diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java index 07ddbb00e9..b5587c6b7e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java @@ -10,6 +10,7 @@ public class Dataset extends Result implements Serializable { private Field storagedate; + // candidate for removal private Field device; private Field size; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 11fdaa4f92..09e77a244e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -2,8 +2,10 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.ArrayList; import java.util.Comparator; import java.util.List; +import java.util.stream.Collectors; public class Result extends OafEntity implements Serializable { @@ -248,13 +250,24 @@ public class Result extends OafEntity implements Serializable { StructuredProperty baseMainTitle = null; if (title != null) { baseMainTitle = getMainTitle(title); - title.remove(baseMainTitle); + if (baseMainTitle != null) { + final StructuredProperty p = baseMainTitle; + title = title.stream().filter(t -> t != p).collect(Collectors.toList()); + } +// +// +// title.remove(baseMainTitle); } StructuredProperty newMainTitle = null; if (r.getTitle() != null) { newMainTitle = getMainTitle(r.getTitle()); - r.getTitle().remove(newMainTitle); + if (newMainTitle != null) { + final StructuredProperty p = newMainTitle; + title = title.stream().filter(t -> t != p).collect(Collectors.toList()); + } + + // r.getTitle().remove(newMainTitle); } if (newMainTitle != null && compareTrust(this, r) < 0) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java index 40332bf53c..d25b5c9cec 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java @@ -10,8 +10,10 @@ public class Software extends Result implements Serializable { private List> documentationUrl; + // candidate for removal private List license; + // candidate for removal private Field codeRepositoryUrl; private Qualifier programmingLanguage; diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 0e84d99a45..59ff05ed3f 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -57,7 +57,7 @@ eu.dnetlib dnet-openaire-broker-common - [2.0.0,3.0.0) + [2.0.1,3.0.0) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java index 9e5d986448..df33fae0da 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -12,7 +12,6 @@ import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DateUtils; -import eu.dnetlib.broker.objects.OpenAireEventPayload; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.KeyValue; @@ -37,15 +36,13 @@ public class EventFactory { final Map map = createMapFromResult(updateInfo); - final String payload = createPayload(updateInfo); - final String eventId = calculateEventId( updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0), updateInfo.getHighlightValueAsString()); res.setEventId(eventId); res.setProducerId(PRODUCER_ID); - res.setPayload(payload); + res.setPayload(updateInfo.asBrokerPayload().toJSON()); res.setMap(map); res.setTopic(updateInfo.getTopicPath()); res.setCreationDate(now); @@ -54,15 +51,6 @@ public class EventFactory { return res; } - private static String createPayload(final UpdateInfo updateInfo) { - final OpenAireEventPayload payload = new OpenAireEventPayload(); - // TODO - - updateInfo.compileHighlight(payload); - - return payload.toJSON(); - } - private static Map createMapFromResult(final UpdateInfo updateInfo) { final Map map = new HashMap<>(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index d5e577972d..a38e760c51 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -43,21 +43,21 @@ import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublic import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedBy; import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedTo; import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationReferences; +import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMissingSoftware; +import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMoreSoftware; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAbstract; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAuthorOrcid; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingOpenAccess; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPid; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate; -import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSoftware; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSubject; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid; -import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSoftware; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -128,10 +128,13 @@ public class GenerateEventsApplication { final JavaRDD eventsRdd = sc.emptyRDD(); - eventsRdd.union(generateSimpleEvents(spark, graphPath, Publication.class)); - eventsRdd.union(generateSimpleEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class)); - eventsRdd.union(generateSimpleEvents(spark, graphPath, Software.class)); - eventsRdd.union(generateSimpleEvents(spark, graphPath, OtherResearchProduct.class)); + for (final Class r1 : BrokerConstants.RESULT_CLASSES) { + eventsRdd.union(generateSimpleEvents(spark, graphPath, r1)); + + for (final Class r2 : BrokerConstants.RESULT_CLASSES) { + eventsRdd.union(generateRelationEvents(spark, graphPath, r1, r2)); + } + } eventsRdd.saveAsTextFile(eventsPath, GzipCodec.class); }); @@ -187,6 +190,38 @@ public class GenerateEventsApplication { return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); } + private static JavaRDD generateRelationEvents( + final SparkSession spark, + final String graphPath, + final Class sourceClass, + final Class targetClass) { + + final Dataset sources = readPath( + spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) + .filter(r -> r.getDataInfo().getDeletedbyinference()); + + final Dataset targets = readPath( + spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass); + + final Dataset mergedRels = readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); + + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); + + if (targetClass == Project.class) { + // TODO join using: generateProjectsEvents + } else if (targetClass == Software.class) { + // TODO join using: generateSoftwareEvents + } else if (targetClass == Publication.class) { + // TODO join using: generatePublicationRelatedEvents + } else if (targetClass == eu.dnetlib.dhp.schema.oaf.Dataset.class) { + // TODO join using: generateDatasetRelatedEvents + } + + return null; + } + private List generateProjectsEvents(final Collection>> childrenWithProjects) { final List> list = new ArrayList<>(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java index 461266d567..ed5e71d52d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java @@ -3,11 +3,13 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.Arrays; import java.util.List; +import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; @@ -22,8 +24,17 @@ public class EnrichMissingProject @Override protected List> findUpdates(final Pair> source, final Pair> target) { - // TODO - return Arrays.asList(); + + if (source.getRight().isEmpty()) { + return Arrays.asList(); + } else { + return target + .getRight() + .stream() + .map(ConversionUtils::oafProjectToBrokerProject) + .map(p -> generateUpdateInfo(p, source, target)) + .collect(Collectors.toList()); + } } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java index d9bfb62d59..753166a824 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java @@ -1,13 +1,15 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; -import java.util.Arrays; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; @@ -21,8 +23,20 @@ public class EnrichMoreProject extends UpdateMatcher> @Override protected List> findUpdates(final Pair> source, final Pair> target) { - // TODO - return Arrays.asList(); + + final Set existingProjects = source + .getRight() + .stream() + .map(Project::getId) + .collect(Collectors.toSet()); + + return target + .getRight() + .stream() + .filter(p -> !existingProjects.contains(p.getId())) + .map(ConversionUtils::oafProjectToBrokerProject) + .map(p -> generateUpdateInfo(p, source, target)) + .collect(Collectors.toList()); } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java index 75e77b3c6f..074b6043a4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -39,7 +39,7 @@ public abstract class AbstractEnrichMissingPublication .getRight() .stream() .filter(d -> !existingPublications.contains(d.getId())) - .map(ConversionUtils::oafPublicationToBrokerPublication) + .map(ConversionUtils::oafResultToBrokerPublication) .map(i -> generateUpdateInfo(i, source, target)) .collect(Collectors.toList()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java similarity index 72% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java index 4fcba43a40..fd9091dc1a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java @@ -1,13 +1,15 @@ -package eu.dnetlib.dhp.broker.oa.matchers.simple; +package eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware; import java.util.Arrays; import java.util.List; +import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; @@ -23,8 +25,17 @@ public class EnrichMissingSoftware protected List> findUpdates( final Pair> source, final Pair> target) { - // TODO - return Arrays.asList(); + + if (source.getRight().isEmpty()) { + return Arrays.asList(); + } else { + return target + .getRight() + .stream() + .map(ConversionUtils::oafSoftwareToBrokerSoftware) + .map(p -> generateUpdateInfo(p, source, target)) + .collect(Collectors.toList()); + } } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java similarity index 66% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java index a1affff623..cb649dffff 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java @@ -1,13 +1,15 @@ -package eu.dnetlib.dhp.broker.oa.matchers.simple; +package eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware; -import java.util.Arrays; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; @@ -23,8 +25,20 @@ public class EnrichMoreSoftware protected List> findUpdates( final Pair> source, final Pair> target) { - // TODO - return Arrays.asList(); + + final Set existingSoftwares = source + .getRight() + .stream() + .map(Software::getId) + .collect(Collectors.toSet()); + + return target + .getRight() + .stream() + .filter(p -> !existingSoftwares.contains(p.getId())) + .map(ConversionUtils::oafSoftwareToBrokerSoftware) + .map(p -> generateUpdateInfo(p, source, target)) + .collect(Collectors.toList()); } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index c7e9dcbc11..30638cefbb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -37,7 +37,7 @@ public class EnrichMissingOpenAccess extends UpdateMatcher { .stream() .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(s -> s) + .flatMap(List::stream) .map(i -> generateUpdateInfo(i, source, target)) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index c376da44d2..f9c5f81da1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -34,7 +34,7 @@ public class EnrichMoreOpenAccess extends UpdateMatcher { .stream() .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(s -> s) + .flatMap(List::stream) .filter(i -> !urls.contains(i.getUrl())) .map(i -> generateUpdateInfo(i, source, target)) .collect(Collectors.toList()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java index 8e97192bfb..f4da59518d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java @@ -1,9 +1,21 @@ package eu.dnetlib.dhp.broker.oa.util; +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; + public class BrokerConstants { - public final static String OPEN_ACCESS = "OPEN"; - public final static String IS_MERGED_IN_CLASS = "isMergedIn"; + public static final String OPEN_ACCESS = "OPEN"; + public static final String IS_MERGED_IN_CLASS = "isMergedIn"; + + public static final List> RESULT_CLASSES = Arrays + .asList(Publication.class, Dataset.class, Software.class, OtherResearchProduct.class); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 2f87d0ee76..2b39115b16 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -1,49 +1,184 @@ package eu.dnetlib.dhp.broker.oa.util; -import java.util.stream.Stream; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Pair; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.DocumentHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; -import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.ExternalReference; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ConversionUtils { - public static Stream oafInstanceToBrokerInstances(final eu.dnetlib.dhp.schema.oaf.Instance i) { + private static final Logger log = LoggerFactory.getLogger(ConversionUtils.class); + + public static List oafInstanceToBrokerInstances(final Instance i) { return i.getUrl().stream().map(url -> { - final Instance r = new Instance(); - r.setUrl(url); - r.setInstancetype(i.getInstancetype().getClassid()); - r.setLicense(BrokerConstants.OPEN_ACCESS); - r.setHostedby(i.getHostedby().getValue()); - return r; - }); + return new eu.dnetlib.broker.objects.Instance() + .setUrl(url) + .setInstancetype(i.getInstancetype().getClassid()) + .setLicense(BrokerConstants.OPEN_ACCESS) + .setHostedby(i.getHostedby().getValue()); + }).collect(Collectors.toList()); } public static Pid oafPidToBrokerPid(final StructuredProperty sp) { - final Pid pid = new Pid(); - pid.setValue(sp.getValue()); - pid.setType(sp.getQualifier().getClassid()); - return pid; + return sp != null ? new Pid() + .setValue(sp.getValue()) + .setType(sp.getQualifier().getClassid()) : null; } public static final Pair oafSubjectToPair(final StructuredProperty sp) { - return Pair.of(sp.getQualifier().getClassid(), sp.getValue()); + return sp != null ? Pair.of(sp.getQualifier().getClassid(), sp.getValue()) : null; } public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) { - final eu.dnetlib.broker.objects.Dataset res = new eu.dnetlib.broker.objects.Dataset(); - // TODO + return d != null ? new eu.dnetlib.broker.objects.Dataset() + .setOriginalId(d.getOriginalId().get(0)) + .setTitles(structPropList(d.getTitle())) + .setPids(d.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) + .setInstances( + d + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) + .setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList())) + : null; + } + + public static final eu.dnetlib.broker.objects.Publication oafResultToBrokerPublication(final Result result) { + + return result != null ? new eu.dnetlib.broker.objects.Publication() + .setOriginalId(result.getOriginalId().get(0)) + .setTitles(structPropList(result.getTitle())) + .setAbstracts(fieldList(result.getDescription())) + .setLanguage(result.getLanguage().getClassid()) + .setSubjects(structPropList(result.getSubject())) + .setCreators(result.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList())) + .setPublicationdate(result.getDateofcollection()) + .setPublisher(fieldValue(result.getPublisher())) + .setEmbargoenddate(fieldValue(result.getEmbargoenddate())) + .setContributor(fieldList(result.getContributor())) + .setJournal( + result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) + .setCollectedFrom(result.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList())) + .setPids(result.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) + .setInstances( + result + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) + .setExternalReferences( + result + .getExternalReference() + .stream() + .map(ConversionUtils::oafExtRefToBrokerExtRef) + .collect(Collectors.toList())) + : null; + } + + private static eu.dnetlib.broker.objects.Journal oafJournalToBrokerJournal(final Journal journal) { + return journal != null ? new eu.dnetlib.broker.objects.Journal() + .setName(journal.getName()) + .setIssn(journal.getIssnPrinted()) + .setEissn(journal.getIssnOnline()) + .setLissn(journal.getIssnLinking()) : null; + } + + private static eu.dnetlib.broker.objects.ExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) { + return ref != null ? new eu.dnetlib.broker.objects.ExternalReference() + .setRefidentifier(ref.getRefidentifier()) + .setSitename(ref.getSitename()) + .setType(ref.getQualifier().getClassid()) + .setUrl(ref.getUrl()) + : null; + } + + public static final eu.dnetlib.broker.objects.Project oafProjectToBrokerProject(final Project p) { + if (p == null) { + return null; + } + + final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project() + .setTitle(fieldValue(p.getTitle())) + .setAcronym(fieldValue(p.getAcronym())) + .setCode(fieldValue(p.getCode())); + + final String ftree = fieldValue(p.getFundingtree()); + if (StringUtils.isNotBlank(ftree)) { + try { + final Document fdoc = DocumentHelper.parseText(ftree); + res.setFunder(fdoc.valueOf("/fundingtree/funder/shortname")); + res.setJurisdiction(fdoc.valueOf("/fundingtree/funder/jurisdiction")); + res.setFundingProgram(fdoc.valueOf("//funding_level_0/name")); + } catch (final DocumentException e) { + log.error("Error in record " + p.getId() + ": invalid fundingtree: " + ftree); + } + } + return res; } - public static final eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication d) { - final eu.dnetlib.broker.objects.Publication res = new eu.dnetlib.broker.objects.Publication(); - // TODO - return res; + public static final eu.dnetlib.broker.objects.Software oafSoftwareToBrokerSoftware(final Software sw) { + return sw != null ? new eu.dnetlib.broker.objects.Software() + .setName(structPropValue(sw.getTitle())) + .setDescription(fieldValue(sw.getDescription())) + .setRepository(fieldValue(sw.getCodeRepositoryUrl())) + .setLandingPage(fieldValue(sw.getDocumentationUrl())) + : null; + } + + private static String fieldValue(final Field f) { + return f != null ? f.getValue() : null; + } + + private static String fieldValue(final List> fl) { + return fl != null ? fl.stream().map(Field::getValue).filter(StringUtils::isNotBlank).findFirst().orElse(null) + : null; + } + + private static String structPropValue(final List props) { + return props != null + ? props.stream().map(StructuredProperty::getValue).filter(StringUtils::isNotBlank).findFirst().orElse(null) + : null; + } + + private static List fieldList(final List> fl) { + return fl != null + ? fl.stream().map(Field::getValue).filter(StringUtils::isNotBlank).collect(Collectors.toList()) + : new ArrayList<>(); + } + + private static List structPropList(final List props) { + return props != null + ? props + .stream() + .map(StructuredProperty::getValue) + .filter(StringUtils::isNotBlank) + .collect(Collectors.toList()) + : new ArrayList<>(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index 5cc0d371db..04b426a1c2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -1,12 +1,16 @@ package eu.dnetlib.dhp.broker.oa.util; +import java.util.List; import java.util.function.BiConsumer; import java.util.function.Function; import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.Provenance; import eu.dnetlib.broker.objects.Publication; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Result; public final class UpdateInfo { @@ -66,12 +70,41 @@ public final class UpdateInfo { return trust; } - public void compileHighlight(final OpenAireEventPayload payload) { - compileHighlight.accept(payload.getHighlight(), getHighlightValue()); - } - public String getHighlightValueAsString() { return highlightToString.apply(getHighlightValue()); } + public OpenAireEventPayload asBrokerPayload() { + + final Publication p = ConversionUtils.oafResultToBrokerPublication(getSource()); + compileHighlight.accept(p, getHighlightValue()); + + final Publication hl = new Publication(); + compileHighlight.accept(hl, getHighlightValue()); + + final String provId = getSource().getOriginalId().stream().findFirst().orElse(null); + final String provRepo = getSource() + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .findFirst() + .orElse(null); + final String provUrl = getSource() + .getInstance() + .stream() + .map(Instance::getUrl) + .flatMap(List::stream) + .findFirst() + .orElse(null); + ; + + final Provenance provenance = new Provenance().setId(provId).setRepositoryName(provRepo).setUrl(provUrl); + + return new OpenAireEventPayload() + .setPublication(p) + .setHighlight(hl) + .setTrust(trust) + .setProvenance(provenance); + } + } diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml new file mode 100644 index 0000000000..1684429421 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -0,0 +1,93 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.2-SNAPSHOT + + 4.0.0 + + dhp-doiboost + + + + + net.alchim31.maven + scala-maven-plugin + 4.0.1 + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + + ${scala.version} + + + + + + + + + + + + org.apache.hadoop + hadoop-client + + + org.apache.httpcomponents + httpclient + 4.3.4 + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + org.apache.cxf + cxf-rt-transports-http + + + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + + com.jayway.jsonpath + json-path + + + + org.apache.spark + spark-core_2.11 + + + + org.apache.spark + spark-sql_2.11 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala new file mode 100644 index 0000000000..90bfacdc91 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -0,0 +1,374 @@ +package eu.dnetlib.doiboost + +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import org.codehaus.jackson.map.ObjectMapper +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ +import scala.io.Source + + +case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} + +case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){} + +object DoiBoostMappingUtil { + def getUnknownCountry(): Qualifier = { + createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries") + } + + + + def generateMAGAffiliationId(affId: String): String = { + s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}" + } + + + val logger: Logger = LoggerFactory.getLogger(getClass) + + //STATIC STRING + val MAG = "microsoft" + val MAG_NAME = "Microsoft Academic Graph" + val ORCID = "ORCID" + val CROSSREF = "Crossref" + val UNPAYWALL = "UnpayWall" + val GRID_AC = "grid.ac" + val WIKPEDIA = "wikpedia" + val doiBoostNSPREFIX = "doiboost____" + val OPENAIRE_PREFIX = "openaire____" + val SEPARATOR = "::" + val DNET_LANGUAGES = "dnet:languages" + val PID_TYPES = "dnet:pid_types" + + val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;") + + def toActionSet(item:Oaf) :(String, String) = { + val mapper = new ObjectMapper() + + item match { + case dataset: Dataset => + val a: AtomicAction[Dataset] = new AtomicAction[Dataset] + a.setClazz(classOf[Dataset]) + a.setPayload(dataset) + (dataset.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case publication: Publication => + val a: AtomicAction[Publication] = new AtomicAction[Publication] + a.setClazz(classOf[Publication]) + a.setPayload(publication) + (publication.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case organization: Organization => + val a: AtomicAction[Organization] = new AtomicAction[Organization] + a.setClazz(classOf[Organization]) + a.setPayload(organization) + (organization.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case relation: Relation => + val a: AtomicAction[Relation] = new AtomicAction[Relation] + a.setClazz(classOf[Relation]) + a.setPayload(relation) + (relation.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case _ => + null + } + + } + + + def toHostedByItem(input:String): (String, HostedByItemType) = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + + lazy val json: json4s.JValue = parse(input) + val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]] + (c.keys.head, c.values.head) + } + + + def toISSNPair(publication: Publication) : (String, Publication) = { + val issn = if (publication.getJournal == null) null else publication.getJournal.getIssnPrinted + val eissn =if (publication.getJournal == null) null else publication.getJournal.getIssnOnline + val lissn =if (publication.getJournal == null) null else publication.getJournal.getIssnLinking + + if (issn!= null && issn.nonEmpty) + (issn, publication) + else if(eissn!= null && eissn.nonEmpty) + (eissn, publication) + else if(lissn!= null && lissn.nonEmpty) + (lissn, publication) + else + (publication.getId, publication) + } + + + + + def generateGridAffiliationId(gridId:String) :String = { + s"20|grid________::${DHPUtils.md5(gridId.toLowerCase().trim())}" + } + + + def fixResult(result: Dataset) :Dataset = { + val instanceType = result.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty) + if (instanceType.isDefined) { + result.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype)) + } + result.getInstance().asScala.foreach(i => { + i.setHostedby(getUbknownHostedBy()) + }) + result + } + + def getUbknownHostedBy():KeyValue = { + val hb = new KeyValue + hb.setValue("Unknown Repository") + hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c") + hb + + } + + + def getOpenAccessQualifier():Qualifier = { + createQualifier("OPEN","Open Access","dnet:access_modes", "dnet:access_modes") + + } + + def getRestrictedQualifier():Qualifier = { + createQualifier("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes") + + } + + def fixPublication(input:((String,Publication), (String,HostedByItemType))): Publication = { + + val publication = input._1._2 + + val item = if (input._2 != null) input._2._2 else null + + + val instanceType = publication.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty) + + if (instanceType.isDefined) { + publication.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype)) + } + + + publication.getInstance().asScala.foreach(i => { + val hb = new KeyValue + if (item != null) { + hb.setValue(item.officialname) + hb.setKey(generateDSId(item.id)) + if (item.openAccess) + i.setAccessright(getOpenAccessQualifier()) + publication.setBestaccessright(getOpenAccessQualifier()) + } + else { + hb.setValue("Unknown Repository") + hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c") + } + i.setHostedby(hb) + }) + + val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid) + if (ar.nonEmpty) { + if(ar.contains("OPEN")){ + publication.setBestaccessright(getOpenAccessQualifier()) + } + else { + publication.setBestaccessright(getRestrictedQualifier()) + } + } + publication + } + + + def generateDSId(input: String): String = { + + val b = StringUtils.substringBefore(input, "::") + val a = StringUtils.substringAfter(input, "::") + s"10|${b}::${DHPUtils.md5(a)}" + } + + + def generateDataInfo(): DataInfo = { + generateDataInfo("0.9") + } + + + def filterPublication(publication: Publication): Boolean = { + + //Case empty publication + if (publication == null) + return false + + //Case publication with no title + if (publication.getTitle == null || publication.getTitle.size == 0) + return false + + + val s = publication.getTitle.asScala.count(p => p.getValue != null + && p.getValue.nonEmpty && !p.getValue.equalsIgnoreCase("[NO TITLE AVAILABLE]")) + + if (s == 0) + return false + + // fixes #4360 (test publisher) + val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null + + if (publisher != null && (publisher.equalsIgnoreCase("Test accounts") || publisher.equalsIgnoreCase("CrossRef Test Account"))) { + return false; + } + + //Publication with no Author + if (publication.getAuthor == null || publication.getAuthor.size() == 0) + return false + + + //filter invalid author + val authors = publication.getAuthor.asScala.map(s => { + if (s.getFullname.nonEmpty) { + s.getFullname + } + else + s"${ + s.getName + } ${ + s.getSurname + }" + }) + + val c = authors.count(isValidAuthorName) + if (c == 0) + return false + + // fixes #4368 + if (authors.count(s => s.equalsIgnoreCase("Addie Jackson")) > 0 && "Elsevier BV".equalsIgnoreCase(publication.getPublisher.getValue)) + return false + + true + } + + + def isValidAuthorName(fullName: String): Boolean = { + if (fullName == null || fullName.isEmpty) + return false + if (invalidName.contains(fullName.toLowerCase.trim)) + return false + true + } + + + def generateDataInfo(trust: String): DataInfo = { + val di = new DataInfo + di.setDeletedbyinference(false) + di.setInferred(false) + di.setInvisible(false) + di.setTrust(trust) + di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions")) + di + } + + + def createSP(value: String, classId: String, schemeId: String): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier(createQualifier(classId, schemeId)) + sp.setValue(value) + sp + + } + + def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier(createQualifier(classId, schemeId)) + sp.setValue(value) + sp.setDataInfo(dataInfo) + sp + + } + + def createCrossrefCollectedFrom(): KeyValue = { + + val cf = new KeyValue + cf.setValue(CROSSREF) + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase)) + cf + + } + + + def createUnpayWallCollectedFrom(): KeyValue = { + + val cf = new KeyValue + cf.setValue(UNPAYWALL) + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase)) + cf + + } + + def createORIDCollectedFrom(): KeyValue = { + + val cf = new KeyValue + cf.setValue(ORCID) + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase)) + cf + + } + + + def generateIdentifier (oaf: Result, doi: String): String = { + val id = DHPUtils.md5 (doi.toLowerCase) + if (oaf.isInstanceOf[Dataset] ) + return s"60|${ + doiBoostNSPREFIX + }${ + SEPARATOR + }${ + id + }" + s"50|${ + doiBoostNSPREFIX + }${ + SEPARATOR + }${ + id + }" + } + + + + + def createMAGCollectedFrom(): KeyValue = { + + val cf = new KeyValue + cf.setValue(MAG_NAME) + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(MAG)) + cf + + } + + def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = { + val q = new Qualifier + q.setClassid(clsName) + q.setClassname(clsValue) + q.setSchemeid(schName) + q.setSchemename(schValue) + q + } + + def createQualifier(cls: String, sch: String): Qualifier = { + createQualifier(cls, cls, sch, sch) + } + + + def asField[T](value: T): Field[T] = { + val tmp = new Field[T] + tmp.setValue(value) + tmp + + + } + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala new file mode 100644 index 0000000000..7a6cd3faaa --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -0,0 +1,80 @@ +package eu.dnetlib.doiboost + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} +import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.Text +import org.apache.hadoop.io.compress.GzipCodec +import org.apache.hadoop.mapred.SequenceFileOutputFormat +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkGenerateDOIBoostActionSet { + val logger: Logger = LoggerFactory.getLogger(getClass) + def main(args: Array[String]): Unit = { + + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] + implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] + implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] + implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] + implicit val mapEncoderAS: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING) + + implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]] + + val dbPublicationPath = parser.get("dbPublicationPath") + val dbDatasetPath = parser.get("dbDatasetPath") + val crossRefRelation = parser.get("crossRefRelation") + val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath") + val dbOrganizationPath = parser.get("dbOrganizationPath") + val workingDirPath = parser.get("targetPath") + + spark.read.load(dbDatasetPath).as[OafDataset] + .map(d =>DoiBoostMappingUtil.fixResult(d)) + .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) + .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet") + + spark.read.load(dbPublicationPath).as[Publication] + .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) + .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") + + spark.read.load(dbOrganizationPath).as[Organization] + .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) + .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") + + + spark.read.load(crossRefRelation).as[Relation] + .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) + .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") + + spark.read.load(dbaffiliationRelationPath).as[Relation] + .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) + .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") + + + val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] + + d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) + + + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala new file mode 100644 index 0000000000..772af010fd --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -0,0 +1,140 @@ +package eu.dnetlib.doiboost + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset, Organization} +import eu.dnetlib.doiboost.mag.ConversionUtil +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.functions.col +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ + +object SparkGenerateDoiBoost { + + def main(args: Array[String]): Unit = { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + import spark.implicits._ + + val hostedByMapPath = parser.get("hostedByMapPath") + val workingDirPath = parser.get("workingDirPath") + + + implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] + implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] + implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] + implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub) + implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] + + logger.info("Phase 2) Join Crossref with UnpayWall") + + val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p)) + val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p)) + + def applyMerge(item:((String, Publication), (String, Publication))) : Publication = + { + val crossrefPub = item._1._2 + if (item._2!= null) { + val otherPub = item._2._2 + if (otherPub != null) { + crossrefPub.mergeFrom(otherPub) + } + } + crossrefPub + } + crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin") + logger.info("Phase 3) Join Result with ORCID") + val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p)) + val orcidPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p)) + fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/secondJoin") + + logger.info("Phase 3) Join Result with MAG") + val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) + + val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) + sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication") + + + val doiBoostPublication: Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder) + + val hostedByDataset : Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem)) + + + doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left") + .map(DoiBoostMappingUtil.fixPublication) + .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered") + + val affiliationPath = parser.get("affiliationPath") + val paperAffiliationPath = parser.get("paperAffiliationPath") + + val affiliation = spark.read.load(affiliationPath).select(col("AffiliationId"), col("GridId"), col("OfficialPage"), col("DisplayName")) + + val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId")) + + + val a:Dataset[DoiBoostAffiliation] = paperAffiliation + .joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId"))) + .select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation] + + + + val magPubs:Dataset[(String,Publication)]= spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s =>s._1!= null ) + + + magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => { + val pub:Publication = item._1._2 + val affiliation = item._2 + val affId:String = if (affiliation.GridId.isDefined) DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId.get) else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString) + val r:Relation = new Relation + r.setSource(pub.getId) + r.setTarget(affId) + r.setRelType("resultOrganization") + r.setRelClass("hasAuthorInstitution") + r.setSubRelType("affiliation") + r.setDataInfo(pub.getDataInfo) + r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava) + val r1:Relation = new Relation + r1.setTarget(pub.getId) + r1.setSource(affId) + r1.setRelType("resultOrganization") + r1.setRelClass("isAuthorInstitutionOf") + r1.setSubRelType("affiliation") + r1.setDataInfo(pub.getDataInfo) + r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava) + List(r, r1) + })(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation") + + + magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => { + val affiliation = item._2 + if (affiliation.GridId.isEmpty) { + val o = new Organization + o.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava) + o.setDataInfo(DoiBoostMappingUtil.generateDataInfo()) + o.setId(DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)) + o.setOriginalId(List(affiliation.AffiliationId.toString).asJava) + if (affiliation.DisplayName.nonEmpty) + o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get)) + if (affiliation.OfficialPage.isDefined) + o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get)) + o.setCountry(DoiBoostMappingUtil.getUnknownCountry()) + o + } + else + null + }).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization") + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala new file mode 100644 index 0000000000..cc2c9d5860 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -0,0 +1,440 @@ +package eu.dnetlib.doiboost.crossref + +import eu.dnetlib.dhp.schema.oaf._ +import eu.dnetlib.dhp.utils.DHPUtils +import eu.dnetlib.doiboost.DoiBoostMappingUtil._ +import org.apache.commons.lang.StringUtils +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.JsonAST._ +import org.json4s.jackson.JsonMethods._ +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ +import scala.collection.mutable +import scala.util.matching.Regex + +case class mappingAffiliation(name: String) {} + +case class mappingAuthor(given: Option[String], family: String, ORCID: Option[String], affiliation: Option[mappingAffiliation]) {} + +case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {} + + +case object Crossref2Oaf { + val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) + + val mappingCrossrefType = Map( + "book-section" -> "publication", + "book" -> "publication", + "book-chapter" -> "publication", + "book-part" -> "publication", + "book-series" -> "publication", + "book-set" -> "publication", + "book-track" -> "publication", + "edited-book" -> "publication", + "reference-book" -> "publication", + "monograph" -> "publication", + "journal-article" -> "publication", + "dissertation" -> "publication", + "other" -> "publication", + "peer-review" -> "publication", + "proceedings" -> "publication", + "proceedings-article" -> "publication", + "reference-entry" -> "publication", + "report" -> "publication", + "report-series" -> "publication", + "standard" -> "publication", + "standard-series" -> "publication", + "posted-content" -> "publication", + "dataset" -> "dataset" + ) + + + val mappingCrossrefSubType = Map( + "book-section" -> "0013 Part of book or chapter of book", + "book" -> "0002 Book", + "book-chapter" -> "0013 Part of book or chapter of book", + "book-part" -> "0013 Part of book or chapter of book", + "book-series" -> "0002 Book", + "book-set" -> "0002 Book", + "book-track" -> "0002 Book", + "edited-book" -> "0002 Book", + "reference-book" -> "0002 Book", + "monograph" -> "0002 Book", + "journal-article" -> "0001 Article", + "dissertation" -> "0006 Doctoral thesis", + "other" -> "0038 Other literature type", + "peer-review" -> "0015 Review", + "proceedings" -> "0004 Conference object", + "proceedings-article" -> "0004 Conference object", + "reference-entry" -> "0013 Part of book or chapter of book", + "report" -> "0017 Report", + "report-series" -> "0017 Report", + "standard" -> "0038 Other literature type", + "standard-series" -> "0038 Other literature type", + "dataset" -> "0021 Dataset", + "preprint" -> "0016 Preprint", + "report" -> "0017 Report" + ) + + def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + + //MAPPING Crossref DOI into PID + val doi: String = (json \ "DOI").extract[String] + result.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava) + + //MAPPING Crossref DOI into OriginalId + //and Other Original Identifier of dataset like clinical-trial-number + val clinicalTrialNumbers = for (JString(ctr) <- json \ "clinical-trial-number") yield ctr + val alternativeIds = for (JString(ids) <- json \ "alternative-id") yield ids + val tmp = clinicalTrialNumbers ::: alternativeIds ::: List(doi) + + result.setOriginalId(tmp.filter(id => id != null).asJava) + + //Set identifier as {50|60} | doiboost____::md5(DOI) + result.setId(generateIdentifier(result, doi)) + + // Add DataInfo + result.setDataInfo(generateDataInfo()) + + result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long]) + result.setDateofcollection((json \ "indexed" \ "date-time").extract[String]) + + result.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava) + + // Publisher ( Name of work's publisher mapped into Result/Publisher) + val publisher = (json \ "publisher").extractOrElse[String](null) + if (publisher!= null && publisher.nonEmpty) + result.setPublisher(asField(publisher)) + + + // TITLE + val mainTitles = for {JString(title) <- json \ "title" if title.nonEmpty} yield createSP(title, "main title", "dnet:dataCite_title") + val originalTitles = for {JString(title) <- json \ "original-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title") + val shortTitles = for {JString(title) <- json \ "short-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title") + val subtitles = for {JString(title) <- json \ "subtitle" if title.nonEmpty} yield createSP(title, "subtitle", "dnet:dataCite_title") + result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava) + + // DESCRIPTION + val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description) + result.setDescription(descriptionList.asJava) + + // Source + val sourceList = for {JString(source) <- json \ "source" if source!= null && source.nonEmpty} yield asField(source) + result.setSource(sourceList.asJava) + + //RELEVANT DATE Mapping + val createdDate = generateDate((json \ "created" \ "date-time").extract[String], (json \ "created" \ "date-parts").extract[List[List[Int]]], "created", "dnet:dataCite_date") + val postedDate = generateDate((json \ "posted" \ "date-time").extractOrElse[String](null), (json \ "posted" \ "date-parts").extract[List[List[Int]]], "available", "dnet:dataCite_date") + val acceptedDate = generateDate((json \ "accepted" \ "date-time").extractOrElse[String](null), (json \ "accepted" \ "date-parts").extract[List[List[Int]]], "accepted", "dnet:dataCite_date") + val publishedPrintDate = generateDate((json \ "published-print" \ "date-time").extractOrElse[String](null), (json \ "published-print" \ "date-parts").extract[List[List[Int]]], "published-print", "dnet:dataCite_date") + val publishedOnlineDate = generateDate((json \ "published-online" \ "date-time").extractOrElse[String](null), (json \ "published-online" \ "date-parts").extract[List[List[Int]]], "published-online", "dnet:dataCite_date") + + val issuedDate = extractDate((json \ "issued" \ "date-time").extractOrElse[String](null), (json \ "issued" \ "date-parts").extract[List[List[Int]]]) + if (StringUtils.isNotBlank(issuedDate)) { + result.setDateofacceptance(asField(issuedDate)) + } + else { + result.setDateofacceptance(asField(createdDate.getValue)) + } + result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava) + + //Mapping Subject + val subjectList:List[String] = (json \ "subject").extractOrElse[List[String]](List()) + + if (subjectList.nonEmpty) { + result.setSubject(subjectList.map(s=> createSP(s, "keywords", "dnet:subject_classification_typologies")).asJava) + } + + + + //Mapping Author + val authorList: List[mappingAuthor] = (json \ "author").extractOrElse[List[mappingAuthor]](List()) + result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava) + + // Mapping instance + val instance = new Instance() + val license = for { + JString(lic) <- json \ "license" \ "URL" + } yield asField(lic) + val l = license.filter(d => StringUtils.isNotBlank(d.getValue)) + if (l.nonEmpty) + instance.setLicense(l.head) + + + val has_review = (json \ "relation" \"has-review" \ "id") + + if(has_review != JNothing) + instance.setRefereed(asField("peerReviewed")) + + + instance.setAccessright(getRestrictedQualifier()) + result.setInstance(List(instance).asJava) + instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource")) + result.setResourcetype(createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource")) + + instance.setCollectedfrom(createCrossrefCollectedFrom()) + if (StringUtils.isNotBlank(issuedDate)) { + instance.setDateofacceptance(asField(issuedDate)) + } + val s: String = (json \ "URL").extract[String] + val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct + if (links.nonEmpty) + instance.setUrl(links.asJava) + result + } + + + def generateAuhtor(given: String, family: String, orcid: String): Author = { + val a = new Author + a.setName(given) + a.setSurname(family) + a.setFullname(s"$given $family") + if (StringUtils.isNotBlank(orcid)) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + + a + } + + def convert(input: String): List[Oaf] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + + var resultList: List[Oaf] = List() + + + val objectType = (json \ "type").extractOrElse[String](null) + val objectSubType = (json \ "subtype").extractOrElse[String](null) + if (objectType == null) + return resultList + + + val result = generateItemFromType(objectType, objectSubType) + if (result == null) + return List() + val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type")); + mappingResult(result, json, cOBJCategory) + + + val funderList: List[mappingFunder] = (json \ "funder").extractOrElse[List[mappingFunder]](List()) + + if (funderList.nonEmpty) { + resultList = resultList ::: mappingFunderToRelations(funderList, result.getId, createCrossrefCollectedFrom(), result.getDataInfo, result.getLastupdatetimestamp) + } + + + result match { + case publication: Publication => convertPublication(publication, json, cOBJCategory) + case dataset: Dataset => convertDataset(dataset) + } + + resultList = resultList ::: List(result) + resultList + } + + + def mappingFunderToRelations(funders: List[mappingFunder], sourceId: String, cf: KeyValue, di: DataInfo, ts: Long): List[Relation] = { + + val queue = new mutable.Queue[Relation] + + + def snfRule(award:String): String = { + var tmp1 = StringUtils.substringAfter(award,"_") + val tmp2 = StringUtils.substringBefore(tmp1,"/") + logger.debug(s"From $award to $tmp2") + tmp2 + + + } + + + def extractECAward(award: String): String = { + val awardECRegex: Regex = "[0-9]{4,9}".r + if (awardECRegex.findAllIn(award).hasNext) + return awardECRegex.findAllIn(award).max + null + } + + + def generateRelation(sourceId:String, targetId:String, nsPrefix:String) :Relation = { + + val r = new Relation + r.setSource(sourceId) + r.setTarget(s"$nsPrefix::$targetId") + r.setRelType("resultProject") + r.setRelClass("isProducedBy") + r.setSubRelType("outcome") + r.setCollectedfrom(List(cf).asJava) + r.setDataInfo(di) + r.setLastupdatetimestamp(ts) + r + } + + + def generateSimpleRelationFromAward(funder: mappingFunder, nsPrefix: String, extractField: String => String): Unit = { + if (funder.award.isDefined && funder.award.get.nonEmpty) + funder.award.get.map(extractField).filter(a => a!= null && a.nonEmpty).foreach( + award => { + val targetId = DHPUtils.md5(award) + queue += generateRelation(sourceId, targetId, nsPrefix) + } + ) + } + + if (funders != null) + funders.foreach(funder => { + if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) { + funder.DOI.get match { + case "10.13039/100010663" | + "10.13039/100010661" | + "10.13039/501100007601" | + "10.13039/501100000780" | + "10.13039/100010665" => generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + case "10.13039/100011199" | + "10.13039/100004431" | + "10.13039/501100004963" | + "10.13039/501100000780" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) + case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) + generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) + case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) + case "10.13039/501100001602" => generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) + case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) + case "10.13039/501100000038"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "nserc_______" ) + case "10.13039/501100000155"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "sshrc_______" ) + case "10.13039/501100000024"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "cihr________" ) + case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a) + case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) + case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a=>a) + case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) + case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a=>a) + queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "miur________" ) + case "10.13039/501100006588" | + "10.13039/501100004488" => generateSimpleRelationFromAward(funder, "irb_hr______", a=>a.replaceAll("Project No.", "").replaceAll("HRZZ-","") ) + case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a) + case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snfRule) + case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a) + case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a) + case "10.13039/100004440"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" ) + case _ => logger.debug("no match for "+funder.DOI.get ) + + + } + + + } else { + funder.name match { + case "European Union’s Horizon 2020 research and innovation program" => generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + case "European Union's" => + generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + generateSimpleRelationFromAward(funder, "corda_______", extractECAward) + case "The French National Research Agency (ANR)" | + "The French National Research Agency" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) + case "Wellcome Trust Masters Fellowship" => queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" ) + case _ => logger.debug("no match for "+funder.name ) + + } + } + + } + ) + queue.toList + } + + def convertDataset(dataset: Dataset): Unit = { + // TODO check if there are other info to map into the Dataset + } + + + def convertPublication(publication: Publication, json: JValue, cobjCategory: String): Unit = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + val containerTitles = for {JString(ct) <- json \ "container-title"} yield ct + + + //Mapping book + if (cobjCategory.toLowerCase.contains("book")) { + val ISBN = for {JString(isbn) <- json \ "ISBN"} yield isbn + if (ISBN.nonEmpty && containerTitles.nonEmpty) { + val source = s"${containerTitles.head} ISBN: ${ISBN.head}" + if (publication.getSource != null) { + val l: List[Field[String]] = publication.getSource.asScala.toList + val ll: List[Field[String]] = l ::: List(asField(source)) + publication.setSource(ll.asJava) + } + else + publication.setSource(List(asField(source)).asJava) + } + } else { + // Mapping Journal + + val issnInfos = for {JArray(issn_types) <- json \ "issn-type" + JObject(issn_type) <- issn_types + JField("type", JString(tp)) <- issn_type + JField("value", JString(vl)) <- issn_type + } yield Tuple2(tp, vl) + + val volume = (json \ "volume").extractOrElse[String](null) + if (containerTitles.nonEmpty) { + val journal = new Journal + journal.setName(containerTitles.head) + if (issnInfos.nonEmpty) { + + issnInfos.foreach(tp => { + tp._1 match { + case "electronic" => journal.setIssnOnline(tp._2) + case "print" => journal.setIssnPrinted(tp._2) + } + }) + } + journal.setVol(volume) + val page = (json \ "page").extractOrElse[String](null) + if (page != null) { + val pp = page.split("-") + if (pp.nonEmpty) + journal.setSp(pp.head) + if (pp.size > 1) + journal.setEp(pp(1)) + } + publication.setJournal(journal) + } + } + } + + def extractDate(dt: String, datePart: List[List[Int]]): String = { + if (StringUtils.isNotBlank(dt)) + return dt + if (datePart != null && datePart.size == 1) { + val res = datePart.head + if (res.size == 3) { + val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d" + if (dp.length == 10) { + return dp + } + } + } + null + + } + + def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = { + val dp = extractDate(dt, datePart) + if (StringUtils.isNotBlank(dp)) + return createSP(dp, classId, schemeId) + null + } + + def generateItemFromType(objectType: String, objectSubType: String): Result = { + if (mappingCrossrefType.contains(objectType)) { + if (mappingCrossrefType(objectType).equalsIgnoreCase("publication")) + return new Publication() + if (mappingCrossrefType(objectType).equalsIgnoreCase("dataset")) + return new Dataset() + } + null + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java new file mode 100644 index 0000000000..f69a05da1c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java @@ -0,0 +1,103 @@ + +package eu.dnetlib.doiboost.crossref; + +import java.io.ByteArrayOutputStream; +import java.util.zip.Inflater; + +import org.apache.commons.codec.binary.Base64; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IntWritable; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class CrossrefImporter { + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + CrossrefImporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/import_from_es.json"))); + + parser.parseArgument(args); + + final String hdfsuri = parser.get("namenode"); + System.out.println("HDFS URI" + hdfsuri); + Path hdfswritepath = new Path(parser.get("targetPath")); + System.out.println("TargetPath: " + hdfsuri); + + final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp")) + ? Long.parseLong(parser.get("timestamp")) + : -1; + + if (timestamp > 0) + System.out.println("Timestamp added " + timestamp); + + // ====== Init HDFS File System Object + Configuration conf = new Configuration(); + // Set FileSystem URI + conf.set("fs.defaultFS", hdfsuri); + // Because of Maven + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + + ESClient client = timestamp > 0 + ? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp) + : new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref"); + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.keyClass(IntWritable.class), + SequenceFile.Writer.valueClass(Text.class))) { + + int i = 0; + long start = System.currentTimeMillis(); + long end = 0; + final IntWritable key = new IntWritable(i); + final Text value = new Text(); + while (client.hasNext()) { + key.set(i++); + value.set(client.next()); + writer.append(key, value); + if (i % 100000 == 0) { + end = System.currentTimeMillis(); + final float time = (end - start) / 1000.0F; + System.out + .println( + String.format("Imported %d records last 100000 imported in %f seconds", i, time)); + start = System.currentTimeMillis(); + } + } + } + } + + public static String decompressBlob(final String blob) { + try { + byte[] byteArray = Base64.decodeBase64(blob.getBytes()); + final Inflater decompresser = new Inflater(); + decompresser.setInput(byteArray); + final ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length); + byte[] buffer = new byte[8192]; + while (!decompresser.finished()) { + int size = decompresser.inflate(buffer); + bos.write(buffer, 0, size); + } + byte[] unzippeddata = bos.toByteArray(); + decompresser.end(); + return new String(unzippeddata); + } catch (Throwable e) { + throw new RuntimeException("Wrong record:" + blob, e); + } + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java new file mode 100644 index 0000000000..e31ccf399b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java @@ -0,0 +1,114 @@ + +package eu.dnetlib.doiboost.crossref; + +import java.io.IOException; +import java.util.Iterator; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpPost; +import org.apache.http.entity.StringEntity; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.jayway.jsonpath.JsonPath; + +public class ESClient implements Iterator { + private static final Logger logger = LoggerFactory.getLogger(ESClient.class); + + static final String blobPath = "$.hits[*].hits[*]._source.blob"; + static final String scrollIdPath = "$._scroll_id"; + static final String JSON_NO_TS = "{\"size\":1000}"; + static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; + static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}"; + + private final String scrollId; + + private List buffer; + + private final String esHost; + + public ESClient(final String esHost, final String esIndex) throws IOException { + + this.esHost = esHost; + final String body = getResponse( + String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS); + scrollId = getJPathString(scrollIdPath, body); + buffer = getBlobs(body); + } + + public ESClient(final String esHost, final String esIndex, final long timestamp) + throws IOException { + this.esHost = esHost; + final String body = getResponse( + String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), + String.format(JSON_WITH_TS, timestamp)); + scrollId = getJPathString(scrollIdPath, body); + buffer = getBlobs(body); + } + + private String getResponse(final String url, final String json) { + CloseableHttpClient client = HttpClients.createDefault(); + try { + + HttpPost httpPost = new HttpPost(url); + if (json != null) { + StringEntity entity = new StringEntity(json); + httpPost.setEntity(entity); + httpPost.setHeader("Accept", "application/json"); + httpPost.setHeader("Content-type", "application/json"); + } + CloseableHttpResponse response = client.execute(httpPost); + + return IOUtils.toString(response.getEntity().getContent()); + } catch (Throwable e) { + throw new RuntimeException("Error on executing request ", e); + } finally { + try { + client.close(); + } catch (IOException e) { + throw new RuntimeException("Unable to close client ", e); + } + } + } + + private String getJPathString(final String jsonPath, final String json) { + try { + Object o = JsonPath.read(json, jsonPath); + if (o instanceof String) + return (String) o; + return null; + } catch (Exception e) { + return ""; + } + } + + private List getBlobs(final String body) { + final List res = JsonPath.read(body, "$.hits.hits[*]._source.blob"); + return res; + } + + @Override + public boolean hasNext() { + return (buffer != null && !buffer.isEmpty()); + } + + @Override + public String next() { + final String nextItem = buffer.remove(0); + if (buffer.isEmpty()) { + + final String json_param = String.format(JSON_SCROLL, scrollId); + final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param); + try { + buffer = getBlobs(body); + } catch (Throwable e) { + logger.error("Error on get next page: body:" + body); + } + } + return nextItem; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala new file mode 100644 index 0000000000..fac4c90b47 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala @@ -0,0 +1,98 @@ +package eu.dnetlib.doiboost.crossref + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf +import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset} +import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.{IntWritable, Text} +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + + +case class Reference(author: String, firstPage: String) {} + +object SparkMapDumpIntoOAF { + + def main(args: Array[String]): Unit = { + + + val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(SparkMapDumpIntoOAF.getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation] + implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset] + + val sc = spark.sparkContext + val targetPath = parser.get("targetPath") + + + sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text]) + .map(k => k._2.toString).map(CrossrefImporter.decompressBlob) + .flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject") + + val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null) + + val distinctPubs:RDD[Publication] = inputRDD.filter(k => k != null && k.isInstanceOf[Publication]) + .map(k => k.asInstanceOf[Publication]).map { p: Publication => Tuple2(p.getId, p) }.reduceByKey { case (p1: Publication, p2: Publication) => + var r = if (p1 == null) p2 else p1 + if (p1 != null && p2 != null) { + if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) { + if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp) + r = p2 + else + r = p1 + } else { + r = if (p1.getLastupdatetimestamp == null) p2 else p1 + } + } + r + }.map(_._2) + + val pubs:Dataset[Publication] = spark.createDataset(distinctPubs) + pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication") + + + val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset]) + .map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) => + var r = if (p1 == null) p2 else p1 + if (p1 != null && p2 != null) { + if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) { + if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp) + r = p2 + else + r = p1 + } else { + r = if (p1.getLastupdatetimestamp == null) p2 else p1 + } + } + r + }.map(_._2) + + spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset") + + + + val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation]) + .map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r)) + .reduceByKey { case (p1: Relation, p2: Relation) => + if (p1 == null) p2 else p1 + }.map(_._2) + + val rels: Dataset[Relation] = spark.createDataset(distinctRels) + + rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations") + } + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala new file mode 100644 index 0000000000..1c6e1b0e65 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -0,0 +1,314 @@ +package eu.dnetlib.doiboost.mag + + +import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty} +import eu.dnetlib.doiboost.DoiBoostMappingUtil +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse +import eu.dnetlib.doiboost.DoiBoostMappingUtil._ + +import scala.collection.JavaConverters._ +import scala.collection.mutable +import scala.util.matching.Regex + + +case class MagPapers(PaperId: Long, Rank: Integer, Doi: String, + DocType: String, PaperTitle: String, OriginalTitle: String, + BookTitle: String, Year: Option[Integer], Date: Option[java.sql.Timestamp], Publisher: String, + JournalId: Option[Long], ConferenceSeriesId: Option[Long], ConferenceInstanceId: Option[Long], + Volume: String, Issue: String, FirstPage: String, LastPage: String, + ReferenceCount: Option[Long], CitationCount: Option[Long], EstimatedCitation: Option[Long], + OriginalVenue: String, FamilyId: Option[Long], CreatedDate: java.sql.Timestamp) {} + + +case class MagPaperAbstract(PaperId: Long, IndexedAbstract: String) {} + +case class MagAuthor(AuthorId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], LastKnownAffiliationId: Option[Long], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {} + +case class MagAffiliation(AffiliationId: Long, Rank: Int, NormalizedName: String, DisplayName: String, GridId: String, OfficialPage: String, WikiPage: String, PaperCount: Long, CitationCount: Long, Latitude: Option[Float], Longitude: Option[Float], CreatedDate: java.sql.Timestamp) {} + +case class MagPaperAuthorAffiliation(PaperId: Long, AuthorId: Long, AffiliationId: Option[Long], AuthorSequenceNumber: Int, OriginalAuthor: String, OriginalAffiliation: String) {} + + +case class MagAuthorAffiliation(author: MagAuthor, affiliation:String) + +case class MagPaperWithAuthorList(PaperId: Long, authors: List[MagAuthorAffiliation]) {} + +case class MagPaperAuthorDenormalized(PaperId: Long, author: MagAuthor, affiliation:String) {} + +case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option[String], LanguageCode: Option[String]) {} + +case class MagUrlInstance(SourceUrl:String){} + +case class MagUrl(PaperId: Long, instances: List[MagUrlInstance]) + +case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){} + +case class MagFieldOfStudy(PaperId:Long, subjects:List[MagSubject]) {} + +case class MagJournal(JournalId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], Issn: Option[String], Publisher: Option[String], Webpage: Option[String], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {} + + +case class MagConferenceInstance(ci:Long, DisplayName:Option[String], Location:Option[String], StartDate:Option[java.sql.Timestamp], EndDate:Option[java.sql.Timestamp], PaperId:Long){} + +case object ConversionUtil { + + def extractMagIdentifier(pids:mutable.Buffer[String]) :String ={ + val magIDRegex: Regex = "^[0-9]+$".r + val s =pids.filter(p=> magIDRegex.findAllIn(p).hasNext) + + if (s.nonEmpty) + return s.head + null + } + + + def mergePublication(a: Publication, b:Publication) : Publication = { + if ((a != null) && (b != null)) { + a.mergeFrom(b) + a + } else { + if (a == null) b else a + } + + + } + + def choiceLatestMagArtitcle(p1: MagPapers, p2:MagPapers) :MagPapers = { + var r = if (p1 == null) p2 else p1 + if (p1 != null && p2 != null) { + if (p1.CreatedDate != null && p2.CreatedDate != null) { + if (p1.CreatedDate.before(p2.CreatedDate)) + r = p2 + else + r = p1 + } else { + r = if (p1.CreatedDate == null) p2 else p1 + } + } + r + + } + + + def updatePubsWithDescription(inputItem:((String, Publication), MagPaperAbstract)) : Publication = { + val pub = inputItem._1._2 + val abst = inputItem._2 + if (abst != null) { + pub.setDescription(List(asField(abst.IndexedAbstract)).asJava) + } + pub + + } + + + def updatePubsWithConferenceInfo(inputItem:((String, Publication), MagConferenceInstance)) : Publication = { + val publication:Publication= inputItem._1._2 + val ci:MagConferenceInstance = inputItem._2 + + if (ci!= null){ + + val j:Journal = new Journal + if (ci.Location.isDefined) + j.setConferenceplace(ci.Location.get) + j.setName(ci.DisplayName.get) + if (ci.StartDate.isDefined && ci.EndDate.isDefined) + { + j.setConferencedate(s"${ci.StartDate.get.toString.substring(0,10)} - ${ci.EndDate.get.toString.substring(0,10)}") + } + + publication.setJournal(j) + } + publication + } + + def updatePubsWithSubject(item:((String, Publication), MagFieldOfStudy)) : Publication = { + + val publication = item._1._2 + val fieldOfStudy = item._2 + if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) { + val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => { + val s1 = createSP(s.DisplayName, "keywords", "dnet:subject_classification_typologies") + val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString) + var resList: List[StructuredProperty] = List(s1) + if (s.MainType.isDefined) { + val maintp = s.MainType.get + val s2 = createSP(s.MainType.get, "keywords", "dnet:subject_classification_typologies") + s2.setDataInfo(di) + resList = resList ::: List(s2) + if (maintp.contains(".")) { + val s3 = createSP(maintp.split("\\.").head, "keywords", "dnet:subject_classification_typologies") + s3.setDataInfo(di) + resList = resList ::: List(s3) + } + } + resList + }) + publication.setSubject(p.asJava) + } + publication + } + + + + def addInstances(a: (Publication, MagUrl)): Publication = { + val pub = a._1 + val urls = a._2 + + + + val i = new Instance + + + if (urls!= null) { + + val l:List[String] = urls.instances.filter(k=>k.SourceUrl.nonEmpty).map(k=>k.SourceUrl):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}") + + i.setUrl(l.asJava) + } + else + i.setUrl(List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}").asJava) + + i.setCollectedfrom(createMAGCollectedFrom()) + pub.setInstance(List(i).asJava) + pub + } + + + def transformPaperAbstract(input: MagPaperAbstract): MagPaperAbstract = { + MagPaperAbstract(input.PaperId, convertInvertedIndexString(input.IndexedAbstract)) + } + + + def createOAFFromJournalAuthorPaper(inputParams: ((MagPapers, MagJournal), MagPaperWithAuthorList)): Publication = { + val paper = inputParams._1._1 + val journal = inputParams._1._2 + val authors = inputParams._2 + + val pub = new Publication + pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava) + pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava) + + //Set identifier as {50|60} | doiboost____::md5(DOI) + pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase)) + + val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title") + val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title") + pub.setTitle(List(mainTitles, originalTitles).asJava) + + pub.setSource(List(asField(paper.BookTitle)).asJava) + + val authorsOAF = authors.authors.map { f: MagAuthorAffiliation => + + val a: eu.dnetlib.dhp.schema.oaf.Author = new eu.dnetlib.dhp.schema.oaf.Author + + a.setFullname(f.author.DisplayName.get) + + if(f.affiliation!= null) + a.setAffiliation(List(asField(f.affiliation)).asJava) + a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava) + a + } + pub.setAuthor(authorsOAF.asJava) + + + if (paper.Date != null && paper.Date.isDefined) { + pub.setDateofacceptance(asField(paper.Date.get.toString.substring(0,10))) + } + pub.setPublisher(asField(paper.Publisher)) + + + if (journal != null && journal.DisplayName.isDefined) { + val j = new Journal + + j.setName(journal.DisplayName.get) + j.setSp(paper.FirstPage) + j.setEp(paper.LastPage) + if (journal.Publisher.isDefined) + pub.setPublisher(asField(journal.Publisher.get)) + if (journal.Issn.isDefined) + j.setIssnPrinted(journal.Issn.get) + pub.setJournal(j) + } + pub.setCollectedfrom(List(createMAGCollectedFrom()).asJava) + pub.setDataInfo(generateDataInfo()) + pub + } + + + def createOAF(inputParams: ((MagPapers, MagPaperWithAuthorList), MagPaperAbstract)): Publication = { + + val paper = inputParams._1._1 + val authors = inputParams._1._2 + val description = inputParams._2 + + val pub = new Publication + pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava) + pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava) + + //Set identifier as {50|60} | doiboost____::md5(DOI) + pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase)) + + val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title") + val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title") + pub.setTitle(List(mainTitles, originalTitles).asJava) + + pub.setSource(List(asField(paper.BookTitle)).asJava) + + + if (description != null) { + pub.setDescription(List(asField(description.IndexedAbstract)).asJava) + } + + + val authorsOAF = authors.authors.map { f: MagAuthorAffiliation => + + val a: eu.dnetlib.dhp.schema.oaf.Author = new eu.dnetlib.dhp.schema.oaf.Author + + a.setFullname(f.author.DisplayName.get) + + if(f.affiliation!= null) + a.setAffiliation(List(asField(f.affiliation)).asJava) + + + a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava) + + a + + } + + + if (paper.Date != null) { + pub.setDateofacceptance(asField(paper.Date.toString.substring(0,10))) + } + + pub.setAuthor(authorsOAF.asJava) + + + pub + + } + + + def convertInvertedIndexString(json_input: String): String = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(json_input) + val idl = (json \ "IndexLength").extract[Int] + if (idl > 0) { + val res = Array.ofDim[String](idl) + + val iid = (json \ "InvertedIndex").extract[Map[String, List[Int]]] + + for {(k: String, v: List[Int]) <- iid} { + v.foreach(item => res(item) = k) + } + (0 until idl).foreach(i => { + if (res(i) == null) + res(i) = "" + }) + return res.mkString(" ") + } + "" + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala new file mode 100644 index 0000000000..f291a92f99 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala @@ -0,0 +1,92 @@ +package eu.dnetlib.doiboost.mag + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{SaveMode, SparkSession} +import org.apache.spark.sql.types._ +import org.slf4j.{Logger, LoggerFactory} +import org.apache.spark.sql.functions._ + +object SparkImportMagIntoDataset { + val datatypedict = Map( + "int" -> IntegerType, + "uint" -> IntegerType, + "long" -> LongType, + "ulong" -> LongType, + "float" -> FloatType, + "string" -> StringType, + "DateTime" -> DateType + ) + + + val stream = Map( + "Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")), + "FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")), + "FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")), + "FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")), + "PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")), + "PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")), + "PaperExtendedAttributes" -> Tuple2("mag/PaperExtendedAttributes.txt", Seq("PaperId:long", "AttributeType:int", "AttributeValue:string")), + "PaperFieldsOfStudy" -> Tuple2("advanced/PaperFieldsOfStudy.txt", Seq("PaperId:long", "FieldOfStudyId:long", "Score:float")), + "PaperRecommendations" -> Tuple2("advanced/PaperRecommendations.txt", Seq("PaperId:long", "RecommendedPaperId:long", "Score:float")), + "PaperReferences" -> Tuple2("mag/PaperReferences.txt", Seq("PaperId:long", "PaperReferenceId:long")), + "PaperResources" -> Tuple2("mag/PaperResources.txt", Seq("PaperId:long", "ResourceType:int", "ResourceUrl:string", "SourceUrl:string", "RelationshipType:int")), + "PaperUrls" -> Tuple2("mag/PaperUrls.txt", Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")), + "Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "CreatedDate:DateTime")), + "RelatedFieldOfStudy" -> Tuple2("advanced/RelatedFieldOfStudy.txt", Seq("FieldOfStudyId1:long", "Type1:string", "FieldOfStudyId2:long", "Type2:string", "Rank:float")) + ) + + + def getSchema(streamName: String): StructType = { + var schema = new StructType() + val d: Seq[String] = stream(streamName)._2 + d.foreach { case t => + val currentType = t.split(":") + val fieldName: String = currentType.head + var fieldType: String = currentType.last + val nullable: Boolean = fieldType.endsWith("?") + if (nullable) + fieldType = fieldType.replace("?", "") + schema = schema.add(StructField(fieldName, datatypedict(fieldType), nullable)) + } + schema + } + + + def main(args: Array[String]): Unit = { + val logger: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + + stream.foreach { case (k, v) => + val s: StructType = getSchema(k) + val df = spark.read + .option("header", "false") + .option("charset", "UTF8") + .option("delimiter", "\t") + .schema(s) + .csv(s"${parser.get("sourcePath")}/${v._1}") + logger.info(s"Converting $k") + + df.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/$k") + } + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala new file mode 100644 index 0000000000..f3d051bd66 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala @@ -0,0 +1,157 @@ +package eu.dnetlib.doiboost.mag + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Publication +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.functions._ +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ + +object SparkPreProcessMAG { + def main(args: Array[String]): Unit = { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val sourcePath = parser.get("sourcePath") + import spark.implicits._ + implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication] + implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) + + logger.info("Phase 1) make uninque DOI in Papers:") + val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers] + + // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one + val result: RDD[MagPapers] = d.where(col("Doi").isNotNull) + .rdd + .map{ p: MagPapers => Tuple2(p.Doi, p) } + .reduceByKey((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2)) + .map(_._2) + + val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) + distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct") + + logger.info("Phase 6) Enrich Publication with description") + val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] + pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") + + logger.info("Phase 3) Group Author by PaperId") + val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor] + + val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation] + val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation] + + paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId"))) + .map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null)) } + .joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left") + .map(s => { + val mpa = s._1._2 + val af = s._2 + if (af != null) { + MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName) + } else + mpa + }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors")) + .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors") + + logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors") + + val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal] + + val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers] + + val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList] + + val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left") + firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left") + .map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) } + .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2") + + + var magPubs: Dataset[(String, Publication)] = + spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + + val conference = spark.read.load(s"$sourcePath/ConferenceInstances") + .select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" ) + val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci"))) + .select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance] + + + magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left") + .map(item => ConversionUtil.updatePubsWithConferenceInfo(item)) + .write + .mode(SaveMode.Overwrite) + .save(s"${parser.get("targetPath")}/merge_step_2_conference") + + + magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] + + + logger.info("Phase 5) enrich publication with URL and Instances") + magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") + .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } + .write.mode(SaveMode.Overwrite) + .save(s"${parser.get("targetPath")}/merge_step_3") + + +// logger.info("Phase 6) Enrich Publication with description") +// val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] +// pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") + + val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract] + + + magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left") + .map(item => ConversionUtil.updatePubsWithDescription(item) + ).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4") + + + logger.info("Phase 7) Enrich Publication with FieldOfStudy") + + magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType") + + val pfos = spark.read.load(s"$sourcePath/PaperFieldsOfStudy") + + val paperField = pfos.joinWith(fos, fos("fos").equalTo(pfos("FieldOfStudyId"))) + .select($"_1.FieldOfStudyId", $"_2.DisplayName", $"_2.MainType", $"_1.PaperId", $"_1.Score") + .groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects")) + .as[MagFieldOfStudy] + + magPubs.joinWith(paperField, col("_1") + .equalTo(paperField("PaperId")), "left") + .map(item => ConversionUtil.updatePubsWithSubject(item)) + .write.mode(SaveMode.Overwrite) + .save(s"${parser.get("targetPath")}/mag_publication") + + + val s:RDD[Publication] = spark.read.load(s"${parser.get("targetPath")}/mag_publication").as[Publication] + .map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b)) + .map(_._2) + + spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication_u") + + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java new file mode 100644 index 0000000000..570fdef17c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java @@ -0,0 +1,146 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.URI; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.mortbay.log.Log; + +import eu.dnetlib.doiboost.orcid.json.JsonWriter; +import eu.dnetlib.doiboost.orcid.model.WorkData; +import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; + +public class ActivitiesDecompressor { + + private static final int MAX_XML_WORKS_PARSED = -1; + private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000; + + public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + parseTarActivities(fs, conf, gzipInputStream, outputPath); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + + private static void parseTarActivities( + FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) { + int counter = 0; + int doiFound = 0; + int errorFromOrcidFound = 0; + int xmlParserErrorFound = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + + try { + if (entry.isDirectory() || !filename.contains("works")) { + + } else { + Log.debug("XML work entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from + // tarInput + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + WorkData workData = XMLRecordParser.VTDParseWorkData(buffer.toString().getBytes()); + if (workData != null) { + if (workData.getErrorCode() != null) { + errorFromOrcidFound += 1; + Log + .debug( + "error from Orcid with code " + + workData.getErrorCode() + + " for entry " + + entry.getName()); + continue; + } + if (workData.isDoiFound()) { + String jsonData = JsonWriter.create(workData); + Log.debug("oid: " + workData.getOid() + " data: " + jsonData); + + final Text key = new Text(workData.getOid()); + final Text value = new Text(jsonData); + + try { + writer.append(key, value); + } catch (IOException e) { + Log.debug("Writing to sequence file: " + e.getMessage()); + Log.debug(e); + throw new RuntimeException(e); + } + doiFound += 1; + } + + } else { + Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); + xmlParserErrorFound += 1; + } + } + } catch (Exception e) { + Log + .warn( + "Parsing work from tar archive and xml work: " + filename + " " + e.getMessage()); + Log.warn(e); + } + + if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log.info("Current xml works parsed: " + counter); + } + + if ((MAX_XML_WORKS_PARSED > -1) && (counter > MAX_XML_WORKS_PARSED)) { + break; + } + } + } + } catch (IOException e) { + Log.warn("Parsing work from gzip archive: " + e.getMessage()); + Log.warn(e); + throw new RuntimeException(e); + } + Log.info("Activities parse completed"); + Log.info("Total XML works parsed: " + counter); + Log.info("Total doi found: " + doiFound); + Log.info("Error from Orcid found: " + errorFromOrcidFound); + Log.info("Error parsing xml work found: " + xmlParserErrorFound); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala new file mode 100644 index 0000000000..7b344f4a5c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -0,0 +1,87 @@ +package eu.dnetlib.doiboost.orcid + +import java.io.IOException + +import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import eu.dnetlib.doiboost.DoiBoostMappingUtil +import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier} +import eu.dnetlib.doiboost.crossref.Crossref2Oaf +import org.apache.commons.lang.StringUtils +import org.codehaus.jackson.map.ObjectMapper +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ + + +case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,errorCode:String){} + + + +case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {} +object ORCIDToOAF { + val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) + val mapper = new ObjectMapper + + def isJsonValid(inputStr: String): Boolean = { + import java.io.IOException + try { + mapper.readTree(inputStr) + true + } catch { + case e: IOException => + false + } + } + + def extractValueFromInputString(input: String): (String, String) = { + val i = input.indexOf('[') + if (i <5) { + return null + } + val orcidList = input.substring(i, input.length - 1) + val doi = input.substring(1, i - 1) + if (isJsonValid(orcidList)) { + (doi, orcidList) + } else null + } + + + def convertTOOAF(input:ORCIDElement) :Publication = { + val doi = input.doi + val pub:Publication = new Publication + pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava) + pub.setDataInfo(generateDataInfo()) + pub.setId(generateIdentifier(pub, doi.toLowerCase)) + try{ + pub.setAuthor(input.authors.map(a=> { + generateAuhtor(a.name, a.surname, a.creditName, a.oid) + }).asJava) + pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava) + pub.setDataInfo(DoiBoostMappingUtil.generateDataInfo()) + pub + } catch { + case e: Throwable => + logger.info(s"ERROR ON GENERATE Publication from $input") + null + } + } + + def generateAuhtor(given: String, family: String, fullName:String, orcid: String): Author = { + val a = new Author + a.setName(given) + a.setSurname(family) + if (fullName!= null && fullName.nonEmpty) + a.setFullname(fullName) + else + a.setFullname(s"$given $family") + if (StringUtils.isNotBlank(orcid)) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + + a + } + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java new file mode 100644 index 0000000000..70528a8f60 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java @@ -0,0 +1,51 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class OrcidAuthorsDOIsDataGen extends OrcidDSManager { + + private String activitiesFileNameTarGz; + private String outputAuthorsDOIsPath; + + public static void main(String[] args) throws IOException, Exception { + OrcidAuthorsDOIsDataGen orcidAuthorsDOIsDataGen = new OrcidAuthorsDOIsDataGen(); + orcidAuthorsDOIsDataGen.loadArgs(args); + orcidAuthorsDOIsDataGen.generateAuthorsDOIsData(); + } + + public void generateAuthorsDOIsData() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsDOIsPath)); + ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + OrcidAuthorsDOIsDataGen.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); + Log.info("Default Path: " + hdfsOrcidDefaultPath); + activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); + Log.info("Activities File Name: " + activitiesFileNameTarGz); + outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath"); + Log.info("Output Authors DOIs Data: " + outputAuthorsDOIsPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java new file mode 100644 index 0000000000..4f846bdf3c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -0,0 +1,81 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; +import java.net.URI; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class OrcidDSManager { + + protected String hdfsServerUri; + protected String hdfsOrcidDefaultPath; + private String summariesFileNameTarGz; + private String outputAuthorsPath; + + public static void main(String[] args) throws IOException, Exception { + OrcidDSManager orcidDSManager = new OrcidDSManager(); + orcidDSManager.loadArgs(args); + orcidDSManager.generateAuthors(); + } + + public void generateAuthors() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz); + Path outputPath = new Path( + hdfsServerUri + .concat(hdfsOrcidDefaultPath) + .concat(outputAuthorsPath) + .concat("authors.seq")); + SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath); + } + + protected Configuration initConfigurationObject() { + // ====== Init HDFS File System Object + Configuration conf = new Configuration(); + // Set FileSystem URI + conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath)); + // Because of Maven + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + return conf; + } + + protected FileSystem initFileSystemObject(Configuration conf) { + // Get the filesystem - HDFS + FileSystem fs = null; + try { + fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + return fs; + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + OrcidDSManager.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); + Log.info("Default Path: " + hdfsOrcidDefaultPath); + summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); + Log.info("Summaries File Name: " + summariesFileNameTarGz); + outputAuthorsPath = parser.get("outputAuthorsPath"); + Log.info("Output Authors Data: " + outputAuthorsPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java new file mode 100644 index 0000000000..2e1a199da9 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java @@ -0,0 +1,203 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.text.SimpleDateFormat; +import java.util.Arrays; +import java.util.Date; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class OrcidDownloader extends OrcidDSManager { + + static final int REQ_LIMIT = 24; +// static final int REQ_MAX_TEST = 100; + static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 10000; + static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + static final String lastUpdate = "2019-09-30 00:00:00"; + private String lambdaFileName; + private String outputPath; + private String token; + + public static void main(String[] args) throws IOException, Exception { + OrcidDownloader orcidDownloader = new OrcidDownloader(); + orcidDownloader.loadArgs(args); + orcidDownloader.parseLambdaFile(); + } + + private String downloadRecord(String orcidId) { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", String.format("Bearer %s", token)); + CloseableHttpResponse response = client.execute(httpGet); + if (response.getStatusLine().getStatusCode() != 200) { + Log + .warn( + "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); + return new String(""); + } + return IOUtils.toString(response.getEntity().getContent()); + + } catch (Throwable e) { + Log.warn("Downloading " + orcidId, e.getMessage()); + + } + return new String(""); + } + + public void parseLambdaFile() throws Exception { + int parsedRecordsCounter = 0; + int downloadedRecordsCounter = 0; + int savedRecordsCounter = 0; + long startDownload = 0; + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName); + Path hdfsreadpath = new Path(lambdaFileUri); + FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath); + Path hdfsoutputPath = new Path( + hdfsServerUri + .concat(hdfsOrcidDefaultPath) + .concat(outputPath) + .concat("orcid_records.seq")); + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(hdfsoutputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class))) { + + try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) { + String line; + int nReqTmp = 0; + startDownload = System.currentTimeMillis(); + long startReqTmp = System.currentTimeMillis(); + while ((line = br.readLine()) != null) { + parsedRecordsCounter++; + // skip headers line + if (parsedRecordsCounter == 1) { + continue; + } + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + if (isModified(orcidId, recordInfo.get(3))) { + String record = downloadRecord(orcidId); + downloadedRecordsCounter++; + if (!record.isEmpty()) { + String compressRecord = ArgumentApplicationParser.compressArgument(record); + final Text key = new Text(recordInfo.get(0)); + final Text value = new Text(compressRecord); + + try { + writer.append(key, value); + savedRecordsCounter++; + } catch (IOException e) { + Log.warn("Writing to sequence file: " + e.getMessage()); + Log.warn(e); + throw new RuntimeException(e); + } + } + } + long endReq = System.currentTimeMillis(); + nReqTmp++; + if (nReqTmp == REQ_LIMIT) { + long reqSessionDuration = endReq - startReqTmp; + if (reqSessionDuration <= 1000) { + Log + .warn( + "\nreqSessionDuration: " + + reqSessionDuration + + " nReqTmp: " + + nReqTmp + + " wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } else { + nReqTmp = 0; + startReqTmp = System.currentTimeMillis(); + } + } + +// if (parsedRecordsCounter > REQ_MAX_TEST) { +// break; +// } + if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log + .info( + "Current parsed: " + + parsedRecordsCounter + + " downloaded: " + + downloadedRecordsCounter + + " saved: " + + savedRecordsCounter); +// if (parsedRecordsCounter > REQ_MAX_TEST) { +// break; +// } + } + } + long endDownload = System.currentTimeMillis(); + long downloadTime = endDownload - startDownload; + Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); + } + } + lambdaFileStream.close(); + Log.info("Download started at: " + new Date(startDownload).toString()); + Log.info("Parsed Records Counter: " + parsedRecordsCounter); + Log.info("Downloaded Records Counter: " + downloadedRecordsCounter); + Log.info("Saved Records Counter: " + savedRecordsCounter); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + OrcidDownloader.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); + Log.info("Default Path: " + hdfsOrcidDefaultPath); + lambdaFileName = parser.get("lambdaFileName"); + Log.info("Lambda File Name: " + lambdaFileName); + outputPath = parser.get("outputPath"); + Log.info("Output Data: " + outputPath); + token = parser.get("token"); + } + + private boolean isModified(String orcidId, String modifiedDate) { + Date modifiedDateDt = null; + Date lastUpdateDt = null; + try { + if (modifiedDate.length() != 19) { + modifiedDate = modifiedDate.substring(0, 19); + } + modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); + lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); + } catch (Exception e) { + Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); + return true; + } + return modifiedDateDt.after(lastUpdateDt); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala new file mode 100644 index 0000000000..1cd9ba4d42 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -0,0 +1,44 @@ +package eu.dnetlib.doiboost.orcid + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.mag.ConversionUtil +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkConvertORCIDToOAF { + + + + def main(args: Array[String]): Unit = { + + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) + import spark.implicits._ + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + val dataset:Dataset[ORCIDElement] = spark.read.json(sourcePath).as[ORCIDElement] + + + logger.info("Converting ORCID to OAF") + val d:RDD[Publication] = dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null).map(p=>(p.getId,p)).rdd.reduceByKey(ConversionUtil.mergePublication) + .map(_._2) + + spark.createDataset(d).as[Publication].write.mode(SaveMode.Overwrite).save(targetPath) + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java new file mode 100644 index 0000000000..b4239bba29 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java @@ -0,0 +1,180 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.hadoop.mapreduce.Job; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.esotericsoftware.minlog.Log; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcid.model.WorkData; +import scala.Tuple2; + +public class SparkGenerateDoiAuthorList { + + public static void main(String[] args) throws IOException, Exception { + Logger logger = LoggerFactory.getLogger(SparkGenerateDoiAuthorList.class); + logger.info("[ SparkGenerateDoiAuthorList STARTED]"); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkGenerateDoiAuthorList.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String workingPath = parser.get("workingPath"); + logger.info("workingPath: ", workingPath); + final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath"); + logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaPairRDD summariesRDD = sc + .sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class); + Dataset summariesDataset = spark + .createDataset( + summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(AuthorData.class)); + + JavaPairRDD activitiesRDD = sc + .sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class); + Dataset activitiesDataset = spark + .createDataset( + activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(WorkData.class)); + + Function, Tuple2>> toAuthorListFunction = data -> { + try { + String doi = data._1(); + if (doi == null) { + return null; + } + AuthorData author = data._2(); + if (author == null) { + return null; + } + List toAuthorList = Arrays.asList(author); + return new Tuple2<>(doi, toAuthorList); + } catch (Exception e) { + Log.error("toAuthorListFunction ERROR", e); + return null; + } + }; + + JavaRDD>> doisRDD = activitiesDataset + .joinWith( + summariesDataset, + activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") + .map( + (MapFunction, Tuple2>) value -> { + WorkData w = value._1; + AuthorData a = value._2; + return new Tuple2<>(w.getDoi(), a); + }, + Encoders.tuple(Encoders.STRING(), Encoders.bean(AuthorData.class))) + .filter(Objects::nonNull) + .toJavaRDD() + .map(toAuthorListFunction); + + JavaPairRDD + .fromJavaRDD(doisRDD) + .reduceByKey((d1, d2) -> { + try { + if (d1 != null && d2 != null) { + Stream mergedStream = Stream + .concat( + d1.stream(), + d2.stream()); + List mergedAuthors = mergedStream.collect(Collectors.toList()); + return mergedAuthors; + } + if (d1 != null) { + return d1; + } + if (d2 != null) { + return d2; + } + } catch (Exception e) { + Log.error("mergeAuthorsFunction ERROR", e); + return null; + } + return null; + }) + .mapToPair( + s -> { + ObjectMapper mapper = new ObjectMapper(); + return new Tuple2<>(s._1(), mapper.writeValueAsString(s._2())); + }) + .repartition(10) + .saveAsTextFile(workingPath + outputDoiAuthorListPath); + }); + + } + + private static AuthorData loadAuthorFromJson(Text orcidId, Text json) { + AuthorData authorData = new AuthorData(); + authorData.setOid(orcidId.toString()); + JsonElement jElement = new JsonParser().parse(json.toString()); + authorData.setName(getJsonValue(jElement, "name")); + authorData.setSurname(getJsonValue(jElement, "surname")); + authorData.setCreditName(getJsonValue(jElement, "creditname")); + return authorData; + } + + private static WorkData loadWorkFromJson(Text orcidId, Text json) { + WorkData workData = new WorkData(); + workData.setOid(orcidId.toString()); + JsonElement jElement = new JsonParser().parse(json.toString()); + workData.setDoi(getJsonValue(jElement, "doi")); + return workData; + } + + private static String getJsonValue(JsonElement jElement, String property) { + if (jElement.getAsJsonObject().has(property)) { + JsonElement name = null; + name = jElement.getAsJsonObject().get(property); + if (name != null && !name.isJsonNull()) { + return name.getAsString(); + } + } + return null; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java new file mode 100644 index 0000000000..4e18ab8401 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.util.LongAccumulator; +import org.mortbay.log.Log; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; +import scala.Tuple2; + +public class SparkOrcidGenerateAuthors { + + static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + static final String lastUpdate = "2019-09-30 00:00:00"; + + public static void main(String[] args) throws IOException, Exception { + Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); + logger.info("[ SparkOrcidGenerateAuthors STARTED]"); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkOrcidGenerateAuthors.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String workingPath = parser.get("workingPath"); + logger.info("workingPath: ", workingPath); + final String outputAuthorsPath = parser.get("outputAuthorsPath"); + logger.info("outputAuthorsPath: ", outputAuthorsPath); + final String token = parser.get("token"); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + LongAccumulator parsedRecordsAcc = sc.sc().longAccumulator("parsedRecords"); + LongAccumulator modifiedRecordsAcc = sc.sc().longAccumulator("modifiedRecords"); + LongAccumulator downloadedRecordsAcc = sc.sc().longAccumulator("downloadedRecords"); + LongAccumulator alreadyDownloadedRecords = sc.sc().longAccumulator("alreadyDownloadedRecords"); + JavaRDD lamdaFileRDD = sc.textFile(workingPath + "lamdafiles"); + + JavaRDD downloadedRDD = sc.textFile(workingPath + "downloaded"); + Function getOrcidIdFunction = line -> { + try { + String[] values = line.split(","); + return values[0].substring(1); + } catch (Exception e) { + return new String(""); + } + }; + List downloadedRecords = downloadedRDD.map(getOrcidIdFunction).collect(); + + Function isModifiedAfterFilter = line -> { + String[] values = line.split(","); + String orcidId = values[0]; + parsedRecordsAcc.add(1); + if (isModified(orcidId, values[3])) { + modifiedRecordsAcc.add(1); + return true; + } + return false; + }; + Function isNotDownloadedFilter = line -> { + String[] values = line.split(","); + String orcidId = values[0]; + if (downloadedRecords.contains(orcidId)) { + alreadyDownloadedRecords.add(1); + return false; + } + return true; + }; + Function> downloadRecordFunction = line -> { + String[] values = line.split(","); + String orcidId = values[0]; + String modifiedDate = values[3]; + return downloadRecord(orcidId, modifiedDate, token, downloadedRecordsAcc); + }; + + lamdaFileRDD + .filter(isModifiedAfterFilter) + .filter(isNotDownloadedFilter) + .map(downloadRecordFunction) + .rdd() + .saveAsTextFile(workingPath.concat(outputAuthorsPath)); + }); + + } + + private static boolean isModified(String orcidId, String modifiedDate) { + Date modifiedDateDt = null; + Date lastUpdateDt = null; + try { + if (modifiedDate.length() != 19) { + modifiedDate = modifiedDate.substring(0, 19); + } + modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); + lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); + } catch (Exception e) { + Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); + return true; + } + return modifiedDateDt.after(lastUpdateDt); + } + + private static Tuple2 downloadRecord(String orcidId, String modifiedDate, String token, + LongAccumulator downloadedRecordsAcc) { + final DownloadedRecordData data = new DownloadedRecordData(); + data.setOrcidId(orcidId); + data.setModifiedDate(modifiedDate); + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", String.format("Bearer %s", token)); + CloseableHttpResponse response = client.execute(httpGet); + int statusCode = response.getStatusLine().getStatusCode(); + data.setStatusCode(statusCode); + if (statusCode != 200) { + Log + .warn( + "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); + return data.toTuple2(); + } + downloadedRecordsAcc.add(1); + data + .setCompressedData( + ArgumentApplicationParser.compressArgument(IOUtils.toString(response.getEntity().getContent()))); + } catch (Throwable e) { + Log.warn("Downloading " + orcidId, e.getMessage()); + data.setErrorMessage(e.getMessage()); + return data.toTuple2(); + } + return data.toTuple2(); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java new file mode 100644 index 0000000000..ca6f0f6c4c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java @@ -0,0 +1,50 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class SparkPartitionLambdaFile { + + public static void main(String[] args) throws IOException, Exception { + Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkOrcidGenerateAuthors.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + final String workingPath = parser.get("workingPath"); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD lamdaFileRDD = sc.textFile(workingPath + "last_modified.csv"); + + lamdaFileRDD + .repartition(20) + .saveAsTextFile(workingPath.concat("lamdafiles")); + }); + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java new file mode 100644 index 0000000000..f0bbb5c327 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -0,0 +1,158 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.URI; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.mortbay.log.Log; + +import eu.dnetlib.doiboost.orcid.json.JsonWriter; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; + +public class SummariesDecompressor { + + private static final int MAX_XML_RECORDS_PARSED = -1; + + public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + parseTarSummaries(fs, conf, gzipInputStream, outputPath); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + + private static void parseTarSummaries( + FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) { + int counter = 0; + int nameFound = 0; + int surnameFound = 0; + int creditNameFound = 0; + int errorFromOrcidFound = 0; + int xmlParserErrorFound = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + try { + if (entry.isDirectory()) { + Log.debug("Directory entry name: " + entry.getName()); + } else { + Log.debug("XML record entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from + // tarInput + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + AuthorData authorData = XMLRecordParser.VTDParseAuthorData(buffer.toString().getBytes()); + if (authorData != null) { + if (authorData.getErrorCode() != null) { + errorFromOrcidFound += 1; + Log + .debug( + "error from Orcid with code " + + authorData.getErrorCode() + + " for oid " + + entry.getName()); + continue; + } + String jsonData = JsonWriter.create(authorData); + Log.debug("oid: " + authorData.getOid() + " data: " + jsonData); + + final Text key = new Text(authorData.getOid()); + final Text value = new Text(jsonData); + + try { + writer.append(key, value); + } catch (IOException e) { + Log.debug("Writing to sequence file: " + e.getMessage()); + Log.debug(e); + throw new RuntimeException(e); + } + + if (authorData.getName() != null) { + nameFound += 1; + } + if (authorData.getSurname() != null) { + surnameFound += 1; + } + if (authorData.getCreditName() != null) { + creditNameFound += 1; + } + + } else { + Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); + xmlParserErrorFound += 1; + } + } + } catch (Exception e) { + Log + .warn( + "Parsing record from tar archive and xml record: " + + filename + + " " + + e.getMessage()); + Log.warn(e); + } + + if ((counter % 100000) == 0) { + Log.info("Current xml records parsed: " + counter); + } + + if ((MAX_XML_RECORDS_PARSED > -1) && (counter > MAX_XML_RECORDS_PARSED)) { + break; + } + } + } + } catch (IOException e) { + Log.warn("Parsing record from gzip archive: " + e.getMessage()); + Log.warn(e); + throw new RuntimeException(e); + } + Log.info("Summaries parse completed"); + Log.info("Total XML records parsed: " + counter); + Log.info("Name found: " + nameFound); + Log.info("Surname found: " + surnameFound); + Log.info("Credit name found: " + creditNameFound); + Log.info("Error from Orcid found: " + errorFromOrcidFound); + Log.info("Error parsing xml record found: " + xmlParserErrorFound); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java new file mode 100644 index 0000000000..35676d5bab --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.doiboost.orcid.json; + +import com.google.gson.JsonObject; + +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcid.model.WorkData; + +public class JsonWriter { + + public static String create(AuthorData authorData) { + JsonObject author = new JsonObject(); + author.addProperty("oid", authorData.getOid()); + author.addProperty("name", authorData.getName()); + author.addProperty("surname", authorData.getSurname()); + if (authorData.getCreditName() != null) { + author.addProperty("creditname", authorData.getCreditName()); + } + return author.toString(); + } + + public static String create(WorkData workData) { + JsonObject work = new JsonObject(); + work.addProperty("oid", workData.getOid()); + work.addProperty("doi", workData.getDoi()); + return work.toString(); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java new file mode 100644 index 0000000000..29551c347a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.doiboost.orcid.model; + +import java.io.Serializable; + +public class AuthorData implements Serializable { + + private String oid; + private String name; + private String surname; + private String creditName; + private String errorCode; + + public String getErrorCode() { + return errorCode; + } + + public void setErrorCode(String errorCode) { + this.errorCode = errorCode; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getSurname() { + return surname; + } + + public void setSurname(String surname) { + this.surname = surname; + } + + public String getCreditName() { + return creditName; + } + + public void setCreditName(String creditName) { + this.creditName = creditName; + } + + public String getOid() { + return oid; + } + + public void setOid(String oid) { + this.oid = oid; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java new file mode 100644 index 0000000000..f66ef82a2f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java @@ -0,0 +1,76 @@ + +package eu.dnetlib.doiboost.orcid.model; + +import java.io.Serializable; + +import org.apache.hadoop.io.Text; + +import com.google.gson.JsonObject; + +import scala.Tuple2; + +public class DownloadedRecordData implements Serializable { + + private String orcidId; + private String modifiedDate; + private String statusCode; + private String compressedData; + private String errorMessage; + + public Tuple2 toTuple2() { + JsonObject data = new JsonObject(); + data.addProperty("statusCode", getStatusCode()); + data.addProperty("modifiedDate", getModifiedDate()); + if (getCompressedData() != null) { + data.addProperty("compressedData", getCompressedData()); + } + if (getErrorMessage() != null) { + data.addProperty("errorMessage", getErrorMessage()); + } + return new Tuple2<>(orcidId, data.toString()); + } + + public String getErrorMessage() { + return errorMessage; + } + + public void setErrorMessage(String errorMessage) { + this.errorMessage = errorMessage; + } + + public String getOrcidId() { + return orcidId; + } + + public void setOrcidId(String orcidId) { + this.orcidId = orcidId; + } + + public int getStatusCode() { + try { + return Integer.parseInt(statusCode); + } catch (Exception e) { + return -2; + } + } + + public void setStatusCode(int statusCode) { + this.statusCode = Integer.toString(statusCode); + } + + public String getCompressedData() { + return compressedData; + } + + public void setCompressedData(String compressedData) { + this.compressedData = compressedData; + } + + public String getModifiedDate() { + return modifiedDate; + } + + public void setModifiedDate(String modifiedDate) { + this.modifiedDate = modifiedDate; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/WorkData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/WorkData.java new file mode 100644 index 0000000000..db1728a9b4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/WorkData.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.doiboost.orcid.model; + +import java.io.Serializable; + +public class WorkData implements Serializable { + + private String oid; + private String doi; + private boolean doiFound = false; + + public boolean isDoiFound() { + return doiFound; + } + + public void setDoiFound(boolean doiFound) { + this.doiFound = doiFound; + } + + public String getOid() { + return oid; + } + + public void setOid(String oid) { + this.oid = oid; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getErrorCode() { + return errorCode; + } + + public void setErrorCode(String errorCode) { + this.errorCode = errorCode; + } + + private String errorCode; +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java new file mode 100644 index 0000000000..2e43f4d3e6 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -0,0 +1,123 @@ + +package eu.dnetlib.doiboost.orcid.xml; + +import java.util.Arrays; +import java.util.List; + +import com.ximpleware.AutoPilot; +import com.ximpleware.EOFException; +import com.ximpleware.EncodingException; +import com.ximpleware.EntityException; +import com.ximpleware.ParseException; +import com.ximpleware.VTDGen; +import com.ximpleware.VTDNav; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcid.model.WorkData; + +public class XMLRecordParser { + + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; + private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; + private static final String NS_PERSON = "person"; + private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; + private static final String NS_DETAILS = "personal-details"; + private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; + private static final String NS_OTHER = "other-name"; + private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; + private static final String NS_RECORD = "record"; + private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; + + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + + private static final String NS_ERROR = "error"; + + public static AuthorData VTDParseAuthorData(byte[] bytes) + throws VtdException, EncodingException, EOFException, EntityException, ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); + ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); + ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); + ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + + AuthorData authorData = new AuthorData(); + final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); + if (!errors.isEmpty()) { + authorData.setErrorCode(errors.get(0)); + return authorData; + } + + List recordNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, "//record:record", Arrays.asList("path")); + if (!recordNodes.isEmpty()) { + final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); + authorData.setOid(oid); + } else { + return null; + } + + final List names = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names"); + if (!names.isEmpty()) { + authorData.setName(names.get(0)); + } + + final List surnames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name"); + if (!surnames.isEmpty()) { + authorData.setSurname(surnames.get(0)); + } + + final List creditNames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name"); + if (!creditNames.isEmpty()) { + authorData.setCreditName(creditNames.get(0)); + } + return authorData; + } + + public static WorkData VTDParseWorkData(byte[] bytes) + throws VtdException, EncodingException, EOFException, EntityException, ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + + WorkData workData = new WorkData(); + final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); + if (!errors.isEmpty()) { + workData.setErrorCode(errors.get(0)); + return workData; + } + + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path")); + if (!workNodes.isEmpty()) { + final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + workData.setOid(oid); + } else { + return null; + } + + final List dois = VtdUtilityParser + .getTextValue( + ap, vn, "//common:external-id-type[text()=\"doi\"]/../common:external-id-value"); + if (!dois.isEmpty()) { + workData.setDoi(dois.get(0)); + workData.setDoiFound(true); + } + return workData; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala new file mode 100644 index 0000000000..a72e4b0d6e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala @@ -0,0 +1,43 @@ +package eu.dnetlib.doiboost.uw + +import eu.dnetlib.dhp.application.ArgumentApplicationParser + +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + + +object SparkMapUnpayWallToOAF { + + def main(args: Array[String]): Unit = { + + + val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + + + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath") + + logger.info("Converting UnpayWall to OAF") + + val d:Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication] + d.write.mode(SaveMode.Overwrite).save(targetPath) + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala new file mode 100644 index 0000000000..08cd4ee8ee --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala @@ -0,0 +1,63 @@ +package eu.dnetlib.doiboost.uw + +import eu.dnetlib.dhp.schema.oaf.{Instance, Publication} +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ +import eu.dnetlib.doiboost.DoiBoostMappingUtil._ + + + +case class OALocation(evidence:Option[String], host_type:Option[String], is_best:Option[Boolean], license: Option[String], pmh_id:Option[String], updated:Option[String], + url:Option[String], url_for_landing_page:Option[String], url_for_pdf:Option[String], version:Option[String]) {} + + + + +object UnpayWallToOAF { + val logger: Logger = LoggerFactory.getLogger(getClass) + + def convertToOAF(input:String):Publication = { + val pub = new Publication + + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + + val doi = (json \"doi").extract[String] + + + val is_oa = (json\ "is_oa").extract[Boolean] + + val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null) + pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava) + pub.setId(generateIdentifier(pub, doi.toLowerCase)) + + pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava) + pub.setDataInfo(generateDataInfo()) + + if (!is_oa) + return null + + if(oaLocation== null || oaLocation.url.isEmpty) + return null + val i :Instance= new Instance() + + i.setCollectedfrom(createUnpayWallCollectedFrom()) + i.setAccessright(getOpenAccessQualifier()) + i.setUrl(List(oaLocation.url.get).asJava) + + if (oaLocation.license.isDefined) + i.setLicense(asField(oaLocation.license.get)) + pub.setInstance(List(i).asJava) + + pub + + } + + + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json new file mode 100644 index 0000000000..312bd0751e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json new file mode 100644 index 0000000000..bf992b5086 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json @@ -0,0 +1,6 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json new file mode 100644 index 0000000000..131c301257 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json @@ -0,0 +1,6 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml new file mode 100644 index 0000000000..508202e301 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml new file mode 100644 index 0000000000..db4ac96f94 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml @@ -0,0 +1,80 @@ + + + + workingPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + timestamp + Timestamp for incremental Harvesting + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.crossref.CrossrefImporter + -t${workingPath}/input/crossref/index_dump + -n${nameNode} + -ts${timestamp} + + + + + + + + + yarn-cluster + cluster + ExtractCrossrefToOAF + eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + ${sparkExtraOPT} + + --sourcePath${workingPath}/input/crossref/index_dump,${workingPath}/crossref/index_dump + --targetPath${workingPath}/input/crossref + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json new file mode 100644 index 0000000000..444e487f7b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json @@ -0,0 +1,7 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, + {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json new file mode 100644 index 0000000000..b894177b3b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json @@ -0,0 +1,3 @@ +[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputDoiAuthorListPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json new file mode 100644 index 0000000000..35bfe1b415 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json @@ -0,0 +1,4 @@ +[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write the authors data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json new file mode 100644 index 0000000000..6eb1ec6f16 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json @@ -0,0 +1,9 @@ +[ + {"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}, + {"paramName": "dp", "paramLongName":"dbPublicationPath", "paramDescription": "the Crossref Publication Path", "paramRequired": true}, + {"paramName": "dd", "paramLongName":"dbDatasetPath", "paramDescription": "the Crossref Dataset Path", "paramRequired": true}, + {"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true}, + {"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, + {"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, + {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true} +] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json new file mode 100644 index 0000000000..ea08f47d43 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json @@ -0,0 +1,7 @@ +[ + {"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}, + {"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true}, + {"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, + {"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true}, + {"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true} +] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json new file mode 100644 index 0000000000..87a138d525 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json @@ -0,0 +1,5 @@ +[ + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true}, + {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true}, + {"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml new file mode 100644 index 0000000000..cf617a84c4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + 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 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml new file mode 100644 index 0000000000..34ba5d89da --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml @@ -0,0 +1,103 @@ + + + + hostedByMapPath + the Hosted By Map Path + + + affiliationPath + the Affliation Path + + + paperAffiliationPath + the paperAffiliation Path + + + workingDirPath + the Working Path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + yarn-cluster + cluster + Create DOIBoost Infospace + eu.dnetlib.doiboost.SparkGenerateDoiBoost + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --hostedByMapPath${hostedByMapPath} + --affiliationPath${affiliationPath} + --paperAffiliationPath${paperAffiliationPath} + --workingDirPath${workingDirPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Generate DOIBoost ActionSet + eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --dbPublicationPath${workingDirPath}/doiBoostPublicationFiltered + --dbDatasetPath${workingDirPath}/crossrefDataset + --crossRefRelation/data/doiboost/input/crossref/relations + --dbaffiliationRelationPath${workingDirPath}/doiBoostPublicationAffiliation + -do${workingDirPath}/doiBoostOrganization + --targetPath${workingDirPath}/actionDataSet + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json new file mode 100644 index 0000000000..bf0b80f69f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml new file mode 100644 index 0000000000..59e5c059fc --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.wf.rerun.failnodes + false + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml new file mode 100644 index 0000000000..2277b79b0f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml @@ -0,0 +1,87 @@ + + + + sourcePath + the working dir base path + + + targetPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + yarn-cluster + cluster + Convert Mag to Dataset + eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + ${sparkExtraOPT} + + --sourcePath${sourcePath} + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + + + + yarn-cluster + cluster + Convert Mag to Dataset + eu.dnetlib.doiboost.mag.SparkPreProcessMAG + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${sourcePath} + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json new file mode 100644 index 0000000000..bf0b80f69f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml new file mode 100644 index 0000000000..5621415d97 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx4g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml new file mode 100644 index 0000000000..7a8d041870 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml @@ -0,0 +1,41 @@ + + + + workingPath + the working dir base path + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDSManager + -d${workingPath}/ + -n${nameNode} + -fORCID_2019_summaries.tar.gz + -ooutput/ + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml new file mode 100644 index 0000000000..5621415d97 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx4g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml new file mode 100644 index 0000000000..1c2ae89ddc --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml @@ -0,0 +1,505 @@ + + + + workingPath_activities + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 0 + + + shell_cmd_1 + wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 1 + + + shell_cmd_2 + wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 2 + + + shell_cmd_3 + wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 3 + + + shell_cmd_4 + wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 4 + + + shell_cmd_5 + wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 5 + + + shell_cmd_6 + wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 6 + + + shell_cmd_7 + wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 7 + + + shell_cmd_8 + wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 8 + + + shell_cmd_9 + wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 9 + + + shell_cmd_X + wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file X + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_0.tar.gz + -ooutput/authors_dois_0.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_1} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_1.tar.gz + -ooutput/authors_dois_1.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_2} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_2.tar.gz + -ooutput/authors_dois_2.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_3} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_3.tar.gz + -ooutput/authors_dois_3.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_4} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_4.tar.gz + -ooutput/authors_dois_4.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_5} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_5.tar.gz + -ooutput/authors_dois_5.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_6} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_6.tar.gz + -ooutput/authors_dois_6.seq + + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_7} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_7.tar.gz + -ooutput/authors_dois_7.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_8} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_8.tar.gz + -ooutput/authors_dois_8.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_9} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_9.tar.gz + -ooutput/authors_dois_9.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_X} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen + -d${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_X.tar.gz + -ooutput/authors_dois_X.seq + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/config-default.xml new file mode 100644 index 0000000000..3726022cbf --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + hadoop-rm3.garr-pa1.d4science.org:8032 + + + nameNode + hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 + + + queueName + default + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml new file mode 100644 index 0000000000..21d092a83e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + workingPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + Gen_Doi_Author_List + eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList + dhp-doiboost-1.2.1-SNAPSHOT.jar + --num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + + -w${workingPath}/ + -odoi_author_list/ + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml new file mode 100644 index 0000000000..5621415d97 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx4g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml new file mode 100644 index 0000000000..1f9adeb4d8 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml @@ -0,0 +1,45 @@ + + + + workingPathOrcid + the working dir base path + + + token + access token + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDownloader + -d${workingPathOrcid}/ + -n${nameNode} + -flast_modified.csv + -odownload/ + -t${token} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml new file mode 100644 index 0000000000..a720e75923 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + hadoop-rm3.garr-pa1.d4science.org:8032 + + + nameNode + hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 + + + queueName + default + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml new file mode 100644 index 0000000000..7ebc5f0a0b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml @@ -0,0 +1,83 @@ + + + + workingPath + the working dir base path + + + token + access token + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + outputPath + the working dir base path + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + Split_Lambda_File + eu.dnetlib.doiboost.orcid.SparkPartitionLambdaFile + dhp-doiboost-1.2.1-SNAPSHOT.jar + --num-executors 24 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + + -w${workingPath}/ + -oauthors/ + -t${token} + + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + Gen_Orcid_Authors + eu.dnetlib.doiboost.orcid.SparkOrcidGenerateAuthors + dhp-doiboost-1.2.1-SNAPSHOT.jar + --num-executors 20 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + + -w${workingPath}/ + -oauthors/ + -t${token} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml new file mode 100644 index 0000000000..cf617a84c4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + 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 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml new file mode 100644 index 0000000000..bffde793ba --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + sourcePath + the working dir base path + + + targetPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${sourcePath} + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml new file mode 100644 index 0000000000..cf617a84c4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml new file mode 100644 index 0000000000..d2a69752ea --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + sourcePath + the working dir base path + + + targetPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + Convert UnpayWall to Dataset + eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${sourcePath}/uw_extracted + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala new file mode 100644 index 0000000000..4912648bea --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala @@ -0,0 +1,70 @@ +package eu.dnetlib.dhp.doiboost + +import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset} +import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType} +import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass +import eu.dnetlib.doiboost.mag.ConversionUtil +import eu.dnetlib.doiboost.orcid.ORCIDElement +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Test + +import scala.io.Source + +class DoiBoostHostedByMapTest { + + + +// @Test +// def testMerge():Unit = { +// val conf: SparkConf = new SparkConf() +// val spark: SparkSession = +// SparkSession +// .builder() +// .config(conf) +// .appName(getClass.getSimpleName) +// .master("local[*]").getOrCreate() +// +// +// +// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] +// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] +// implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub) +// +// +// import spark.implicits._ +// val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz") +// +// +// val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem)) +// +// +// hbMap.show() +// +// +// +// +// +// +// +// +// +// +// } + + + @Test + def idDSGeneration():Unit = { + val s ="doajarticles::0066-782X" + + + + println(DoiBoostMappingUtil.generateDSId(s)) + + + } + + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala new file mode 100644 index 0000000000..d31f80248f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -0,0 +1,365 @@ +package eu.dnetlib.doiboost.crossref + +import eu.dnetlib.dhp.schema.oaf._ +import eu.dnetlib.dhp.utils.DHPUtils +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Assertions._ +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} + +import scala.collection.JavaConverters._ +import scala.io.Source +import scala.util.matching.Regex + + +class CrossrefMappingTest { + + val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) + val mapper = new ObjectMapper() + + + @Test + def testFunderRelationshipsMapping(): Unit = { + val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString + val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString + val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString + + + for (line <- funder_doi.lines) { + val json = template.replace("%s", line) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + checkRelation(resultList) + } + for (line <- funder_name.lines) { + val json = template.replace("%s", line) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + checkRelation(resultList) + } + } + + def checkRelation(generatedOAF: List[Oaf]): Unit = { + + val rels: List[Relation] = generatedOAF.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]] + assertFalse(rels.isEmpty) + rels.foreach(relation => { + val relJson = mapper.writeValueAsString(relation) + + assertNotNull(relation.getSource, s"Source of relation null $relJson") + assertNotNull(relation.getTarget, s"Target of relation null $relJson") + assertFalse(relation.getTarget.isEmpty, s"Target is empty: $relJson") + assertFalse(relation.getRelClass.isEmpty, s"RelClass is empty: $relJson") + assertFalse(relation.getRelType.isEmpty, s"RelType is empty: $relJson") + assertFalse(relation.getSubRelType.isEmpty, s"SubRelType is empty: $relJson") + + }) + + } + + + @Test + def testEmptyTitle() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + items.foreach(p => println(mapper.writeValueAsString(p))) + + + } + + + @Test + def testPeerReviewed(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + + items.foreach(p => logger.info(mapper.writeValueAsString(p))) + + + + + } + + def extractECAward(award: String): String = { + val awardECRegex: Regex = "[0-9]{4,9}".r + if (awardECRegex.findAllIn(award).hasNext) + return awardECRegex.findAllIn(award).max + null + } + + + @Test + def extractECTest(): Unit = { + val s = "FP7/2007-2013" + val awardExtracted = extractECAward(s) + println(awardExtracted) + + println(DHPUtils.md5(awardExtracted)) + + + } + + @Test + def testJournalRelation(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("awardTest.json")).mkString + assertNotNull(json) + + assertFalse(json.isEmpty) + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + val rels:List[Relation] = resultList.filter(p => p.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation]) + + + + rels.foreach(s => logger.info(s.getTarget)) + assertEquals(rels.size, 3 ) + + + } + + + @Test + def testConvertBookFromCrossRef2Oaf(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("book.json")).mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + assert(items.nonEmpty) + assert(items.size == 1) + val result: Result = items.head.asInstanceOf[Result] + assertNotNull(result) + + logger.info(mapper.writeValueAsString(result)); + + assertNotNull(result.getDataInfo, "Datainfo test not null Failed"); + assertNotNull( + result.getDataInfo.getProvenanceaction, + "DataInfo/Provenance test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassid.isEmpty, + "DataInfo/Provenance/classId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassname.isEmpty, + "DataInfo/Provenance/className test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty, + "DataInfo/Provenance/SchemeId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemename.isEmpty, + "DataInfo/Provenance/SchemeName test not null Failed"); + + assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed"); + assertFalse(result.getCollectedfrom.isEmpty); + + val collectedFromList = result.getCollectedfrom.asScala + assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion") + + assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion") + + + val relevantDates = result.getRelevantdate.asScala + + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-online")), "Missing relevant date of type published-online") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-print")), "Missing relevant date of type published-print") + val rels = resultList.filter(p => p.isInstanceOf[Relation]) + assert(rels.isEmpty) + } + + + @Test + def testConvertPreprintFromCrossRef2Oaf(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("preprint.json")).mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val result: Result = items.head.asInstanceOf[Publication] + assertNotNull(result) + + logger.info(mapper.writeValueAsString(result)); + + assertNotNull(result.getDataInfo, "Datainfo test not null Failed"); + assertNotNull( + result.getDataInfo.getProvenanceaction, + "DataInfo/Provenance test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassid.isEmpty, + "DataInfo/Provenance/classId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassname.isEmpty, + "DataInfo/Provenance/className test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty, + "DataInfo/Provenance/SchemeId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemename.isEmpty, + "DataInfo/Provenance/SchemeName test not null Failed"); + + assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed"); + assertFalse(result.getCollectedfrom.isEmpty); + + val collectedFromList = result.getCollectedfrom.asScala + assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion") + + assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion") + + + val relevantDates = result.getRelevantdate.asScala + + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("available")), "Missing relevant date of type available") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("accepted")), "Missing relevant date of type accepted") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-online")), "Missing relevant date of type published-online") + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-print")), "Missing relevant date of type published-print") + val rels = resultList.filter(p => p.isInstanceOf[Relation]) + assert(rels.isEmpty) + } + + + @Test + def testConvertDatasetFromCrossRef2Oaf(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Dataset]) + + assert(items.nonEmpty) + assert(items.size == 1) + val result: Result = items.head.asInstanceOf[Dataset] + assertNotNull(result) + + logger.info(mapper.writeValueAsString(result)); + + assertNotNull(result.getDataInfo, "Datainfo test not null Failed"); + assertNotNull( + result.getDataInfo.getProvenanceaction, + "DataInfo/Provenance test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassid.isEmpty, + "DataInfo/Provenance/classId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassname.isEmpty, + "DataInfo/Provenance/className test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty, + "DataInfo/Provenance/SchemeId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemename.isEmpty, + "DataInfo/Provenance/SchemeName test not null Failed"); + + assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed"); + assertFalse(result.getCollectedfrom.isEmpty); + } + + @Test + def testConvertArticleFromCrossRef2Oaf(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val result: Result = items.head.asInstanceOf[Publication] + assertNotNull(result) + + logger.info(mapper.writeValueAsString(result)); + + assertNotNull(result.getDataInfo, "Datainfo test not null Failed"); + assertNotNull( + result.getDataInfo.getProvenanceaction, + "DataInfo/Provenance test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassid.isEmpty, + "DataInfo/Provenance/classId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassname.isEmpty, + "DataInfo/Provenance/className test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty, + "DataInfo/Provenance/SchemeId test not null Failed"); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemename.isEmpty, + "DataInfo/Provenance/SchemeName test not null Failed"); + + assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed"); + assertFalse(result.getCollectedfrom.isEmpty); + + val collectedFromList = result.getCollectedfrom.asScala + assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion") + + assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion") + + + val relevantDates = result.getRelevantdate.asScala + + assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created") + + val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]] + assertFalse(rels.isEmpty) + rels.foreach(relation => { + assertNotNull(relation) + assertFalse(relation.getSource.isEmpty) + assertFalse(relation.getTarget.isEmpty) + assertFalse(relation.getRelClass.isEmpty) + assertFalse(relation.getRelType.isEmpty) + assertFalse(relation.getSubRelType.isEmpty) + + }) + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala new file mode 100644 index 0000000000..88b1669f48 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala @@ -0,0 +1,69 @@ +package eu.dnetlib.doiboost.mag + +import java.sql.Timestamp + +import eu.dnetlib.dhp.schema.oaf.Publication +import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature +import org.apache.spark.SparkConf +import org.apache.spark.api.java.function.MapFunction +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} +import org.junit.jupiter.api.Assertions._ +import org.apache.spark.sql.functions._ + +import scala.collection.JavaConverters._ +import scala.io.Source +import scala.reflect.ClassTag +import scala.util.matching.Regex + + + +class MAGMappingTest { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + + + + @Test + def testSplitter():Unit = { + val s = "sports.team" + + + if (s.contains(".")) { + println(s.split("\\.")head) + } + + } + + + + @Test + def testDate() :Unit = { + + val p:Timestamp = Timestamp.valueOf("2011-10-02 00:00:00") + + println(p.toString.substring(0,10)) + + } + + + + @Test + def buildInvertedIndexTest(): Unit = { + val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString + val description = ConversionUtil.convertInvertedIndexString(json_input) + assertNotNull(description) + assertTrue(description.nonEmpty) + + logger.debug(description) + + } + + +} + + diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/ElasticSearchTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/ElasticSearchTest.java new file mode 100644 index 0000000000..69a2547fd9 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/ElasticSearchTest.java @@ -0,0 +1,192 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; +import java.net.ConnectException; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Future; + +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpPost; +import org.apache.http.entity.StringEntity; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; +import org.junit.jupiter.api.Test; + +import com.google.common.collect.Lists; +import com.google.common.collect.Maps; + +public class ElasticSearchTest { + + private static final String BASE_CFG_URL = "http://%s:9200/%s/%s/%s?pretty"; + + private String indexHost; + private String indexName; + private String indexType; + private String record; + private int readTimeout = 30000; + + private int nThreads = 4; + private int nTasks = 150; + private ExecutorService executorService = Executors.newFixedThreadPool(nThreads); + private List> resList = Lists.newArrayList(); + + public void setup() { + indexHost = "ip-90-147-167-25.ct1.garrservices.it"; + indexName = "orcid_update"; + indexType = "record"; + record = "{\n" + + " \"timestamp\": 1540825815212,\n" + + " \"pid\": \"0000-0002-5214-479X\",\n" + + " \"blob\": \"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\"\n" + + " }"; + } + + // @Test + public void testSingleFeed() throws Exception { + setup(); + String url = String.format(BASE_CFG_URL, indexHost, indexName, indexType, "0000-0002-5214-479X"); + System.out.println("Sending to: " + url); + System.out.println("record: " + record); + + System.out.println("response from ES: " + getResponse(url, record)); + } + +// @Test + public void testMultipleFeed() throws Exception { + setup(); + String recordTemplate = "{\n" + + " \"timestamp\": 1540825815212,\n" + + " \"pid\": \"0000-0000-0000-%s\",\n" + + " \"blob\": \"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\"\n" + + " }"; + for (int i = 0; i < 10000; i++) { + String orcidId = String.format("0000-0000-0000-%s", Integer.toString(i)); + String url = String.format(BASE_CFG_URL, indexHost, indexName, indexType, orcidId); + String recordTs = String.format(recordTemplate, Integer.toString(i)); + getResponse(url, recordTs); + } + System.out.println(""); + } + + private String getResponse(final String url, final String json) { + CloseableHttpClient client = HttpClients.createDefault(); + try { + + HttpPost httpPost = new HttpPost(url); + if (json != null) { + StringEntity entity = new StringEntity(json); + httpPost.setEntity(entity); + httpPost.setHeader("Accept", "application/json"); + httpPost.setHeader("Content-type", "application/json"); + } + CloseableHttpResponse response = client.execute(httpPost); + + return IOUtils.toString(response.getEntity().getContent()); + } catch (Throwable e) { + throw new RuntimeException("Error on executing request ", e); + } finally { + try { + client.close(); + } catch (IOException e) { + throw new RuntimeException("Unable to close client ", e); + } + } + } + +// @Test + public void testMultiThreadFeed() throws Exception { + setup(); + int countAll = 0; + int countOk = 0; + int partial = 0; + String recordTemplate = "{\n" + + " \"timestamp\": 1540825815212,\n" + + " \"pid\": \"%s\",\n" + + " \"blob\": \"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\"\n" + + " }"; + Map errors = Maps.newHashMap(); + PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager(); + cm.setMaxTotal(nThreads); + CloseableHttpClient client = HttpClients.custom().setConnectionManager(cm).build(); + for (int i = 40000; i < 41000; i++) { + String orcidId = String.format("%s", i); + String record = String.format(recordTemplate, orcidId); + countAll++; + if (partial == nTasks) { + System.out + .println( + "Waiting for tasks to complete before resubmitting to executor (countAll = " + countAll + + ") . . . "); + System.out.println("Getting replies"); + long startWait = System.currentTimeMillis(); + for (Future res : resList) { + if (res.get() == 200) + countOk++; + } + resList.clear(); + partial = 0; + System.out + .println(". . . Ready to submit again after " + (System.currentTimeMillis() - startWait) + " ms"); + } + partial++; + Future res = executorService.submit(() -> { + CloseableHttpResponse responsePPOST = null; + try { + + String url = String.format(BASE_CFG_URL, indexHost, indexName, indexType, orcidId); + HttpPost post = new HttpPost(url); + post.setHeader("Accept", "application/json"); + post.setHeader("Content-type", "application/json"); + StringEntity entity = new StringEntity(record); + post.setEntity(entity); + responsePPOST = client.execute(post); + int statusCode = responsePPOST.getStatusLine().getStatusCode(); + switch (statusCode) { + case 200: + case 201: + return statusCode; + default: + System.out + .println( + responsePPOST.getStatusLine().getStatusCode() + ": " + + responsePPOST.getStatusLine().getReasonPhrase()); + System.out.println("Source record causing error: " + record); + errors.merge(statusCode, 1, Integer::sum); + return statusCode; + } + } catch (ConnectException ce) { + throw ce; + } catch (IOException e) { + e.printStackTrace(); + errors.merge(-1, 1, Integer::sum); + } finally { + if (responsePPOST != null) + responsePPOST.close(); + } + return -1; + }); + resList.add(res); + } + executorService.shutdown(); + + // now let's wait for the results. We can block ourselves here: we have nothing else to do + System.out.println("Waiting for responses"); + for (Future res : resList) { + if (res.get() == 200) + countOk++; + } + client.close(); + cm.shutdown(); + + System.out.println("countOk: " + countOk); + System.out.println("countAll: " + countAll); + System.out.println("errors count: " + errors.size()); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala new file mode 100644 index 0000000000..158746ab52 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -0,0 +1,30 @@ +package eu.dnetlib.doiboost.orcid + +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.crossref.Crossref2Oaf +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} +import org.junit.jupiter.api.Assertions._ + +import scala.io.Source + +class MappingORCIDToOAFTest { + val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) + val mapper = new ObjectMapper() + + @Test + def testExtractData():Unit ={ + val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString + assertNotNull(json) + assertFalse(json.isEmpty) + json.lines.foreach(s => { + assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) + }) + } + + + + + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java new file mode 100644 index 0000000000..75f857ca44 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -0,0 +1,136 @@ + +package eu.dnetlib.doiboost.orcid; + +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Arrays; +import java.util.Date; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class OrcidClientTest { + final String orcidId = "0000-0001-7291-3210"; + final int REQ_LIMIT = 24; + final int REQ_MAX_TEST = 100; + final int RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL = 10; + final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + final String toRetrieveDate = "2020-05-06 23:59:46.031145"; + String toNotRetrieveDate = "2019-09-29 23:59:59.000000"; + String lastUpdate = "2019-09-30 00:00:00"; + String shortDate = "2020-05-06 16:06:11"; + +// curl -i -H "Accept: application/vnd.orcid+xml" +// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d' +// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record' + + public String testDownloadRecord(String orcidId) throws Exception { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d"); + CloseableHttpResponse response = client.execute(httpGet); + if (response.getStatusLine().getStatusCode() != 200) { + System.out + .println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); + } + return IOUtils.toString(response.getEntity().getContent()); + } catch (Throwable e) { + e.printStackTrace(); + } + return new String(""); + } + +// @Test + public void testLambdaFileParser() throws Exception { + try (BufferedReader br = new BufferedReader( + new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) { + String line; + int counter = 0; + int nReqTmp = 0; + long startDownload = System.currentTimeMillis(); + long startReqTmp = System.currentTimeMillis(); + while ((line = br.readLine()) != null) { + counter++; +// skip headers line + if (counter == 1) { + continue; + } + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + testDownloadRecord(recordInfo.get(0)); + long endReq = System.currentTimeMillis(); + nReqTmp++; + if (nReqTmp == REQ_LIMIT) { + long reqSessionDuration = endReq - startReqTmp; + if (reqSessionDuration <= 1000) { + System.out + .println( + "\nreqSessionDuration: " + reqSessionDuration + " nReqTmp: " + nReqTmp + " wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } else { + nReqTmp = 0; + startReqTmp = System.currentTimeMillis(); + } + } + + if (counter > REQ_MAX_TEST) { + break; + } + if ((counter % RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL) == 0) { + System.out.println("Current record downloaded: " + counter); + } + } + long endDownload = System.currentTimeMillis(); + long downloadTime = endDownload - startDownload; + System.out.println("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); + } + } + +// @Test + public void getRecordDatestamp() throws ParseException { + Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate); + Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate); + Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); + assertTrue(toRetrieveDateDt.after(lastUpdateDt)); + assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt)); + } + + public void testDate(String value) throws ParseException { + System.out.println(value.toString()); + if (value.length() != 19) { + value = value.substring(0, 19); + } + Date valueDt = new SimpleDateFormat(DATE_FORMAT).parse(value); + System.out.println(valueDt.toString()); + } + +// @Test + public void testModifiedDate() throws ParseException { + testDate(toRetrieveDate); + testDate(toNotRetrieveDate); + testDate(shortDate); + } + +// @Test + public void testReadBase64CompressedRecord() throws Exception { + final String base64CompressedRecord = IOUtils + .toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64")); + final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); + System.out.println(recordFromSeqFile); + final String downloadedRecord = testDownloadRecord("0000-0001-6645-509X"); + assertTrue(recordFromSeqFile.equals(downloadedRecord)); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java new file mode 100644 index 0000000000..d5da4eec02 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.doiboost.orcid.xml; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcid.model.WorkData; + +public class XMLRecordParserTest { + + @Test + public void testOrcidAuthorDataXMLParser() throws Exception { + + String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml")); + + XMLRecordParser p = new XMLRecordParser(); + + AuthorData authorData = p.VTDParseAuthorData(xml.getBytes()); + assertNotNull(authorData); + assertNotNull(authorData.getName()); + System.out.println("name: " + authorData.getName()); + assertNotNull(authorData.getSurname()); + System.out.println("surname: " + authorData.getSurname()); + } + + @Test + public void testOrcidXMLErrorRecordParser() throws Exception { + + String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml")); + + XMLRecordParser p = new XMLRecordParser(); + + AuthorData authorData = p.VTDParseAuthorData(xml.getBytes()); + assertNotNull(authorData); + assertNotNull(authorData.getErrorCode()); + System.out.println("error: " + authorData.getErrorCode()); + } + + @Test + public void testOrcidWorkDataXMLParser() throws Exception { + + String xml = IOUtils + .toString( + this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml")); + + XMLRecordParser p = new XMLRecordParser(); + + WorkData workData = p.VTDParseWorkData(xml.getBytes()); + assertNotNull(workData); + assertNotNull(workData.getOid()); + System.out.println("oid: " + workData.getOid()); + assertNotNull(workData.getDoi()); + System.out.println("doi: " + workData.getDoi()); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala new file mode 100644 index 0000000000..8a6dd279b6 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala @@ -0,0 +1,49 @@ +package eu.dnetlib.doiboost.uw + +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Test + +import scala.io.Source +import org.junit.jupiter.api.Assertions._ +import org.slf4j.{Logger, LoggerFactory} + +class UnpayWallMappingTest { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + + @Test + def testMappingToOAF():Unit ={ + + val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString + + + for (line <-Ilist.lines) { + + + val p = UnpayWallToOAF.convertToOAF(line) + + if(p!= null) { + assertTrue(p.getPid.size()==1) + logger.info(p.getId) + } + assertNotNull(line) + assertTrue(line.nonEmpty) + } + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + + + val l = Ilist.lines.next() + + logger.info(mapper.writeValueAsString(UnpayWallToOAF.convertToOAF(l))) + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json new file mode 100644 index 0000000000..4e6db2a124 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json @@ -0,0 +1,20 @@ +[{"journal":{"issnOnline":null,"vol":"37","issnLinking":null,"edition":null,"issnPrinted":"2415-8038","dataInfo":null,"conferencedate":null,"iss":null,"ep":"34","sp":"30","conferenceplace":null,"name":"Scientific Herald of Uzhhorod University.Series Physics"},"format":[],"source":[{"dataInfo":null,"value":"Crossref"},{"dataInfo":null,"value":null}],"description":[],"subject":[{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Instability"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Softening"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Composite material"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Self-organization"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Materials science"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Crystalline materials"}],"author":[{"surname":"Мар’ян","affiliation":null,"fullname":"М. 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MC activation/degranulation, as judged by diffuse extracellular tryptase staining, was a common feature within RAU-inflammatory infiltrates and at RAU-inflammatory infiltrates-connective tissue interfaces, which were often associated with connective tissue disruption. MC counts in the RAU connective tissue, lateral to the inflammatory infiltrates, were significantly greater than in the connective tissue of TUs and of control biopsies (124+/-36 vs 73+/-13 vs 69+/-21 cells/mm2, respectively; P<0.001). Overall, MCs were significantly increased in aphthae (116+/-26 cells/mm2) compared with TU lesions (72+/-11 cells/mm2, P<0.001) and controls (71+/-16 cells/mm2, P<0.001). 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There is no specific pronouncement on the part of the International Accounting Standards Board (IASB) or from the Brazilian Accounting Pronouncements Committee (CPC) regarding the accounting treatment to be applied in operations that use these currencies. Bitcoin is of interest to economists as a virtual currency with the potential to disrupt existing payment systems and even monetary systems. This essay offers a contribution for standard-setters and the tax authority (fisco) by providing the basis for possible guidelines to be issued on the accounting treatment of bitcoin operations, as well as by defining the appropriate tax treatment; in addition, it makes a contribution for accounting professionals by suggesting the accounting policy to be adopted in these operations. Here, the analysis of the characteristics of bitcoins is compared with the guidelines and concepts of IFRS, in order to elaborate the recommendation for accounting treatment, and it suggests that the most adequate procedure would be that of foreign currency, which would go against the tax treatment adopted up until now by the Brazilian Internal Revenue Service (Receita Federal) or the Internal Revenue Service (IRS) of the United States of America (USA), which suggest treating virtual currencies as goods and not as currencies. 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We use the Weather Research and Forecast (WRF) model to simulate a large-scale tropical tropopause layer (TTL) cirrus in order to understand the formation and life cycle of the cloud. This cirrus event has been previously described through satellite observations by Taylor et al. (2011). Comparisons of the simulated and observed cirrus show a fair agreement and validate the reference simulation regarding cloud extension, location and life time. The validated simulation is used to understand the causes of cloud formation. It is shown that several cirrus clouds successively form in the region due to adiabatic cooling and large-scale uplift rather than from convective anvils. The structure of the uplift is tied to the equatorial response (equatorial wave excitation) to a potential vorticity intrusion from the midlatitudes. Sensitivity tests are then performed to assess the relative importance of the choice of the microphysics parameterization and of the initial and boundary conditions. The initial dynamical conditions (wind and temperature) essentially control the horizontal location and area of the cloud. However, the choice of the microphysics scheme influences the ice water content and the cloud vertical position. Last, the fair agreement with the observations allows to estimate the cloud impact in the TTL in the simulations. The cirrus clouds have a small but not negligible impact on the radiative budget of the local TTL. However, for this particular case, the cloud radiative heating does not significantly influence the simulated dynamics. This result is due to (1) the lifetime of air parcels in the cloud system, which is too short to significantly influence the dynamics, and (2) the fact that induced vertical motions would be comparable to or smaller than the typical mesoscale motions present. Finally, the simulation also provides an estimate of the vertical redistribution of water by the cloud and the results emphasize the importance in our case of both rehydration and dehydration in the vicinity of the cirrus.\n "}],"subject":[{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Atmospheric Science"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Cirrus"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Weather Research and Forecasting 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The greatest obstacle to reduction was a constriction of the capsule. At a mean follow-up of 13.2 months (9 to 24), all eight hips remained stable. Three developed avascular necrosis. The mean acetabular index decreased from 35.5° (30° to 40°) pre-operatively to 23.3° (17° to 28°).\n\nThis study demonstrates that arthroscopic reduction is feasible using two standardised portals. 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It therefore allows the study of how the healthy brain functions, how it is affected by different diseases, how it attempts to recover after damage and how drugs can modulate activity or post-damage recovery. After an fMRI experiment has been designed and carried out, the resulting data must be passed through various analysis steps before the experimenter can get answers to questions about experimentally related activations at the individual or multi-subject level. This paper gives a brief overview of the most commonly used analysis pipeline: data pre-processing, temporal linear modelling and activation thresholding. For more details, see Jezzard et al [1]. fMRI Data In a typical fMRI session a low-resolution functional volume is acquired every few seconds. (MR volumes are often also referred to as ‘‘images’’ or ‘‘scans’’). Over the course of the experiment, 100 volumes or more are typically recorded. In the simplest possible experiment, some images will be taken whilst stimulation (for the remainder of this chapter, reference to ‘‘stimulation’’ should be taken to include also the carrying out of physical or cognitive activity) is applied, and some will be taken with the subject at rest. Because the images are taken using an MR sequence which is sensitive to changes in local blood oxygenation level (BOLD imaging; see Chapters 2 and 3 in Jezzard et al [1]), parts of the images taken during stimulation should show increased intensity, compared with those taken whilst at rest. The parts of these images that show increased intensity should correspond to the brain areas which are activated by the stimulation. The goal of fMRI analysis is to detect, in a robust, sensitive and valid way, those parts of the brain that show increased intensity at the points in time that stimulation was applied. A single volume is made up of individual cuboid elements called voxels (Figure 1). An fMRI data set from a single session can either be thought of as t volumes, one taken every few seconds, or as v voxels, each with an associated time series of t time points. It is important to be able to conceptualize both of these representations, as some analysis steps make more sense when thinking of the data in one way, and others make more sense the other way. An example time-series from a single voxel is shown in Figure 2. Image intensity is shown on the y axis, and time (in scans) on the x axis. As described above, for some of the time points, stimulation was applied, (the higher intensity periods), and at some time points the subject was at rest. As well as the effect of the stimulation being clear, the high frequency noise is also apparent. 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Abstract Micropropagated shoot explants fromPinus radiataD. Don were used to produce stable transgenic plants byAgrobacterium tumefaciensmediated transformation. Using this method any genotype that can be micropropagated could produce stable transgenic lines. As over 80% ofP. radiatagenotypes tested can be micropropagated, this effectively means that any line chosen for superior characteristics could be transformed. There are well established protocols for progressing such germplasm to field deployment. Here we used open and control pollinated seed lines and embryogenic clones. The method developed was faster than other methods previously developed using mature cotyledons. PCR positive shoots could be obtain within 6 months ofAgrobacteriumcocultivation compared with 12 months for cotyledon methods. Transformed shoots were obtained using either kanamycin or geneticin as the selectable marker gene. Shoots were recovered from selection, were tested and were not chimeric, indicating that the selection pressure was optimal for this explant type. GFP was used as a vital marker, and the bar gene, (for resistance to the herbicide Buster\\u00ae/Basta\\u00ae) was used to produce lines that could potentially be used in commercial application. As expected, a range of expression phenotypes were identified for both these reporter genes and the analyses for expression were relatively easy.", + "prefix": "10.1101", + "author": [ + { + "affiliation": [], + "given": "Jan E", + "family": "Grant", + "sequence": "first" + }, + { + "affiliation": [], + "given": "Pauline A", + "family": "Cooper", + "sequence": "additional" + }, + { + "affiliation": [], + "given": "Tracy M", + "family": "Dale", + "sequence": "additional" + } + ], + "reference-count": 0, + "member": "246", + "source": "Crossref", + "score": 1.0, + "deposited": { + "timestamp": 1483495053000, + "date-time": "2017-01-04T01:57:33Z", + "date-parts": [ + [ + 2017, + 1, + 4 + ] + ] + }, + "indexed": { + "timestamp": 1550234353119, + "date-time": "2019-02-15T12:39:13Z", + "date-parts": [ + [ + 2019, + 2, + 15 + ] + ] + }, + "type": "posted-content", + "URL": "http://dx.doi.org/10.1101/030080", + "is-referenced-by-count": 2, + "link": [ + { + "URL": 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"published_date": "1959-10-01", "best_oa_location": null, "journal_is_in_doaj": false, "has_repository_copy": false} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties b/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties new file mode 100644 index 0000000000..20f56e38dd --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties @@ -0,0 +1,11 @@ +# Set root logger level to DEBUG and its only appender to A1. +log4j.rootLogger=INFO, A1 + +# A1 is set to be a ConsoleAppender. +log4j.appender.A1=org.apache.log4j.ConsoleAppender + +# A1 uses PatternLayout. +log4j.logger.org = ERROR +log4j.logger.eu.dnetlib = DEBUG +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n \ No newline at end of file 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 3becdec448..8e5ba9cd11 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 @@ -39,9 +39,6 @@ import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; public class GenerateEntitiesApplication { @@ -66,15 +63,15 @@ public class GenerateEntitiesApplication { log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String sourcePaths = parser.get("sourcePaths"); - final String targetPath = parser.get("targetPath"); + log.info("sourcePaths: {}", sourcePaths); - // final String dbUrl = parser.get("postgresUrl"); - // final String dbUser = parser.get("postgresUser"); - // final String dbPassword = parser.get("postgresPassword"); + final String targetPath = parser.get("targetPath"); + log.info("targetPath: {}", targetPath); final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); - final VocabularyGroup vocs = loadVocsFromIS(isLookupUrl); // MAP: vocId -> voc + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { @@ -165,35 +162,6 @@ public class GenerateEntitiesApplication { } } - private static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException { - final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); - - final String xquery = IOUtils - .toString( - GenerateEntitiesApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery")); - - final VocabularyGroup vocs = new VocabularyGroup(); - - for (final String s : isLookUpService.quickSearchProfile(xquery)) { - final String[] arr = s.split("@=@"); - if (arr.length == 4) { - final String vocId = arr[0].trim(); - final String vocName = arr[1].trim(); - final String termId = arr[2].trim(); - final String termName = arr[3].trim(); - - if (!vocs.vocabularyExists(vocId)) { - vocs.addVocabulary(vocId, vocName); - } - - vocs.addTerm(vocId, termId, termName); - } - } - - return vocs; - } - private static Oaf convertFromJson(final String s, final Class clazz) { try { return OBJECT_MAPPER.readValue(s, clazz); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 5b8296c19b..653027039a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -10,7 +10,28 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; +import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; +import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTICIPANT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; +import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; import java.io.Closeable; import java.io.IOException; @@ -26,12 +47,13 @@ import java.util.function.Function; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -52,7 +74,7 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { - private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + private static final Logger log = LoggerFactory.getLogger(MigrateDbEntitiesApplication.class); public static final String SOURCE_TYPE = "source_type"; public static final String TARGET_TYPE = "target_type"; @@ -61,6 +83,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i private final long lastUpdateTimestamp; + private final VocabularyGroup vocs; + public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -71,15 +95,25 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i parser.parseArgument(args); final String dbUrl = parser.get("postgresUrl"); + log.info("postgresUrl: {}", dbUrl); + final String dbUser = parser.get("postgresUser"); + log.info("postgresUser: {}", dbUser); + final String dbPassword = parser.get("postgresPassword"); + log.info("postgresPassword: xxx"); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); + log.info("processClaims: {}", processClaims); try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, - dbPassword)) { + dbPassword, isLookupUrl)) { if (processClaims) { log.info("Processing claims..."); smdbe.execute("queryClaims.sql", smdbe::processClaims); @@ -103,18 +137,21 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } - protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST + protected MigrateDbEntitiesApplication(final VocabularyGroup vocs) { // ONLY FOR UNIT TEST super(); this.dbClient = null; this.lastUpdateTimestamp = new Date().getTime(); + this.vocs = vocs; } public MigrateDbEntitiesApplication( - final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) + final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword, + final String isLookupUrl) throws Exception { super(hdfsPath); this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); this.lastUpdateTimestamp = new Date().getTime(); + this.vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); } public void execute(final String sqlFile, final Function> producer) @@ -453,12 +490,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Boolean inferred = rs.getBoolean("inferred"); final String trust = rs.getString("trust"); return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - ENTITYREGISTRY_PROVENANCE_ACTION, - trust); + deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); } private Qualifier prepareQualifierSplitting(final String s) { @@ -466,7 +498,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i return null; } final String[] arr = s.split("@@@"); - return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; + return arr.length == 2 ? vocs.getTermAsQualifier(arr[1], arr[0]) : null; } private List> prepareListFields(final Array array, final DataInfo info) { @@ -485,8 +517,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i if (parts.length == 2) { final String value = parts[0]; final String[] arr = parts[1].split("@@@"); - if (arr.length == 4) { - return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); + if (arr.length == 2) { + return structuredProperty(value, vocs.getTermAsQualifier(arr[1], arr[0]), dataInfo); } } return null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java index 7714f6d90c..c955ee6404 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java @@ -1,10 +1,11 @@ package eu.dnetlib.dhp.oa.graph.raw.common; +import java.io.Serializable; import java.util.HashMap; import java.util.Map; -public class Vocabulary { +public class Vocabulary implements Serializable { private final String id; private final String name; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 127f73e220..43ed7f2d9e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -1,12 +1,50 @@ package eu.dnetlib.dhp.oa.graph.raw.common; +import java.io.IOException; +import java.io.Serializable; import java.util.HashMap; import java.util.Map; -import eu.dnetlib.dhp.schema.oaf.Qualifier; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; -public class VocabularyGroup { +import eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class VocabularyGroup implements Serializable { + + public static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException { + final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + final String xquery = IOUtils + .toString( + GenerateEntitiesApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery")); + + final VocabularyGroup vocs = new VocabularyGroup(); + + for (final String s : isLookUpService.quickSearchProfile(xquery)) { + final String[] arr = s.split("@=@"); + if (arr.length == 4) { + final String vocId = arr[0].trim(); + final String vocName = arr[1].trim(); + final String termId = arr[2].trim(); + final String termName = arr[3].trim(); + + if (!vocs.vocabularyExists(vocId)) { + vocs.addVocabulary(vocId, vocName); + } + + vocs.addTerm(vocId, termId, termName); + } + } + + return vocs; + } private final Map vocs = new HashMap<>(); @@ -29,7 +67,9 @@ public class VocabularyGroup { } public Qualifier getTermAsQualifier(final String vocId, final String id) { - if (termExists(vocId, id)) { + if (StringUtils.isBlank(id)) { + return OafMapperUtils.qualifier("UNKNOWN", "UNKNOWN", vocId, vocId); + } else if (termExists(vocId, id)) { final Vocabulary v = vocs.get(vocId.toLowerCase()); final VocabularyTerm t = v.getTerm(id); return OafMapperUtils.qualifier(t.getId(), t.getName(), v.getId(), v.getName()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java index b3c7859231..1aa1b82539 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java @@ -1,7 +1,9 @@ package eu.dnetlib.dhp.oa.graph.raw.common; -public class VocabularyTerm { +import java.io.Serializable; + +public class VocabularyTerm implements Serializable { private final String id; private final String name; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index 9e3992bcfb..8342dde959 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -18,8 +18,8 @@ "paramRequired": true }, { - "paramName": "islookup", - "paramLongName": "islookup", + "paramName": "isu", + "paramLongName": "isLookupUrl", "paramDescription": "the url of the ISLookupService", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json index cb13ff0242..4e838561d5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "action", "paramDescription": "process claims", "paramRequired": false + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the url of the ISLookupService", + "paramRequired": true } ] \ No newline at end of file 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 f8426c35f2..c2bea9f8a2 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 @@ -123,6 +123,7 @@ --postgresUrl${postgresURL} --postgresUser${postgresUser} --postgresPassword${postgresPassword} + --isLookupUrl${isLookupUrl} --actionclaims @@ -173,6 +174,7 @@ --postgresUrl${postgresURL} --postgresUser${postgresUser} --postgresPassword${postgresPassword} + --isLookupUrl${isLookupUrl} @@ -237,7 +239,7 @@ --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims --targetPath${workingDir}/entities_claim - --islookup${isLookupUrl} + --isLookupUrl${isLookupUrl} @@ -284,7 +286,7 @@ --sourcePaths${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records --targetPath${workingDir}/entities - --islookup${isLookupUrl} + --isLookupUrl${isLookupUrl} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 05b85a5615..575f9229ed 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -16,6 +16,10 @@ postgresPassword the password postgres + + isLookupUrl + the address of the lookUp service + sparkDriverMemory @@ -88,6 +92,7 @@ --postgresUrl${postgresURL} --postgresUser${postgresUser} --postgresPassword${postgresPassword} + --isLookupUrl${isLookupUrl} @@ -103,6 +108,7 @@ --postgresUrl${postgresURL} --postgresUser${postgresUser} --postgresPassword${postgresPassword} + --isLookupUrl${isLookupUrl} --actionclaims diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml index f16e22f957..8684181526 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml @@ -24,6 +24,10 @@ mongoDb mongo database + + isLookupUrl + the address of the lookUp service + sparkDriverMemory memory for driver process @@ -62,6 +66,7 @@ -pgurl${postgresURL} -pguser${postgresUser} -pgpasswd${postgresPassword} + -islookup${isLookupUrl} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql index 745f83971a..687377aa48 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql @@ -1,17 +1,16 @@ SELECT - dor.datasource AS datasource, - dor.organization AS organization, - NULL AS startdate, - NULL AS enddate, - false AS inferred, - false AS deletedbyinference, - 0.9 AS trust, - NULL AS inferenceprovenance, - dc.id AS collectedfromid, - dc.officialname AS collectedfromname, - 'providedBy@@@provided by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS semantics, - d.provenanceaction || '@@@' || d.provenanceaction || '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction - + dor.datasource AS datasource, + dor.organization AS organization, + NULL AS startdate, + NULL AS enddate, + false AS inferred, + false AS deletedbyinference, + 0.9 AS trust, + NULL AS inferenceprovenance, + dc.id AS collectedfromid, + dc.officialname AS collectedfromname, + 'providedBy@@@dnet:datasources_organizations_typologies' AS semantics, + d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction FROM dsm_datasource_organization dor - LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) + LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql index ff1178c711..43b0f8f4b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql @@ -7,36 +7,36 @@ SELECT CASE WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire-cris_1.1']) THEN - 'openaire-cris_1.1@@@OpenAIRE CRIS v1.1@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) THEN - 'openaire4.0@@@OpenAIRE 4.0@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'openaire4.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN - 'driver-openaire2.0@@@OpenAIRE 2.0+ (DRIVER OA, EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['driver']) THEN - 'driver@@@OpenAIRE Basic (DRIVER OA)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'driver@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0']) THEN - 'openaire2.0@@@OpenAIRE 2.0 (EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'openaire2.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire3.0']) THEN - 'openaire3.0@@@OpenAIRE 3.0 (OA, funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'openaire3.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0_data']) THEN - 'openaire2.0_data@@@OpenAIRE Data (funded, referenced datasets)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'openaire2.0_data@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['native']) THEN - 'native@@@proprietary@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'native@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['hostedBy']) THEN - 'hostedBy@@@collected from a compatible aggregator@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'hostedBy@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['notCompatible']) THEN - 'notCompatible@@@under validation@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'notCompatible@@@dnet:datasourceCompatibilityLevel' ELSE - 'UNKNOWN@@@not available@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + 'UNKNOWN@@@dnet:datasourceCompatibilityLevel' END AS openairecompatibility, d.websiteurl AS websiteurl, d.logourl AS logourl, @@ -47,7 +47,7 @@ SELECT NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - (SELECT array_agg(s|| '###keywords@@@keywords@@@dnet:subject_classification_typologies@@@dnet:subject_classification_typologies') + (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( SELECT trim(s) @@ -83,32 +83,9 @@ SELECT ARRAY[]::text[] AS policies, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - d.typology || '@@@' || CASE - WHEN (d.typology = 'crissystem') THEN 'CRIS System' - WHEN (d.typology = 'datarepository::unknown') THEN 'Data Repository' - WHEN (d.typology = 'aggregator::datarepository') THEN 'Data Repository Aggregator' - WHEN (d.typology = 'infospace') THEN 'Information Space' - WHEN (d.typology = 'pubsrepository::institutional') THEN 'Institutional Repository' - WHEN (d.typology = 'aggregator::pubsrepository::institutional') THEN 'Institutional Repository Aggregator' - WHEN (d.typology = 'pubsrepository::journal') THEN 'Journal' - WHEN (d.typology = 'aggregator::pubsrepository::journals') THEN 'Journal Aggregator/Publisher' - WHEN (d.typology = 'pubsrepository::mock') THEN 'Other' - WHEN (d.typology = 'pubscatalogue::unknown') THEN 'Publication Catalogue' - WHEN (d.typology = 'pubsrepository::unknown') THEN 'Publication Repository' - WHEN (d.typology = 'aggregator::pubsrepository::unknown') THEN 'Publication Repository Aggregator' - WHEN (d.typology = 'entityregistry') THEN 'Registry' - WHEN (d.typology = 'scholarcomminfra') THEN 'Scholarly Comm. Infrastructure' - WHEN (d.typology = 'pubsrepository::thematic') THEN 'Thematic Repository' - WHEN (d.typology = 'websource') THEN 'Web Source' - WHEN (d.typology = 'entityregistry::projects') THEN 'Funder database' - WHEN (d.typology = 'entityregistry::repositories') THEN 'Registry of repositories' - WHEN (d.typology = 'softwarerepository') THEN 'Software Repository' - WHEN (d.typology = 'aggregator::softwarerepository') THEN 'Software Repository Aggregator' - WHEN (d.typology = 'orprepository') THEN 'Repository' - ELSE 'Other' - END || '@@@dnet:datasource_typologies@@@dnet:datasource_typologies' AS datasourcetype, - 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, - CONCAT(d.issn, ' @@@ ', d.eissn, ' @@@ ', d.lissn) AS journal + d.typology||'@@@dnet:datasource_typologies' AS datasourcetype, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, + d.issn || ' @@@ ' || d.eissn || ' @@@ ' || d.lissn AS journal FROM dsm_datasources d diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index d13bd43425..3e5de80711 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -22,13 +22,12 @@ SELECT '' AS inferenceprovenance, d.id AS collectedfromid, d.officialname AS collectedfromname, - o.country || '@@@' || COALESCE(cntr.name,o.country) || '@@@dnet:countries@@@dnet:countries' AS country, - 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, ARRAY[]::text[] AS pid FROM dsm_organizations o LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) - LEFT OUTER JOIN class cntr ON (cntr.code = o.country) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql index 99c8e04b4b..3396f365c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql @@ -11,8 +11,8 @@ SELECT '' AS inferenceprovenance, 'openaire____::openorgs' AS collectedfromid, 'OpenOrgs Database' AS collectedfromname, - o.country || '@@@' || o.country || '@@@dnet:countries@@@dnet:countries' AS country, - 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid FROM organizations o LEFT OUTER JOIN acronyms a ON (a.id = o.id) @@ -40,8 +40,8 @@ SELECT '' AS inferenceprovenance, 'openaire____::openorgs' AS collectedfromid, 'OpenOrgs Database' AS collectedfromname, - o.country || '@@@' || o.country || '@@@dnet:countries@@@dnet:countries' AS country, - 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid FROM other_names n LEFT OUTER JOIN organizations o ON (n.id = o.id) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index 4c06ca5b9a..13cfca8715 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -11,8 +11,8 @@ SELECT NULL AS inferenceprovenance, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - po.semanticclass || '@@@' || po.semanticclass || '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics, - 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction + po.semanticclass || '@@@dnet:project_organization_relations' AS semantics, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction FROM project_organization po LEFT OUTER JOIN projects p ON (p.id = po.project) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql index 685b57ab65..db0da83f77 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql @@ -31,17 +31,14 @@ SELECT p.fundedamount AS fundedamount, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - p.contracttype || '@@@' || p.contracttypename || '@@@' || p.contracttypescheme || '@@@' || p.contracttypescheme AS contracttype, - pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction, + p.contracttype || '@@@' || p.contracttypescheme AS contracttype, + p.provenanceactionclass || '@@@' || p.provenanceactionscheme AS provenanceaction, array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, - array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects, + array_agg(DISTINCT s.name || '###' || s.semanticclass || '@@@' || s.semanticscheme) AS subjects, array_agg(DISTINCT fp.path) AS fundingtree FROM projects p - LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass) - LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme) - LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) @@ -53,9 +50,6 @@ SELECT LEFT OUTER JOIN project_subject ps ON (ps.project = p.id) LEFT OUTER JOIN subjects s ON (s.id = ps.subject) - LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass) - LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme) - GROUP BY p.id, p.code, @@ -85,5 +79,6 @@ SELECT p.fundedamount, dc.id, dc.officialname, - pac.code, pac.name, pas.code, pas.name, - p.contracttype , p.contracttypename, p.contracttypescheme; \ No newline at end of file + p.contracttype, + p.contracttypescheme; + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql index 6cff188756..234bb7c3eb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql @@ -28,18 +28,15 @@ SELECT p.summary AS summary, p.currency AS currency, p.totalcost AS totalcost, - p.fundedamount AS fundedamount, + p.fundedamount AS fundedamount, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name AS contracttype, - pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction, + p.contracttypeclass || '@@@' || p.contracttypescheme AS contracttype, + p.provenanceactionclass || '@@@' || p.provenanceactionscheme AS provenanceaction, array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, - array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects, + array_agg(DISTINCT s.name || '###' || s.semanticclass || '@@@' || s.semanticscheme) AS subjects, array_agg(DISTINCT fp.path) AS fundingtree FROM projects p - LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass) - LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme) - LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) @@ -51,12 +48,6 @@ SELECT LEFT OUTER JOIN project_subject ps ON (ps.project = p.id) LEFT OUTER JOIN subjects s ON (s.id = ps.subject) - LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass) - LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme) - - LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass) - LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme) - GROUP BY p.id, p.code, @@ -85,6 +76,6 @@ SELECT p.totalcost, p.fundedamount, dc.id, - dc.officialname, - pac.code, pac.name, pas.code, pas.name, - ctc.code, ctc.name, cts.code, cts.name; \ No newline at end of file + dc.officialname + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 1bbe57ee83..22fcb36c98 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -4,6 +4,8 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.lenient; import java.io.IOException; import java.sql.Array; @@ -25,6 +27,8 @@ import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Organization; @@ -40,9 +44,22 @@ public class MigrateDbEntitiesApplicationTest { @Mock private ResultSet rs; + @Mock + private VocabularyGroup vocs; + @BeforeEach public void setUp() { - this.app = new MigrateDbEntitiesApplication(); + lenient() + .when(vocs.getTermAsQualifier(anyString(), anyString())) + .thenAnswer( + invocation -> OafMapperUtils + .qualifier( + invocation.getArgument(1), invocation.getArgument(1), invocation.getArgument(0), + invocation.getArgument(0))); + + lenient().when(vocs.termExists(anyString(), anyString())).thenReturn(true); + + this.app = new MigrateDbEntitiesApplication(vocs); } @Test @@ -61,8 +78,7 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals(ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); - assertEquals( - ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); + assertEquals(ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); } @Test @@ -78,8 +94,7 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(p.getCollectedfrom().get(0).getKey()); assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); - assertEquals( - p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); + assertEquals(p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); } @Test @@ -99,13 +114,10 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); - assertEquals( - o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); - assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); - assertEquals( - o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); - assertEquals( - o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); + assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[0]); + assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[1]); + assertEquals(o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[1]); + assertEquals(o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json index 3a0318ed7b..2baf7c8f17 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json @@ -52,7 +52,7 @@ { "field": "semantics", "type": "not_used", - "value": "providedBy@@@provided by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies" + "value": "providedBy@@@dnet:datasources_organizations_typologies" }, { "field": "provenanceaction", diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json index 71e84954f6..f4c5f97ed1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json @@ -30,7 +30,7 @@ { "field": "openairecompatibility", "type": "string", - "value": "hostedBy@@@collected from a compatible aggregator@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel" + "value": "hostedBy@@@dnet:datasourceCompatibilityLevel" }, { "field": "websiteurl", @@ -219,16 +219,16 @@ { "field": "datasourcetype", "type": "string", - "value": "pubsrepository::journal@@@Journal@@@dnet:datasource_typologies@@@dnet:datasource_typologies" + "value": "pubsrepository::journal@@@dnet:datasource_typologies" }, { "field": "provenanceaction", "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions" + "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" }, { "field": "journal", "type": "string", - "value": "2579-5449@@@2597-6540@@@" + "value": "2579-5449 @@@ 2597-6540 @@@ " } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json index f766246bcc..38657a1e1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json @@ -117,11 +117,11 @@ { "field": "country", "type": "string", - "value": "US@@@US@@@dnet:countries@@@dnet:countries" + "value": "US@@@dnet:countries" }, { "field": "provenanceaction", "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions" + "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json index 855e1a4839..4311086e74 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json @@ -62,11 +62,11 @@ { "field": "semantics", "type": "not_used", - "value": "coordinator@@@coordinator@@@dnet:project_organization_relations@@@dnet:project_organization_relations" + "value": "coordinator@@@dnet:project_organization_relations" }, { "field": "provenanceaction", "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions" + "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json index 7d6ebffbee..d6109cac1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json @@ -167,7 +167,7 @@ { "field": "provenanceaction", "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@Harvested@@@dnet:provenanceActions@@@dnet:provenanceActions" + "value": "sysimport:crosswalk:entityregistry@@@dnet:provenanceActions" }, { "field": "pid", diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java index e79dad8d3e..78d8730806 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java @@ -40,6 +40,7 @@ public class SparkIndexCollectionOnES { final String index = parser.get("index"); final String idPath = parser.get("idPath"); final String type = parser.get("type"); + final String indexHost = parser.get("esHost"); final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); @@ -63,7 +64,8 @@ public class SparkIndexCollectionOnES { inputRdd = sc.textFile(sourcePath); Map esCfg = new HashMap<>(); - esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); + // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); + esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", idPath); esCfg.put("es.batch.write.retry.count", "8"); esCfg.put("es.batch.write.retry.wait", "60s"); diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json index 905b6d5146..f70f7dd799 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json @@ -17,6 +17,13 @@ "paramDescription": "the index name", "paramRequired": true }, + { + "paramName": "h", + "paramLongName": "esHost", + "paramDescription": "the index host name", + "paramRequired": true + }, + { "paramName": "t", diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml index 9fc86e0146..4f5c7bbf6e 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml @@ -16,6 +16,11 @@ index index name + + + indexHost + index host name + @@ -37,6 +42,7 @@ -mt yarn-cluster --sourcePath${workingDirPath}/summary --index${index}_object + --esHost${indexHost} --idPathid --typesummary @@ -57,6 +63,7 @@ -mt yarn-cluster --sourcePath${workingDirPath}/scholix_json --index${index}_scholix + --esHost${indexHost} --idPathidentifier --typescholix diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 6f63893621..efc301573b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -21,6 +21,10 @@ hiveJdbcUrl hive server jdbc url + + hive_timeout + the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds. + @@ -31,6 +35,10 @@ hive.metastore.uris ${hiveMetastoreUris} + + hive.txn.timeout + ${hive_timeout} + diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index cf9753da40..11e5be0b63 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -29,6 +29,7 @@ dhp-blacklist dhp-stats-update dhp-broker-events + dhp-doiboost diff --git a/pom.xml b/pom.xml index e0ee189001..f4b96fefb3 100644 --- a/pom.xml +++ b/pom.xml @@ -193,6 +193,7 @@ net.sf.saxon Saxon-HE 9.9.1-6 + provided