codeRegex", "(?=[\\w-]*[a-zA-Z])(?=[\\w-]*\\d)[\\w-]+"); + CodeMatch codeMatch = new CodeMatch(params); + + // names have different codes + assertEquals( + 0.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998 ev02a", + "physical oceanography at ctd station june 1998 ir02", conf)); + + // names have same code + assertEquals( + 1.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998 ev02a", + "physical oceanography at ctd station june 1998 ev02a", conf)); + + // code is not in both names + assertEquals( + -1, + codeMatch + .distance( + "physical oceanography at ctd station june 1998", + "physical oceanography at ctd station june 1998 ev02a", conf)); + assertEquals( + 1.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", + conf)); + } + @Test public void listContainsMatchTest() { @@ -257,15 +294,15 @@ public class ComparatorTest extends AbstractPaceTest { List a = createFieldList( Arrays .asList( - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"doi\",\"classname\":\"Digital Object Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"10.1111/pbi.12655\"}"), + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}", + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"), "authors"); List b = createFieldList( Arrays .asList( - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC5399005\"}", - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"27775869\"}", - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"user:claim\",\"classname\":\"Linked by user\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"doi\",\"classname\":\"Digital Object Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"10.1111/pbi.12655\"}", - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"handle\",\"classname\":\"Handle\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"1854/LU-8523529\"}"), + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}", + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_2\"}", + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"user:claim\",\"classname\":\"Linked by user\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"isni\",\"classname\":\"ISNI Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"isni_1\"}"), "authors"); double result = jsonListMatch.compare(a, b, conf); @@ -277,6 +314,13 @@ public class ComparatorTest extends AbstractPaceTest { result = jsonListMatch.compare(a, b, conf); assertEquals(1.0, result); + + params.put("mode", "type"); + jsonListMatch = new JsonListMatch(params); + result = jsonListMatch.compare(a, b, conf); + + assertEquals(0.5, result); + } @Test @@ -327,6 +371,24 @@ public class ComparatorTest extends AbstractPaceTest { } + @Test + public void dateMatch() { + + DateRange dateRange = new DateRange(params); + + double result = dateRange.distance("2021-05-13", "2023-05-13", conf); + assertEquals(1.0, result); + + result = dateRange.distance("2021-05-13", "2025-05-13", conf); + assertEquals(0.0, result); + + result = dateRange.distance("", "2020-05-05", conf); + assertEquals(-1.0, result); + + result = dateRange.distance("invalid date", "2021-05-02", conf); + assertEquals(-1.0, result); + } + @Test public void titleVersionMatchTest() { diff --git a/dhp-shade-package/pom.xml b/dhp-shade-package/pom.xml index d8e17ed46..c4f9b262e 100644 --- a/dhp-shade-package/pom.xml +++ b/dhp-shade-package/pom.xml @@ -26,16 +26,16 @@ - - eu.dnetlib.dhp - dhp-actionmanager - ${project.version} - - + + + eu.dnetlib.dhp + dhp-aggregation + ${project.version} + @@ -56,61 +56,61 @@ - - eu.dnetlib.dhp - dhp-graph-mapper - ${project.version} - - - eu.dnetlib.dhp - dhp-graph-provision - ${project.version} - - - eu.dnetlib.dhp - dhp-impact-indicators - ${project.version} - - - eu.dnetlib.dhp - dhp-stats-actionsets - ${project.version} - - - eu.dnetlib.dhp - dhp-stats-hist-snaps - ${project.version} - - - eu.dnetlib.dhp - dhp-stats-monitor-irish - ${project.version} - - - eu.dnetlib.dhp - dhp-stats-promote - ${project.version} - - - eu.dnetlib.dhp - dhp-stats-update - ${project.version} - - - eu.dnetlib.dhp - dhp-swh - ${project.version} - - - eu.dnetlib.dhp - dhp-usage-raw-data-update - ${project.version} - - - eu.dnetlib.dhp - dhp-usage-stats-build - ${project.version} - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml index 7ccfb342e..cdb4de908 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml @@ -135,22 +135,10 @@ --outputPath${workingDir}/action_payload_by_type --isLookupUrl${isLookupUrl} - + - - - - - - - - - - - - ${wf:appPath()}/promote_action_payload_for_dataset_table @@ -162,7 +150,7 @@ - + @@ -177,7 +165,7 @@ - + @@ -192,7 +180,7 @@ - + @@ -207,7 +195,7 @@ - + @@ -222,7 +210,7 @@ - + @@ -237,7 +225,7 @@ - + @@ -252,7 +240,7 @@ - + @@ -267,26 +255,9 @@ - + - - - ${wf:appPath()}/promote_action_payload_for_person_table - - - - inputActionPayloadRootPath - ${workingDir}/action_payload_by_type - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index 73b4b77cb..d7ad7fcb9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -13,6 +13,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 15c1cc376..75e58e665 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -104,22 +104,22 @@ public class PrepareAffiliationRelations implements Serializable { .listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); JavaPairRDD crossrefRelations = prepareAffiliationRelationsNewModel( - spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::crossref"); + spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":crossref"); JavaPairRDD pubmedRelations = prepareAffiliationRelations( - spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::pubmed"); + spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":pubmed"); JavaPairRDD openAPCRelations = prepareAffiliationRelationsNewModel( - spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::openapc"); + spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":openapc"); JavaPairRDD dataciteRelations = prepareAffiliationRelationsNewModel( - spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::datacite"); + spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":datacite"); JavaPairRDD webCrawlRelations = prepareAffiliationRelationsNewModel( - spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::rawaff"); + spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":rawaff"); JavaPairRDD publisherRelations = prepareAffiliationRelationFromPublisherNewModel( - spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::webcrawl"); + spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":webcrawl"); crossrefRelations .union(pubmedRelations) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java index bf2c19c3d..05f083740 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java @@ -15,6 +15,7 @@ import java.util.stream.Collectors; import org.apache.commons.cli.ParseException; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; @@ -29,7 +30,6 @@ import org.apache.spark.sql.Dataset; import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.spark_project.jetty.util.StringUtil; import com.fasterxml.jackson.databind.ObjectMapper; @@ -193,8 +193,8 @@ public class ExtractPerson implements Serializable { private static Relation getProjectRelation(String project, String orcid, String role) { String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid); - String target = PROJECT_ID_PREFIX + project.substring(0, 14) - + IdentifierFactory.md5(project.substring(15)); + String target = PROJECT_ID_PREFIX + StringUtils.substringBefore(project, "::") + "::" + + IdentifierFactory.md5(StringUtils.substringAfter(project, "::")); List properties = new ArrayList<>(); Relation relation = OafMapperUtils @@ -206,7 +206,7 @@ public class ExtractPerson implements Serializable { null); relation.setValidated(true); - if (StringUtil.isNotBlank(role)) { + if (StringUtils.isNotBlank(role)) { KeyValue kv = new KeyValue(); kv.setKey("role"); kv.setValue(role); @@ -345,7 +345,20 @@ public class ExtractPerson implements Serializable { OafMapperUtils .structuredProperty( op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME, - ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null)); + ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, + OafMapperUtils + .dataInfo( + false, + null, + false, + false, + OafMapperUtils + .qualifier( + ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY, + ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES), + "0.91"))); person.setDateofcollection(op.getLastModifiedDate()); person.setOriginalId(Arrays.asList(op.getOrcid())); person.setDataInfo(ORCIDDATAINFO); @@ -439,13 +452,13 @@ public class ExtractPerson implements Serializable { null); relation.setValidated(true); - if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) { + if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtils.isNotBlank(row.getStartDate())) { KeyValue kv = new KeyValue(); kv.setKey("startDate"); kv.setValue(row.getStartDate()); properties.add(kv); } - if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) { + if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtils.isNotBlank(row.getEndDate())) { KeyValue kv = new KeyValue(); kv.setKey("endDate"); kv.setValue(row.getEndDate()); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java new file mode 100644 index 000000000..e67e7171f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java @@ -0,0 +1,203 @@ + +package eu.dnetlib.dhp.actionmanager.raid; + +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID; +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME; +import static eu.dnetlib.dhp.common.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; + +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +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 eu.dnetlib.dhp.utils.DHPUtils; +import scala.Tuple2; + +public class GenerateRAiDActionSetJob { + + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final List RAID_COLLECTED_FROM = listKeyValues( + OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); + + private static final Qualifier RAID_QUALIFIER = qualifier( + "0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE); + + private static final Qualifier RAID_INFERENCE_QUALIFIER = qualifier( + "raid:openaireinference", "Inferred by OpenAIRE", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + + private static final DataInfo RAID_DATA_INFO = dataInfo( + false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_INFERENCE_QUALIFIER, "0.92"); + + public static void main(final String[] args) throws Exception { + + final String jsonConfiguration = IOUtils + .toString( + eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); + processRAiDEntities(spark, inputPath, outputPath); + }); + } + + private static void removeOutputDir(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + static void processRAiDEntities(final SparkSession spark, + final String inputPath, + final String outputPath) { + readInputPath(spark, inputPath) + .map(GenerateRAiDActionSetJob::prepareRAiD) + .flatMap(List::iterator) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + + } + + protected static List> prepareRAiD(final RAiDEntity r) { + + final Date now = new Date(); + final OtherResearchProduct orp = new OtherResearchProduct(); + final List> res = new ArrayList<>(); + String raidId = calculateOpenaireId(r.getRaid()); + + orp.setId(raidId); + orp.setCollectedfrom(RAID_COLLECTED_FROM); + orp.setDataInfo(RAID_DATA_INFO); + orp + .setTitle( + Collections + .singletonList( + structuredProperty( + r.getTitle(), + qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE), + RAID_DATA_INFO))); + orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary())); + + Instance instance = new Instance(); + instance.setInstancetype(RAID_QUALIFIER); + orp.setInstance(Collections.singletonList(instance)); + orp + .setSubject( + r + .getSubjects() + .stream() + .map( + s -> subject( + s, + qualifier( + DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, + DNET_SUBJECT_TYPOLOGIES), + RAID_DATA_INFO)) + .collect(Collectors.toList())); + orp + .setRelevantdate( + Arrays + .asList( + structuredProperty( + r.getEndDate(), qualifier(END_DATE, END_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE), + RAID_DATA_INFO), + structuredProperty( + r.getStartDate(), + qualifier(START_DATE, START_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE), + RAID_DATA_INFO))); + orp.setLastupdatetimestamp(now.getTime()); + orp.setDateofacceptance(field(r.getStartDate(), RAID_DATA_INFO)); + + res.add(new AtomicAction<>(OtherResearchProduct.class, orp)); + + for (String resultId : r.getIds()) { + Relation rel1 = OafMapperUtils + .getRelation( + raidId, + resultId, + ModelConstants.RESULT_RESULT, + PART, + HAS_PART, + orp); + Relation rel2 = OafMapperUtils + .getRelation( + resultId, + raidId, + ModelConstants.RESULT_RESULT, + PART, + IS_PART_OF, + orp); + res.add(new AtomicAction<>(Relation.class, rel1)); + res.add(new AtomicAction<>(Relation.class, rel2)); + } + + return res; + } + + public static String calculateOpenaireId(final String raid) { + return String.format("50|%s::%s", RAID_NS_PREFIX, DHPUtils.md5(raid)); + } + + public static List createAuthors(final List author) { + return author.stream().map(s -> { + Author a = new Author(); + a.setFullname(s); + return a; + }).collect(Collectors.toList()); + } + + private static JavaRDD readInputPath( + final SparkSession spark, + final String path) { + + return spark + .read() + .json(path) + .as(Encoders.bean(RAiDEntity.class)) + .toJavaRDD(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java new file mode 100644 index 000000000..856b52e18 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java @@ -0,0 +1,5 @@ + +package eu.dnetlib.dhp.actionmanager.raid.model; + +public class GenerateRAiDActionSetJob { +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java new file mode 100644 index 000000000..1203b28a7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java @@ -0,0 +1,106 @@ + +package eu.dnetlib.dhp.actionmanager.raid.model; + +import java.io.Serializable; +import java.util.List; + +public class RAiDEntity implements Serializable { + + String raid; + List authors; + String startDate; + String endDate; + List subjects; + List titles; + List ids; + String title; + String summary; + + public RAiDEntity() { + } + + public RAiDEntity(String raid, List authors, String startDate, String endDate, List subjects, + List titles, List ids, String title, String summary) { + this.raid = raid; + this.authors = authors; + this.startDate = startDate; + this.endDate = endDate; + this.subjects = subjects; + this.titles = titles; + this.ids = ids; + this.title = title; + this.summary = summary; + } + + public String getRaid() { + return raid; + } + + public void setRaid(String raid) { + this.raid = raid; + } + + public List getAuthors() { + return authors; + } + + public void setAuthors(List authors) { + this.authors = authors; + } + + public String getStartDate() { + return startDate; + } + + public void setStartDate(String startDate) { + this.startDate = startDate; + } + + public String getEndDate() { + return endDate; + } + + public void setEndDate(String endDate) { + this.endDate = endDate; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public List getTitles() { + return titles; + } + + public void setTitles(List titles) { + this.titles = titles; + } + + public List getIds() { + return ids; + } + + public void setIds(List ids) { + this.ids = ids; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getSummary() { + return summary; + } + + public void setSummary(String summary) { + this.summary = summary; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 5f3493d56..6e8f48bda 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -44,13 +44,7 @@ import eu.dnetlib.dhp.common.Constants; 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.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index f63bfcb48..67966d523 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -28,6 +28,7 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpClientParams; @@ -129,6 +130,8 @@ public class CollectorWorker extends ReportingJob { return new Gtr2PublicationsCollectorPlugin(this.clientParams); case osfPreprints: return new OsfPreprintsCollectorPlugin(this.clientParams); + case zenodoDump: + return new CollectZenodoDumpCollectorPlugin(); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(this.api.getParams().get("other_plugin_type")) 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 index 11f4c55d8..8172456bb 100644 --- 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 @@ -154,7 +154,6 @@ public class ORCIDExtractor extends Thread { extractedItem++; if (extractedItem % 100000 == 0) { log.info("Thread {}: Extracted {} items", id, extractedItem); - break; } } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 72e691579..ef0ff00c4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -11,7 +11,7 @@ public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints; + oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints, zenodoDump, research_fi; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java index 5b8f48680..1b1ff8db4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java @@ -1,6 +1,9 @@ package eu.dnetlib.dhp.collection.plugin.gtr2; +import java.nio.charset.StandardCharsets; +import java.time.LocalDate; +import java.time.format.DateTimeFormatter; import java.util.ArrayList; import java.util.HashMap; import java.util.Iterator; @@ -16,9 +19,6 @@ import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.DocumentHelper; import org.dom4j.Element; -import org.joda.time.DateTime; -import org.joda.time.format.DateTimeFormat; -import org.joda.time.format.DateTimeFormatter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -33,7 +33,7 @@ public class Gtr2PublicationsIterator implements Iterator { private static final Logger log = LoggerFactory.getLogger(Gtr2PublicationsIterator.class); private final HttpConnector2 connector; - private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd"); + private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); private static final int MAX_ATTEMPTS = 10; @@ -41,7 +41,7 @@ public class Gtr2PublicationsIterator implements Iterator { private int currPage; private int endPage; private boolean incremental = false; - private DateTime fromDate; + private LocalDate fromDate; private final Map cache = new HashMap<>(); @@ -188,28 +188,28 @@ public class Gtr2PublicationsIterator implements Iterator { private Document loadURL(final String cleanUrl, final int attempt) { try { - log.debug(" * Downloading Url: " + cleanUrl); - final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes("UTF-8"); + log.debug(" * Downloading Url: {}", cleanUrl); + final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes(StandardCharsets.UTF_8); return DocumentHelper.parseText(new String(bytes)); } catch (final Throwable e) { - log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e); + log.error("Error dowloading url: {}, attempt = {}", cleanUrl, attempt, e); if (attempt >= MAX_ATTEMPTS) { - throw new RuntimeException("Error dowloading url: " + cleanUrl, e); + throw new RuntimeException("Error downloading url: " + cleanUrl, e); } try { Thread.sleep(60000); // I wait for a minute } catch (final InterruptedException e1) { - throw new RuntimeException("Error dowloading url: " + cleanUrl, e); + throw new RuntimeException("Error downloading url: " + cleanUrl, e); } return loadURL(cleanUrl, attempt + 1); } } - private DateTime parseDate(final String s) { - return DateTime.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter); + private LocalDate parseDate(final String s) { + return LocalDate.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter); } - private boolean isAfter(final String d, final DateTime fromDate) { + private boolean isAfter(final String d, final LocalDate fromDate) { return StringUtils.isNotBlank(d) && parseDate(d).isAfter(fromDate); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java index 269a89f71..cad499962 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java @@ -6,7 +6,7 @@ import java.util.Queue; import java.util.concurrent.PriorityBlockingQueue; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.math.NumberUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.http.Header; @@ -27,25 +27,25 @@ public class ResearchFiIterator implements Iterator { private final String baseUrl; private final String authToken; - private int currPage; - private int nPages; + private String nextUrl; + private int nCalls = 0; private final Queue queue = new PriorityBlockingQueue<>(); public ResearchFiIterator(final String baseUrl, final String authToken) { this.baseUrl = baseUrl; this.authToken = authToken; - this.currPage = 0; - this.nPages = 0; + this.nextUrl = null; } private void verifyStarted() { - if (this.currPage == 0) { - try { - nextCall(); - } catch (final CollectorException e) { - throw new IllegalStateException(e); + + try { + if (this.nCalls == 0) { + this.nextUrl = invokeUrl(this.baseUrl); } + } catch (final CollectorException e) { + throw new IllegalStateException(e); } } @@ -62,9 +62,9 @@ public class ResearchFiIterator implements Iterator { synchronized (this.queue) { verifyStarted(); final String res = this.queue.poll(); - while (this.queue.isEmpty() && (this.currPage < this.nPages)) { + while (this.queue.isEmpty() && StringUtils.isNotBlank(this.nextUrl)) { try { - nextCall(); + this.nextUrl = invokeUrl(this.nextUrl); } catch (final CollectorException e) { throw new IllegalStateException(e); } @@ -73,18 +73,11 @@ public class ResearchFiIterator implements Iterator { } } - private void nextCall() throws CollectorException { + private String invokeUrl(final String url) throws CollectorException { - this.currPage += 1; + this.nCalls += 1; + String next = null; - final String url; - if (!this.baseUrl.contains("?")) { - url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE); - } else if (!this.baseUrl.contains("PageSize=")) { - url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE); - } else { - url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage); - } log.info("Calling url: " + url); try (final CloseableHttpClient client = HttpClients.createDefault()) { @@ -94,11 +87,15 @@ public class ResearchFiIterator implements Iterator { try (final CloseableHttpResponse response = client.execute(req)) { for (final Header header : response.getAllHeaders()) { log.debug("HEADER: " + header.getName() + " = " + header.getValue()); - if ("x-page-count".equals(header.getName())) { - final int totalPages = NumberUtils.toInt(header.getValue()); - if (this.nPages != totalPages) { - this.nPages = NumberUtils.toInt(header.getValue()); - log.info("Total pages: " + totalPages); + if ("link".equals(header.getName())) { + final String s = StringUtils.substringBetween(header.getValue(), "<", ">"); + final String token = StringUtils + .substringBefore(StringUtils.substringAfter(s, "NextPageToken="), "&"); + + if (this.baseUrl.contains("?")) { + next = this.baseUrl + "&NextPageToken=" + token; + } else { + next = this.baseUrl + "?NextPageToken=" + token; } } } @@ -108,6 +105,9 @@ public class ResearchFiIterator implements Iterator { jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString()))); } + + return next; + } catch (final Throwable e) { log.warn("Error calling url: " + url, e); throw new CollectorException("Error calling url: " + url, e); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java new file mode 100644 index 000000000..9513cab51 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java @@ -0,0 +1,109 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.IOException; +import java.io.InputStream; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +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.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +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 eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class CollectZenodoDumpCollectorPlugin implements CollectorPlugin { + + final private Logger log = LoggerFactory.getLogger(getClass()); + + private void downloadItem(final String name, final String itemURL, final String basePath, + final FileSystem fileSystem) { + 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); + fsDataOutputStream.flush(); + fsDataOutputStream.hflush(); + fsDataOutputStream.close(); + } + } catch (Throwable eu) { + throw new RuntimeException(eu); + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + public FileSystem initializeFileSystem(final String hdfsURI) { + try { + return FileSystem.get(getHadoopConfiguration(hdfsURI)); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + + final String zenodoURL = api.getBaseUrl(); + final String hdfsURI = api.getParams().get("hdfsURI"); + final FileSystem fileSystem = initializeFileSystem(hdfsURI); + return doStream(fileSystem, zenodoURL, "/tmp"); + } + + public Stream doStream(FileSystem fileSystem, String zenodoURL, String basePath) throws CollectorException { + try { + + downloadItem("zenodoDump.tar.gz", zenodoURL, basePath, fileSystem); + CompressionCodecFactory factory = new CompressionCodecFactory(fileSystem.getConf()); + Path sourcePath = new Path(basePath + "/zenodoDump.tar.gz"); + CompressionCodec codec = factory.getCodec(sourcePath); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fileSystem.open(sourcePath)); + return iterateTar(gzipInputStream); + + } catch (IOException e) { + throw new CollectorException(e); + } + } catch (Exception e) { + throw new CollectorException(e); + } + } + + private Stream iterateTar(InputStream gzipInputStream) throws Exception { + + Iterable iterable = () -> new ZenodoTarIterator(gzipInputStream); + return StreamSupport.stream(iterable.spliterator(), false); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java new file mode 100644 index 000000000..8e627683e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java @@ -0,0 +1,59 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import java.io.Closeable; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.Iterator; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.io.IOUtils; + +public class ZenodoTarIterator implements Iterator, Closeable { + + private final InputStream gzipInputStream; + private final StringBuilder currentItem = new StringBuilder(); + private TarArchiveInputStream tais; + private boolean hasNext; + + public ZenodoTarIterator(InputStream gzipInputStream) { + this.gzipInputStream = gzipInputStream; + tais = new TarArchiveInputStream(gzipInputStream); + hasNext = getNextItem(); + } + + private boolean getNextItem() { + try { + TarArchiveEntry entry; + while ((entry = tais.getNextTarEntry()) != null) { + if (entry.isFile()) { + currentItem.setLength(0); + currentItem.append(IOUtils.toString(new InputStreamReader(tais))); + return true; + } + } + return false; + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + @Override + public boolean hasNext() { + return hasNext; + } + + @Override + public String next() { + final String data = currentItem.toString(); + hasNext = getNextItem(); + return data; + } + + @Override + public void close() throws IOException { + gzipInputStream.close(); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java new file mode 100644 index 000000000..427eb2725 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.sx.bio.pubmed; + +/** + * The type Pubmed Affiliation. + * + * @author Sandro La Bruzzo + */ +public class PMAffiliation { + + private String name; + + private PMIdentifier identifier; + + public PMAffiliation() { + + } + + public PMAffiliation(String name, PMIdentifier identifier) { + this.name = name; + this.identifier = identifier; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public PMIdentifier getIdentifier() { + return identifier; + } + + public void setIdentifier(PMIdentifier identifier) { + this.identifier = identifier; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index 3fb814606..6191f6446 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -8,259 +8,115 @@ import java.util.List; /** * This class represent an instance of Pubmed Article extracted from the native XML * - * @author Sandro La Bruzzo */ - public class PMArticle implements Serializable { - /** - * the Pubmed Identifier - */ private String pmid; - private String pmcId; - - /** - * the DOI - */ private String doi; - /** - * the Pubmed Date extracted from Specifies a date significant to either the article's history or the citation's processing. - * All dates will have a , , and elements. Some may have an , , and element(s). - */ private String date; - /** - * This is an 'envelop' element that contains various elements describing the journal cited; i.e., ISSN, Volume, Issue, and PubDate and author name(s), however, it does not contain data itself. - */ private PMJournal journal; - /** - * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. The NLM journal title abbreviation is exported in the element. - */ private String title; - /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. - */ private String description; - /** - * the language in which an article was published is recorded in . - * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single - * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value. - * Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined. - */ private String language; - - /** - * NLM controlled vocabulary, Medical Subject Headings (MeSH®), is used to characterize the content of the articles represented by MEDLINE citations. * - */ - private final List subjects = new ArrayList<>(); - /** - * This element is used to identify the type of article indexed for MEDLINE; - * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of - * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). - */ - private final List publicationTypes = new ArrayList<>(); - /** - * Personal and collective (corporate) author names published with the article are found in . - */ + private List subjects; + private List publicationTypes = new ArrayList<>(); private List authors = new ArrayList<>(); + private List grants = new ArrayList<>(); - /** - * contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service - * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations. - */ - private final List grants = new ArrayList<>(); - - /** - * get the DOI - * @return a DOI - */ - public String getDoi() { - return doi; - } - - /** - * Set the DOI - * @param doi a DOI - */ - public void setDoi(String doi) { - this.doi = doi; - } - - /** - * get the Pubmed Identifier - * @return the PMID - */ public String getPmid() { return pmid; } - /** - * set the Pubmed Identifier - * @param pmid the Pubmed Identifier - */ public void setPmid(String pmid) { this.pmid = pmid; } - /** - * the Pubmed Date extracted from Specifies a date significant to either the article's history or the citation's processing. - * All dates will have a , , and elements. Some may have an , , and element(s). - * - * @return the Pubmed Date - */ - public String getDate() { - return date; - } - - /** - * Set the pubmed Date - * @param date - */ - public void setDate(String date) { - this.date = date; - } - - /** - * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. - * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. - * The NLM journal title abbreviation is exported in the element. - * - * @return the pubmed Journal Extracted - */ - public PMJournal getJournal() { - return journal; - } - - /** - * Set the mapped pubmed Journal - * @param journal - */ - public void setJournal(PMJournal journal) { - this.journal = journal; - } - - /** - * contains the entire title of the journal article. is always in English; - * those titles originally published in a non-English language and translated for are enclosed in square brackets. - * All titles end with a period unless another punctuation mark such as a question mark or bracket is present. - * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl). - * Corporate/collective authors may appear at the end of for citations up to about the year 2000. - * - * @return the extracted pubmed Title - */ - public String getTitle() { - return title; - } - - /** - * set the pubmed title - * @param title - */ - public void setTitle(String title) { - this.title = title; - } - - /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. - * - * @return the Mapped Pubmed Article Abstracts - */ - public String getDescription() { - return description; - } - - /** - * Set the Mapped Pubmed Article Abstracts - * @param description - */ - public void setDescription(String description) { - this.description = description; - } - - /** - * Personal and collective (corporate) author names published with the article are found in . - * - * @return get the Mapped Authors lists - */ - public List getAuthors() { - return authors; - } - - /** - * Set the Mapped Authors lists - * @param authors - */ - public void setAuthors(List authors) { - this.authors = authors; - } - - /** - * This element is used to identify the type of article indexed for MEDLINE; - * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of - * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). - * - * @return the mapped Subjects - */ - public List getSubjects() { - return subjects; - } - - /** - * - * the language in which an article was published is recorded in . - * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single - * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value. - * Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined. - * - * @return The mapped Language - */ - public String getLanguage() { - return language; - } - - /** - * - * Set The mapped Language - * - * @param language the mapped Language - */ - public void setLanguage(String language) { - this.language = language; - } - - /** - * This element is used to identify the type of article indexed for MEDLINE; - * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of - * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). - * - * @return the mapped Publication Type - */ - public List getPublicationTypes() { - return publicationTypes; - } - - /** - * contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service - * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations. - * @return the mapped grants - */ - - public List getGrants() { - return grants; - } - public String getPmcId() { return pmcId; } - public PMArticle setPmcId(String pmcId) { + public void setPmcId(String pmcId) { this.pmcId = pmcId; - return this; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getDate() { + return date; + } + + public void setDate(String date) { + this.date = date; + } + + public PMJournal getJournal() { + return journal; + } + + public void setJournal(PMJournal journal) { + this.journal = journal; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public String getLanguage() { + return language; + } + + public void setLanguage(String language) { + this.language = language; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public List getPublicationTypes() { + return publicationTypes; + } + + public void setPublicationTypes(List publicationTypes) { + this.publicationTypes = publicationTypes; + } + + public List getAuthors() { + return authors; + } + + public void setAuthors(List authors) { + this.authors = authors; + } + + public List getGrants() { + return grants; + } + + public void setGrants(List grants) { + this.grants = grants; } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java index 68ef6459e..e023f2e62 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java @@ -12,6 +12,8 @@ public class PMAuthor implements Serializable { private String lastName; private String foreName; + private PMIdentifier identifier; + private PMAffiliation affiliation; /** * Gets last name. @@ -59,4 +61,40 @@ public class PMAuthor implements Serializable { .format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : ""); } + /** + * Gets identifier. + * + * @return the identifier + */ + public PMIdentifier getIdentifier() { + return identifier; + } + + /** + * Sets identifier. + * + * @param identifier the identifier + */ + public void setIdentifier(PMIdentifier identifier) { + this.identifier = identifier; + } + + /** + * Gets affiliation. + * + * @return the affiliation + */ + public PMAffiliation getAffiliation() { + return affiliation; + } + + /** + * Sets affiliation. + * + * @param affiliation the affiliation + */ + public void setAffiliation(PMAffiliation affiliation) { + this.affiliation = affiliation; + } + } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java new file mode 100644 index 000000000..6cd17a90c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.sx.bio.pubmed; + +public class PMIdentifier { + + private String pid; + private String type; + + public PMIdentifier(String pid, String type) { + this.pid = cleanPid(pid); + this.type = type; + } + + public PMIdentifier() { + + } + + private String cleanPid(String pid) { + + if (pid == null) { + return null; + } + + // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705 + if (pid.matches("[0-9]{15}[0-9X]")) { + return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4"); + } + + // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543 + if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) { + return pid.replaceAll("http://orcid.org/", ""); + } + return pid; + } + + public String getPid() { + return pid; + } + + public PMIdentifier setPid(String pid) { + this.pid = cleanPid(pid); + return this; + } + + public String getType() { + return type; + } + + public PMIdentifier setType(String type) { + this.type = type; + return this; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json new file mode 100644 index 000000000..2049630d2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "i", + "paramLongName": "inputPath", + "paramDescription": "the path of the input json", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml new file mode 100644 index 000000000..a1755f329 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml new file mode 100644 index 000000000..d3392596f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml @@ -0,0 +1,53 @@ + + + + raidJsonInputPath + the path of the json + + + raidActionSetPath + path where to store the action set + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + yarn + cluster + ProcessRAiDFile + eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --inputPath${raidJsonInputPath} + --outputPath${raidActionSetPath} + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json index 3ba83764d..0fcc03266 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json @@ -1,8 +1,7 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"mo", "paramLongName":"mdstoreOutputVersion", "paramDescription": "the oaf path ", "paramRequired": true}, - {"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false}, - {"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true} + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the baseline path", "paramRequired": true}, + {"paramName":"mo", "paramLongName":"mdstoreOutputVersion", "paramDescription": "the mdstore path to save", "paramRequired": true} + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml index 30eb41469..2a51b4050 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + baselineWorkingPath @@ -16,11 +16,6 @@ mdStoreManagerURI the path of the cleaned mdstore - - skipUpdate - false - The request block size - @@ -44,16 +39,16 @@ --mdStoreManagerURI${mdStoreManagerURI} - + - + yarn cluster - Convert Baseline to OAF Dataset - eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame + Convert Baseline Pubmed to OAF Dataset + eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -65,12 +60,10 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --workingPath${baselineWorkingPath} + --sourcePath${baselineWorkingPath} --mdstoreOutputVersion${wf:actionData('StartTransaction')['mdStoreVersion']} --masteryarn --isLookupUrl${isLookupUrl} - --hdfsServerUri${nameNode} - --skipUpdate${skipUpdate} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala index e7d68920b..ea2177497 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala @@ -37,7 +37,7 @@ case class mappingAuthor( family: Option[String], sequence: Option[String], ORCID: Option[String], - affiliation: Option[mappingAffiliation] + affiliation: Option[List[mappingAffiliation]] ) {} case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {} @@ -457,15 +457,14 @@ case object Crossref2Oaf { } //Mapping Author - val authorList: List[mappingAuthor] = - (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined) + val authorList: List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined) val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) => a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first") ) result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) => - generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index) + generateAuthor(a.given.orNull, a.family.get, a.ORCID.orNull, index, a.affiliation) }.asJava) // Mapping instance @@ -504,19 +503,6 @@ case object Crossref2Oaf { ) } - val is_review = json \ "relation" \ "is-review-of" \ "id" - - if (is_review != JNothing) { - instance.setInstancetype( - OafMapperUtils.qualifier( - "0015", - "peerReviewed", - ModelConstants.DNET_REVIEW_LEVELS, - ModelConstants.DNET_REVIEW_LEVELS - ) - ) - } - if (doi.startsWith("10.3410") || doi.startsWith("10.12703")) instance.setHostedby( OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect") @@ -574,12 +560,23 @@ case object Crossref2Oaf { s"50|doiboost____|$id" } - def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = { + private def generateAuthor( + given: String, + family: String, + orcid: String, + index: Int, + affiliation: Option[List[mappingAffiliation]] + ): Author = { val a = new Author a.setName(given) a.setSurname(family) a.setFullname(s"$given $family") a.setRank(index + 1) + + // Adding Raw affiliation if it's defined + if (affiliation.isDefined) { + a.setRawAffiliationString(affiliation.get.map(a => a.name).asJava) + } if (StringUtils.isNotBlank(orcid)) a.setPid( List( @@ -673,11 +670,11 @@ case object Crossref2Oaf { val doi = input.getString(0) val rorId = input.getString(1) - val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.clean(doi)}" + val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true) val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId) val r: Relation = new Relation - DoiCleaningRule.clean(doi) + r.setSource(pubId) r.setTarget(affId) r.setRelType(ModelConstants.RESULT_ORGANIZATION) @@ -705,7 +702,15 @@ case object Crossref2Oaf { val objectType = (json \ "type").extractOrElse[String](null) if (objectType == null) return resultList - val typology = getTypeQualifier(objectType, vocabularies) + + // If the item has a relations is-review-of, then we force it to a peer-review + val is_review = json \ "relation" \ "is-review-of" \ "id" + var force_to_review = false + if (is_review != JNothing) { + force_to_review = true + } + + val typology = getTypeQualifier(if (force_to_review) "peer-review" else objectType, vocabularies) if (typology == null) return List() @@ -757,33 +762,6 @@ case object Crossref2Oaf { else resultList } - - // if (uw != null) { -// result.getCollectedfrom.add(createUnpayWallCollectedFrom()) -// val i: Instance = new Instance() -// i.setCollectedfrom(createUnpayWallCollectedFrom()) -// if (uw.best_oa_location != null) { -// -// i.setUrl(List(uw.best_oa_location.url).asJava) -// if (uw.best_oa_location.license.isDefined) { -// i.setLicense(field[String](uw.best_oa_location.license.get, null)) -// } -// -// val colour = get_unpaywall_color(uw.oa_status) -// if (colour.isDefined) { -// val a = new AccessRight -// a.setClassid(ModelConstants.ACCESS_RIGHT_OPEN) -// a.setClassname(ModelConstants.ACCESS_RIGHT_OPEN) -// a.setSchemeid(ModelConstants.DNET_ACCESS_MODES) -// a.setSchemename(ModelConstants.DNET_ACCESS_MODES) -// a.setOpenAccessRoute(colour.get) -// i.setAccessright(a) -// } -// i.setPid(result.getPid) -// result.getInstance().add(i) -// } -// } - } private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = { @@ -978,7 +956,26 @@ case object Crossref2Oaf { case "10.13039/501100010790" => generateSimpleRelationFromAward(funder, "erasmusplus_", a => a) case _ => logger.debug("no match for " + funder.DOI.get) - + //Add for Danish funders + //Independent Research Fund Denmark (IRFD) + case "10.13039/501100004836" => + generateSimpleRelationFromAward(funder, "irfd________", a => a) + val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //Carlsberg Foundation (CF) + case "10.13039/501100002808" => + generateSimpleRelationFromAward(funder, "cf__________", a => a) + val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //Novo Nordisk Foundation (NNF) + case "10.13039/501100009708" => + generateSimpleRelationFromAward(funder, "nnf___________", a => a) + val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + case _ => logger.debug("no match for " + funder.DOI.get) } } else { diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala new file mode 100644 index 000000000..adac9ffb6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala @@ -0,0 +1,104 @@ +package eu.dnetlib.dhp.sx.bio.ebi + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.common.Constants +import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup +import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser2, PubMedToOaf} +import eu.dnetlib.dhp.transformation.TransformSparkJobNode +import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile +import eu.dnetlib.dhp.utils.ISLookupClientFactory +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +class SparkCreatePubmedDump(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 isLookupUrl: String = parser.get("isLookupUrl") + log.info("isLookupUrl: {}", isLookupUrl) + val sourcePath = parser.get("sourcePath") + log.info(s"SourcePath is '$sourcePath'") + val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") + log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'") + val mapper = new ObjectMapper() + val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) + val outputBasePath = cleanedMdStoreVersion.getHdfsPath + log.info(s"outputBasePath is '$outputBasePath'") + + val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) + val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) + + createPubmedDump(spark, sourcePath, outputBasePath, vocabularies) + + } + + /** This method creates a dump of the pubmed articles + * @param spark the spark session + * @param sourcePath the path of the source file + * @param targetPath the path of the target file + * @param vocabularies the vocabularies + */ + def createPubmedDump( + spark: SparkSession, + sourcePath: String, + targetPath: String, + vocabularies: VocabularyGroup + ): Unit = { + require(spark != null) + + implicit val PMEncoder: Encoder[PMArticle] = Encoders.bean(classOf[PMArticle]) + + import spark.implicits._ + val df = spark.read.option("lineSep", "").text(sourcePath) + val mapper = new ObjectMapper() + df.as[String] + .map(s => { + val id = s.indexOf("") + if (id >= 0) s"${s.substring(id)}" else null + }) + .filter(s => s != null) + .map { i => + //remove try catch + try { + new PMParser2().parse(i) + } catch { + case _: Exception => { + throw new RuntimeException(s"Error parsing article: $i") + } + } + } + .dropDuplicates("pmid") + .map { a => + val oaf = PubMedToOaf.convert(a, vocabularies) + if (oaf != null) + mapper.writeValueAsString(oaf) + else + null + } + .as[String] + .filter(s => s != null) + .write + .option("compression", "gzip") + .mode("overwrite") + .text(targetPath + MDSTORE_DATA_PATH) + + val mdStoreSize = spark.read.text(targetPath + MDSTORE_DATA_PATH).count + writeHdfsFile(spark.sparkContext.hadoopConfiguration, "" + mdStoreSize, targetPath + MDSTORE_SIZE_PATH) + } +} + +object SparkCreatePubmedDump { + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + + new SparkCreatePubmedDump("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json", args, log).initialize().run() + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala new file mode 100644 index 000000000..bc9a2cf02 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala @@ -0,0 +1,277 @@ +package eu.dnetlib.dhp.sx.bio.pubmed + +import org.apache.commons.lang3.StringUtils + +import javax.xml.stream.XMLEventReader +import scala.collection.JavaConverters._ +import scala.xml.{MetaData, NodeSeq} +import scala.xml.pull.{EvElemEnd, EvElemStart, EvText} + +class PMParser2 { + + /** Extracts the value of an attribute from a MetaData object. + * @param attrs the MetaData object + * @param key the key of the attribute + * @return the value of the attribute or null if the attribute is not found + */ + private def extractAttributes(attrs: MetaData, key: String): String = { + + val res = attrs.get(key) + if (res.isDefined) { + val s = res.get + if (s != null && s.nonEmpty) + s.head.text + else + null + } else null + } + + /** Validates and formats a date given the year, month, and day as strings. + * + * @param year the year as a string + * @param month the month as a string + * @param day the day as a string + * @return the formatted date as "YYYY-MM-DD" or null if the date is invalid + */ + private def validate_Date(year: String, month: String, day: String): String = { + try { + f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d" + + } catch { + case _: Throwable => null + } + } + + /** Extracts the grant information from a NodeSeq object. + * + * @param gNode the NodeSeq object + * @return the grant information or an empty list if the grant information is not found + */ + private def extractGrant(gNode: NodeSeq): List[PMGrant] = { + gNode + .map(node => { + val grantId = (node \ "GrantID").text + val agency = (node \ "Agency").text + val country = (node \ "Country").text + new PMGrant(grantId, agency, country) + }) + .toList + } + + /** Extracts the journal information from a NodeSeq object. + * + * @param jNode the NodeSeq object + * @return the journal information or null if the journal information is not found + */ + private def extractJournal(jNode: NodeSeq): PMJournal = { + val journal = new PMJournal + journal.setTitle((jNode \ "Title").text) + journal.setIssn((jNode \ "ISSN").text) + journal.setVolume((jNode \ "JournalIssue" \ "Volume").text) + journal.setIssue((jNode \ "JournalIssue" \ "Issue").text) + if (journal.getTitle != null && StringUtils.isNotEmpty(journal.getTitle)) + journal + else + null + } + + private def extractAuthors(aNode: NodeSeq): List[PMAuthor] = { + aNode + .map(author => { + val a = new PMAuthor + a.setLastName((author \ "LastName").text) + a.setForeName((author \ "ForeName").text) + val id = (author \ "Identifier").text + val idType = (author \ "Identifier" \ "@Source").text + + if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) { + a.setIdentifier(new PMIdentifier(id, idType)) + } + + val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text + val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text + val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text + + if (affiliation != null && affiliation.nonEmpty) { + val aff = new PMAffiliation() + aff.setName(affiliation) + if ( + affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty + ) { + aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType)) + } + a.setAffiliation(aff) + } + a + }) + .toList + } + + def parse(input: String): PMArticle = { + val xml = scala.xml.XML.loadString(input) + val article = new PMArticle + + val grantNodes = xml \ "MedlineCitation" \\ "Grant" + article.setGrants(extractGrant(grantNodes).asJava) + + val journal = xml \ "MedlineCitation" \ "Article" \ "Journal" + article.setJournal(extractJournal(journal)) + + val authors = xml \ "MedlineCitation" \ "Article" \ "AuthorList" \ "Author" + + article.setAuthors( + extractAuthors(authors).asJava + ) + + val pmId = xml \ "MedlineCitation" \ "PMID" + + val articleIds = xml \ "PubmedData" \ "ArticleIdList" \ "ArticleId" + articleIds.foreach(articleId => { + val idType = (articleId \ "@IdType").text + val id = articleId.text + if ("doi".equalsIgnoreCase(idType)) article.setDoi(id) + if ("pmc".equalsIgnoreCase(idType)) article.setPmcId(id) + }) + article.setPmid(pmId.text) + + val pubMedPubDate = xml \ "MedlineCitation" \ "DateCompleted" + val currentDate = + validate_Date((pubMedPubDate \ "Year").text, (pubMedPubDate \ "Month").text, (pubMedPubDate \ "Day").text) + if (currentDate != null) article.setDate(currentDate) + + val articleTitle = xml \ "MedlineCitation" \ "Article" \ "ArticleTitle" + article.setTitle(articleTitle.text) + + val abstractText = xml \ "MedlineCitation" \ "Article" \ "Abstract" \ "AbstractText" + if (abstractText != null && abstractText.text != null && abstractText.text.nonEmpty) + article.setDescription(abstractText.text.split("\n").map(s => s.trim).mkString(" ").trim) + + val language = xml \ "MedlineCitation" \ "Article" \ "Language" + article.setLanguage(language.text) + + val subjects = xml \ "MedlineCitation" \ "MeshHeadingList" \ "MeshHeading" + article.setSubjects( + subjects + .take(20) + .map(subject => { + val descriptorName = (subject \ "DescriptorName").text + val ui = (subject \ "DescriptorName" \ "@UI").text + val s = new PMSubject + s.setValue(descriptorName) + s.setMeshId(ui) + s + }) + .toList + .asJava + ) + val publicationTypes = xml \ "MedlineCitation" \ "Article" \ "PublicationTypeList" \ "PublicationType" + article.setPublicationTypes( + publicationTypes + .map(pt => { + val s = new PMSubject + s.setValue(pt.text) + s + }) + .toList + .asJava + ) + + article + } + + def parse2(xml: XMLEventReader): PMArticle = { + var currentArticle: PMArticle = null + var currentSubject: PMSubject = null + var currentAuthor: PMAuthor = null + var currentJournal: PMJournal = null + var currentGrant: PMGrant = null + var currNode: String = null + var currentYear = "0" + var currentMonth = "01" + var currentDay = "01" + var currentArticleType: String = null + + while (xml.hasNext) { + val ne = xml.next + ne match { + case EvElemStart(_, label, attrs, _) => + currNode = label + + label match { + case "PubmedArticle" => currentArticle = new PMArticle + case "Author" => currentAuthor = new PMAuthor + case "Journal" => currentJournal = new PMJournal + case "Grant" => currentGrant = new PMGrant + case "PublicationType" | "DescriptorName" => + currentSubject = new PMSubject + currentSubject.setMeshId(extractAttributes(attrs, "UI")) + case "ArticleId" => currentArticleType = extractAttributes(attrs, "IdType") + case _ => + } + case EvElemEnd(_, label) => + label match { + case "PubmedArticle" => return currentArticle + case "Author" => currentArticle.getAuthors.add(currentAuthor) + case "Journal" => currentArticle.setJournal(currentJournal) + case "Grant" => currentArticle.getGrants.add(currentGrant) + case "PubMedPubDate" => + if (currentArticle.getDate == null) + currentArticle.setDate(validate_Date(currentYear, currentMonth, currentDay)) + case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay") + case "DescriptorName" => currentArticle.getSubjects.add(currentSubject) + case "PublicationType" => currentArticle.getPublicationTypes.add(currentSubject) + case _ => + } + case EvText(text) => + if (currNode != null && text.trim.nonEmpty) + currNode match { + case "ArticleTitle" => { + if (currentArticle.getTitle == null) + currentArticle.setTitle(text.trim) + else + currentArticle.setTitle(currentArticle.getTitle + text.trim) + } + case "AbstractText" => { + if (currentArticle.getDescription == null) + currentArticle.setDescription(text.trim) + else + currentArticle.setDescription(currentArticle.getDescription + text.trim) + } + case "PMID" => currentArticle.setPmid(text.trim) + case "ArticleId" => + if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim) + case "Language" => currentArticle.setLanguage(text.trim) + case "ISSN" => currentJournal.setIssn(text.trim) + case "GrantID" => currentGrant.setGrantID(text.trim) + case "Agency" => currentGrant.setAgency(text.trim) + case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim) + case "Year" => currentYear = text.trim + case "Month" => currentMonth = text.trim + case "Day" => currentDay = text.trim + case "Volume" => currentJournal.setVolume(text.trim) + case "Issue" => currentJournal.setIssue(text.trim) + case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim) + case "LastName" => { + if (currentAuthor != null) + currentAuthor.setLastName(text.trim) + } + case "ForeName" => + if (currentAuthor != null) + currentAuthor.setForeName(text.trim) + case "Title" => + if (currentJournal.getTitle == null) + currentJournal.setTitle(text.trim) + else + currentJournal.setTitle(currentJournal.getTitle + text.trim) + case _ => + + } + case _ => + } + + } + null + } + +} 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 d59d73bd0..281ca0e07 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 @@ -294,6 +294,24 @@ object PubMedToOaf { author.setName(a.getForeName) author.setSurname(a.getLastName) author.setFullname(a.getFullName) + if (a.getIdentifier != null) { + author.setPid( + List( + OafMapperUtils.structuredProperty( + a.getIdentifier.getPid, + OafMapperUtils.qualifier( + a.getIdentifier.getType, + a.getIdentifier.getType, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES + ), + dataInfo + ) + ).asJava + ) + } + if (a.getAffiliation != null) + author.setRawAffiliationString(List(a.getAffiliation.getName).asJava) author.setRank(index + 1) author }(collection.breakOut) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java new file mode 100644 index 000000000..9417822af --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.dhp.actionmanager.raid; + +import static java.nio.file.Files.createTempDirectory; + +import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.File; +import java.nio.file.Paths; +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat; +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.rdd.RDD; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +public class GenerateRAiDActionSetJobTest { + private static String input_path; + private static String output_path; + static SparkSession spark; + + @BeforeEach + void setUp() throws Exception { + + input_path = Paths + .get( + GenerateRAiDActionSetJobTest.class + .getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json") + .toURI()) + .toFile() + .getAbsolutePath(); + + output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + SparkConf conf = new SparkConf(); + conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", output_path); + conf.set("hive.metastore.warehouse.dir", output_path); + + spark = SparkSession + .builder() + .appName(GenerateRAiDActionSetJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + static void cleanUp() throws Exception { + FileUtils.deleteDirectory(new File(output_path)); + } + + @Test + @Disabled + void testProcessRAiDEntities() { + GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set"); + + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD result = sc + .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(AtomicAction::getPayload); + + assertEquals(80, result.count()); + } + + @Test + void testPrepareRAiD() { + + List> atomicActions = GenerateRAiDActionSetJob + .prepareRAiD( + new RAiDEntity( + "-92190526", + Arrays + .asList( + "Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", + "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", + "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", + "Maïeul GRUGET", "Cécile Duchêne"), + "2021-09-10", + "2024-02-16", + Arrays + .asList( + "cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", + "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", + "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", + "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", + "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", + "General Medicine", "Geography, Planning and Development", "multi-scales", + "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", + "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", + "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", + "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", + "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", + "open source", "drawing", "Constraint", "Multi-scale maps"), + Arrays + .asList( + "Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", + "Collection of cartographic disorientation stories", "Anchorwhat dataset", + "BasqueRoads: A Benchmark for Road Network Selection", + "Progressive river network selection for pan-scalar maps", + "BasqueRoads, a dataset to benchmark road selection algorithms", + "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", + "Empirical approach to advance the generalisation of multi-scale maps", + "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", + "eye-tracking data from a survey on zooming in a pan-scalar map", + "Material of the experiment 'More is Less' from the MapMuxing project", + "Cartagen4py, an open source Python library for map generalisation", + "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"), + Arrays + .asList( + "50|doi_dedup___::6915135e0aa39f913394513f809ae58a", + "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", + "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", + "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", + "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", + "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", + "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", + "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", + "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", + "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", + "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", + "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", + "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", + "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"), + "Exploring Multi-Scale Map Generalization and Design", + "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval.")); + + OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload(); + Relation rel = (Relation) atomicActions.get(1).getPayload(); + + assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue()); + assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource()); + assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget()); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java new file mode 100644 index 000000000..3592ad6a5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import java.util.zip.GZIPInputStream; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +public class ZenodoPluginCollectionTest { + + @Test + public void testZenodoIterator() throws Exception { + + final GZIPInputStream gis = new GZIPInputStream( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz")); + try (ZenodoTarIterator it = new ZenodoTarIterator(gis)) { + Assertions.assertTrue(it.hasNext()); + int i = 0; + while (it.hasNext()) { + Assertions.assertNotNull(it.next()); + i++; + } + Assertions.assertEquals(10, i); + + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json new file mode 100644 index 000000000..7694b605c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json @@ -0,0 +1,6 @@ +{"raid": "-9222092103004099540", "authors": ["Department of Archaeology & Museums", "Department of Archaeology and Museums", "Department Of Archaeology & Museums"], "subjects": ["Begamganj", "Raisen", "Bhopal", "Budhni", "Malwa site survey", "सीहोर", "Gauharganj", "बुधनी", "Budni", "Berasia"], "titles": ["Malwa site survey : Raisen District, Begamganj Tahsīl, photographic documentation", "Malwa site survey : Bhopal District, photographic documentation (version 1, TIFF files)", "Malwa site survey : Raisen District, Gauharganj Tahsīl, village finds", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 1)", "Malwa site survey: Bhopal District, Berasia Tahsīl, photographic documentation (with villages named)", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 2)", "Malwa site survey : Bhopal District, photographic documentation (version 2, JPEG files)"], "ids": ["50|doi_dedup___::7523d165970830dd857e6cbea4302adf", "50|doi_dedup___::02309ae8a9fae291df321e317f5c5330", "50|doi_dedup___::95347ba2c4264414fab39712ee7fe481", "50|doi_dedup___::970aa708fe667596754fd02a708780f5", "50|doi_dedup___::b7cd9128cc53b1257a4f000347f339b0", "50|doi_dedup___::c7d65da0ecedef4d2c702b9db197d90c", "50|doi_dedup___::addbb67cf5046e340f342ba091bcebfa"], "title": "Documentation of Malwa Region", "summary": "This project involves the documentation of the Malwa region through photographic surveys. The surveys were conducted by the Department of Archaeology and Museums, Madhya Pradesh, and cover various districts and tahsils. The documentation includes photographic records of sites, villages, and other relevant features. The project aims to provide a comprehensive understanding of the region's cultural and historical significance.", "startDate": "2019-03-06", "endDate": "2019-03-08"} +{"raid": "-9221424331076109424", "authors": ["Hutchings, Judy", "Ward, Catherine", "Baban, Adriana", "D��nil��, Ingrid", "Frantz, Inga", "Gardner, Frances", "Lachman, Jamie", "Lachman, Jamie M.", "Foran, Heather", "Heinrichs, Nina", "Murphy, Hugh", "B��ban, Adriana", "Raleva, Marija", "Fang, Xiangming", "Jansen, Elena", "Taut, Diana", "Foran, Heather M.", "T��ut, Diana", "Ward, Catherine L.", "Williams, Margiad", "Lesco, Galina", "Brühl, Antonia"], "subjects": ["3. Good health", "5. Gender equality", "Criminology not elsewhere classified", "1. No poverty", "2. Zero hunger"], "titles": ["sj-docx-1-vaw-10.1177_10778012231188090 - Supplemental material for Co-Occurrence of Intimate Partner Violence Against Mothers and Maltreatment of Their Children With Behavioral Problems in Eastern Europe", "Hunger in vulnerable families in Southeastern Europe: Associations with health and violence", "Prevention of child mental health problems through parenting interventions in Southeastern Europe (RISE): study protocol for a multi-site randomised controlled trial"], "ids": ["50|doi_dedup___::a70015063e5400dae2e097ee10b4a589", "50|doi_dedup___::6e1d12026fcde9087724622ccdeed430", "50|doi_dedup___::5b7bd5d46c5d95e2ef5b36663504a67e"], "title": "Exploring the Impact of Hunger and Violence on Child Health in Southeastern Europe", "summary": "This study aims to investigate the relationship between hunger, violence, and child health in vulnerable families in Southeastern Europe. The research will explore the experiences of families in FYR Macedonia, Republic of Moldova, and Romania, and examine the associations between hunger, maltreatment, and other health indicators. The study will also test the efficacy of a parenting intervention targeting child behavioral problems in alleviating these issues. The findings of this research will contribute to the development of effective interventions to address the complex needs of vulnerable families in the region.", "startDate": "2019-06-04", "endDate": "2023-01-01"} +{"raid": "-9219052635741785098", "authors": ["Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"], "subjects": ["cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"], "titles": ["Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment \"More is Less\" from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"], "ids": ["50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"], "title": "Exploring Multi-Scale Map Generalization and Design", "summary": "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval.", "startDate": "2021-09-10", "endDate": "2024-02-16"} +{"raid": "-9216828847055450272", "authors": ["Grey, Alan", "Gorelov, Sergey", "Pall, Szilard", "Merz, Pascal", "Justin A., Lemkul", "Szilárd Páll", "Pasquadibisceglie, Andrea", "Kutzner, Carsten", "Schulz, Roland", "Nabet, Julien", "Abraham, Mark", "Jalalypour, Farzaneh", "Lundborg, Magnus", "Gray, Alan", "Villa, Alessandra", "Berk Hess", "Santuz, Hubert", "Irrgang, M. Eric", "Wingbermuehle, Sebastian", "Lemkul, Justin A.", "Jordan, Joe", "Pellegrino, Michele", "Doijade, Mahesh", "Shvetsov, Alexey", "Hess, Berk", "Behera, Sudarshan", "Andrey Alekseenko", "Shugaeva, Tatiana", "Fleischmann, Stefan", "Bergh, Cathrine", "Morozov, Dmitry", "Adam Hospital", "Briand, Eliane", "Lindahl, Erik", "Brown, Ania", "Marta Lloret Llinares", "Miletic, Vedran", "Alekseenko, Andrey", "Gouaillardet, Gilles", "Fiorin, Giacomo", "Basov, Vladimir"], "subjects": ["webinar"], "titles": ["Introduction to HPC: molecular dynamics simulations with GROMACS: log files", "BioExcel webinar #73: Competency frameworks to support training design and professional development", "Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana", "GROMACS 2024.0 Manual", "BioExcel Webinar #71: GROMACS-PMX for accurate estimation of free energy differences", "Introduction to HPC: molecular dynamics simulations with GROMACS: input files", "BioExcel Webinar #68: What's new in GROMACS 2023", "BioExcel Webinar #69: BioBB-Wfs and BioBB-API, integrated web-based platform and programmatic interface for biomolecular simulations workflows using the BioExcel Building Blocks library", "GROMACS 2024-beta Source code"], "ids": ["50|doi_dedup___::8318fbc815ee1943c3269be7567f220b", "50|doi_dedup___::9530e03fb2aac63e82b18a40dc09e32c", "50|doi_dedup___::30174ab31075e76a428ca5b4f4d236b8", "50|doi_________::70b7c6dce09ae6f1361d22913fdf95eb", "50|doi_dedup___::337dd48600618f3c06257edd750d6201", "50|doi_dedup___::d622992ba9077617f37ebd268b3e806d", "50|doi_dedup___::0b0bcc6825d6c052c37882fd5cfc1e8c", "50|doi_dedup___::4b1541a7cee32527c65ace5d1ed57335", "50|doi_dedup___::1379861df59bd755e4fb39b9f95ffbd3"], "title": "Exploring High-Performance Computing and Biomolecular Simulations", "summary": "This project involves exploring high-performance computing (HPC) and biomolecular simulations using GROMACS. The objectives include understanding molecular dynamics simulations, log files, input files, and output files. Additionally, the project aims to explore competency frameworks for professional development, specifically in the field of computational biomolecular research. The tools and techniques used will include GROMACS, BioExcel Building Blocks, and competency frameworks. The expected outcomes include a deeper understanding of HPC and biomolecular simulations, as well as the development of skills in using GROMACS and BioExcel Building Blocks. The project will also contribute to the development of competency frameworks for professional development in the field of computational biomolecular research.", "startDate": "2023-04-25", "endDate": "2024-01-30"} +{"raid": "-9210544816395499758", "authors": ["Bateson, Melissa", "Andrews, Clare", "Verhulst, Simon", "Nettle, Daniel", "Zuidersma, Erica"], "subjects": ["2. Zero hunger"], "titles": ["Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings", "Data and code archive for Andrews et al. 'Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings'"], "ids": ["50|doi_dedup___::176117239be06189523c253e0ca9c5ec", "50|doi_dedup___::343e0b0ddf0d54763a89a62af1f7a379"], "title": "Investigating the Effects of Food Insecurity on Energy Storage and Somatic Maintenance in European Starlings", "summary": "This study examines the impact of food insecurity on energy storage and somatic maintenance in European starlings. The research involved exposing juvenile starlings to either uninterrupted food availability or a regime of unpredictable food unavailability. The results show that birds exposed to food insecurity stored more energy, but at the expense of somatic maintenance and repair. The study provides insights into the adaptive responses of birds to food scarcity and the trade-offs involved in energy storage and maintenance.", "startDate": "2021-06-28", "endDate": "2021-06-28"} +{"raid": "-9208499171224730388", "authors": ["Maniati, Eleni", "Bakker, Bjorn", "McClelland, Sarah E.", "Shaikh, Nadeem", "De Angelis, Simone", "Johnson, Sarah C.", "Wang, Jun", "Foijer, Floris", "Spierings, Diana C. J.", "Boemo, Michael A.", "Wardenaar, René", "Mazzagatti, Alice"], "subjects": [], "titles": ["Additional file 2 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses", "Additional file 5 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses"], "ids": ["50|doi_dedup___::a1bfeb173971f74a274fab8bdd78a4bc", "50|doi_dedup___::3d6e151aaeb2f7c40a320207fdd80ade"], "title": "Analysis of DNA Copy Number Alterations and Chromosome Scale Losses", "summary": "This study analyzed the effects of replication stress on DNA copy number alterations and chromosome scale losses. The results show distinctive landscapes of these alterations and losses, which were further investigated in additional files. The study provides valuable insights into the mechanisms of replication stress and its impact on genomic stability.", "startDate": "2022-01-01", "endDate": "2022-01-01"} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json new file mode 100644 index 000000000..201138e45 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json @@ -0,0 +1,232 @@ +{ + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 3 + ] + ], + "date-time": "2022-04-03T01:45:59Z", + "timestamp": 1648950359167 + }, + "reference-count": 0, + "publisher": "American Society of Clinical Oncology (ASCO)", + "issue": "18_suppl", + "content-domain": { + "domain": [], + "crossmark-restriction": false + }, + "short-container-title": [ + "JCO" + ], + "published-print": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + }, + "abstract": " 3507 Purpose: To detect IGF-1R on circulating tumor cells (CTCs) as a biomarker in the clinical development of a monoclonal human antibody, CP-751,871, targeting IGF-1R. Experimental Design: An automated sample preparation and analysis system for enumerating CTCs (Celltracks) was adapted for detecting IGF-1R positive CTCs with a diagnostic antibody targeting a different IGF-1R epitope to CP-751,871. This assay was utilized in three phase I trials of CP-751,871 as a single agent or with chemotherapy and was validated using cell lines and blood samples from healthy volunteers and patients with metastatic carcinoma. Results: There was no interference between the analytical and therapeutic antibodies. CP-751,871 was well tolerated as a single agent, and in combination with docetaxel or carboplatin and paclitaxel, at doses ranging from 0.05 mg/kg to 20 mg/kg. Eighty patients were enrolled on phase 1 studies of CP-751,871, with 47 (59%) patients having CTCs detected during the study. Prior to treatment 26 patients (33%) had CTCs, with 23 having detectable IGF-1R positive CTCs. CP-751,871 alone, and CP-751,871 with cytotoxic chemotherapy, decreased CTCs and IGF-1R positive CTCs; these increased towards the end of the 21-day cycle in some patients, falling again with retreatment. CTCs were commonest in advanced hormone refractory prostate cancer (11/20). Detectable IGF-1R expression on CTCs before treatment with CP-751,871 and docetaxel was associated with a higher frequency of PSA decline by more than 50% (6/10 vs 2/8 patients). A relationship was observed between sustained falls in CTCs counts and PSA declines by more than 50%. Conclusions: IGF-1R expression is detectable by immunofluorescence on CTCs. These data support the further evaluation of CTCs in pharmacodynamic studies and patient selection, particularly in advanced prostate cancer. No significant financial relationships to disclose. ", + "DOI": "10.1200/jco.2007.25.18_suppl.3507", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2020, + 3, + 6 + ] + ], + "date-time": "2020-03-06T20:50:42Z", + "timestamp": 1583527842000 + }, + "page": "3507-3507", + "source": "Crossref", + "is-referenced-by-count": 0, + "title": [ + "Circulating tumor cells expressing the insulin growth factor-1 receptor (IGF-1R): Method of detection, incidence and potential applications" + ], + "prefix": "10.1200", + "volume": "25", + "author": [ + { + "given": "J. S.", + "family": "de Bono", + "sequence": "first", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "A.", + "family": "Adjei", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "G.", + "family": "Attard", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "M.", + "family": "Pollak", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "P.", + "family": "Fong", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "P.", + "family": "Haluska", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "L.", + "family": "Roberts", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "D.", + "family": "Chainese", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "L.", + "family": "Terstappen", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "A.", + "family": "Gualberto", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + } + ], + "member": "233", + "container-title": [ + "Journal of Clinical Oncology" + ], + "original-title": [], + "language": "en", + "deposited": { + "date-parts": [ + [ + 2020, + 3, + 6 + ] + ], + "date-time": "2020-03-06T20:51:03Z", + "timestamp": 1583527863000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "http://ascopubs.org/doi/10.1200/jco.2007.25.18_suppl.3507" + } + }, + "subtitle": [], + "short-title": [], + "issued": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + }, + "references-count": 0, + "journal-issue": { + "issue": "18_suppl", + "published-print": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + } + }, + "alternative-id": [ + "10.1200/jco.2007.25.18_suppl.3507" + ], + "URL": "http://dx.doi.org/10.1200/jco.2007.25.18_suppl.3507", + "relation": {}, + "ISSN": [ + "0732-183X", + "1527-7755" + ], + "issn-type": [ + { + "value": "0732-183X", + "type": "print" + }, + { + "value": "1527-7755", + "type": "electronic" + } + ], + "subject": [], + "published": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz new file mode 100644 index 000000000..6c06bf4e5 Binary files /dev/null and b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz differ diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml new file mode 100644 index 000000000..c2e503f57 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml @@ -0,0 +1,157 @@ + + + 37318999 + + 2024 + 02 + 09 + + + 2024 + 02 + 09 + +
+ + 1522-1229 + + 47 + 3 + + 2023 + Sep + 01 + + + Advances in physiology education + Adv Physiol Educ + + Providing the choice of in-person or videoconference attendance in a clinical physiology course may harm learning outcomes for the entire cohort. + + 548-556 + + 10.1152/advan.00160.2022 + + Clinical Physiology 1 and 2 are flipped classes in which students watch prerecorded videos before class. During the 3-h class, students take practice assessments, work in groups on critical thinking exercises, work through case studies, and engage in drawing exercises. Due to the COVID pandemic, these courses were transitioned from in-person classes to online classes. Despite the university's return-to-class policy, some students were reluctant to return to in-person classes; therefore during the 2021-2022 academic year, Clinical Physiology 1 and 2 were offered as flipped, hybrid courses. In a hybrid format, students either attended the synchronous class in person or online. Here we evaluate the learning outcomes and the perceptions of the learning experience for students who attended Clinical Physiology 1 and 2 either online (2020-2021) or in a hybrid format (2021-2022). In addition to exam scores, in-class surveys and end of course evaluations were compiled to describe the student experience in the flipped hybrid setting. Retrospective linear mixed-model regression analysis of exam scores revealed that a hybrid modality (2021-2022) was associated with lower exam scores when controlling for sex, graduate/undergraduate status, delivery method, and the order in which the courses were taken (F test: F = 8.65, df1 = 2, df2 = 179.28, P = 0.0003). In addition, being a Black Indigenous Person of Color (BIPOC) student is associated with a lower exam score, controlling for the same previous factors (F test: F = 4.23, df1 = 1, df2 = 130.28, P = 0.04), albeit with lower confidence; the BIPOC representation in this sample is small (BIPOC: n = 144; total: n = 504). There is no significant interaction between the hybrid modality and race, meaning that BIPOC and White students are both negatively affected in a hybrid flipped course. Instructors should consider carefully about offering hybrid courses and build in extra student support.NEW & NOTEWORTHY The transition from online to in-person teaching has been as challenging as the original transition to remote teaching with the onset of the pandemic. Since not all students were ready to return to the classroom, students could choose to take this course in person or online. This arrangement provided flexibility and opportunities for innovative class activities for students but introduced tradeoffs in lower test scores from the hybrid modality than fully online or fully in-person modalities. + + + + Anderson + Lisa Carney + LC + 0000-0003-2261-1921 + + Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota, United States. + https://ror.org/017zqws13 + + + + Jacobson + Tate + T + + Department of Statistics, University of Minnesota, Minneapolis, Minnesota, United States. + + + + eng + + Journal Article + + + 2023 + 06 + 15 + +
+ + United States + Adv Physiol Educ + 100913944 + 1043-4046 + + IM + + + Physiology + education + + + Retrospective Studies + + + Learning + + + Pandemics + + + COVID-19 + + + Regression Analysis + + + Students + + + Humans + + + Male + + + Female + + + White People + + + Black People + + + Education, Distance + + + Curriculum + + + + flipped teaching + hybrid teaching + inequity + learning outcomes + responsive teaching + + + + + + 2023 + 7 + 21 + 6 + 44 + + + 2023 + 6 + 15 + 19 + 14 + + + 2023 + 6 + 15 + 12 + 53 + + + ppublish + + 37318999 + 10.1152/advan.00160.2022 + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala index c3ea884eb..ebe247d8a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala @@ -3,12 +3,15 @@ package eu.dnetlib.dhp.collection.crossref import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType +import eu.dnetlib.dhp.schema.oaf.Publication import org.apache.commons.io.IOUtils -import org.junit.jupiter.api.{BeforeEach, Test} +import org.junit.jupiter.api.{Assertions, BeforeEach, Test} import org.junit.jupiter.api.extension.ExtendWith import org.mockito.junit.jupiter.MockitoExtension import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters.asScalaBufferConverter + @ExtendWith(Array(classOf[MockitoExtension])) class CrossrefMappingTest extends AbstractVocabularyTest { @@ -25,8 +28,32 @@ class CrossrefMappingTest extends AbstractVocabularyTest { val input = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8") - println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All)) + Crossref2Oaf + .convert(input, vocabularies, TransformationType.All) + .foreach(record => { + Assertions.assertNotNull(record) + }) } + @Test + def mappingAffiliation(): Unit = { + val input = + IOUtils.toString( + getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), + "utf-8" + ) + val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult) + data.foreach(record => { + Assertions.assertNotNull(record) + Assertions.assertTrue(record.isInstanceOf[Publication]) + val publication = record.asInstanceOf[Publication] + publication.getAuthor.asScala.foreach(author => { + Assertions.assertNotNull(author.getRawAffiliationString) + Assertions.assertTrue(author.getRawAffiliationString.size() > 0) + + }) + }) + println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head)) + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index c4af14c40..cb7826dbf 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -5,7 +5,10 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.utils.PidType import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump +import eu.dnetlib.dhp.sx.bio.pubmed._ +import org.apache.commons.io.IOUtils +import org.apache.spark.sql.SparkSession import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -13,14 +16,16 @@ import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{BeforeEach, Test} import org.mockito.junit.jupiter.MockitoExtension +import org.slf4j.LoggerFactory import java.io.{BufferedReader, InputStream, InputStreamReader} +import java.util.regex.Pattern import java.util.zip.GZIPInputStream import javax.xml.stream.XMLInputFactory import scala.collection.JavaConverters._ +import scala.collection.mutable import scala.collection.mutable.ListBuffer import scala.io.Source -import scala.xml.pull.XMLEventReader @ExtendWith(Array(classOf[MockitoExtension])) class BioScholixTest extends AbstractVocabularyTest { @@ -48,6 +53,76 @@ class BioScholixTest extends AbstractVocabularyTest { } } + @Test + def testPid(): Unit = { + val pids = List( + "0000000163025705", + "000000018494732X", + "0000000308873343", + "0000000335964515", + "0000000333457333", + "0000000335964515", + "0000000302921949", + "http://orcid.org/0000-0001-8567-3543", + "http://orcid.org/0000-0001-7868-8528", + "0000-0001-9189-1440", + "0000-0003-3727-9247", + "0000-0001-7246-1058", + "000000033962389X", + "0000000330371470", + "0000000171236123", + "0000000272569752", + "0000000293231371", + "http://orcid.org/0000-0003-3345-7333", + "0000000340145688", + "http://orcid.org/0000-0003-4894-1689" + ) + + pids.foreach(pid => { + val pidCleaned = new PMIdentifier(pid, "ORCID").getPid + // assert pid is in the format of ORCID + println(pidCleaned) + assertTrue(pidCleaned.matches("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]")) + }) + } + + def extractAffiliation(s: String): List[String] = { + val regex: String = "(.*)<\\/Affiliation>" + val pattern = Pattern.compile(regex, Pattern.MULTILINE) + val matcher = pattern.matcher(s) + val l: mutable.ListBuffer[String] = mutable.ListBuffer() + while (matcher.find()) { + l += matcher.group(1) + } + l.toList + } + + case class AuthorPID(pidType: String, pid: String) {} + + def extractAuthorIdentifier(s: String): List[AuthorPID] = { + val regex: String = "(.*)<\\/Identifier>" + val pattern = Pattern.compile(regex, Pattern.MULTILINE) + val matcher = pattern.matcher(s) + val l: mutable.ListBuffer[AuthorPID] = mutable.ListBuffer() + while (matcher.find()) { + l += AuthorPID(pidType = matcher.group(1), pid = matcher.group(2)) + } + l.toList + } + + @Test + def testParsingPubmed2(): Unit = { + val mapper = new ObjectMapper() + val xml = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml")) + val parser = new PMParser2() + val article = parser.parse(xml) + +// println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(article)) + + println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(PubMedToOaf.convert(article, vocabularies))) + + } + @Test def testEBIData() = { val inputFactory = XMLInputFactory.newInstance @@ -124,6 +199,14 @@ class BioScholixTest extends AbstractVocabularyTest { } } + def testPubmedSplitting(): Unit = { + + val spark: SparkSession = SparkSession.builder().appName("test").master("local").getOrCreate() + new SparkCreatePubmedDump("", Array.empty, LoggerFactory.getLogger(getClass)) + .createPubmedDump(spark, "/home/sandro/Downloads/pubmed", "/home/sandro/Downloads/pubmed_mapped", vocabularies) + + } + @Test def testPubmedOriginalID(): Unit = { val article: PMArticle = new PMArticle diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 44482cfdb..f6a436543 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -135,7 +135,7 @@ public class DedupRecordFactory { return Collections.emptyIterator(); } - OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator()); + OafEntity mergedEntity = MergeUtils.mergeGroup(cliques.iterator()); // dedup records do not have date of transformation attribute mergedEntity.setDateoftransformation(null); mergedEntity diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index c7efce4d7..b0bc314e2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -69,6 +69,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { Dataset mergeRels = spark .read() + .schema(REL_BEAN_ENC.schema()) .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) .as(REL_BEAN_ENC); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java index 726814c43..a79047590 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java @@ -46,8 +46,8 @@ class DatasetMergerTest implements Serializable { } @Test - void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException { - Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator()); + void datasetMergerTest() { + Dataset pub_merged = MergeUtils.mergeGroup(datasets.stream().map(Tuple2::_2).iterator()); // verify id assertEquals(dedupId, pub_merged.getId()); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java index 6acc65e05..217840c86 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java @@ -21,17 +21,19 @@ class DecisionTreeTest { void testJPath() throws IOException { DedupConfig conf = DedupConfig - .load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_organization.json"))); + .load( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/jpath/dedup_conf_organization.json"))); - final String org = IOUtils.toString(getClass().getResourceAsStream("organization.json")); + final String org = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/jpath/organization.json")); Row row = SparkModel.apply(conf).rowFromJson(org); System.out.println("row = " + row); Assertions.assertNotNull(row); Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier"))); - - System.out.println("row = " + row.getAs("countrytitle")); } @Test @@ -44,7 +46,8 @@ class DecisionTreeTest { .getResourceAsStream( "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); - final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json")); + final String org = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/jpath/organization_example1.json")); Row row = SparkModel.apply(conf).rowFromJson(org); // to check that the same parsing returns the same row diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 3bfd861f8..a3004c25a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -190,7 +190,7 @@ public class SparkDedupTest implements Serializable { System.out.println("orp_simrel = " + orp_simrel); if (CHECK_CARDINALITIES) { - assertEquals(742, orgs_simrel); + assertEquals(720, orgs_simrel); assertEquals(566, pubs_simrel); assertEquals(113, sw_simrel); assertEquals(148, ds_simrel); @@ -251,7 +251,7 @@ public class SparkDedupTest implements Serializable { // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) if (CHECK_CARDINALITIES) { - assertEquals(742, orgs_simrel); + assertEquals(720, orgs_simrel); assertEquals(566, pubs_simrel); assertEquals(148, ds_simrel); assertEquals(280, orp_simrel); @@ -440,25 +440,27 @@ public class SparkDedupTest implements Serializable { .count(); final List merges = pubs - .filter("source == '50|arXiv_dedup_::c93aeb433eb90ed7a86e29be00791b7c'") + .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")// and relClass = + // '"+ModelConstants.MERGES+"'") .collectAsList(); - assertEquals(1, merges.size()); + assertEquals(4, merges.size()); Set dups = Sets .newHashSet( "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", - "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); + "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c", + "50|arXiv_dedup_::c93aeb433eb90ed7a86e29be00791b7c"); merges.forEach(r -> { assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); assertEquals(ModelConstants.DEDUP, r.getSubRelType()); - assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass()); + assertEquals(ModelConstants.MERGES, r.getRelClass()); assertTrue(dups.contains(r.getTarget())); }); final List mergedIn = pubs - .filter("target == '50|arXiv_dedup_::c93aeb433eb90ed7a86e29be00791b7c'") + .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") .collectAsList(); - assertEquals(3, mergedIn.size()); + assertEquals(4, mergedIn.size()); mergedIn.forEach(r -> { assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); assertEquals(ModelConstants.DEDUP, r.getSubRelType()); @@ -473,8 +475,8 @@ public class SparkDedupTest implements Serializable { System.out.println("orp_mergerel = " + orp_mergerel); if (CHECK_CARDINALITIES) { - assertEquals(1268, orgs_mergerel); - assertEquals(1156, pubs.count()); + assertEquals(1280, orgs_mergerel); + assertEquals(1158, pubs.count()); assertEquals(292, sw_mergerel); assertEquals(476, ds_mergerel); assertEquals(742, orp_mergerel); @@ -561,7 +563,7 @@ public class SparkDedupTest implements Serializable { System.out.println("orp_mergerel = " + orp_mergerel); if (CHECK_CARDINALITIES) { - assertEquals(1278, orgs_mergerel); + assertEquals(1280, orgs_mergerel); assertEquals(1156, pubs.count()); assertEquals(292, sw_mergerel); assertEquals(476, ds_mergerel); @@ -618,7 +620,7 @@ public class SparkDedupTest implements Serializable { System.out.println("orp_deduprecord = " + orp_deduprecord); if (CHECK_CARDINALITIES) { - assertEquals(78, orgs_deduprecord); + assertEquals(87, orgs_deduprecord); assertEquals(96, pubs.count()); assertEquals(47, sw_deduprecord); assertEquals(97, ds_deduprecord); @@ -761,7 +763,7 @@ public class SparkDedupTest implements Serializable { if (CHECK_CARDINALITIES) { assertEquals(930, publications); - assertEquals(831, organizations); + assertEquals(840, organizations); assertEquals(100, projects); assertEquals(100, datasource); assertEquals(196, softwares); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java index b2b5d824b..6b3ef8a20 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java @@ -146,7 +146,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(92, orgs_simrel); + assertEquals(91, orgs_simrel); } @Test @@ -175,7 +175,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(128, orgs_simrel); + assertEquals(127, orgs_simrel); } @Test diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java index 9d73475be..2efa26c02 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java @@ -324,7 +324,7 @@ public class SparkPublicationRootsTest implements Serializable { private void verifyRoot_case_3(Dataset roots, Dataset pubs) { Publication root = roots - .filter("id = '50|dedup_wf_001::31ca734cc22181b704c4aa8fd050062a'") + .filter("id = '50|dedup_wf_002::7143f4ff5708f3657db0b7e68ea74d55'") .first(); assertNotNull(root); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java index 9afe1e34b..1e73801ff 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java @@ -143,7 +143,9 @@ public class SparkPublicationRootsTest2 implements Serializable { "--graphBasePath", graphInputPath, "--actionSetId", testActionSetId, "--isLookUpUrl", "lookupurl", - "--workingPath", workingPath + "--workingPath", workingPath, + "--hiveMetastoreUris", "", + }), spark) .run(isLookUpService); @@ -153,7 +155,7 @@ public class SparkPublicationRootsTest2 implements Serializable { .as(Encoders.bean(Relation.class)); assertEquals( - 3, merges + 4, merges .filter("relclass == 'isMergedIn'") .map((MapFunction) Relation::getTarget, Encoders.STRING()) .distinct() @@ -178,7 +180,7 @@ public class SparkPublicationRootsTest2 implements Serializable { .textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord") .map(asEntity(Publication.class), Encoders.bean(Publication.class)); - assertEquals(3, roots.count()); + assertEquals(4, roots.count()); final Dataset pubs = spark .read() @@ -195,7 +197,6 @@ public class SparkPublicationRootsTest2 implements Serializable { .collectAsList() .get(0); - assertEquals(crossref_duplicate.getDateofacceptance().getValue(), root.getDateofacceptance().getValue()); assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java index 19f2c8102..d21a0dcf4 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java @@ -168,7 +168,7 @@ public class SparkStatsTest implements Serializable { .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats") .count(); - assertEquals(414, orgs_blocks); + assertEquals(406, orgs_blocks); assertEquals(221, pubs_blocks); assertEquals(134, sw_blocks); assertEquals(196, ds_blocks); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java index 18c9ce18d..d54f608ac 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java @@ -19,17 +19,19 @@ class JsonPathTest { void testJPath() throws IOException { DedupConfig conf = DedupConfig - .load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_organization.json"))); + .load( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/jpath/dedup_conf_organization.json"))); - final String org = IOUtils.toString(getClass().getResourceAsStream("organization.json")); + final String org = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/jpath/organization.json")); Row row = SparkModel.apply(conf).rowFromJson(org); System.out.println("row = " + row); Assertions.assertNotNull(row); Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier"))); - - System.out.println("row = " + row.getAs("countrytitle")); } @Test diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json index f00f6198e..388f0b6ff 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json @@ -24,22 +24,19 @@ "start": { "fields": [ { - "field": "gridid", - "comparator": "exactMatch", + "field": "pid", + "comparator": "jsonListMatch", "weight": 1, "countIfUndefined": "false", - "params": {} - }, - { - "field": "rorid", - "comparator": "exactMatch", - "weight": 1, - "countIfUndefined": "false", - "params": {} + "params": { + "jpath_classid": "$.qualifier.classid", + "jpath_value": "$.value", + "mode": "type" + } } ], "threshold": 1, - "aggregation": "OR", + "aggregation": "MAX", "positive": "MATCH", "negative": "NO_MATCH", "undefined": "necessaryConditions", @@ -149,11 +146,10 @@ "model" : [ { "name" : "country", "type" : "String", "path" : "$.country.classid", "infer" : "country", "inferenceFrom" : "$.legalname.value"}, { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value", "infer" : "city_keyword"}, - { "name" : "original_legalname", "type" : "String", "path" : "$.legalname.value" }, + { "name" : "original_legalname", "type" : "String", "path" : "$.legalname.value", "clean": "title"}, { "name" : "legalname", "type" : "String", "path" : "$.legalname.value", "infer" : "city_keyword"}, { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, - { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"}, - { "name" : "rorid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='ROR')].value"}, + { "name": "pid", "type": "JSON", "path": "$.pid[*]", "overrideMatch": "true"}, { "name" : "originalId", "type" : "String", "path" : "$.id" } ], "blacklists" : {}, 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 f284a063e..031a04058 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 @@ -566,7 +566,26 @@ case object Crossref2Oaf { queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) case _ => logger.debug("no match for " + funder.DOI.get) - + //Add for Danish funders + //Independent Research Fund Denmark (IRFD) + case "10.13039/501100004836" => + generateSimpleRelationFromAward(funder, "irfd________", a => a) + val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //Carlsberg Foundation (CF) + case "10.13039/501100002808" => + generateSimpleRelationFromAward(funder, "cf__________", a => a) + val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //Novo Nordisk Foundation (NNF) + case "10.13039/501100009708" => + generateSimpleRelationFromAward(funder, "nnf___________", a => a) + val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + case _ => logger.debug("no match for " + funder.DOI.get) } } else { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 8dd6e38ba..c28610e1e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp; +import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; + import java.util.ArrayList; import java.util.List; import java.util.Optional; @@ -21,8 +23,6 @@ import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; -import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; - public class PropagationConstant { private PropagationConstant() { @@ -48,7 +48,7 @@ public class PropagationConstant { public static final String INSTITUTIONAL_REPO_TYPE = "institutional"; - //public static final String PROPAGATION_DATA_INFO_TYPE = "propagation"; + // public static final String PROPAGATION_DATA_INFO_TYPE = "propagation"; public static final String TRUE = "true"; 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 6079da365..1e39d99c3 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 @@ -171,7 +171,7 @@ public class Utils implements Serializable { public static List getCommunityIdList(String baseURL) throws IOException { return getValidCommunities(baseURL) .stream() - .map(community -> community.getId()) + .map(CommunityModel::getId) .collect(Collectors.toList()); } 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 2ea229e3e..0d6c81627 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 @@ -130,6 +130,7 @@ public class ResultTagger implements Serializable { // log.info("Remove constraints for " + communityId); if (conf.getRemoveConstraintsMap().keySet().contains(communityId) && conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && + !conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() && conf .getRemoveConstraintsMap() .get(communityId) @@ -161,29 +162,30 @@ public class ResultTagger implements Serializable { // Tagging for datasource final Set datasources = new HashSet<>(); - final Set collfrom = new HashSet<>(); + final Set cfhb = new HashSet<>(); final Set hostdby = new HashSet<>(); if (Objects.nonNull(result.getInstance())) { for (Instance i : result.getInstance()) { if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) { - collfrom.add(i.getCollectedfrom().getKey()); + cfhb.add(i.getCollectedfrom().getKey()); } if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) { + cfhb.add(i.getHostedby().getKey()); hostdby.add(i.getHostedby().getKey()); } } - collfrom + cfhb .forEach( dsId -> datasources .addAll( conf.getCommunityForDatasource(dsId, param))); hostdby.forEach(dsId -> { - datasources - .addAll( - conf.getCommunityForDatasource(dsId, param)); +// datasources +// .addAll( +// conf.getCommunityForDatasource(dsId, param)); if (conf.isEoscDatasource(dsId)) { datasources.add("eosc"); } @@ -226,6 +228,7 @@ public class ResultTagger implements Serializable { .forEach(communityId -> { if (!removeCommunities.contains(communityId) && conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && + !conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() && conf .getSelectionConstraintsMap() .get(communityId) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java index 57cc658fc..8a23a7017 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java @@ -33,6 +33,8 @@ public class SelectionConstraints implements Serializable { // Constraints in or public boolean verifyCriteria(final Map> param) { + if (criteria.isEmpty()) + return true; for (Constraints selc : criteria) { if (selc.verifyCriteria(param)) { return true; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidAuthors.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidAuthors.java index 0c687b991..582823660 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidAuthors.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidAuthors.java @@ -1,18 +1,19 @@ -package eu.dnetlib.dhp.orcidtoresultfromsemrel; -import eu.dnetlib.dhp.utils.OrcidAuthor; +package eu.dnetlib.dhp.orcidtoresultfromsemrel; import java.io.Serializable; import java.util.List; +import eu.dnetlib.dhp.utils.OrcidAuthor; + public class OrcidAuthors implements Serializable { - List orcidAuthorList; + List orcidAuthorList; - public List getOrcidAuthorList() { - return orcidAuthorList; - } + public List getOrcidAuthorList() { + return orcidAuthorList; + } - public void setOrcidAuthorList(List orcidAuthorList) { - this.orcidAuthorList = orcidAuthorList; - } + public void setOrcidAuthorList(List orcidAuthorList) { + this.orcidAuthorList = orcidAuthorList; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkPropagateOrcidAuthor.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkPropagateOrcidAuthor.java index 5c13cba3c..86a042b21 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkPropagateOrcidAuthor.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkPropagateOrcidAuthor.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.orcidtoresultfromsemrel; import java.util.List; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index a6466716a..a28aba5d3 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.projecttoresult; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; import java.util.ArrayList; import java.util.List; 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 f84a10d1c..c51e1fa78 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 @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.resulttocommunityfromorganization; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; import java.util.ArrayList; import java.util.Arrays; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index 7a6238940..916af964e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; import java.io.Serializable; import java.util.ArrayList; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index aede9ef05..ecb7cc827 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -1,11 +1,14 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; +import static java.lang.String.join; + import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.io.IOException; import java.util.Arrays; +import java.util.Collections; import java.util.List; import org.apache.commons.io.IOUtils; @@ -19,6 +22,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.api.Utils; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -45,7 +49,7 @@ public class PrepareResultCommunitySetStep1 { /** * a dataset for example could be linked to more than one publication. For each publication linked to that dataset - * the previous query will produce a row: targetId set of community context the target could possibly inherit with + * the previous query will produce a row: targetId, set of community context the target could possibly inherit. With * the following query there will be a single row for each result linked to more than one result of the result type * currently being used */ @@ -56,6 +60,27 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target as resultId, community_context " + + + "from resultWithContext rwc " + + "join relatedToRelations r " + + "join patents p " + + "on rwc.id = r.source and r.target = p.id"; + + private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" + + " from result " + + " lateral view explode (context) c as co " + + " where lower(co.id) IN %s" + + " group by id"; + + private static final String RESULT_PATENT = "select id " + + " from result " + + " where array_contains(instance.instancetype.classname, 'Patent')"; + + private static final String IS_RELATED_TO_RELATIONS = "select source, target " + + " from relation " + + " where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false"; + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -82,14 +107,25 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final List allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";")); - log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); + final String allowedsemrel = "(" + join( + ",", + Arrays + .asList(parser.get("allowedsemrels").split(";")) + .stream() + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + + ")"; + log.info("allowedSemRel: {}", allowedsemrel); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", baseURL); - final List communityIdList = getCommunityList(baseURL); - log.info("communityIdList: {}", new Gson().toJson(communityIdList)); + final String communityIdList = "(" + join( + ",", getCommunityList(baseURL) + .stream() + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + + ")"; final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -118,10 +154,10 @@ public class PrepareResultCommunitySetStep1 { SparkSession spark, String inputPath, String outputPath, - List allowedsemrel, + String allowedsemrel, Class resultClazz, String resultType, - List communityIdList) { + String communityIdList) { final String inputResultPath = inputPath + "/" + resultType; log.info("Reading Graph table from: {}", inputResultPath); @@ -132,7 +168,8 @@ public class PrepareResultCommunitySetStep1 { Dataset relation = readPath(spark, inputRelationPath, Relation.class); relation.createOrReplaceTempView("relation"); - Dataset result = readPath(spark, inputResultPath, resultClazz); + Dataset result = readPath(spark, inputResultPath, resultClazz) + .where("datainfo.deletedbyinference != true AND datainfo.invisible != true"); result.createOrReplaceTempView("result"); final String outputResultPath = outputPath + "/" + resultType; @@ -141,10 +178,20 @@ public class PrepareResultCommunitySetStep1 { String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - getConstraintList(" lower(co.id) = '", communityIdList), - getConstraintList(" lower(relClass) = '", allowedsemrel)); - + "AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); + + Dataset rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList)); + Dataset patents = spark.sql(RESULT_PATENT); + Dataset relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS); + + rwc.createOrReplaceTempView("resultWithContext"); + patents.createOrReplaceTempView("patents"); + relatedToRelations.createOrReplaceTempView("relatedTorelations"); + + result_context = result_context.unionAll(spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO)); + result_context.createOrReplaceTempView("result_context"); spark @@ -152,8 +199,9 @@ public class PrepareResultCommunitySetStep1 { .as(Encoders.bean(ResultCommunityList.class)) .write() .option("compression", "gzip") - .mode(SaveMode.Overwrite) + .mode(SaveMode.Append) .json(outputResultPath); + } public static List getCommunityList(final String baseURL) throws IOException { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java index a53d3dfe3..9801b1bf6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.ArrayList; import java.util.HashSet; import java.util.Set; @@ -76,22 +77,13 @@ public class PrepareResultCommunitySetStep2 { if (b == null) { return a; } - Set community_set = new HashSet<>(); - a.getCommunityList().stream().forEach(aa -> community_set.add(aa)); - b - .getCommunityList() - .stream() - .forEach( - aa -> { - if (!community_set.contains(aa)) { - a.getCommunityList().add(aa); - community_set.add(aa); - } - }); + Set community_set = new HashSet<>(a.getCommunityList()); + community_set.addAll(b.getCommunityList()); + a.setCommunityList(new ArrayList<>(community_set)); return a; }) .map(Tuple2::_2) - .map(r -> OBJECT_MAPPER.writeValueAsString(r)) + .map(OBJECT_MAPPER::writeValueAsString) .saveAsTextFile(outputPath, GzipCodec.class); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 3cf2f73c3..b923c4c32 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.enrichment.Constants.PROPAGATION_DATA_INFO_TYPE; import java.util.*; import java.util.stream.Collectors; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java index c4141b3e8..bb20291d1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java @@ -7,6 +7,7 @@ import java.nio.file.Path; import java.util.ArrayList; import java.util.List; +import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -33,7 +34,7 @@ public class CountryPropagationJobTest { private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); private static SparkSession spark; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java index d9b879de8..5067b1cf7 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java @@ -5,6 +5,7 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -19,7 +20,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; public class DatasourceCountryPreparationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); private static SparkSession spark; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkJobTest.java index db917658a..10c817ae4 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkJobTest.java @@ -25,6 +25,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.KeyValueSet; import eu.dnetlib.dhp.PropagationConstant; +import eu.dnetlib.dhp.common.enrichment.Constants; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -145,7 +146,7 @@ public class SparkJobTest { .foreach( r -> Assertions .assertEquals( - PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance())); + Constants.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance())); result .foreach( r -> Assertions @@ -428,7 +429,7 @@ public class SparkJobTest { .foreach( r -> Assertions .assertEquals( - PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance())); + Constants.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance())); project .foreach( r -> Assertions diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index 40849132e..59a8f82f3 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -71,23 +71,24 @@ public class OrcidPropagationJobTest { .getResource( "/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc") .getPath(); - SparkOrcidToResultFromSemRelJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-hive_metastore_uris", "", - "-saveGraph", "true", - "-resultTableName", Dataset.class.getCanonicalName(), - "-outputPath", workingDir.toString() + "/dataset", - "-possibleUpdatesPath", possibleUpdatesPath - }); + SparkPropagateOrcidAuthor + .main( + new String[] { + "-graphPath", + getClass() + .getResource( + "/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate") + .getPath(), + "-targetPath", + workingDir.toString() + "/graph", + "-orcidPath", "", + "-workingDir", workingDir.toString() + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") + .textFile(workingDir.toString() + "/graph/dataset") .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); @@ -110,36 +111,24 @@ public class OrcidPropagationJobTest { @Test void oneUpdateTest() throws Exception { - SparkOrcidToResultFromSemRelJob - .main( - new String[] { - "-isTest", - Boolean.TRUE.toString(), - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-sourcePath", - getClass() - .getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate") - .getPath(), - "-hive_metastore_uris", - "", - "-saveGraph", - "true", - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", - workingDir.toString() + "/dataset", - "-possibleUpdatesPath", - getClass() - .getResource( - "/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc") - .getPath() - }); + SparkPropagateOrcidAuthor + .main( + new String[] { + "-graphPath", + getClass() + .getResource( + "/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate") + .getPath(), + "-targetPath", + workingDir.toString() + "/graph", + "-orcidPath", "", + "-workingDir", workingDir.toString() + }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") + .textFile(workingDir.toString() + "/graph/dataset") .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); @@ -177,31 +166,18 @@ public class OrcidPropagationJobTest { @Test void twoUpdatesTest() throws Exception { - SparkOrcidToResultFromSemRelJob + SparkPropagateOrcidAuthor .main( new String[] { - "-isTest", - Boolean.TRUE.toString(), - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-sourcePath", + "-graphPath", getClass() .getResource( "/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/twoupdates") .getPath(), - "-hive_metastore_uris", - "", - "-saveGraph", - "true", - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", + "-targetPath", workingDir.toString() + "/dataset", - "-possibleUpdatesPath", - getClass() - .getResource( - "/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc") - .getPath() + "-orcidPath", "", + "-workingDir", workingDir.toString() }); final JavaSparkContext sc = new JavaSparkContext(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 6440ded92..d3505a604 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 @@ -7,6 +7,7 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -30,7 +31,7 @@ public class ResultToCommunityJobTest { private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); private static SparkSession spark; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index 0d5b12c80..0a7eb414a 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -6,8 +6,11 @@ import static org.apache.spark.sql.functions.desc; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.ArrayList; import java.util.List; +import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -24,13 +27,15 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; import eu.dnetlib.dhp.schema.oaf.Dataset; +import scala.collection.Seq; public class ResultToCommunityJobTest { private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); private static SparkSession spark; @@ -271,4 +276,59 @@ public class ResultToCommunityJobTest { .get(0) .getString(0)); } + + @Test + public void prepareStep1Test() throws Exception { + /* + * final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) .map(value -> + * "'" + value.toLowerCase() + "'") .toArray(String[]::new)); log.info("allowedSemRel: {}", new + * Gson().toJson(allowedsemrel)); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", + * baseURL); + */ + PrepareResultCommunitySetStep1 + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph") + .getPath(), + "-hive_metastore_uris", "", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/preparedInfo", + "-allowedsemrels", "issupplementto;issupplementedby", + "-baseURL", "https://dev-openaire.d4science.org/openaire/community/" + }); + + org.apache.spark.sql.Dataset resultCommunityList = spark + .read() + .schema(Encoders.bean(ResultCommunityList.class).schema()) + .json(workingDir.toString() + "/preparedInfo/publication") + .as(Encoders.bean(ResultCommunityList.class)); + + Assertions.assertEquals(2, resultCommunityList.count()); + Assertions + .assertEquals( + 1, + resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count()); + Assertions + .assertEquals( + 1, + resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count()); + + ArrayList communities = resultCommunityList + .filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'") + .first() + .getCommunityList(); + Assertions.assertEquals(2, communities.size()); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid))); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid))); + + communities = resultCommunityList + .filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'") + .first() + .getCommunityList(); + Assertions.assertEquals(1, communities.size()); + Assertions.assertEquals("dh-ch", communities.get(0)); + } + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/dataset/dataset_10.json.gz b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/dataset/dataset_10.json.gz new file mode 100644 index 000000000..778f72262 Binary files /dev/null and b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/dataset/dataset_10.json.gz differ diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/otherresearchproduct/empty.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/otherresearchproduct/empty.json new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/publication/empty.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/publication/empty.json new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/relation/empty.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/relation/empty.json new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/software/empty.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate/software/empty.json new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate/dataset/dataset_10.json new file mode 100644 index 000000000..215acd239 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate/dataset/dataset_10.json @@ -0,0 +1,10 @@ +{"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":1585055868909,"id":"50|dedup_wf_001::36bcfaa1494c849547a346da688ade24","originalId":["od______3989::02dd5d2c222191b0b9bd4f33c8e96529"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital 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Nicole","name":"Nicole","pid":[{"dataInfo":null,"qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":null,"schemename":null},"value":"0000-0001-9513-2468"}],"rank":1,"surname":"Jung"},{"affiliation":[],"fullname":"Gräßle, Simone","name":"Simone","pid":[],"rank":2,"surname":"Gräßle"}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"esl/spa","classname":"Spanish","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Ciencias de la 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Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.

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Ex situ analyses of the tiles were performed by secondary ion mass spectrometry.
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this.invisible); final long lastUpdateTimestamp = new Date().getTime(); - final List instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy); + final Instance instance = prepareInstances(doc, entityInfo, collectedFrom, hostedBy); - final String type = getResultType(doc, instances); + if (!Optional + .ofNullable(instance.getInstancetype()) + .map(Qualifier::getClassid) + .filter(StringUtils::isNotBlank) + .isPresent()) { + return Lists.newArrayList(); + } - return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + final String type = getResultType(instance); + + return createOafs(doc, type, instance, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (final DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); } } - protected String getResultType(final Document doc, final List instances) { - final String type = doc.valueOf("//dr:CobjCategory/@type"); - - if (StringUtils.isBlank(type) && this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { - final String instanceType = instances - .stream() - .map(i -> i.getInstancetype().getClassid()) - .findFirst() - .filter(s -> !UNKNOWN.equalsIgnoreCase(s)) - .orElse("0000"); // Unknown + protected String getResultType(final Instance instance) { + if (this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { return Optional - .ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) + .ofNullable(instance.getInstancetype()) .map(Qualifier::getClassid) + .map( + instanceType -> Optional + .ofNullable( + this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) + .map(Qualifier::getClassid) + .orElse("0000")) .orElse("0000"); + } else { + throw new IllegalStateException("Missing vocabulary: " + ModelConstants.DNET_RESULT_TYPOLOGIES); } - - return type; } private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { @@ -197,12 +203,12 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, - final List instances, + final Instance instance, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity(doc, type, instance, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -235,19 +241,19 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, - final List instances, + final Instance instance, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, doc, instance, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, doc, instance, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -258,7 +264,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, doc, instance, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -268,7 +274,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, doc, instance, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -415,7 +421,7 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, final Document doc, - final List instances, + final Instance instance, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { @@ -449,8 +455,8 @@ public abstract class AbstractMdRecordToOafMapper { r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); r.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - r.setInstance(instances); - r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); + r.setInstance(Arrays.asList(instance)); + r.setBestaccessright(OafMapperUtils.createBestAccessRights(Arrays.asList(instance))); r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info)); } @@ -509,7 +515,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - protected abstract List prepareInstances( + protected abstract Instance prepareInstances( Document doc, DataInfo info, KeyValue collectedfrom, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index c3806c211..357fae470 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -133,7 +133,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication { inputRdd .keyBy(oaf -> ModelSupport.idFn().apply(oaf)) .groupByKey() - .map(t -> MergeUtils.mergeGroup(t._1, t._2.iterator())), + .map(t -> MergeUtils.mergeGroup(t._2.iterator())), // .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf)) // .reduceByKey(MergeUtils::merge) // .map(Tuple2::_2), 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 98da48f9e..33351e91f 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 @@ -135,7 +135,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { } @Override - protected List prepareInstances( + protected Instance prepareInstances( final Document doc, final DataInfo info, final KeyValue collectedfrom, @@ -197,7 +197,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { instance.getUrl().addAll(validUrl); } - return Lists.newArrayList(instance); + return instance; } /** 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 ad61304a0..efe05eb68 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 @@ -126,7 +126,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } @Override - protected List prepareInstances( + protected Instance prepareInstances( final Document doc, final DataInfo info, final KeyValue collectedfrom, @@ -210,7 +210,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { instance.setUrl(new ArrayList<>()); instance.getUrl().addAll(validUrl); } - return Arrays.asList(instance); + return instance; } protected String trimAndDecodeUrl(String url) { @@ -319,7 +319,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List> prepareDescriptions(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//*[local-name()='description' and ./@descriptionType='Abstract']", info); + return prepareListFields(doc, "//datacite:description[./@descriptionType='Abstract'] | //dc:description", info); } @Override 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 index 4031da15a..1ece2c0be 100644 --- 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 @@ -51,6 +51,7 @@ --orcidPath${orcidPath} --targetPath${targetPath} --graphPath${graphPath} + --workingDir${workingDir} --masteryarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 2512fc5bc..01aaadae5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -162,6 +162,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=15000 --inputPath${graphInputPath}/publication @@ -197,6 +198,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=8000 --inputPath${graphInputPath}/dataset @@ -232,6 +234,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=5000 --inputPath${graphInputPath}/otherresearchproduct @@ -267,6 +270,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/software @@ -302,6 +306,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/datasource @@ -337,6 +342,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/organization @@ -372,6 +378,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/project @@ -407,6 +414,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/person @@ -442,6 +450,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.autoBroadcastJoinThreshold=-1 --conf spark.sql.shuffle.partitions=20000 --inputPath${graphInputPath}/relation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml index a8d0d5068..3444e3afe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml @@ -68,6 +68,7 @@ + @@ -260,6 +261,33 @@ + + + yarn + cluster + Merge person + eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob + dhp-graph-mapper-${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.sql.shuffle.partitions=7680 + + --betaInputPath${betaInputGraphPath}/person + --prodInputPath${prodInputGraphPath}/person + --outputPath${graphOutputPath}/person + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Person + --priority${priority} + + + + + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index ff927fe52..1b3cb1111 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -649,6 +649,7 @@ + @@ -860,6 +861,32 @@ + + + yarn + cluster + MergeClaims_person + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=200 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Person + + + + + 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 index f10a9e56f..7478225b5 100644 --- 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 @@ -11,7 +11,12 @@ import scala.collection.JavaConverters._ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) extends SparkEnrichWithOrcidAuthors(propertyPath, args, log: Logger) { - override def createTemporaryData(spark:SparkSession, graphPath: String, orcidPath: String, targetPath: String): Unit = { + override def createTemporaryData( + spark: SparkSession, + graphPath: String, + orcidPath: String, + targetPath: String + ): Unit = { val orcidAuthors = spark.read.load(s"$orcidPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") @@ -82,14 +87,13 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] } } - object SparkEnrichGraphWithOrcidAuthors { +object SparkEnrichGraphWithOrcidAuthors { - val log: Logger = LoggerFactory.getLogger(SparkEnrichGraphWithOrcidAuthors.getClass) + 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() - } + 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/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala index d94a23947..42299cd34 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala @@ -133,7 +133,7 @@ object SparkCreateInputGraph { val ds: Dataset[T] = spark.read.load(sourcePath).as[T] ds.groupByKey(_.getId) - .mapGroups { (id, it) => MergeUtils.mergeGroup(id, it.asJava).asInstanceOf[T] } + .mapGroups { (id, it) => MergeUtils.mergeGroup(it.asJava).asInstanceOf[T] } // .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] } // .map(_) .write 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 2cf3ea0c0..e1710db54 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 @@ -906,6 +906,30 @@ class MappersTest { assertEquals("IT", p.getCountry().get(0).getClassid()); assertEquals("FR", p.getCountry().get(1).getClassid()); assertEquals("DE", p.getCountry().get(2).getClassid()); + + assertNotNull(p.getDescription()); + assertEquals(1, p.getDescription().size()); + assertNotNull(p.getDescription().get(0)); + assertTrue(StringUtils.isNotBlank(p.getDescription().get(0).getValue())); + } + + @Test + void testODFRecord_guidelines4() throws IOException { + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + + assertNotNull(p.getDescription()); + assertEquals(2, p.getDescription().size()); + assertNotNull(p.getDescription().get(0)); + assertTrue(StringUtils.isNotBlank(p.getDescription().get(0).getValue())); + assertNotNull(p.getDescription().get(1)); + assertTrue(StringUtils.isNotBlank(p.getDescription().get(1).getValue())); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml new file mode 100644 index 000000000..4f390afb7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml @@ -0,0 +1,95 @@ + + +
+ od______1261::66de86a37fa980b9b8f4cefdf1c5a0c5 + oai:air.unimi.it:2434/636308 + 2020-09-04T14:36:48.411Z + od______1261 + oai:air.unimi.it:2434/636308 + 2022-10-14T14:17:28Z + com_2434_73555 + col_2434_73557 + openaire + 2024-11-07T06:17:52.454Z +
+ + + + I processi incorpati di costruzione della conoscenza nelle pratiche di cura + + + + S. Visioli + rp17381 + University of Milan + 53567 + + + L. Zannini + 0000-0001-7287-6616 + rp31993 + University of Milan + 5556 + + + 487 + 2 + 506 + 8 + METIS + + 10.30557/MT00041 + http://hdl.handle.net/2434/636308 + + + 2018 + 2018 + 2019-05-23 + + ita + journal article + In ambito educativo, il corpo è stato tradizionalmente marginalizzato o rifiutato come fonte di conoscenza. Negli ultimi decenni, la letteratura pedagogica ha manifestato crescente interesse per il ruolo che ha il corpo dell’insegnante, nel pianificare e realizzare l’insegnamento, sfidando le ideologie e le epistemologie dominanti, secondo le quali la nostra mente è la fonte primaria di apprendimento. Al contrario, una pedagogia della conoscenza incorpata (embodiment) considera il corpo centrale nel nostro conoscere (le pratiche d’insegnamento) e nel nostro essere (insegnanti). Analogamente, la letteratura delle professioni del caring si è rivelata molto attenta ai temi della conoscenza incorpata, ossia di quel sapere che è presente in un corpo, spesso in modo tacito. Le infermiere hanno da tempo esplorato il ruolo del loro corpo nei processi di costruzione della conoscenza, come anche il ruolo del corpo dello studente, e addirittura del paziente, nel conoscere la malattia. In questo paper riportiamo alcune riflessioni ed esperienze sulla conoscenza incorpata nelle pratiche assistenziali, mettendo in luce come questa, benché spesso tacita, abbia un ruolo centrale nell’aver cura delle persone malate. + In educational contexts, the body has been traditionally marginalized or rejected as a source of knowledge. In the last decades, some pedagogical contributions have shown interest for the role that the teacher’s body has in planning and implementing teaching, challenging dominant ideologies and epistemologies that tell us our minds are the primary sources of learning. Conversely, a pedagogy of embodiment makes the body central in our knowing (educational practices) and being (a teacher). Similarly, literature from the caring professions has revealed very receptive to-ward issues related to embodied knowledge, that is to say the knowledge that the body owns, which is frequently tacit. Since many years, nurses have explored the role of body in the processes of knowledge building, as well as the role of the student’s body, and even the patient’s body, in knowing the illness. In this paper we report some reflections and experiences concerning embodied knowledge in the nursing practice, highlighting that embodied knowledge, even if tacit, has a pivotal role when caring for sick people. + application/pdf + 2434/636308 + open access + + body; educational practices; embodied knowledge; nursing; teaching + + + + 413926 bytes + + + https://air.unimi.it/bitstream/2434/636308/2/Finale%20pubblicato.pdf + + https://air.unimi.it/bitstream/2434/636308/2/Finale%20pubblicato.pdf + 0001 + 2018-01-01 + OPEN + ita + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java index 738d75189..2c977a390 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java @@ -174,6 +174,8 @@ public class ProvisionModelSupport { && StringUtils.isNotBlank(relation.getValidationDate())) { rr.setValidationDate(relation.getValidationDate()); } + rr.setGivenName(re.getGivenName()); + rr.setFamilyName(re.getFamilyName()); return rr; } @@ -208,11 +210,31 @@ public class ProvisionModelSupport { ps.setAlternativeNames(p.getAlternativeNames()); ps.setBiography(p.getBiography()); ps.setConsent(p.getConsent()); - // ps.setSubject(...)); + ps.setSubject(mapPersonTopics(p.getSubject())); return ps; } + private static List mapPersonTopics(List subjects) { + return Optional + .ofNullable(subjects) + .map( + ss -> ss + .stream() + .map(ProvisionModelSupport::mapPersonTopic) + .collect(Collectors.toList())) + .orElse(null); + } + + private static PersonTopic mapPersonTopic(eu.dnetlib.dhp.schema.oaf.PersonTopic pt) { + PersonTopic topic = new PersonTopic(); + topic.setValue(pt.getValue()); + topic.setSchema(pt.getSchema()); + topic.setFromYear(pt.getFromYear()); + topic.setToYear(pt.getToYear()); + return topic; + } + private static Funding mapFunding(List fundingtree, VocabularyGroup vocs) { SAXReader reader = new SAXReader(); return Optional diff --git a/pom.xml b/pom.xml index 9480ddfc0..033d88b0b 100644 --- a/pom.xml +++ b/pom.xml @@ -937,7 +937,7 @@ 1.1.3 1.7 1.0.7 - [9.0.0] + [10.0.0] cdh5.9.2 3.5 11.0.2