diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 9b03536dd..92a939d19 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 4d40edd99..551f04154 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 5e896e7a5..4bf8ef4b6 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -1,13 +1,11 @@ - + 4.0.0 eu.dnetlib.dhp dhp-code-style - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 041641fcf..44c0763d6 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 51af8d954..388998b94 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index 4a123ceda..fab26b384 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT ../ diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index c6bfff12d..accc06d12 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -6,36 +6,86 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier; public class ModelConstants { public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies"; + public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource"; + public static final String DNET_ACCESS_MODES = "dnet:access_modes"; + public static final String DNET_LANGUAGES = "dnet:languages"; + public static final String DNET_PID_TYPES = "dnet:pid_types"; + public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date"; + public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource"; + public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; + + public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository"; + public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry"; + public static final String USER_CLAIM = "user:claim"; public static final String DATASET_RESULTTYPE_CLASSID = "dataset"; public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication"; public static final String SOFTWARE_RESULTTYPE_CLASSID = "software"; public static final String ORP_RESULTTYPE_CLASSID = "other"; - public static Qualifier PUBLICATION_DEFAULT_RESULTTYPE = new Qualifier(); - public static Qualifier DATASET_DEFAULT_RESULTTYPE = new Qualifier(); - public static Qualifier SOFTWARE_DEFAULT_RESULTTYPE = new Qualifier(); - public static Qualifier ORP_DEFAULT_RESULTTYPE = new Qualifier(); + public static final String RESULT_RESULT = "resultResult"; + public static final String PUBLICATION_DATASET = "publicationDataset"; + public static final String IS_RELATED_TO = "isRelatedTo"; + public static final String SUPPLEMENT = "supplement"; + public static final String IS_SUPPLEMENT_TO = "isSupplementTo"; + public static final String IS_SUPPLEMENTED_BY = "isSupplementedBy"; + public static final String PART = "part"; + public static final String IS_PART_OF = "IsPartOf"; + public static final String HAS_PARTS = "HasParts"; + public static final String RELATIONSHIP = "relationship"; - static { - PUBLICATION_DEFAULT_RESULTTYPE.setClassid(PUBLICATION_RESULTTYPE_CLASSID); - PUBLICATION_DEFAULT_RESULTTYPE.setClassname(PUBLICATION_RESULTTYPE_CLASSID); - PUBLICATION_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES); - PUBLICATION_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES); + public static final String RESULT_PROJECT = "resultProject"; + public static final String OUTCOME = "outcome"; + public static final String IS_PRODUCED_BY = "isProducedBy"; + public static final String PRODUCES = "produces"; - DATASET_DEFAULT_RESULTTYPE.setClassid(DATASET_RESULTTYPE_CLASSID); - DATASET_DEFAULT_RESULTTYPE.setClassname(DATASET_RESULTTYPE_CLASSID); - DATASET_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES); - DATASET_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES); + public static final String DATASOURCE_ORGANIZATION = "datasourceOrganization"; + public static final String PROVISION = "provision"; + public static final String IS_PROVIDED_BY = "isProvidedBy"; + public static final String PROVIDES = "provides"; - SOFTWARE_DEFAULT_RESULTTYPE.setClassid(SOFTWARE_RESULTTYPE_CLASSID); - SOFTWARE_DEFAULT_RESULTTYPE.setClassname(SOFTWARE_RESULTTYPE_CLASSID); - SOFTWARE_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES); - SOFTWARE_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES); + public static final String PROJECT_ORGANIZATION = "projectOrganization"; + public static final String PARTICIPATION = "participation"; + public static final String HAS_PARTICIPANT = "hasParticipant"; + public static final String IS_PARTICIPANT = "isParticipant"; - ORP_DEFAULT_RESULTTYPE.setClassid(ORP_RESULTTYPE_CLASSID); - ORP_DEFAULT_RESULTTYPE.setClassname(ORP_RESULTTYPE_CLASSID); - ORP_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES); - ORP_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES); + public static final String UNKNOWN = "UNKNOWN"; + public static final String NOT_AVAILABLE = "not available"; + + public static final Qualifier PUBLICATION_DEFAULT_RESULTTYPE = qualifier( + PUBLICATION_RESULTTYPE_CLASSID, PUBLICATION_RESULTTYPE_CLASSID, + DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES); + + public static final Qualifier DATASET_DEFAULT_RESULTTYPE = qualifier( + DATASET_RESULTTYPE_CLASSID, DATASET_RESULTTYPE_CLASSID, + DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES); + + public static final Qualifier SOFTWARE_DEFAULT_RESULTTYPE = qualifier( + SOFTWARE_RESULTTYPE_CLASSID, SOFTWARE_RESULTTYPE_CLASSID, + DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES); + + public static final Qualifier ORP_DEFAULT_RESULTTYPE = qualifier( + ORP_RESULTTYPE_CLASSID, ORP_RESULTTYPE_CLASSID, + DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES); + + public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS = qualifier( + SYSIMPORT_CROSSWALK_REPOSITORY, SYSIMPORT_CROSSWALK_REPOSITORY, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + + public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = qualifier( + SYSIMPORT_CROSSWALK_ENTITYREGISTRY, SYSIMPORT_CROSSWALK_ENTITYREGISTRY, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + + private static Qualifier qualifier( + final String classid, + final String classname, + final String schemeid, + final String schemename) { + final Qualifier q = new Qualifier(); + q.setClassid(classid); + q.setClassname(classname); + q.setSchemeid(schemeid); + q.setSchemename(schemename); + return q; } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 4bfc05039..3496492e8 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -7,6 +7,9 @@ import java.util.Objects; public abstract class Oaf implements Serializable { + /** + * The list of datasource id/name pairs providing this relationship. + */ protected List collectedfrom; private DataInfo dataInfo; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 2c282c29e..ad5e9cebe 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -7,16 +7,38 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; +/** + * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to + * graph node identifiers and it is further characterised by the semantic of the link through the fields relType, + * subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, while + * individual relationship types can provide extra information via the properties field. + */ public class Relation extends Oaf { + /** + * Main relationship classifier, values include 'resultResult', 'resultProject', 'resultOrganization', etc. + */ private String relType; + /** + * Further classifies a relationship, values include 'affiliation', 'similarity', 'supplement', etc. + */ private String subRelType; + /** + * Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges, + * 'isMergedIn'. + */ private String relClass; + /** + * The source entity id. + */ private String source; + /** + * The target entity id. + */ private String target; public String getRelType() { diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 22ca7504d..2327b97e2 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -1,11 +1,10 @@ - + 4.0.0 eu.dnetlib.dhp dhp-workflows - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java index 89cb63fab..77be7652e 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java @@ -84,8 +84,11 @@ public class MigrateActionSet { final List sourcePaths = getSourcePaths(sourceNN, isLookUp); log .info( - "paths to process:\n{}", - sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n"))); + "paths to process:\n{}", sourcePaths + .stream() + .map(p -> p.toString()) + .collect(Collectors.joining("\n"))); + for (Path source : sourcePaths) { if (!sourceFS.exists(source)) { @@ -119,9 +122,8 @@ public class MigrateActionSet { } } - props - .setProperty( - TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(","))); + final String targetPathsCsv = targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")); + props.setProperty(TARGET_PATHS, targetPathsCsv); File file = new File(System.getProperty("oozie.action.output.properties")); try (OutputStream os = new FileOutputStream(file)) { diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index 456113c43..90d573ac0 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -1,12 +1,10 @@ package eu.dnetlib.dhp.actionmanager.migration; -import static eu.dnetlib.data.proto.KindProtos.Kind.entity; -import static eu.dnetlib.data.proto.KindProtos.Kind.relation; -import static eu.dnetlib.data.proto.TypeProtos.*; -import static eu.dnetlib.data.proto.TypeProtos.Type.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.io.Serializable; +import java.util.ArrayList; import java.util.List; import java.util.Optional; import java.util.stream.Collectors; @@ -21,10 +19,6 @@ import eu.dnetlib.dhp.schema.oaf.*; public class ProtoConverter implements Serializable { - public static final String UNKNOWN = "UNKNOWN"; - public static final String NOT_AVAILABLE = "not available"; - public static final String DNET_ACCESS_MODES = "dnet:access_modes"; - public static Oaf convert(OafProtos.Oaf oaf) { try { switch (oaf.getKind()) { @@ -64,6 +58,7 @@ public class ProtoConverter implements Serializable { case result: final Result r = convertResult(oaf); r.setInstance(convertInstances(oaf)); + r.setExternalReference(convertExternalRefs(oaf)); return r; case project: return convertProject(oaf); @@ -94,13 +89,44 @@ public class ProtoConverter implements Serializable { i.setHostedby(mapKV(ri.getHostedby())); i.setInstancetype(mapQualifier(ri.getInstancetype())); i.setLicense(mapStringField(ri.getLicense())); - i.setUrl(ri.getUrlList()); + i + .setUrl( + ri.getUrlList() != null ? ri + .getUrlList() + .stream() + .distinct() + .collect(Collectors.toCollection(ArrayList::new)) : null); i.setRefereed(mapStringField(ri.getRefereed())); i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount())); i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency())); return i; } + private static List convertExternalRefs(OafProtos.Oaf oaf) { + ResultProtos.Result r = oaf.getEntity().getResult(); + if (r.getExternalReferenceCount() > 0) { + return r + .getExternalReferenceList() + .stream() + .map(e -> convertExtRef(e)) + .collect(Collectors.toList()); + } + return Lists.newArrayList(); + } + + private static ExternalReference convertExtRef(ResultProtos.Result.ExternalReference e) { + ExternalReference ex = new ExternalReference(); + ex.setUrl(e.getUrl()); + ex.setSitename(e.getSitename()); + ex.setRefidentifier(e.getRefidentifier()); + ex.setQuery(e.getQuery()); + ex.setQualifier(mapQualifier(e.getQualifier())); + ex.setLabel(e.getLabel()); + ex.setDescription(e.getDescription()); + ex.setDataInfo(ex.getDataInfo()); + return ex; + } + private static Organization convertOrganization(OafProtos.Oaf oaf) { final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata(); final Organization org = setOaf(new Organization(), oaf); diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 3e7b1a375..19237a5a8 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java index 9811fb707..861ae5201 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java @@ -1,17 +1,21 @@ package eu.dnetlib.dhp.collection; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.ByteArrayInputStream; import java.nio.charset.StandardCharsets; import java.util.HashMap; import java.util.Map; import java.util.Objects; +import java.util.Optional; import org.apache.commons.cli.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.Text; +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; @@ -23,6 +27,8 @@ import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; @@ -35,6 +41,8 @@ import eu.dnetlib.message.MessageType; public class GenerateNativeStoreSparkJob { + private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class); + public static MetadataRecord parseRecord( final String input, final String xpath, @@ -78,84 +86,90 @@ public class GenerateNativeStoreSparkJob { final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class); final long dateOfCollection = new Long(parser.get("dateOfCollection")); - final SparkSession spark = SparkSession - .builder() - .appName("GenerateNativeStoreSparkJob") - .master(parser.get("master")) - .getOrCreate(); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final Map ongoingMap = new HashMap<>(); final Map reportMap = new HashMap<>(); final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaPairRDD inputRDD = sc - .sequenceFile(parser.get("input"), IntWritable.class, Text.class); + final JavaPairRDD inputRDD = sc + .sequenceFile(parser.get("input"), IntWritable.class, Text.class); - final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems"); + final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems"); + final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords"); - final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords"); + final MessageManager manager = new MessageManager( + parser.get("rabbitHost"), + parser.get("rabbitUser"), + parser.get("rabbitPassword"), + false, + false, + null); - final MessageManager manager = new MessageManager( - parser.get("rabbitHost"), - parser.get("rabbitUser"), - parser.get("rabbitPassword"), - false, - false, - null); + final JavaRDD mappeRDD = inputRDD + .map( + item -> parseRecord( + item._2().toString(), + parser.get("xpath"), + parser.get("encoding"), + provenance, + dateOfCollection, + totalItems, + invalidRecords)) + .filter(Objects::nonNull) + .distinct(); - final JavaRDD mappeRDD = inputRDD - .map( - item -> parseRecord( - item._2().toString(), - parser.get("xpath"), - parser.get("encoding"), - provenance, - dateOfCollection, - totalItems, - invalidRecords)) - .filter(Objects::nonNull) - .distinct(); + ongoingMap.put("ongoing", "0"); + if (!test) { + manager + .sendMessage( + new Message( + parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), + parser.get("rabbitOngoingQueue"), + true, + false); + } - ongoingMap.put("ongoing", "0"); - if (!test) { - manager - .sendMessage( - new Message( - parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), - parser.get("rabbitOngoingQueue"), - true, - false); - } + final Encoder encoder = Encoders.bean(MetadataRecord.class); + final Dataset mdstore = spark.createDataset(mappeRDD.rdd(), encoder); + final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords"); + mdStoreRecords.add(mdstore.count()); + ongoingMap.put("ongoing", "" + totalItems.value()); + if (!test) { + manager + .sendMessage( + new Message( + parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), + parser.get("rabbitOngoingQueue"), + true, + false); + } + mdstore.write().format("parquet").save(parser.get("output")); + reportMap.put("inputItem", "" + totalItems.value()); + reportMap.put("invalidRecords", "" + invalidRecords.value()); + reportMap.put("mdStoreSize", "" + mdStoreRecords.value()); + if (!test) { + manager + .sendMessage( + new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), + parser.get("rabbitReportQueue"), + true, + false); + manager.close(); + } + }); - final Encoder encoder = Encoders.bean(MetadataRecord.class); - final Dataset mdstore = spark.createDataset(mappeRDD.rdd(), encoder); - final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords"); - mdStoreRecords.add(mdstore.count()); - ongoingMap.put("ongoing", "" + totalItems.value()); - if (!test) { - manager - .sendMessage( - new Message( - parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), - parser.get("rabbitOngoingQueue"), - true, - false); - } - mdstore.write().format("parquet").save(parser.get("output")); - reportMap.put("inputItem", "" + totalItems.value()); - reportMap.put("invalidRecords", "" + invalidRecords.value()); - reportMap.put("mdStoreSize", "" + mdStoreRecords.value()); - if (!test) { - manager - .sendMessage( - new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), - parser.get("rabbitReportQueue"), - true, - false); - manager.close(); - } } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java index 5f39717d0..8737d36ef 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java @@ -1,13 +1,17 @@ package eu.dnetlib.dhp.transformation; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.ByteArrayInputStream; import java.util.HashMap; import java.util.Map; import java.util.Objects; +import java.util.Optional; import org.apache.commons.cli.*; import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; @@ -17,8 +21,11 @@ import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper; @@ -29,6 +36,8 @@ import eu.dnetlib.message.MessageType; public class TransformSparkJobNode { + private static final Logger log = LoggerFactory.getLogger(TransformSparkJobNode.class); + public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -40,12 +49,18 @@ public class TransformSparkJobNode { parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("input"); final String outputPath = parser.get("output"); final String workflowId = parser.get("workflowId"); final String trasformationRule = extractXSLTFromTR( Objects.requireNonNull(DHPUtils.decompressString(parser.get("transformationRule")))); - final String master = parser.get("master"); + final String rabbitUser = parser.get("rabbitUser"); final String rabbitPassword = parser.get("rabbitPassword"); final String rabbitHost = parser.get("rabbitHost"); @@ -53,46 +68,48 @@ public class TransformSparkJobNode { final long dateOfCollection = new Long(parser.get("dateOfCollection")); final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); - final SparkSession spark = SparkSession - .builder() - .appName("TransformStoreSparkJob") - .master(master) - .getOrCreate(); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + final Encoder encoder = Encoders.bean(MetadataRecord.class); + final Dataset mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder); + final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems"); + final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems"); + final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems"); + final Map vocabularies = new HashMap<>(); + vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); + final TransformFunction transformFunction = new TransformFunction( + totalItems, + errorItems, + transformedItems, + trasformationRule, + dateOfCollection, + vocabularies); + mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath); + if (rabbitHost != null) { + System.out.println("SEND FINAL REPORT"); + final Map reportMap = new HashMap<>(); + reportMap.put("inputItem", "" + totalItems.value()); + reportMap.put("invalidRecords", "" + errorItems.value()); + reportMap.put("mdStoreSize", "" + transformedItems.value()); + System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap)); + if (!test) { + final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false, + false, + null); + manager + .sendMessage( + new Message(workflowId, "Transform", MessageType.REPORT, reportMap), + rabbitReportQueue, + true, + false); + manager.close(); + } + } + }); - final Encoder encoder = Encoders.bean(MetadataRecord.class); - final Dataset mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder); - final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems"); - final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems"); - final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems"); - final Map vocabularies = new HashMap<>(); - vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); - final TransformFunction transformFunction = new TransformFunction( - totalItems, - errorItems, - transformedItems, - trasformationRule, - dateOfCollection, - vocabularies); - mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath); - if (rabbitHost != null) { - System.out.println("SEND FINAL REPORT"); - final Map reportMap = new HashMap<>(); - reportMap.put("inputItem", "" + totalItems.value()); - reportMap.put("invalidRecords", "" + errorItems.value()); - reportMap.put("mdStoreSize", "" + transformedItems.value()); - System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap)); - if (!test) { - final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false, false, - null); - manager - .sendMessage( - new Message(workflowId, "Transform", MessageType.REPORT, reportMap), - rabbitReportQueue, - true, - false); - manager.close(); - } - } } private static String extractXSLTFromTR(final String tr) throws DocumentException { diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json index 4b4925f27..4a6aec5ee 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json @@ -1,16 +1,86 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"e", "paramLongName":"encoding", "paramDescription": "the encoding of the input record should be JSON or XML", "paramRequired": true}, - {"paramName":"d", "paramLongName":"dateOfCollection", "paramDescription": "the date when the record has been stored", "paramRequired": true}, - {"paramName":"p", "paramLongName":"provenance", "paramDescription": "the infos about the provenance of the collected records", "paramRequired": true}, - {"paramName":"x", "paramLongName":"xpath", "paramDescription": "the xpath to identify the record ifentifier", "paramRequired": true}, - {"paramName":"i", "paramLongName":"input", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"o", "paramLongName":"output", "paramDescription": "the path of the result DataFrame on HDFS", "paramRequired": true}, - {"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true}, - {"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true}, - {"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}, - {"paramName":"t", "paramLongName":"isTest", "paramDescription": "the name of the report queue", "paramRequired": false} + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "e", + "paramLongName": "encoding", + "paramDescription": "the encoding of the input record should be JSON or XML", + "paramRequired": true + }, + { + "paramName": "d", + "paramLongName": "dateOfCollection", + "paramDescription": "the date when the record has been stored", + "paramRequired": true + }, + { + "paramName": "p", + "paramLongName": "provenance", + "paramDescription": "the infos about the provenance of the collected records", + "paramRequired": true + }, + { + "paramName": "x", + "paramLongName": "xpath", + "paramDescription": "the xpath to identify the record identifier", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "input", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "output", + "paramDescription": "the path of the result DataFrame on HDFS", + "paramRequired": true + }, + { + "paramName": "ru", + "paramLongName": "rabbitUser", + "paramDescription": "the user to connect with RabbitMq for messaging", + "paramRequired": true + }, + { + "paramName": "rp", + "paramLongName": "rabbitPassword", + "paramDescription": "the password to connect with RabbitMq for messaging", + "paramRequired": true + }, + { + "paramName": "rh", + "paramLongName": "rabbitHost", + "paramDescription": "the host of the RabbitMq server", + "paramRequired": true + }, + { + "paramName": "ro", + "paramLongName": "rabbitOngoingQueue", + "paramDescription": "the name of the ongoing queue", + "paramRequired": true + }, + { + "paramName": "rr", + "paramLongName": "rabbitReportQueue", + "paramDescription": "the name of the report queue", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workflowId", + "paramDescription": "the identifier of the dnet Workflow", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "isTest", + "paramDescription": "the name of the report queue", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json index 3af21f53f..4bb5fd56a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json @@ -1,16 +1,74 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"d", "paramLongName":"dateOfCollection", "paramDescription": "the date when the record has been stored", "paramRequired": true}, - {"paramName":"i", "paramLongName":"input", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"o", "paramLongName":"output", "paramDescription": "the path of the result DataFrame on HDFS", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}, - {"paramName":"tr", "paramLongName":"transformationRule","paramDescription": "the transformation Rule to apply to the input MDStore", "paramRequired": true}, - {"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true}, - {"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true}, - {"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true}, - {"paramName":"t", "paramLongName":"isTest", "paramDescription": "the name of the report queue", "paramRequired": false} - - + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "d", + "paramLongName": "dateOfCollection", + "paramDescription": "the date when the record has been stored", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "input", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "output", + "paramDescription": "the path of the result DataFrame on HDFS", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workflowId", + "paramDescription": "the identifier of the dnet Workflow", + "paramRequired": true + }, + { + "paramName": "tr", + "paramLongName": "transformationRule", + "paramDescription": "the transformation Rule to apply to the input MDStore", + "paramRequired": true + }, + { + "paramName": "ru", + "paramLongName": "rabbitUser", + "paramDescription": "the user to connect with RabbitMq for messaging", + "paramRequired": true + }, + { + "paramName": "rp", + "paramLongName": "rabbitPassword", + "paramDescription": "the password to connect with RabbitMq for messaging", + "paramRequired": true + }, + { + "paramName": "rh", + "paramLongName": "rabbitHost", + "paramDescription": "the host of the RabbitMq server", + "paramRequired": true + }, + { + "paramName": "ro", + "paramLongName": "rabbitOngoingQueue", + "paramDescription": "the name of the ongoing queue", + "paramRequired": true + }, + { + "paramName": "rr", + "paramLongName": "rabbitReportQueue", + "paramDescription": "the name of the report queue", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "isTest", + "paramDescription": "the name of the report queue", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java index 44364b30a..c3b05f5c9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java @@ -9,65 +9,60 @@ import java.nio.file.Path; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.io.TempDir; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.model.mdstore.Provenance; +import eu.dnetlib.dhp.schema.common.ModelSupport; public class CollectionJobTest { - private Path testDir; + private static SparkSession spark; - @BeforeEach - public void setup() throws IOException { - testDir = Files.createTempDirectory("dhp-collection"); + @BeforeAll + public static void beforeAll() { + SparkConf conf = new SparkConf(); + conf.setAppName(CollectionJobTest.class.getSimpleName()); + conf.setMaster("local"); + spark = SparkSession.builder().config(conf).getOrCreate(); } - @AfterEach - public void teadDown() throws IOException { - FileUtils.deleteDirectory(testDir.toFile()); + @AfterAll + public static void afterAll() { + spark.stop(); } @Test - public void tesCollection() throws Exception { + public void tesCollection(@TempDir Path testDir) throws Exception { final Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix"); + Assertions.assertNotNull(new ObjectMapper().writeValueAsString(provenance)); + GenerateNativeStoreSparkJob .main( new String[] { - "-mt", - "local", - "-w", - "wid", - "-e", - "XML", - "-d", - "" + System.currentTimeMillis(), - "-p", - new ObjectMapper().writeValueAsString(provenance), - "-x", - "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", - "-i", - this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(), - "-o", - testDir.toString() + "/store", - "-t", - "true", - "-ru", - "", - "-rp", - "", - "-rh", - "", - "-ro", - "", - "-rr", - "" + "issm", "true", + "-w", "wid", + "-e", "XML", + "-d", "" + System.currentTimeMillis(), + "-p", new ObjectMapper().writeValueAsString(provenance), + "-x", "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", + "-i", this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(), + "-o", testDir.toString() + "/store", + "-t", "true", + "-ru", "", + "-rp", "", + "-rh", "", + "-ro", "", + "-rr", "" }); - System.out.println(new ObjectMapper().writeValueAsString(provenance)); + + // TODO introduce useful assertions + } @Test @@ -85,9 +80,8 @@ public class CollectionJobTest { null, null); - assert record != null; - System.out.println(record.getId()); - System.out.println(record.getOriginalId()); + assertNotNull(record.getId()); + assertNotNull(record.getOriginalId()); } @Test @@ -112,10 +106,12 @@ public class CollectionJobTest { System.currentTimeMillis(), null, null); - assert record != null; + record.setBody("ciao"); - assert record1 != null; record1.setBody("mondo"); + + assertNotNull(record); + assertNotNull(record1); assertEquals(record, record1); } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 01c9e3103..98c8cf66c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -12,10 +12,14 @@ import java.util.Map; import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.DisplayName; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -23,6 +27,7 @@ import org.junit.jupiter.api.io.TempDir; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.collection.CollectionJobTest; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.transformation.functions.Cleaner; import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; @@ -33,6 +38,21 @@ import net.sf.saxon.s9api.*; @ExtendWith(MockitoExtension.class) public class TransformationJobTest { + private static SparkSession spark; + + @BeforeAll + public static void beforeAll() { + SparkConf conf = new SparkConf(); + conf.setAppName(CollectionJobTest.class.getSimpleName()); + conf.setMaster("local"); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + @Mock private LongAccumulator accumulator; @@ -78,31 +98,21 @@ public class TransformationJobTest { TransformSparkJobNode .main( new String[] { - "-mt", - "local", - "-i", - mdstore_input, - "-o", - mdstore_output, - "-d", - "1", - "-w", - "1", - "-tr", - xslt, - "-t", - "true", - "-ru", - "", - "-rp", - "", - "-rh", - "", - "-ro", - "", - "-rr", - "" + "-issm", "true", + "-i", mdstore_input, + "-o", mdstore_output, + "-d", "1", + "-w", "1", + "-tr", xslt, + "-t", "true", + "-ru", "", + "-rp", "", + "-rh", "", + "-ro", "", + "-rr", "" }); + + // TODO introduce useful assertions } @Test diff --git a/dhp-workflows/dhp-broker-events/README.md b/dhp-workflows/dhp-broker-events/README.md new file mode 100644 index 000000000..bee6e9995 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/README.md @@ -0,0 +1,3 @@ +# dhp-broker-events +dhp-broker-events is a DNET module responsible +of the production of events for the OpenAIRE Broker Service. diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml new file mode 100644 index 000000000..c94c79f2c --- /dev/null +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -0,0 +1,66 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.8-SNAPSHOT + + 4.0.0 + + dhp-broker-events + + + + + commons-io + commons-io + + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + org.apache.spark + spark-hive_2.11 + test + + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + + + com.jayway.jsonpath + json-path + + + dom4j + dom4j + + + jaxen + jaxen + + + + eu.dnetlib + dnet-openaire-broker-common + [1.0.0,2.0.0) + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java new file mode 100644 index 000000000..0512a3813 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java @@ -0,0 +1,104 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.util.Map; + +public class Event { + + private String eventId; + + private String producerId; + + private String topic; + + private String payload; + + private Long creationDate; + + private Long expiryDate; + + private boolean instantMessage; + + private Map map; + + public Event() { + } + + public Event(final String producerId, final String eventId, final String topic, final String payload, + final Long creationDate, final Long expiryDate, + final boolean instantMessage, + final Map map) { + this.producerId = producerId; + this.eventId = eventId; + this.topic = topic; + this.payload = payload; + this.creationDate = creationDate; + this.expiryDate = expiryDate; + this.instantMessage = instantMessage; + this.map = map; + } + + public String getProducerId() { + return this.producerId; + } + + public void setProducerId(final String producerId) { + this.producerId = producerId; + } + + public String getEventId() { + return this.eventId; + } + + public void setEventId(final String eventId) { + this.eventId = eventId; + } + + public String getTopic() { + return this.topic; + } + + public void setTopic(final String topic) { + this.topic = topic; + } + + public String getPayload() { + return this.payload; + } + + public void setPayload(final String payload) { + this.payload = payload; + } + + public Long getCreationDate() { + return this.creationDate; + } + + public void setCreationDate(final Long creationDate) { + this.creationDate = creationDate; + } + + public Long getExpiryDate() { + return this.expiryDate; + } + + public void setExpiryDate(final Long expiryDate) { + this.expiryDate = expiryDate; + } + + public boolean isInstantMessage() { + return this.instantMessage; + } + + public void setInstantMessage(final boolean instantMessage) { + this.instantMessage = instantMessage; + } + + public Map getMap() { + return this.map; + } + + public void setMap(final Map map) { + this.map = map; + } +} 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 new file mode 100644 index 000000000..0694556b2 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -0,0 +1,140 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.text.ParseException; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +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; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class EventFactory { + + private final static String PRODUCER_ID = "OpenAIRE"; + + private static final int TTH_DAYS = 365; + + private final static String[] DATE_PATTERNS = { + "yyyy-MM-dd" + }; + + public static Event newBrokerEvent(final Result source, final Result target, final UpdateInfo updateInfo) { + + final long now = new Date().getTime(); + + final Event res = new Event(); + + final Map map = createMapFromResult(target, source, updateInfo); + + final String payload = createPayload(target, updateInfo); + + final String eventId = calculateEventId( + updateInfo.getTopic(), target.getOriginalId().get(0), updateInfo.getHighlightValueAsString()); + + res.setEventId(eventId); + res.setProducerId(PRODUCER_ID); + res.setPayload(payload); + res.setMap(map); + res.setTopic(updateInfo.getTopic()); + res.setCreationDate(now); + res.setExpiryDate(calculateExpiryDate(now)); + res.setInstantMessage(false); + return res; + } + + private static String createPayload(final Result result, final UpdateInfo updateInfo) { + final OpenAireEventPayload payload = new OpenAireEventPayload(); + // TODO + + updateInfo.compileHighlight(payload); + + return payload.toJSON(); + } + + private static Map createMapFromResult(final Result oaf, final Result source, + final UpdateInfo updateInfo) { + final Map map = new HashMap<>(); + + final List collectedFrom = oaf.getCollectedfrom(); + if (collectedFrom.size() == 1) { + map.put("target_datasource_id", collectedFrom.get(0).getKey()); + map.put("target_datasource_name", collectedFrom.get(0).getValue()); + } + + final List ids = oaf.getOriginalId(); + if (ids.size() > 0) { + map.put("target_publication_id", ids.get(0)); + } + + final List titles = oaf.getTitle(); + if (titles.size() > 0) { + map.put("target_publication_title", titles.get(0)); + } + + final long date = parseDateTolong(oaf.getDateofacceptance().getValue()); + if (date > 0) { + map.put("target_dateofacceptance", date); + } + + final List subjects = oaf.getSubject(); + if (subjects.size() > 0) { + map + .put( + "target_publication_subject_list", + subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList())); + } + + final List authors = oaf.getAuthor(); + if (authors.size() > 0) { + map + .put( + "target_publication_author_list", + authors.stream().map(Author::getFullname).collect(Collectors.toList())); + } + + // PROVENANCE INFO + map.put("trust", updateInfo.getTrust()); + final List sourceCollectedFrom = source.getCollectedfrom(); + if (sourceCollectedFrom.size() == 1) { + map.put("provenance_datasource_id", sourceCollectedFrom.get(0).getKey()); + map.put("provenance_datasource_name", sourceCollectedFrom.get(0).getValue()); + } + map.put("provenance_publication_id_list", source.getOriginalId()); + + return map; + } + + private static String calculateEventId(final String topic, final String publicationId, final String value) { + return "event-" + + DigestUtils.md5Hex(topic).substring(0, 6) + "-" + + DigestUtils.md5Hex(publicationId).substring(0, 8) + "-" + + DigestUtils.md5Hex(value).substring(0, 8); + } + + private static long calculateExpiryDate(final long now) { + return now + TTH_DAYS * 24 * 60 * 60 * 1000; + } + + private static long parseDateTolong(final String date) { + if (StringUtils.isBlank(date)) { + return -1; + } + try { + return DateUtils.parseDate(date, DATE_PATTERNS).getTime(); + } catch (final ParseException e) { + return -1; + } + } + +} 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 new file mode 100644 index 000000000..54d4ef36a --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -0,0 +1,112 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.model.EventFactory; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAbstract; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAuthorOrcid; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingOpenAccess; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPid; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingProject; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPublicationDate; +import eu.dnetlib.dhp.broker.oa.util.EnrichMissingSubject; +import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess; +import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid; +import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class GenerateEventsApplication { + + private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String graphPath = parser.get("graphPath"); + log.info("graphPath: {}", graphPath); + + final String eventsPath = parser.get("eventsPath"); + log.info("eventsPath: {}", eventsPath); + + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, eventsPath); + generateEvents(spark, graphPath, eventsPath); + }); + + } + + private static void removeOutputDir(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void generateEvents(final SparkSession spark, final String graphPath, final String eventsPath) { + // TODO + } + + private List generateEvents(final Result... children) { + final List list = new ArrayList<>(); + + for (final Result source : children) { + for (final Result target : children) { + if (source != target) { + list + .addAll( + findUpdates(source, target) + .stream() + .map(info -> EventFactory.newBrokerEvent(source, target, info)) + .collect(Collectors.toList())); + } + } + } + + return list; + } + + private List> findUpdates(final Result source, final Result target) { + final List> list = new ArrayList<>(); + list.addAll(EnrichMissingAbstract.findUpdates(source, target)); + list.addAll(EnrichMissingAuthorOrcid.findUpdates(source, target)); + list.addAll(EnrichMissingOpenAccess.findUpdates(source, target)); + list.addAll(EnrichMissingPid.findUpdates(source, target)); + list.addAll(EnrichMissingProject.findUpdates(source, target)); + list.addAll(EnrichMissingPublicationDate.findUpdates(source, target)); + list.addAll(EnrichMissingSubject.findUpdates(source, target)); + list.addAll(EnrichMoreOpenAccess.findUpdates(source, target)); + list.addAll(EnrichMorePid.findUpdates(source, target)); + list.addAll(EnrichMoreSubject.findUpdates(source, target)); + return list; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java new file mode 100644 index 000000000..493d1f97c --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingAbstract extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingAbstract(final String highlightValue, final float trust) { + super("ENRICH/MISSING/ABSTRACT", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getAbstracts().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java new file mode 100644 index 000000000..6899c62a3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingAuthorOrcid extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingAuthorOrcid(final String highlightValue, final float trust) { + super("ENRICH/MISSING/AUTHOR/ORCID", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + // TODO + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java new file mode 100644 index 000000000..9464130f3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingOpenAccess extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingOpenAccess(final Instance highlightValue, final float trust) { + super("ENRICH/MISSING/OPENACCESS_VERSION", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getInstances().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue().getUrl(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java new file mode 100644 index 000000000..293d4993f --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPid extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingPid(final Pid highlightValue, final float trust) { + super("ENRICH/MISSING/PID", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getPids().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue().getType() + "::" + getHighlightValue().getValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java new file mode 100644 index 000000000..a22c179a2 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java @@ -0,0 +1,33 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingProject extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingProject(final Project highlightValue, final float trust) { + super("ENRICH/MISSING/PROJECT", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getProjects().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue().getFunder() + "::" + getHighlightValue().getFundingProgram() + + getHighlightValue().getCode(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java new file mode 100644 index 000000000..869dca264 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationDate extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMissingPublicationDate(final String highlightValue, final float trust) { + super("ENRICH/MISSING/PUBLICATION_DATE", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().setPublicationdate(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java new file mode 100644 index 000000000..a2ed5d043 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingSubject extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // MESHEUROPMC + // ARXIV + // JEL + // DDC + // ACM + + return Arrays.asList(); + } + + private EnrichMissingSubject(final String subjectClassification, final String highlightValue, final float trust) { + super("ENRICH/MISSING/SUBJECT/" + subjectClassification, highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getSubjects().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java new file mode 100644 index 000000000..4f1e88d3d --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMoreOpenAccess extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMoreOpenAccess(final Instance highlightValue, final float trust) { + super("ENRICH/MORE/OPENACCESS_VERSION", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getInstances().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue().getUrl(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java new file mode 100644 index 000000000..ecf2cf310 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMorePid extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); + } + + private EnrichMorePid(final Pid highlightValue, final float trust) { + super("ENRICH/MORE/PID", highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getPids().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue().getType() + "::" + getHighlightValue().getValue(); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java new file mode 100644 index 000000000..f29b86292 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.List; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMoreSubject extends UpdateInfo { + + public static List findUpdates(final Result source, final Result target) { + // MESHEUROPMC + // ARXIV + // JEL + // DDC + // ACM + + return Arrays.asList(); + } + + private EnrichMoreSubject(final String subjectClassification, final String highlightValue, final float trust) { + super("ENRICH/MORE/SUBJECT/" + subjectClassification, highlightValue, trust); + } + + @Override + public void compileHighlight(final OpenAireEventPayload payload) { + payload.getHighlight().getSubjects().add(getHighlightValue()); + } + + @Override + public String getHighlightValueAsString() { + return getHighlightValue(); + } + +} 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 new file mode 100644 index 000000000..f7b6b69e9 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import eu.dnetlib.broker.objects.OpenAireEventPayload; + +public abstract class UpdateInfo { + + private final String topic; + + private final T highlightValue; + + private final float trust; + + protected UpdateInfo(final String topic, final T highlightValue, final float trust) { + this.topic = topic; + this.highlightValue = highlightValue; + this.trust = trust; + } + + public T getHighlightValue() { + return highlightValue; + } + + public float getTrust() { + return trust; + } + + public String getTopic() { + return topic; + } + + abstract public void compileHighlight(OpenAireEventPayload payload); + + abstract public String getHighlightValueAsString(); + +} diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index e7f2a926f..de39401b9 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index a44650823..c0503d991 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -137,10 +137,14 @@ public class SparkCreateMergeRels extends AbstractSparkAction { } private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) { + + String entityType = dedupConf.getWf().getEntityType(); + Relation r = new Relation(); r.setSource(source); r.setTarget(target); r.setRelClass(relClass); + r.setRelType(entityType + entityType.substring(0, 1).toUpperCase() + entityType.substring(1)); r.setSubRelType("dedup"); DataInfo info = new DataInfo(); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 34611db8e..516808511 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -86,7 +86,8 @@ public class SparkPropagateRelation extends AbstractSparkAction { mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET)) - .filter(SparkPropagateRelation::containsDedup); + .filter(SparkPropagateRelation::containsDedup) + .distinct(); Dataset updated = processDataset( processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), @@ -94,7 +95,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { FieldType.TARGET, getDeletedFn()); - save(newRels.union(updated), outputRelationPath, SaveMode.Overwrite); + save(newRels.union(updated).union(mergeRels), outputRelationPath, SaveMode.Overwrite); } private static Dataset processDataset( diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 2451947a1..298a248e3 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -75,12 +75,20 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + yarn diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index a0ae7bc3c..7d2d47eac 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -18,6 +18,7 @@ import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -29,6 +30,8 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -420,7 +423,7 @@ public class SparkDedupTest implements Serializable { long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); - assertEquals(826, relations); + assertEquals(5022, relations); // check deletedbyinference final Dataset mergeRels = spark @@ -450,6 +453,25 @@ public class SparkDedupTest implements Serializable { assertEquals(updated, deletedbyinference); } + @Test + @Order(6) + public void testRelations() throws Exception { + testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10); + testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2); + } + + private void testUniqueness(String path, int expected_total, int expected_unique) { + Dataset rel = spark + .read() + .textFile(getClass().getResource(path).getPath()) + .map( + (MapFunction) s -> new ObjectMapper().readValue(s, Relation.class), + Encoders.bean(Relation.class)); + + assertEquals(expected_total, rel.count()); + assertEquals(expected_unique, rel.distinct().count()); + } + @AfterAll public static void finalCleanUp() throws IOException { FileUtils.deleteDirectory(new File(testOutputBasePath)); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/test/relation_1.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/test/relation_1.json new file mode 100644 index 000000000..c0cf8b695 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/test/relation_1.json @@ -0,0 +1,12 @@ 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+{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681629"} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml index e87811cd5..38f630451 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index d013dd1d9..456e4dfa3 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index d25446bbc..9c407d231 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 82f5cbfd0..fd12716b4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -10,6 +10,7 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; 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 java.util.ArrayList; import java.util.Arrays; @@ -24,7 +25,6 @@ import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; -import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -48,6 +48,21 @@ public abstract class AbstractMdRecordToOafMapper { protected final Map code2name; + protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; + protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; + + protected static final Map nsContext = new HashMap<>(); + + static { + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); + } + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); @@ -57,31 +72,27 @@ public abstract class AbstractMdRecordToOafMapper { public List processMdRecord(final String xml) { try { - final Map nsContext = new HashMap<>(); - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper .parseText( - xml - .replaceAll( - "http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); + xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = keyValue( - createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), - doc.valueOf("//oaf:collectedFrom/@name")); + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + + if (collectedFrom == null) { + return null; + } + final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom - : keyValue( - createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), - doc.valueOf("//oaf:hostedBy/@name")); + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + + if (hostedBy == null) { + return null; + } final DataInfo info = prepareDataInfo(doc); final long lastUpdateTimestamp = new Date().getTime(); @@ -92,6 +103,19 @@ public abstract class AbstractMdRecordToOafMapper { } } + private KeyValue getProvenanceDatasource(Document doc, String xpathId, String xpathName) { + final String dsId = doc.valueOf(xpathId); + final String dsName = doc.valueOf(xpathName); + + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { + return null; + } + + return keyValue( + createOpenaireId(10, dsId, true), + dsName); + } + protected List createOafs( final Document doc, final String type, @@ -107,14 +131,14 @@ public abstract class AbstractMdRecordToOafMapper { case "publication": final Publication p = new Publication(); populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); p.setJournal(prepareJournal(doc, info)); oafs.add(p); break; case "dataset": final Dataset d = new Dataset(); populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER); + d.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -127,7 +151,7 @@ public abstract class AbstractMdRecordToOafMapper { case "software": final Software s = new Software(); populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -138,7 +162,7 @@ public abstract class AbstractMdRecordToOafMapper { default: final OtherResearchProduct o = new OtherResearchProduct(); populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -171,33 +195,36 @@ public abstract class AbstractMdRecordToOafMapper { if (StringUtils.isNotBlank(originalId)) { final String projectId = createOpenaireId(40, originalId, true); - final Relation r1 = new Relation(); - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("isProducedBy"); - r1.setSource(docId); - r1.setTarget(projectId); - r1.setCollectedfrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); - - final Relation r2 = new Relation(); - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("produces"); - r2.setSource(projectId); - r2.setTarget(docId); - r2.setCollectedfrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); + res + .add( + getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp)); + res + .add( + getRelation( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp)); } } return res; } + protected Relation getRelation(String source, String target, String relType, String subRelType, String relClass, + KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { + final Relation rel = new Relation(); + rel.setRelType(relType); + rel.setSubRelType(subRelType); + rel.setRelClass(relClass); + rel.setSource(source); + rel.setTarget(target); + rel.setCollectedfrom(Arrays.asList(collectedFrom)); + rel.setDataInfo(info); + rel.setLastupdatetimestamp(lastUpdateTimestamp); + return rel; + } + protected abstract List addOtherResultRels( final Document doc, final KeyValue collectedFrom, @@ -423,7 +450,7 @@ public abstract class AbstractMdRecordToOafMapper { if (n == null) { return dataInfo( - false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); 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 ccc9f8a89..503e4c504 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 @@ -95,6 +95,7 @@ public class GenerateEntitiesApplication { .sequenceFile(sp, Text.class, Text.class) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> convertToListOaf(k._1(), k._2(), code2name)) + .filter(Objects::nonNull) .flatMap(list -> list.iterator())); } 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 f5ac56b78..e96c41066 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 @@ -10,6 +10,7 @@ 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 java.io.Closeable; import java.io.IOException; @@ -31,7 +32,6 @@ import org.apache.commons.logging.LogFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; -import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -55,6 +55,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + public static final String SOURCE_TYPE = "source_type"; + public static final String TARGET_TYPE = "target_type"; + private final DbClient dbClient; private final long lastUpdateTimestamp; @@ -304,9 +307,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); final Relation r1 = new Relation(); - r1.setRelType("datasourceOrganization"); - r1.setSubRelType("provision"); - r1.setRelClass("isProvidedBy"); + r1.setRelType(DATASOURCE_ORGANIZATION); + r1.setSubRelType(PROVISION); + r1.setRelClass(IS_PROVIDED_BY); r1.setSource(dsId); r1.setTarget(orgId); r1.setCollectedfrom(collectedFrom); @@ -314,9 +317,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setLastupdatetimestamp(lastUpdateTimestamp); final Relation r2 = new Relation(); - r2.setRelType("datasourceOrganization"); - r2.setSubRelType("provision"); - r2.setRelClass("provides"); + r2.setRelType(DATASOURCE_ORGANIZATION); + r2.setSubRelType(PROVISION); + r2.setRelClass(PROVIDES); r2.setSource(orgId); r2.setTarget(dsId); r2.setCollectedfrom(collectedFrom); @@ -338,9 +341,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); final Relation r1 = new Relation(); - r1.setRelType("projectOrganization"); - r1.setSubRelType("participation"); - r1.setRelClass("hasParticipant"); + r1.setRelType(PROJECT_ORGANIZATION); + r1.setSubRelType(PARTICIPATION); + r1.setRelClass(HAS_PARTICIPANT); r1.setSource(projectId); r1.setTarget(orgId); r1.setCollectedfrom(collectedFrom); @@ -348,9 +351,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setLastupdatetimestamp(lastUpdateTimestamp); final Relation r2 = new Relation(); - r2.setRelType("projectOrganization"); - r2.setSubRelType("participation"); - r2.setRelClass("isParticipant"); + r2.setRelType(PROJECT_ORGANIZATION); + r2.setSubRelType(PARTICIPATION); + r2.setRelClass(IS_PARTICIPANT); r2.setSource(orgId); r2.setTarget(projectId); r2.setCollectedfrom(collectedFrom); @@ -367,28 +370,28 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final DataInfo info = dataInfo( false, null, false, false, - qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9"); + qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9"); final List collectedFrom = listKeyValues( createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); try { - if (rs.getString("source_type").equals("context")) { + if (rs.getString(SOURCE_TYPE).equals("context")) { final Result r; - if (rs.getString("target_type").equals("dataset")) { + if (rs.getString(TARGET_TYPE).equals("dataset")) { r = new Dataset(); - r.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER); - } else if (rs.getString("target_type").equals("software")) { + r.setResulttype(DATASET_DEFAULT_RESULTTYPE); + } else if (rs.getString(TARGET_TYPE).equals("software")) { r = new Software(); - r.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER); - } else if (rs.getString("target_type").equals("other")) { + r.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + } else if (rs.getString(TARGET_TYPE).equals("other")) { r = new OtherResearchProduct(); - r.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER); + r.setResulttype(ORP_DEFAULT_RESULTTYPE); } else { r = new Publication(); - r.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER); + r.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); } r.setId(createOpenaireId(50, rs.getString("target_id"), false)); r.setLastupdatetimestamp(lastUpdateTimestamp); @@ -398,32 +401,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication return Arrays.asList(r); } else { - final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false); - final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false); + final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false); + final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false); final Relation r1 = new Relation(); final Relation r2 = new Relation(); - if (rs.getString("source_type").equals("project")) { + if (rs.getString(SOURCE_TYPE).equals("project")) { r1.setCollectedfrom(collectedFrom); - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("produces"); + r1.setRelType(RESULT_PROJECT); + r1.setSubRelType(OUTCOME); + r1.setRelClass(PRODUCES); r2.setCollectedfrom(collectedFrom); - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("isProducedBy"); + r2.setRelType(RESULT_PROJECT); + r2.setSubRelType(OUTCOME); + r2.setRelClass(IS_PRODUCED_BY); } else { r1.setCollectedfrom(collectedFrom); - r1.setRelType("resultResult"); - r1.setSubRelType("relationship"); - r1.setRelClass("isRelatedTo"); + r1.setRelType(RESULT_RESULT); + r1.setSubRelType(RELATIONSHIP); + r1.setRelClass(IS_RELATED_TO); r2.setCollectedfrom(collectedFrom); - r2.setRelType("resultResult"); - r2.setSubRelType("relationship"); - r2.setRelClass("isRelatedTo"); + r2.setRelType(RESULT_RESULT); + r2.setSubRelType(RELATIONSHIP); + r2.setRelClass(IS_RELATED_TO); } r1.setSource(sourceId); @@ -457,8 +460,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final Boolean inferred = rs.getBoolean("inferred"); final String trust = rs.getString("trust"); return dataInfo( - deletedbyinference, inferenceprovenance, inferred, false, - MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION, trust); + deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); } private Qualifier prepareQualifierSplitting(final String s) { @@ -514,9 +516,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication if (arr.length == 3) { final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0].trim() : null; final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1].trim() : null; - ; final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2].trim() : null; - ; + if (issn != null || eissn != null || lissn != null) { return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 286656149..891fee57e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -3,27 +3,19 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -52,7 +44,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Qualifier prepareLanguages(final Document doc) { - return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages"); + return prepareQualifier(doc, "//dc:language", DNET_LANGUAGES, DNET_LANGUAGES); } @Override @@ -96,38 +88,43 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) { - final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//dc:identifier")) { - final String url = ((Node) o).getText().trim(); - if (url.startsWith("http")) { - final Instance instance = new Instance(); - instance.setUrl(Arrays.asList(url)); - instance - .setInstancetype( - prepareQualifier( - doc, - "//dr:CobjCategory", - "dnet:publication_resource", - "dnet:publication_resource")); - instance.setCollectedfrom(collectedfrom); - instance.setHostedby(hostedby); - instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); - instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); - instance - .setAccessright( - prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); - instance.setLicense(field(doc.valueOf("//oaf:license"), info)); - instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); - instance - .setProcessingchargeamount( - field(doc.valueOf("//oaf:processingchargeamount"), info)); - instance - .setProcessingchargecurrency( - field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - res.add(instance); - } - } - return res; + + final Instance instance = new Instance(); + instance + .setInstancetype( + prepareQualifier( + doc, + "//dr:CobjCategory", + DNET_PUBLICATION_RESOURCE, + DNET_PUBLICATION_RESOURCE)); + instance.setCollectedfrom(collectedfrom); + instance.setHostedby(hostedby); + instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); + instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); + instance + .setAccessright( + prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); + instance.setLicense(field(doc.valueOf("//oaf:license"), info)); + instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance + .setProcessingchargeamount( + field(doc.valueOf("//oaf:processingchargeamount"), info)); + instance + .setProcessingchargecurrency( + field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + + List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); + instance + .setUrl( + nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .distinct() + .collect(Collectors.toCollection(ArrayList::new))); + + return Lists.newArrayList(instance); } @Override @@ -241,27 +238,16 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final String otherId = createOpenaireId(50, originalId, false); - final Relation r1 = new Relation(); - r1.setRelType("resultResult"); - r1.setSubRelType("publicationDataset"); - r1.setRelClass("isRelatedTo"); - r1.setSource(docId); - r1.setTarget(otherId); - r1.setCollectedfrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); - - final Relation r2 = new Relation(); - r2.setRelType("resultResult"); - r2.setSubRelType("publicationDataset"); - r2.setRelClass("isRelatedTo"); - r2.setSource(otherId); - r2.setTarget(docId); - r2.setCollectedfrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); + res + .add( + getRelation( + docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, + lastUpdateTimestamp)); + res + .add( + getRelation( + otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, + lastUpdateTimestamp)); } } return res; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 93b0eb29c..04984d008 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -4,16 +4,15 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; @@ -27,6 +26,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { + public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; + public OdfToOafMapper(final Map code2name) { super(code2name); } @@ -62,7 +63,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { structuredProperty( ((Node) o).getText(), prepareQualifier( - (Node) o, "./@nameIdentifierScheme", "dnet:pid_types", "dnet:pid_types"), + (Node) o, "./@nameIdentifierScheme", DNET_PID_TYPES, DNET_PID_TYPES), info)); } return res; @@ -76,18 +77,19 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final KeyValue hostedby) { final Instance instance = new Instance(); + final Set url = new HashSet<>(); instance.setUrl(new ArrayList<>()); instance .setInstancetype( prepareQualifier( - doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource")); + doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); instance.setCollectedfrom(collectedfrom); instance.setHostedby(hostedby); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); instance .setAccessright( - prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); + prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); instance.setLicense(field(doc.valueOf("//oaf:license"), info)); instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); @@ -96,17 +98,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { - instance.getUrl().add(((Node) o).getText().trim()); + url.add(((Node) o).getText().trim()); } for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) { - instance.getUrl().add(((Node) o).getText().trim()); + url.add(((Node) o).getText().trim()); } for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) { - instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim()); + url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); } for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) { - instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim()); + url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); } + instance.getUrl().addAll(url); return Arrays.asList(instance); } @@ -131,8 +134,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { ((Node) o).getText(), "UNKNOWN", "UNKNOWN", - "dnet:dataCite_date", - "dnet:dataCite_date", + DNET_DATA_CITE_DATE, + DNET_DATA_CITE_DATE, info)); } } @@ -171,7 +174,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Qualifier prepareLanguages(final Document doc) { - return prepareQualifier(doc, "//datacite:language", "dnet:languages", "dnet:languages"); + return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES, DNET_LANGUAGES); } @Override @@ -292,36 +295,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String otherId = createOpenaireId(50, originalId, false); final String type = ((Node) o).valueOf("@relationType"); - if (type.equals("IsSupplementTo")) { + if (type.equalsIgnoreCase("IsSupplementTo")) { res .add( - prepareOtherResultRel( - collectedFrom, - info, - lastUpdateTimestamp, - docId, - otherId, - "supplement", - "isSupplementTo")); + getRelation( + docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, + lastUpdateTimestamp)); res .add( - prepareOtherResultRel( - collectedFrom, - info, - lastUpdateTimestamp, - otherId, - docId, - "supplement", - "isSupplementedBy")); + getRelation( + otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, + lastUpdateTimestamp)); } else if (type.equals("IsPartOf")) { + res .add( - prepareOtherResultRel( - collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf")); + getRelation( + docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, + lastUpdateTimestamp)); res .add( - prepareOtherResultRel( - collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts")); + getRelation( + otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, + lastUpdateTimestamp)); } else { } } @@ -329,32 +325,12 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { return res; } - private Relation prepareOtherResultRel( - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp, - final String source, - final String target, - final String subRelType, - final String relClass) { - final Relation r = new Relation(); - r.setRelType("resultResult"); - r.setSubRelType(subRelType); - r.setRelClass(relClass); - r.setSource(source); - r.setTarget(target); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - return r; - } - @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { return prepareQualifier( doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", - "dnet:dataCite_resource", - "dnet:dataCite_resource"); + DNET_DATA_CITE_RESOURCE, + DNET_DATA_CITE_RESOURCE); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MigrationConstants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MigrationConstants.java deleted file mode 100644 index 15bff9565..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MigrationConstants.java +++ /dev/null @@ -1,27 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.raw.common; - -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; - -import eu.dnetlib.dhp.schema.oaf.Qualifier; - -public class MigrationConstants { - - public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = qualifier( - "publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); - public static final Qualifier DATASET_RESULTTYPE_QUALIFIER = qualifier( - "dataset", "dataset", - "dnet:result_typologies", "dnet:result_typologies"); - public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier( - "software", "software", - "dnet:result_typologies", "dnet:result_typologies"); - public static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier( - "other", "other", - "dnet:result_typologies", "dnet:result_typologies"); - public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS = qualifier( - "sysimport:crosswalk:repository", "sysimport:crosswalk:repository", - "dnet:provenanceActions", "dnet:provenanceActions"); - public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = qualifier( - "sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", - "dnet:provenanceActions", "dnet:provenanceActions"); -} 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 9f91380ab..fa015499c 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 @@ -115,11 +115,11 @@ eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication - -p${contentPath}/db_claims - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} - -aclaims + --hdfsPath${contentPath}/db_claims + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + --actionclaims @@ -165,10 +165,10 @@ eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication - -p${contentPath}/db_records - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} + --hdfsPath${contentPath}/db_records + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} @@ -180,12 +180,12 @@ eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication - -p${contentPath}/odf_records - -mongourl${mongoURL} - -mongodb${mongoDb} - -fODF - -lstore - -icleaned + --hdfsPath${contentPath}/odf_records + --mongoBaseUrl${mongoURL} + --mongoDb${mongoDb} + --mdFormatODF + --mdLayoutstore + --mdInterpretationcleaned @@ -197,12 +197,12 @@ eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication - -p${contentPath}/oaf_records - -mongourl${mongoURL} - -mongodb${mongoDb} - -fOAF - -lstore - -icleaned + --hdfsPath${contentPath}/oaf_records + --mongoBaseUrl${mongoURL} + --mongoDb${mongoDb} + --mdFormatOAF + --mdLayoutstore + --mdInterpretationcleaned @@ -231,11 +231,11 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -s${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims - -t${workingDir}/entities_claim - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} + --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims + --targetPath${workingDir}/entities_claim + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} @@ -257,8 +257,8 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -s${workingDir}/entities_claim - -g${workingDir}/graph_claims + --sourcePath${workingDir}/entities_claim + --graphRawPath${workingDir}/graph_claims @@ -280,11 +280,11 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -s${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records - -t${workingDir}/entities - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} + --sourcePaths${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records + --targetPath${workingDir}/entities + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} @@ -307,8 +307,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - -s${workingDir}/entities - -g${workingDir}/graph_raw + --sourcePath${workingDir}/entities + --graphRawPath${workingDir}/graph_raw 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 0730f3a1f..05b85a561 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 @@ -1,8 +1,8 @@ - + - migrationPathStep1 - the base path to store hdfs file + contentPath + path location to store (or reuse) content from the aggregator postgresURL @@ -16,6 +16,7 @@ postgresPassword the password postgres + sparkDriverMemory memory for driver process @@ -28,31 +29,81 @@ sparkExecutorCores number of cores used by single executor + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + - + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication + --hdfsPath${contentPath}/db_records + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + - + - ${jobTracker} - ${nameNode} - eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication - -p${migrationPathStep1}/db_records - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication + --hdfsPath${contentPath}/db_claims + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + --actionclaims diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index 03604f431..65218318a 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index baac163d2..291082df7 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index b9746f153..ede7aa7b4 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -113,7 +113,7 @@ public class XmlIndexingJob { }); } - private static String toIndexRecord(Transformer tr, final String record) { + protected static String toIndexRecord(Transformer tr, final String record) { final StreamResult res = new StreamResult(new StringWriter()); try { tr.transform(new StreamSource(new StringReader(record)), res); @@ -135,7 +135,7 @@ public class XmlIndexingJob { * @throws IOException could happen * @throws TransformerException could happen */ - private static String getLayoutTransformer(String format, String fields, String xslt) + protected static String getLayoutTransformer(String format, String fields, String xslt) throws TransformerException { final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 2cff2124e..ce1c71312 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -9,10 +9,7 @@ import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; import javax.xml.transform.*; @@ -47,7 +44,7 @@ import eu.dnetlib.dhp.schema.oaf.Result; public class XmlRecordFactory implements Serializable { - public static final String REL_SUBTYPE_DEDUP = "dedup"; + private static final String REL_SUBTYPE_DEDUP = "dedup"; private final Map accumulators; private final Set specialDatasourceTypes; @@ -100,8 +97,8 @@ public class XmlRecordFactory implements Serializable { final List relations = je .getLinks() .stream() - .filter(t -> !REL_SUBTYPE_DEDUP.equalsIgnoreCase(t.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, contexts)) + .filter(link -> !isDuplicate(link)) + .map(link -> mapRelation(contexts, templateFactory, type, link)) .collect(Collectors.toCollection(ArrayList::new)); final String mainType = ModelSupport.getMainType(type); @@ -936,7 +933,7 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set contexts) { + private List mapFields(Tuple2 link, Set contexts) { final Relation rel = link.getRelation(); final RelatedEntity re = link.getRelatedEntity(); final String targetType = link.getRelatedEntity().getType(); @@ -1040,38 +1037,47 @@ public class XmlRecordFactory implements Serializable { default: throw new IllegalArgumentException("invalid target type: " + targetType); } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); - - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); - } final String accumulatorName = getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); if (accumulators.containsKey(accumulatorName)) { accumulators.get(accumulatorName).add(1); } + return metadata; + } + + private String mapRelation(Set contexts, TemplateFactory templateFactory, EntityType type, Tuple2 link) { + final Relation rel = link.getRelation(); + final String targetType = link.getRelatedEntity().getType(); + final String scheme = ModelSupport.getScheme(type.toString(), targetType); + + if (StringUtils.isBlank(scheme)) { + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", type.toString(), targetType)); + } + final HashSet fields = Sets.newHashSet(mapFields(link, contexts)); return templateFactory .getRel( - targetType, rel.getTarget(), Sets.newHashSet(metadata), rel.getRelClass(), scheme, info); + targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo()); } private List listChildren( final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { - final List children = Lists.newArrayList(); EntityType entityType = EntityType.valueOf(je.getEntity().getType()); - children - .addAll( - je - .getLinks() - .stream() - .filter(link -> REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, null)) - .collect(Collectors.toCollection(ArrayList::new))); + List children = je + .getLinks() + .stream() + .filter(link -> isDuplicate(link)) + .map(link -> { + final String targetType = link.getRelatedEntity().getType(); + final String name = ModelSupport.getMainType(EntityType.valueOf(targetType)); + final HashSet fields = Sets.newHashSet(mapFields(link, null)); + return templateFactory + .getChild(name, link.getRelatedEntity().getId(), Lists.newArrayList(fields)); + }) + .collect(Collectors.toCollection(ArrayList::new)); if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); @@ -1178,6 +1184,10 @@ public class XmlRecordFactory implements Serializable { return children; } + private boolean isDuplicate(Tuple2 link) { + return REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType()); + } + private List listExtraInfo(OafEntity entity) { final List extraInfo = entity.getExtraInfo(); return extraInfo != null diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 923f6de69..298ac7589 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -405,6 +405,9 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.speculation=false + --conf spark.hadoop.mapreduce.map.speculative=false + --conf spark.hadoop.mapreduce.reduce.speculative=false --inputPath${workingDir}/xml --isLookupUrl ${isLookupUrl} diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st index 89f81e16b..1d3cffea0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st @@ -1,3 +1,3 @@ -> - $metadata:{ it | $it$ }$ - \ No newline at end of file +<$name$$if(hasId)$ objidentifier="$id$"$else$$endif$> + $metadata:{$it$}$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java deleted file mode 100644 index 1336a1cf7..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.oa.provision; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.junit.jupiter.api.BeforeEach; - -public class GraphJoinerTest { - - private final ClassLoader cl = getClass().getClassLoader(); - private Path workingDir; - private Path inputDir; - private Path outputDir; - - @BeforeEach - public void before() throws IOException { - workingDir = Files.createTempDirectory("promote_action_set"); - inputDir = workingDir.resolve("input"); - outputDir = workingDir.resolve("output"); - } - - private static void copyFiles(Path source, Path target) throws IOException { - Files - .list(source) - .forEach( - f -> { - try { - if (Files.isDirectory(f)) { - Path subTarget = Files.createDirectories(target.resolve(f.getFileName())); - copyFiles(f, subTarget); - } else { - Files.copy(f, target.resolve(f.getFileName())); - } - } catch (IOException e) { - e.printStackTrace(); - throw new RuntimeException(e); - } - }); - } -} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java new file mode 100644 index 000000000..b1e39c696 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.io.StringReader; +import java.io.StringWriter; +import java.nio.file.Files; +import java.nio.file.Path; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.stream.StreamResult; +import javax.xml.transform.stream.StreamSource; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; + +public class IndexRecordTransformerTest { + + @Test + public void testTrasformRecord() throws IOException, TransformerException { + String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); + String record = IOUtils.toString(getClass().getResourceAsStream("record.xml")); + String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")); + + String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt); + + Transformer tr = SaxonTransformerFactory.newInstance(transformer); + + String a = XmlIndexingJob.toIndexRecord(tr, record); + + System.out.println(a); + + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml new file mode 100644 index 000000000..f74da5d07 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -0,0 +1,166 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl new file mode 100644 index 000000000..d814baa8e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/layoutToRecordTransformer.xsl @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + . + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml new file mode 100644 index 000000000..b617dbea2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml @@ -0,0 +1,750 @@ + +
+ dedup_wf_001::113ca964590682d906a3588d3d6b4838 + 2020-03-15T05:46:43.509Z + 2020-03-15T21:17:13.902Z +
+ + + + + + + + + + oai:pubmedcentral.nih.gov:5657733 + oai:doaj.org/article:f26495a4c1d149099049e1a604fa1256 + 10.1177/0963689717714320 + 28933215 + PMC5657733 + 10.1177/0963689717714320 + Extract Protects Model Neurons + from Traumatic Injury + + Jain, Subhash C. + Citron, Bruce A. + Vijayalakshmi Ravindranath + Saykally, Jessica N. + Keeley, Kristen L. + Haris Hatic + 2017-06-01 + Withania somnifera has been used in traditional medicine for a variety + of neural disorders. Recently, chronic neurodegenerative conditions have been + shown to benefit from treatment with this extract. To evaluate the action of + this extract on traumatically injured neurons, the efficacy of W. somnifera root + extract as a neuroprotective agent was examined in cultured model neurons + exposed to an in vitro injury system designed to mimic mild traumatic brain + injury (TBI). Neuronal health was evaluated by staining with annexin V (an + early, apoptotic feature) and monitoring released lactate dehydrogenase activity + (a terminal cell loss parameter). Potential mechanisms underlying the observed + neuroprotection were examined. Additionally, morphological changes were + monitored following injury and treatment. Although no differences were found in + the expression of the antioxidant transcription factor nuclear factor erythroid + 2-like 2 (Nrf2) or other Nrf2-related downstream components, significant changes + were seen in apoptotic signaling. Treatment with the extract resulted in an + increased length of neurites projecting from the neuronal cell body after + injury. W. somnifera extract treatment also resulted in reduced cell death in + the model neuron TBI system. The cell death factor Bax was involved (its + expression was reduced 2-fold by the treatment) and injury-induced reduction in + neurite lengths and numbers was reversed by the treatment. This all indicates + that W. somnifera root extract was neuroprotective and could have therapeutic + potential to target factors involved in secondary injury and long-term sequelae + of mild TBI. + + Withania + somnifera + R + Cell Biology + neuroprotection + SH-SY5Y + Biomedical Engineering + Transplantation + traumatic + brain injury + neurites + Ayurveda + Medicine + + 2018-11-13 + 2017-6-30 + 2017-7-1 + SAGE Publishing + Cell Transplantation, Vol 26 (2017) + Cell Transplantation + + + Cell Transplantation + + + + + true + false + 0.9 + dedup-similarity-result-levenstein + + + + + wt__________::4de25ac59f6cb729d5716260164bb67c + Indian Institute Of Science + + + nih_________::ba7da8316fd53d04a985bc935e438555 + INDIAN INSTITUTE OF SCIENCE + + + dedup_wf_001::0047940c0207b6a83e79cd803ecf17d1 + + MRC - MRC Laboratory of Molecular Biology + LMB + + + rcuk________::2558c4f3132f6907f7b23c69009f0d87 + INDIAN INSTUTUTE OF SCIENCE + + + dedup_wf_001::d2fdc8e80f8b4365091bcea83f918ccf + + University of Delhi + University of Delhi + + + doiboost____::d5177e3ad00bd9288201b60206a0b5d0 + 2017-6-30 + + + + 10.1177/0963689717714320 + + + od_______267::fb470352a4b33af7c83391c02117c4fc + + SAGE Publications + PMC5657733 + 28933215 + 2017-06-01 + 10.1177/0963689717714320 + + + nih_________::24e81ae35bbcb50c778df1039f912617 + + + nih_________::NIH::VETERANS_AFFAIRS + + Preventing TBI-Induced Chronic Functional Loss with a Neuroprotective + Antioxidant + 1I01RX001520-01A1 + + + wt__________::52e59d4aa1c57bda1ec144f409de83fc + Indian Institute of Science + + + dedup_wf_001::0499ff413ba8e7fa686531725ba12338 + IISc + + Indian Institute of Science + + + wt__________::ba1db3669859a46e72f222052a9a26d8 + University of Delhi + + + dedup_wf_001::17c785347dfb060aa115af824b0c6789 + IISc + + Indian Institute of Science Bangalore + + + scholexplore::16181ec1a2484116e8ed6b3348858fe7 + + 28933215 + + + doajarticles::cac994ec6c322070c41474486eb5c595 + 2017-07-01 + + SAGE Publishing + 10.1177/0963689717714320 + + + r37980778c78::39a72c53d5801325784f728b543a49a1 + + 10.1371/journal.pone.0006628 + 2016-01-01 + Figshare + + + rcuk________::23feba2a5ca7f6b6016bf3a45180da50 + University of Delhi + + + + + + + + + + https://www.ncbi.nlm.nih.gov/pubmed/28933215 + + + + + + + 2017-06-01 + + + http://europepmc.org/articles/PMC5657733 + + + + + + + + + http://journals.sagepub.com/doi/full-xml/10.1177/0963689717714320 + + + http://journals.sagepub.com/doi/pdf/10.1177/0963689717714320 + + + https://academic.microsoft.com/#/detail/2588640354 + + + + + + + 2017-07-01 + + + https://doi.org/10.1177/0963689717714320 + + + https://doaj.org/toc/0963-6897 + + + https://doaj.org/toc/1555-3892 + + + + + + + + + http://dx.doi.org/10.1177/0963689717714320 + + + + + + + + + https://journals.sagepub.com/doi/pdf/10.1177/0963689717714320 + + + + + + + + 1 Bryan-Hancock C Harrison J The global burden of traumatic brain + injury: preliminary results from the Global Burden of Disease Project. + Inj Prev. 2010;16(Suppl 1):A17. + + + 2 Gardner RC Yaffe K Epidemiology of mild traumatic brain injury + and neurodegenerative disease. Mol Cell Neurosci. 2015;66(Pt + B):75–80.25748121 + + + + + 3 Stern RA Riley DO Daneshvar DH Nowinski CJ Cantu RC McKee AC + Long-term consequences of repetitive brain trauma: chronic traumatic + encephalopathy. PM R. 2011;3(10 Suppl 2):S460–S467.22035690 + + + + + 4 Mac Donald CL Johnson AM Cooper D Nelson EC Werner NJ Shimony JS + Snyder AZ Raichle ME Witherow JR Fang R Detection of blast-related + traumatic brain injury in U.S. military personnel. N Engl J Med. + 2011;364(22):2091–2100.21631321 + + + + + 5 Hatic H Kane MJ Saykally JN Citron BA Modulation of transcription + factor Nrf2 in an in vitro model of traumatic brain injury. J + Neurotrauma. 2012;29(6):1188–1196.22201269 + + + + + 6 Saykally JN Rachmany L Hatic H Shaer A Rubovitch V Pick CG Citron + BA The nuclear factor erythroid 2-like 2 activator, + tert-butylhydroquinone, improves cognitive performance in mice after + mild traumatic brain injury. Neuroscience. + 2012;223:305–314.22890082 + + + + + 7 Hall ED Vaishnav RA Mustafa AG Antioxidant therapies for + traumatic brain injury. Neurotherapeutics. + 2010;7(1):51–61.20129497 + + + + + 8 Scartezzini P Speroni E Review on some plants of Indian + traditional medicine with antioxidant activity. J Ethnopharmacol. + 2000;71(1–2):23–43.10904144 + + + + + 9 Mishra LC Singh BB Dagenais S Scientific basis for the + therapeutic use of Withania somnifera (ashwagandha): a review. Altern + Med Rev. 2000;5(4):334–346.10956379 + + + + + 10 Singh RH Exploring larger evidence-base for contemporary + Ayurveda. Int J Ayurveda Res. 2010;1(2):65–66.20814517 + + + + + 11 Alam N Hossain M Mottalib MA Sulaiman SA Gan SH Khalil MI + Methanolic extracts of Withania somnifera leaves, fruits and roots + possess antioxidant properties and antibacterial activities. BMC + Complement Altern Med. 2012;12:175.23039061 + + + + + 12 Gupta GL Rana AC Withania somnifera (ashwagandha): a review. + Pharmacognosy Rev. 2007;1(1):129–136. + + + 13 Durg S Dhadde SB Vandal R Shivakumar BS Charan CS Withania + somnifera (ashwagandha) in neurobehavioural disorders induced by brain + oxidative stress in rodents: a systematic review and meta-analysis. J + Pharm Pharmacol. 2015;67(7):879–899.25828061 + + + + + 14 Kuboyama T Tohda C Komatsu K Effects of ashwagandha (roots of + Withania somnifera) on neurodegenerative diseases. Biol Pharm Bull. + 2014;37(6):892–897.24882401 + + + + + 15 Mirjalili MH Moyano E Bonfill M Cusido RM Palazon J Steroidal + lactones from Withania somnifera, an ancient plant for novel medicine. + Molecules. 2009;14(7):2373–2393.19633611 + + + + + 16 Ven Murthy MR Ranjekar PK Ramassamy C Deshpande M Scientific + basis for the use of Indian ayurvedic medicinal plants in the treatment + of neurodegenerative disorders: ashwagandha. Cent Nerv Syst Agents Med + Chem. 2010;10(3):238–246.20528765 + + + + + 17 Singh RH Narsimhamurthy K Singh G Neuronutrient impact of + Ayurvedic Rasayana therapy in brain aging. Biogerontology. + 2008;9(6):369–374.18931935 + + + + + 18 Kulkarni SK Dhir A Withania somnifera: an Indian ginseng. Prog + Neuropsychopharmacol Biol Psychiatry. + 2008;32(5):1093–1105.17959291 + + + + + 19 Cooley K Szczurko O Perri D Mills EJ Bernhardt B Zhou Q Seely D + Naturopathic care for anxiety: a randomized controlled trial + ISRCTN78958974. PLoS One. 2009;4(8):e6628.19718255 + + + + + 20 Chopra A Lavin P Patwardhan B Chitre D A 32-week randomized, + placebo-controlled clinical evaluation of RA-11, an Ayurvedic drug, on + osteoarthritis of the knees. J Clin Rheumatol. + 2004;10(5):236–245.17043520 + + + + + 21 Chaudhary G Sharma U Jagannathan NR Gupta YK Evaluation of + Withania somnifera in a middle cerebral artery occlusion model of stroke + in rats. Clin Exp Pharmacol Physiol. + 2003;30(5–6):399–404.12859433 + + + + 22 Adams JD Jr Yang J Mishra LC Singh BB Effects of ashwagandha in + a rat model of stroke. Altern Ther Health Med. + 2002;8(5):18–19. + + + 23 Baitharu I Jain V Deep SN Hota KB Hota SK Prasad D Ilavazhagan G + Withania somnifera root extract ameliorates hypobaric hypoxia induced + memory impairment in rats. J Ethnopharmacol. + 2013;145(2):431–441.23211660 + + + + + 24 RajaSankar S Manivasagam T Sankar V Prakash S Muthusamy R + Krishnamurti A Surendran S Withania somnifera root extract improves + catecholamines and physiological abnormalities seen in a Parkinson’s + disease model mouse. J Ethnopharmacol. + 2009;125(3):369–373.19666100 + + + + + 25 Pingali U Pilli R Fatima N Effect of standardized aqueous + extract of Withania somnifera on tests of cognitive and psychomotor + performanc e in healthy human participants. Pharmacognosy Res. + 2014;6(1):12–18.24497737 + + + + + 26 Prabhakaran Y Dinakaran SK Macharala SP Ghosh S Karanam SR + Kanthasamy N Avasarala H Molecular docking studies of withanolides + against Cox-2 enzyme. Pak J Pharm Sci. + 2012;25(3):595–598.22713947 + + + + + 27 Mohan R Hammers HJ Bargagna-Mohan P Zhan XH Herbstritt CJ Ruiz A + Zhang L Hanson AD Conner BP Rougas J Withaferin A is a potent inhibitor + of angiogenesis. Angiogenesis. 2004;7(2):115–122.15516832 + + + + + 28 Friedemann T Otto B Klatschke K Schumacher U Tao Y Leung AK + Efferth T Schroder S Coptis chinensis Franch. exhibits neuroprotective + properties against oxidative stress in human neuroblastoma cells. J + Ethnopharmacol. 2014;155(1):607–615.24929105 + + + + + 29 Hu S Han R Mak S Han Y Protection against + 1-methyl-4-phenylpyridinium ion (MPP+)-induced apoptosis by water + extract of ginseng (Panax ginseng C.A. Meyer) in SH-SY5Y cells. J + Ethnopharmacol. 2011;135(1):34–42.21349320 + + + + + 30 Kane MJ Hatic H Delic V Dennis JS Butler CL Saykally JN Citron + BA Modeling the pathobiology of repetitive traumatic brain injury in + immortalized neuronal cell lines. Brain Res. + 2011;1425:123–131.22018688 + + + + 31 Sehgal N Gupta A Valli RK Joshi SD Mills JT Hamel E Khanna P + Jain SC Thakur SS Ravindranath V Withania somnifera reverses Alzheimer’s + disease pathology by enhancing low-density lipoprotein receptor-related + protein in liver. Proc Natl Acad Sci U S A. + 2012;109(9):3510–3515.22308347 + + + + + 32 Arundine M Aarts M Lau A Tymianski M Vulnerability of central + neurons to secondary insults after in vitro mechanical stretch. J + Neurosci. 2004;24(37):8106–8123.15371512 + + + + + 33 Lau A Arundine M Sun HS Jones M Tymianski M Inhibition of + caspase-mediated apoptosis by peroxynitrite in traumatic brain injury. J + Neurosci. 2006;26(45):11540–11553.17093075 + + + + 34 Weber JT Rzigalinski BA Ellis EF Traumatic injury of cortical + neurons causes changes in intracellular calcium stores and capacitative + calcium influx. J Biol Chem. 2001;276(3):1800–1807.11050103 + + + + 35 Ellis EF McKinney JS Willoughby KA Liang S Povlishock JT A new + model for rapid stretch-induced injury of cells in culture: + characterization of the model using astrocytes. J Neurotrauma. + 1995;12(3):325–339.7473807 + + + + 36 Zhang Y Ba Y Liu C Sun G Ding L Gao S Hao J Yu Z Zhang J Zen K + PGC-1alpha induces apoptosis in human epithelial ovarian cancer cells + through a PPARgamma-dependent pathway. Cell Res. + 2007;17(4):363–373.17372612 + + + + 37 Brooks AR Lelkes PI Rubanyi GM Gene expression profiling of + human aortic endothelial cells exposed to disturbed flow and steady + laminar flow. Physiol Genomics. 2002;9(1):27–41.11948288 + + + + 38 Du Y Villeneuve NF Wang XJ Sun Z Chen W Li J Lou H Wong PK Zhang + DD Oridonin confers protection against arsenic-induced toxicity through + activation of the Nrf2-mediated defensive response. Environ Health + Perspect. 2008;116(9):1154–1161.18795156 + + + + + 39 Pool M Thiemann J Bar-Or A Fournier AE NeuriteTracer: a novel + ImageJ plugin for automated quantification of neurite outgrowth. J + Neurosci Methods. 2008;168(1):134–139.17936365 + + + + + 40 Chen J Wu X Shao B Zhao W Shi W Zhang S Ni L Shen A Increased + expression of TNF receptor-associated factor 6 after rat traumatic brain + injury. Cell Mol Neurobiol. 2011;31(2):269–275.21072581 + + + + 41 Kuboyama T Tohda C Komatsu K Neuritic regeneration and synaptic + reconstruction induced by withanolide A. Br J Pharmacol. + 2005;144(7):961–971.15711595 + + + + + 42 Kuboyama T Tohda C Komatsu K Withanoside IV and its active + metabolite, sominone, attenuate Abeta(25-35)-induced neurodegeneration + Eur J Neurosci. 2006;23(6):1417–1426.16553605 + + + + + 43 Jarrard LE On the role of the hippocampus in learning and memory + in the rat. Behav Neural Biol. 1993;60(1):9–26.8216164 + + + + + 44 Vareed SK Bauer AK Nair KM Liu Y Jayaprakasam B Nair MG + Blood-brain barrier permeability of bioactive withanamides present in + Withania somnifera fruit extract. Phytother Res. + 2014;28(8):1260–1264.24458838 + + + + + + + + diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 0f5e18082..29015f920 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index e2953693f..ba7002cff 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -15,12 +15,12 @@ oozie.action.sharelib.for.spark spark2 - - hive_metastore_uris + + hiveMetastoreUris thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - hive_jdbc_url + hiveJdbcUrl jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9_6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9_6.sql index d4ca2e10e..461f48bfc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9_6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9_6.sql @@ -1,2 +1,2 @@ DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages; -CREATE TABLE ${stats_db_name}.datasource_languages AS SELECT substr(d.id, 4) as id, langs.languages as language from openaire.datasource d LATERAL VIEW explode(d.odlanguages.value) langs as languages; +CREATE TABLE ${stats_db_name}.datasource_languages AS SELECT substr(d.id, 4) as id, langs.languages as language from ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs as languages; 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 19f3316d8..6f6389362 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 @@ -14,11 +14,11 @@ the external stats that should be added since they are not included in the graph database - hive_metastore_uris + hiveMetastoreUris hive server metastore URIs - hive_jdbc_url + hiveJdbcUrl hive server jdbc url @@ -29,7 +29,7 @@ hive.metastore.uris - ${hive_metastore_uris} + ${hiveMetastoreUris} @@ -42,7 +42,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -53,7 +53,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -64,7 +64,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -75,7 +75,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -86,7 +86,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -97,7 +97,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -108,7 +108,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -119,7 +119,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -130,7 +130,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -141,7 +141,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -152,7 +152,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -163,7 +163,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -174,7 +174,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -185,7 +185,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -196,7 +196,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -207,7 +207,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -218,7 +218,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -229,7 +229,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -240,7 +240,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -251,7 +251,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -262,7 +262,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -273,7 +273,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -284,7 +284,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -295,7 +295,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -306,7 +306,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -317,7 +317,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -328,7 +328,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -339,7 +339,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -350,7 +350,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -361,7 +361,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -372,7 +372,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -383,7 +383,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -394,7 +394,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -405,7 +405,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -416,7 +416,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -427,7 +427,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -438,7 +438,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -449,7 +449,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -460,7 +460,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -471,7 +471,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -482,7 +482,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -493,7 +493,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -504,7 +504,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -515,7 +515,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -526,7 +526,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -537,7 +537,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -548,7 +548,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -559,7 +559,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -570,7 +570,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -581,7 +581,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -592,7 +592,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -603,7 +603,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -614,7 +614,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -625,7 +625,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -636,7 +636,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -647,7 +647,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -658,7 +658,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -669,7 +669,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -680,7 +680,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -691,7 +691,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -702,7 +702,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -713,7 +713,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -724,7 +724,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -735,7 +735,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -746,7 +746,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -757,7 +757,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -768,7 +768,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -779,7 +779,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -790,7 +790,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -801,7 +801,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -813,7 +813,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -824,7 +824,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -835,7 +835,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -846,7 +846,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -857,7 +857,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -868,7 +868,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -879,7 +879,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -890,7 +890,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -901,7 +901,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} @@ -912,7 +912,7 @@ - ${hive_jdbc_url} + ${hiveJdbcUrl} stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index bad72a9ef..b305b5b8c 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 6deabae7f..4c37bcf68 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.1.7-SNAPSHOT + 1.1.8-SNAPSHOT ../ @@ -26,7 +26,7 @@ dhp-dedup-scholexplorer dhp-graph-provision-scholexplorer dhp-stats-update - dhp-doiboost + dhp-broker-events diff --git a/pom.xml b/pom.xml index 0c55bff7d..207151906 100644 --- a/pom.xml +++ b/pom.xml @@ -1,376 +1,376 @@ - + - 4.0.0 - eu.dnetlib.dhp - dhp - 1.1.7-SNAPSHOT - pom + 4.0.0 + eu.dnetlib.dhp + dhp + 1.1.8-SNAPSHOT + pom - - - GNU Affero General Public License v3.0 or later - https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText - repo - This program is free software: you can redistribute it and/or modify it under the terms of the - GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the - License, or (at your option) any later version. - - - + + + GNU Affero General Public License v3.0 or later + https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText + repo + This program is free software: you can redistribute it and/or modify it under the terms of the + GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + - - dhp-build - dhp-schemas - dhp-common - dhp-workflows - + + dhp-build + dhp-schemas + dhp-common + dhp-workflows + - - Redmine - https://issue.openaire.research-infrastructures.eu/projects/openaire - + + Redmine + https://issue.openaire.research-infrastructures.eu/projects/openaire + - - jenkins - https://jenkins-dnet.d4science.org/ - + + jenkins + https://jenkins-dnet.d4science.org/ + - - scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git - scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git - https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD - + + scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git + scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git + https://code-repo.d4science.org/D-Net/dnet-hadoop/ + HEAD + - This module is the root descriptor for the dnet-hadoop project + This module is the root descriptor for the dnet-hadoop project - - + + - - - dnet45-releases - D-Net 45 releases - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases - default - - false - - - true - - - - cloudera - Cloudera Repository - https://repository.cloudera.com/artifactory/cloudera-repos - - true - - - false - - - + + + dnet45-releases + D-Net 45 releases + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases + default + + false + + + true + + + + cloudera + Cloudera Repository + https://repository.cloudera.com/artifactory/cloudera-repos + + true + + + false + + + - - - org.junit.jupiter - junit-jupiter - ${junit-jupiter.version} - test - + + + org.junit.jupiter + junit-jupiter + ${junit-jupiter.version} + test + - - org.mockito - mockito-core - ${mockito-core.version} - test - + + org.mockito + mockito-core + ${mockito-core.version} + test + - - org.mockito - mockito-junit-jupiter - ${mockito-core.version} - test - + + org.mockito + mockito-junit-jupiter + ${mockito-core.version} + test + - - - - - - org.apache.hadoop - hadoop-hdfs - ${dhp.hadoop.version} - provided - - - org.apache.hadoop - hadoop-common - ${dhp.hadoop.version} - provided - - - org.apache.hadoop - hadoop-client - ${dhp.hadoop.version} - provided - - - org.apache.hadoop - hadoop-distcp - ${dhp.hadoop.version} - provided - - - org.apache.spark - spark-core_2.11 - ${dhp.spark.version} - provided - - - org.apache.spark - spark-sql_2.11 - ${dhp.spark.version} - provided - - - org.apache.spark - spark-graphx_2.11 - ${dhp.spark.version} - provided - - - org.apache.spark - spark-hive_2.11 - ${dhp.spark.version} - test - - - - org.slf4j - jcl-over-slf4j - 1.7.25 - provided - - - - org.apache.commons - commons-lang3 - ${dhp.commons.lang.version} - - - - com.google.guava - guava - ${dhp.guava.version} - - - commons-codec - commons-codec - 1.9 - + - - commons-io - commons-io - 2.4 - + + + + org.apache.hadoop + hadoop-hdfs + ${dhp.hadoop.version} + provided + + + org.apache.hadoop + hadoop-common + ${dhp.hadoop.version} + provided + + + org.apache.hadoop + hadoop-client + ${dhp.hadoop.version} + provided + + + org.apache.hadoop + hadoop-distcp + ${dhp.hadoop.version} + provided + + + org.apache.spark + spark-core_2.11 + ${dhp.spark.version} + provided + + + org.apache.spark + spark-sql_2.11 + ${dhp.spark.version} + provided + + + org.apache.spark + spark-graphx_2.11 + ${dhp.spark.version} + provided + + + org.apache.spark + spark-hive_2.11 + ${dhp.spark.version} + test + - - commons-cli - commons-cli - 1.2 - provided - + + org.slf4j + jcl-over-slf4j + 1.7.25 + provided + - - net.sf.saxon - Saxon-HE - 9.9.1-6 - + + org.apache.commons + commons-lang3 + ${dhp.commons.lang.version} + - - dom4j - dom4j - 1.6.1 - + + com.google.guava + guava + ${dhp.guava.version} + - - xml-apis - xml-apis - 1.4.01 - - - jaxen - jaxen - 1.1.6 - + + commons-codec + commons-codec + 1.9 + - - com.mycila.xmltool - xmltool - 3.3 - + + commons-io + commons-io + 2.4 + - - org.apache.solr - solr-solrj - 7.5.0 - - - * - * - - - - - com.lucidworks.spark - spark-solr - 3.6.0 - - - * - * - - - + + commons-cli + commons-cli + 1.2 + provided + - - org.apache.httpcomponents - httpclient - 4.5.3 - - - org.apache.httpcomponents - httpmime - 4.5.3 - - - org.noggit - noggit - 0.8 - - - org.apache.zookeeper - zookeeper - 3.4.11 - + + net.sf.saxon + Saxon-HE + 9.9.1-6 + - - net.schmizz - sshj - 0.10.0 - test - + + dom4j + dom4j + 1.6.1 + - - com.fasterxml.jackson.core - jackson-core - ${dhp.jackson.version} - provided - + + xml-apis + xml-apis + 1.4.01 + - - com.fasterxml.jackson.core - jackson-annotations - ${dhp.jackson.version} - provided - - - com.fasterxml.jackson.core - jackson-databind - ${dhp.jackson.version} - provided - + + jaxen + jaxen + 1.1.6 + - - eu.dnetlib - dnet-actionmanager-common - 6.0.5 - - - org.apache.hadoop - hadoop-common - - - - - eu.dnetlib - dnet-actionmanager-api - [4.0.1,5.0.0) - + + com.mycila.xmltool + xmltool + 3.3 + - - eu.dnetlib - dnet-openaire-data-protos - 3.9.8-proto250 - - - eu.dnetlib - dnet-pace-core - 4.0.1 - - - eu.dnetlib - cnr-rmi-api - [2.0.0,3.0.0) - + + org.apache.solr + solr-solrj + 7.5.0 + + + * + * + + + + + com.lucidworks.spark + spark-solr + 3.6.0 + + + * + * + + + - - org.apache.cxf - cxf-rt-transports-http - 3.1.5 - - - javax.persistence - javax.persistence-api - 2.2 - provided - + + org.apache.httpcomponents + httpclient + 4.5.3 + + + org.apache.httpcomponents + httpmime + 4.5.3 + + + org.noggit + noggit + 0.8 + + + org.apache.zookeeper + zookeeper + 3.4.11 + - - com.rabbitmq - amqp-client - 5.6.0 - - - com.jayway.jsonpath - json-path - 2.4.0 - - - com.arakelian - java-jq - 0.10.1 - - - edu.cmu - secondstring - 1.0.0 - - - org.mongodb - mongo-java-driver - ${mongodb.driver.version} - - - org.postgresql - postgresql - 42.2.10 - + + net.schmizz + sshj + 0.10.0 + test + - - org.antlr - stringtemplate - 4.0 - + + com.fasterxml.jackson.core + jackson-core + ${dhp.jackson.version} + provided + + + + com.fasterxml.jackson.core + jackson-annotations + ${dhp.jackson.version} + provided + + + com.fasterxml.jackson.core + jackson-databind + ${dhp.jackson.version} + provided + + + + eu.dnetlib + dnet-actionmanager-common + 6.0.5 + + + org.apache.hadoop + hadoop-common + + + + + eu.dnetlib + dnet-actionmanager-api + [4.0.1,5.0.0) + + + + eu.dnetlib + dnet-openaire-data-protos + 3.9.8-proto250 + + + eu.dnetlib + dnet-pace-core + 4.0.1 + + + eu.dnetlib + cnr-rmi-api + [2.0.0,3.0.0) + + + + org.apache.cxf + cxf-rt-transports-http + 3.1.5 + + + javax.persistence + javax.persistence-api + 2.2 + provided + + + + com.rabbitmq + amqp-client + 5.6.0 + + + com.jayway.jsonpath + json-path + 2.4.0 + + + com.arakelian + java-jq + 0.10.1 + + + edu.cmu + secondstring + 1.0.0 + + + org.mongodb + mongo-java-driver + ${mongodb.driver.version} + + + org.postgresql + postgresql + 42.2.10 + + + + org.antlr + stringtemplate + 4.0 + com.ximpleware @@ -386,237 +386,237 @@ - org.apache.oozie - oozie-client - ${dhp.oozie.version} - provided - - - - slf4j-simple - org.slf4j - - - - - + org.apache.oozie + oozie-client + ${dhp.oozie.version} + provided + + + + slf4j-simple + org.slf4j + + + + + - - target - target/classes - ${project.artifactId}-${project.version} - target/test-classes - - + + target + target/classes + ${project.artifactId}-${project.version} + target/test-classes + + - - org.apache.maven.plugins - maven-project-info-reports-plugin - 3.0.0 - - - org.apache.maven.plugins - maven-site-plugin - 3.7.1 - + + org.apache.maven.plugins + maven-project-info-reports-plugin + 3.0.0 + + + org.apache.maven.plugins + maven-site-plugin + 3.7.1 + - - org.apache.maven.plugins - maven-compiler-plugin - ${maven.compiler.plugin.version} - - 1.8 - 1.8 - ${project.build.sourceEncoding} - - + + org.apache.maven.plugins + maven-compiler-plugin + ${maven.compiler.plugin.version} + + 1.8 + 1.8 + ${project.build.sourceEncoding} + + - - org.apache.maven.plugins - maven-jar-plugin - 3.0.2 - + + org.apache.maven.plugins + maven-jar-plugin + 3.0.2 + - - org.apache.maven.plugins - maven-source-plugin - 3.0.1 - - - attach-sources - verify - - jar-no-fork - - - - + + org.apache.maven.plugins + maven-source-plugin + 3.0.1 + + + attach-sources + verify + + jar-no-fork + + + + - - org.apache.maven.plugins - maven-surefire-plugin - 3.0.0-M4 - - true - - - - org.apache.maven.plugins - maven-javadoc-plugin - 3.2.0 - - true - none - - - - org.apache.maven.plugins - maven-dependency-plugin - 3.0.0 - + + org.apache.maven.plugins + maven-surefire-plugin + 3.0.0-M4 + + true + + + + org.apache.maven.plugins + maven-javadoc-plugin + 3.2.0 + + true + none + + + + org.apache.maven.plugins + maven-dependency-plugin + 3.0.0 + - - net.revelc.code.formatter - formatter-maven-plugin - 2.11.0 - - - eu.dnetlib.dhp - dhp-code-style - ${project.version} - - - - - - - - org.apache.maven.plugins - maven-site-plugin - - - org.apache.maven.plugins - maven-project-info-reports-plugin - - - net.revelc.code.formatter - formatter-maven-plugin - - - - format - - - eclipse/formatter_dnet.xml - - - - - - net.revelc.code - impsort-maven-plugin - 1.4.1 - - java.,javax.,org.,com. - java,* - - **/thrift/*.java - - - - - sort-imports - - sort - - - - - - org.apache.maven.plugins - maven-release-plugin - 2.5.3 - - - org.jacoco - jacoco-maven-plugin - 0.7.9 - - - **/schemas/* - **/com/cloudera/**/* - **/org/apache/avro/io/**/* - - - - - default-prepare-agent - - prepare-agent - - - - default-report - prepare-package - - report - - - - + + net.revelc.code.formatter + formatter-maven-plugin + 2.11.0 + + + eu.dnetlib.dhp + dhp-code-style + ${project.version} + + + + + + + + org.apache.maven.plugins + maven-site-plugin + + + org.apache.maven.plugins + maven-project-info-reports-plugin + + + net.revelc.code.formatter + formatter-maven-plugin + + + + format + + + eclipse/formatter_dnet.xml + + + + + + net.revelc.code + impsort-maven-plugin + 1.4.1 + + java.,javax.,org.,com. + java,* + + **/thrift/*.java + + + + + sort-imports + + sort + + + + + + org.apache.maven.plugins + maven-release-plugin + 2.5.3 + + + org.jacoco + jacoco-maven-plugin + 0.7.9 + + + **/schemas/* + **/com/cloudera/**/* + **/org/apache/avro/io/**/* + + + + + default-prepare-agent + + prepare-agent + + + + default-report + prepare-package + + report + + + + - + - - - org.apache.maven.wagon - wagon-ssh - 2.10 - - - - - - dnet45-snapshots - DNet45 Snapshots - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots - default - - - dnet45-releases - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases - - - - - - org.apache.maven.plugins - maven-javadoc-plugin - - true - none - - - - + + + org.apache.maven.wagon + wagon-ssh + 2.10 + + + + + + dnet45-snapshots + DNet45 Snapshots + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots + default + + + dnet45-releases + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases + + + + + + org.apache.maven.plugins + maven-javadoc-plugin + + true + none + + + + - - UTF-8 - UTF-8 - 3.6.0 - 2.22.2 - 2.0.1 - cdh5.9.2 - 2.6.0-${dhp.cdh.version} - 4.1.0-${dhp.cdh.version} - 2.4.0.cloudera2 - 2.9.6 - 3.5 - 11.0.2 - 2.11.12 - 5.6.1 - 3.3.3 - 3.4.2 - [2.12,3.0) - + + UTF-8 + UTF-8 + 3.6.0 + 2.22.2 + 2.0.1 + cdh5.9.2 + 2.6.0-${dhp.cdh.version} + 4.1.0-${dhp.cdh.version} + 2.4.0.cloudera2 + 2.9.6 + 3.5 + 11.0.2 + 2.11.12 + 5.6.1 + 3.3.3 + 3.4.2 + [2.12,3.0) +