From d88fe0ac845602eaa929a7454d36864bd3c88f44 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 19 Jun 2020 15:24:30 +0200 Subject: [PATCH 01/16] join methods --- .../broker/oa/GenerateEventsApplication.java | 96 +++++++++++++++---- .../withRels/RelatedEntityFactory.java | 34 ------- 2 files changed, 75 insertions(+), 55 deletions(-) delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 62171ac61..f15d918c9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -28,12 +28,17 @@ import eu.dnetlib.dhp.broker.oa.util.EventGroup; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OpenaireBrokerResultAggregator; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedEntityFactory; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; @@ -84,11 +89,8 @@ public class GenerateEventsApplication { removeOutputDir(spark, eventsPath); // TODO REMOVE THIS - final Dataset projects = readPath(spark, graphPath + "/project", Project.class); - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) - .cache(); - relatedEntities(projects, rels, RelatedProject.class) + + relatedProjects(spark, graphPath) .write() .mode(SaveMode.Overwrite) .json(eventsPath); @@ -144,7 +146,6 @@ public class GenerateEventsApplication { final String graphPath, final Class sourceClass) { - final Dataset projects = readPath(spark, graphPath + "/project", Project.class); // final Dataset datasets = readPath( // spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); // final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); @@ -160,25 +161,78 @@ public class GenerateEventsApplication { .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OpenaireBrokerResult.class)); // TODO UNCOMMENT THIS - final Dataset r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); - // final Dataset r2 = join(r1, rels, relatedEntities(softwares, rels, - // RelatedSoftware.class)); - // final Dataset r3 = join(r2, rels, relatedEntities(datasets, rels, - // RelatedDataset.class)); - // final Dataset r4 = join(r3, rels, relatedEntities(publications, rels, - // RelatedPublication.class));; + final Dataset r1 = join(r0, rels, relatedProjects(spark, graphPath)); + // final Dataset r2 = join(r1, rels, relatedDataset(spark, graphPath)); + // final Dataset r3 = join(r2, rels, relatedPublications(spark, graphPath)); + // final Dataset r4 = join(r3, rels, relatedSoftwares(spark, graphPath)); - return r0; // TODO it should be r4 + return r1; // TODO it should be r4 } - private static Dataset relatedEntities(final Dataset targets, - final Dataset rels, - final Class clazz) { + private static Dataset relatedProjects(final SparkSession spark, final String graphPath) { + + final Dataset projects = readPath(spark, graphPath + "/project", Project.class); + + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)); + return rels - .joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner") + .joinWith(projects, projects.col("id").equalTo(rels.col("target")), "inner") .map( - t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), - Encoders.bean(clazz)); + t -> new RelatedProject( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafProjectToBrokerProject(t._2)), + Encoders.bean(RelatedProject.class)); + } + + private static Dataset relatedDataset(final SparkSession spark, final String graphPath) { + + final Dataset datasets = readPath( + spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); + + return rels + .joinWith(datasets, datasets.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedDataset( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafDatasetToBrokerDataset(t._2)), + Encoders.bean(RelatedDataset.class)); + } + + private static Dataset relatedSoftwares(final SparkSession spark, final String graphPath) { + + final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); + + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); + + return rels + .joinWith(softwares, softwares.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedSoftware( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafSoftwareToBrokerSoftware(t._2)), + Encoders.bean(RelatedSoftware.class)); + } + + private static Dataset relatedPublications(final SparkSession spark, final String graphPath) { + + final Dataset pubs = readPath(spark, graphPath + "/publication", Publication.class); + + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); + + return rels + .joinWith(pubs, pubs.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedPublication( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafPublicationToBrokerPublication(t._2)), + Encoders.bean(RelatedPublication.class)); } private static Dataset join(final Dataset sources, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java deleted file mode 100644 index c60d4f141..000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; - -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; - -public class RelatedEntityFactory { - - @SuppressWarnings("unchecked") - public static RT newRelatedEntity(final String sourceId, - final String relType, - final T target, - final Class clazz) { - - if (clazz == RelatedProject.class) { - return (RT) new RelatedProject(sourceId, relType, - ConversionUtils.oafProjectToBrokerProject((Project) target)); - } else if (clazz == RelatedSoftware.class) { - return (RT) new RelatedSoftware(sourceId, relType, - ConversionUtils.oafSoftwareToBrokerSoftware((Software) target)); - } else if (clazz == RelatedDataset.class) { - return (RT) new RelatedDataset(sourceId, relType, - ConversionUtils.oafDatasetToBrokerDataset((Dataset) target)); - } else if (clazz == RelatedPublication.class) { - return (RT) new RelatedPublication(sourceId, relType, - ConversionUtils.oafPublicationToBrokerPublication((Publication) target)); - } else { - return null; - } - } -} From 16c7a184359a66adc89d2431e2a653653d091ddc Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 22 Jun 2020 08:51:31 +0200 Subject: [PATCH 02/16] refactoring --- dhp-workflows/dhp-broker-events/pom.xml | 2 +- .../dhp/broker/model/EventFactory.java | 6 +- .../broker/oa/GenerateEventsApplication.java | 143 +++--------------- .../broker/oa/GenerateRelatedDatasets.java | 73 +++++++++ .../broker/oa/GenerateRelatedProjects.java | 79 ++++++++++ .../oa/GenerateRelatedPublications.java | 78 ++++++++++ .../broker/oa/GenerateRelatedSoftwares.java | 76 ++++++++++ .../broker/oa/GenerateSimpleEntitities.java | 85 +++++++++++ .../dhp/broker/oa/matchers/UpdateMatcher.java | 16 +- .../AbstractEnrichMissingDataset.java | 13 +- .../relatedProjects/EnrichMissingProject.java | 8 +- .../relatedProjects/EnrichMoreProject.java | 12 +- .../AbstractEnrichMissingPublication.java | 14 +- .../EnrichMissingSoftware.java | 11 +- .../relatedSoftware/EnrichMoreSoftware.java | 14 +- .../simple/EnrichMissingAbstract.java | 4 +- .../simple/EnrichMissingAuthorOrcid.java | 12 +- .../simple/EnrichMissingOpenAccess.java | 14 +- .../oa/matchers/simple/EnrichMissingPid.java | 10 +- .../simple/EnrichMissingPublicationDate.java | 6 +- .../matchers/simple/EnrichMissingSubject.java | 12 +- .../matchers/simple/EnrichMoreOpenAccess.java | 12 +- .../oa/matchers/simple/EnrichMorePid.java | 12 +- .../oa/matchers/simple/EnrichMoreSubject.java | 12 +- .../dhp/broker/oa/util/ClusterUtils.java | 31 ++++ .../dhp/broker/oa/util/ConversionUtils.java | 60 +++++--- .../dhp/broker/oa/util/EventFinder.java | 4 +- .../dhp/broker/oa/util/UpdateInfo.java | 38 ++--- .../aggregators/simple/ResultAggregator.java | 6 +- .../util/aggregators/simple/ResultGroup.java | 8 +- ...java => OaBrokerMainEntityAggregator.java} | 26 ++-- .../aggregators/withRels/RelatedDataset.java | 10 +- .../aggregators/withRels/RelatedProject.java | 10 +- .../withRels/RelatedPublication.java | 11 +- .../aggregators/withRels/RelatedSoftware.java | 10 +- .../dhp/broker/oa/generate_relations.json | 14 ++ .../broker/oa/generate_simple_entities.json | 14 ++ 37 files changed, 669 insertions(+), 297 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/{OpenaireBrokerResultAggregator.java => OaBrokerMainEntityAggregator.java} (59%) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index f943ac93a..8d7d3b88c 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -53,7 +53,7 @@ eu.dnetlib dnet-openaire-broker-common - [3.0.2,4.0.0) + [3.0.3,4.0.0) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java index bf4f62d24..6e38f7448 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -11,7 +11,7 @@ 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.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; public class EventFactory { @@ -49,8 +49,8 @@ public class EventFactory { private static Map createMapFromResult(final UpdateInfo updateInfo) { final Map map = new HashMap<>(); - final OpenaireBrokerResult source = updateInfo.getSource(); - final OpenaireBrokerResult target = updateInfo.getTarget(); + final OaBrokerMainEntity source = updateInfo.getSource(); + final OaBrokerMainEntity target = updateInfo.getTarget(); map.put("target_datasource_id", target.getCollectedFromId()); map.put("target_datasource_name", target.getCollectedFromName()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index f15d918c9..db5992010 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -18,27 +18,20 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.EventFinder; import eu.dnetlib.dhp.broker.oa.util.EventGroup; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OpenaireBrokerResultAggregator; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OaBrokerMainEntityAggregator; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; @@ -48,8 +41,6 @@ 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 @@ -86,11 +77,11 @@ public class GenerateEventsApplication { runWithSparkSession(conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, eventsPath); + ClusterUtils.removeDir(spark, eventsPath); // TODO REMOVE THIS - relatedProjects(spark, graphPath) + expandResultsWithRelations(spark, graphPath, Publication.class) .write() .mode(SaveMode.Overwrite) .json(eventsPath); @@ -110,28 +101,25 @@ public class GenerateEventsApplication { } - private static void removeOutputDir(final SparkSession spark, final String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - private static Dataset generateEvents( final SparkSession spark, final String graphPath, final Class sourceClass, final DedupConfig dedupConfig) { - final Dataset results = expandResultsWithRelations(spark, graphPath, sourceClass); + final Dataset results = expandResultsWithRelations(spark, graphPath, sourceClass); - final Dataset mergedRels = readPath(spark, graphPath + "/relation", Relation.class) + final Dataset mergedRels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - final TypedColumn, ResultGroup> aggr = new ResultAggregator() + final TypedColumn, ResultGroup> aggr = new ResultAggregator() .toColumn(); return results .joinWith(mergedRels, results.col("openaireId").equalTo(mergedRels.col("source")), "inner") .groupByKey( - (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) + (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(aggr) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.bean(ResultGroup.class)) .filter(rg -> rg.getData().size() > 1) @@ -141,7 +129,7 @@ public class GenerateEventsApplication { .flatMap(group -> group.getData().iterator(), Encoders.bean(Event.class)); } - private static Dataset expandResultsWithRelations( + private static Dataset expandResultsWithRelations( final SparkSession spark, final String graphPath, final Class sourceClass) { @@ -151,116 +139,35 @@ public class GenerateEventsApplication { // final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); // final Dataset publications = readPath(spark, graphPath + "/publication", Publication.class); - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) - .cache(); - - final Dataset r0 = readPath( - spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) - .filter(r -> r.getDataInfo().getDeletedbyinference()) - .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OpenaireBrokerResult.class)); + final Dataset r0 = ClusterUtils + .readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) + .filter(r -> r.getDataInfo().getDeletedbyinference()) + .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OaBrokerMainEntity.class)); // TODO UNCOMMENT THIS - final Dataset r1 = join(r0, rels, relatedProjects(spark, graphPath)); - // final Dataset r2 = join(r1, rels, relatedDataset(spark, graphPath)); - // final Dataset r3 = join(r2, rels, relatedPublications(spark, graphPath)); - // final Dataset r4 = join(r3, rels, relatedSoftwares(spark, graphPath)); + // final Dataset r1 = join(r0, relatedProjects(spark, graphPath)); + // final Dataset r2 = join(r1, relatedDataset(spark, graphPath)); + // final Dataset r3 = join(r2, relatedPublications(spark, graphPath)); + // final Dataset r4 = join(r3, relatedSoftwares(spark, graphPath)); - return r1; // TODO it should be r4 + return r0; // TODO it should be r4 } - private static Dataset relatedProjects(final SparkSession spark, final String graphPath) { - - final Dataset projects = readPath(spark, graphPath + "/project", Project.class); - - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)); - - return rels - .joinWith(projects, projects.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedProject( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafProjectToBrokerProject(t._2)), - Encoders.bean(RelatedProject.class)); - } - - private static Dataset relatedDataset(final SparkSession spark, final String graphPath) { - - final Dataset datasets = readPath( - spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); - - return rels - .joinWith(datasets, datasets.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedDataset( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafDatasetToBrokerDataset(t._2)), - Encoders.bean(RelatedDataset.class)); - } - - private static Dataset relatedSoftwares(final SparkSession spark, final String graphPath) { - - final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); - - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); - - return rels - .joinWith(softwares, softwares.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedSoftware( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafSoftwareToBrokerSoftware(t._2)), - Encoders.bean(RelatedSoftware.class)); - } - - private static Dataset relatedPublications(final SparkSession spark, final String graphPath) { - - final Dataset pubs = readPath(spark, graphPath + "/publication", Publication.class); - - final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class); - - return rels - .joinWith(pubs, pubs.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedPublication( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafPublicationToBrokerPublication(t._2)), - Encoders.bean(RelatedPublication.class)); - } - - private static Dataset join(final Dataset sources, - final Dataset rels, + private static Dataset join(final Dataset sources, final Dataset typedRels) { - final TypedColumn, OpenaireBrokerResult> aggr = new OpenaireBrokerResultAggregator() + final TypedColumn, OaBrokerMainEntity> aggr = new OaBrokerMainEntityAggregator() .toColumn(); return sources - .joinWith(typedRels, sources.col("openaireId").equalTo(rels.col("source")), "left_outer") + .joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer") .groupByKey( - (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) + (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) .agg(aggr) - .map(t -> t._2, Encoders.bean(OpenaireBrokerResult.class)); + .map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class)); } - public static Dataset readPath( - final SparkSession spark, - final String inputPath, - final Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java new file mode 100644 index 000000000..4a10fbabf --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java @@ -0,0 +1,73 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class GenerateRelatedDatasets { + + private static final Logger log = LoggerFactory.getLogger(GenerateRelatedDatasets.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenerateRelatedDatasets.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.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 relsPath = parser.get("relsPath"); + log.info("relsPath: {}", relsPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, relsPath); + + final Dataset datasets = ClusterUtils + .readPath(spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + + final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + + rels + .joinWith(datasets, datasets.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedDataset( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafDatasetToBrokerDataset(t._2)), + Encoders.bean(RelatedDataset.class)) + .write() + .mode(SaveMode.Overwrite) + .json(relsPath); + + }); + + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java new file mode 100644 index 000000000..59ed388e7 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java @@ -0,0 +1,79 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +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.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class GenerateRelatedProjects { + + private static final Logger log = LoggerFactory.getLogger(GenerateRelatedProjects.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( + GenerateRelatedProjects.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.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 relsPath = parser.get("relsPath"); + log.info("relsPath: {}", relsPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, relsPath); + + final Dataset projects = ClusterUtils.readPath(spark, graphPath + "/project", Project.class); + + final Dataset rels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)); + + rels + .joinWith(projects, projects.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedProject( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafProjectToBrokerProject(t._2)), + Encoders.bean(RelatedProject.class)) + .write() + .mode(SaveMode.Overwrite) + .json(relsPath); + }); + + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java new file mode 100644 index 000000000..0c20081dc --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java @@ -0,0 +1,78 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +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.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class GenerateRelatedPublications { + + private static final Logger log = LoggerFactory.getLogger(GenerateRelatedPublications.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( + GenerateRelatedPublications.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.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 relsPath = parser.get("relsPath"); + log.info("relsPath: {}", relsPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, relsPath); + + final Dataset pubs = ClusterUtils + .readPath(spark, graphPath + "/publication", Publication.class); + + final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + + rels + .joinWith(pubs, pubs.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedPublication( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafPublicationToBrokerPublication(t._2)), + Encoders.bean(RelatedPublication.class)) + .write() + .mode(SaveMode.Overwrite) + .json(relsPath); + + }); + + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java new file mode 100644 index 000000000..b95788846 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java @@ -0,0 +1,76 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +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.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; + +public class GenerateRelatedSoftwares { + + private static final Logger log = LoggerFactory.getLogger(GenerateRelatedSoftwares.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( + GenerateRelatedSoftwares.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.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 relsPath = parser.get("relsPath"); + log.info("relsPath: {}", relsPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, relsPath); + final Dataset softwares = ClusterUtils.readPath(spark, graphPath + "/software", Software.class); + + final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + + rels + .joinWith(softwares, softwares.col("id").equalTo(rels.col("target")), "inner") + .map( + t -> new RelatedSoftware( + t._1.getSource(), + t._1.getRelType(), + ConversionUtils.oafSoftwareToBrokerSoftware(t._2)), + Encoders.bean(RelatedSoftware.class)) + .write() + .mode(SaveMode.Overwrite) + .json(relsPath); + + }); + + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java new file mode 100644 index 000000000..59485d5cf --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java @@ -0,0 +1,85 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class GenerateSimpleEntitities { + + private static final Logger log = LoggerFactory.getLogger(GenerateSimpleEntitities.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenerateSimpleEntitities.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_simple_entities.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 simpleEntitiesPath = parser.get("simpleEntitiesPath"); + log.info("simpleEntitiesPath: {}", simpleEntitiesPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, simpleEntitiesPath); + + expandResultsWithRelations(spark, graphPath, Publication.class) + .write() + .mode(SaveMode.Overwrite) + .json(simpleEntitiesPath); + + // TODO UNCOMMENT THIS + // spark + // .emptyDataset(Encoders.bean(Event.class)) + // .union(generateEvents(spark, graphPath, Publication.class, dedupConfig)) + // .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig)) + // .union(generateEvents(spark, graphPath, Software.class, dedupConfig)) + // .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig)) + // .write() + // .mode(SaveMode.Overwrite) + // .option("compression", "gzip") + // .json(eventsPath); + }); + + } + + private static Dataset expandResultsWithRelations( + final SparkSession spark, + final String graphPath, + final Class sourceClass) { + + return ClusterUtils + .readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) + .filter(r -> r.getDataInfo().getDeletedbyinference()) + .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OaBrokerMainEntity.class)); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index 13aeefb2f..9aa6f5384 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -12,7 +12,7 @@ import java.util.function.Function; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.lang3.StringUtils; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.pace.config.DedupConfig; @@ -21,11 +21,11 @@ public abstract class UpdateMatcher { private final boolean multipleUpdate; private final Function topicFunction; - private final BiConsumer compileHighlightFunction; + private final BiConsumer compileHighlightFunction; private final Function highlightToStringFunction; public UpdateMatcher(final boolean multipleUpdate, final Function topicFunction, - final BiConsumer compileHighlightFunction, + final BiConsumer compileHighlightFunction, final Function highlightToStringFunction) { this.multipleUpdate = multipleUpdate; this.topicFunction = topicFunction; @@ -33,13 +33,13 @@ public abstract class UpdateMatcher { this.highlightToStringFunction = highlightToStringFunction; } - public Collection> searchUpdatesForRecord(final OpenaireBrokerResult res, - final Collection others, + public Collection> searchUpdatesForRecord(final OaBrokerMainEntity res, + final Collection others, final DedupConfig dedupConfig) { final Map> infoMap = new HashMap<>(); - for (final OpenaireBrokerResult source : others) { + for (final OaBrokerMainEntity source : others) { if (source != res) { for (final T hl : findDifferences(source, res)) { final Topic topic = getTopicFunction().apply(hl); @@ -68,7 +68,7 @@ public abstract class UpdateMatcher { } } - protected abstract List findDifferences(OpenaireBrokerResult source, OpenaireBrokerResult target); + protected abstract List findDifferences(OaBrokerMainEntity source, OaBrokerMainEntity target); protected static boolean isMissing(final List list) { return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0)); @@ -86,7 +86,7 @@ public abstract class UpdateMatcher { return topicFunction; } - public BiConsumer getCompileHighlightFunction() { + public BiConsumer getCompileHighlightFunction() { return compileHighlightFunction; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java index 7a58f986b..c197734a3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java @@ -5,13 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.Dataset; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public abstract class AbstractEnrichMissingDataset - extends UpdateMatcher { +public abstract class AbstractEnrichMissingDataset extends UpdateMatcher { public AbstractEnrichMissingDataset(final Topic topic) { super(true, @@ -23,14 +22,14 @@ public abstract class AbstractEnrichMissingDataset protected abstract boolean filterByType(String relType); @Override - protected final List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected final List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingDatasets = target .getDatasets() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(Dataset::getOriginalId) + .map(OaBrokerRelatedDataset::getOriginalId) .collect(Collectors.toSet()); return source diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java index fa5fde725..49c546bba 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java @@ -4,12 +4,12 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerProject; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMissingProject extends UpdateMatcher { +public class EnrichMissingProject extends UpdateMatcher { public EnrichMissingProject() { super(true, @@ -19,7 +19,7 @@ public class EnrichMissingProject extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, final OaBrokerMainEntity target) { if (target.getProjects().isEmpty()) { return source.getProjects(); } else { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java index ca63aeb49..6954a3fb5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerProject; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMoreProject extends UpdateMatcher { +public class EnrichMoreProject extends UpdateMatcher { public EnrichMoreProject() { super(true, @@ -19,13 +19,13 @@ public class EnrichMoreProject extends UpdateMatcher { prj -> projectAsString(prj)); } - private static String projectAsString(final Project prj) { + private static String projectAsString(final OaBrokerProject prj) { return prj.getFunder() + "::" + prj.getFundingProgram() + "::" + prj.getCode(); } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingProjects = target .getProjects() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java index 300863949..ad6d8263b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.Publication; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public abstract class AbstractEnrichMissingPublication extends UpdateMatcher { +public abstract class AbstractEnrichMissingPublication extends UpdateMatcher { public AbstractEnrichMissingPublication(final Topic topic) { super(true, @@ -23,15 +23,15 @@ public abstract class AbstractEnrichMissingPublication extends UpdateMatcher findDifferences( - final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected final List findDifferences( + final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingPublications = target .getPublications() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(Publication::getOriginalId) + .map(OaBrokerRelatedPublication::getOriginalId) .collect(Collectors.toSet()); return source diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java index 76ae061e6..452caa503 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java @@ -4,12 +4,13 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; public class EnrichMissingSoftware - extends UpdateMatcher { + extends UpdateMatcher { public EnrichMissingSoftware() { super(true, @@ -19,9 +20,9 @@ public class EnrichMissingSoftware } @Override - protected List findDifferences( - final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences( + final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { if (target.getSoftwares().isEmpty()) { return source.getSoftwares(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java index ebd421b8e..aaffe1249 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.Software; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMoreSoftware extends UpdateMatcher { +public class EnrichMoreSoftware extends UpdateMatcher { public EnrichMoreSoftware() { super(true, @@ -20,14 +20,14 @@ public class EnrichMoreSoftware extends UpdateMatcher { } @Override - protected List findDifferences( - final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences( + final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingSoftwares = source .getSoftwares() .stream() - .map(Software::getName) + .map(OaBrokerRelatedSoftware::getName) .collect(Collectors.toSet()); return target diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java index b2cbbce2c..73462bae8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java @@ -5,7 +5,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; @@ -19,7 +19,7 @@ public class EnrichMissingAbstract extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, final OaBrokerMainEntity target) { if (isMissing(target.getAbstracts()) && !isMissing(source.getAbstracts())) { return Arrays.asList(source.getAbstracts().get(0)); } else { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index c4b96e67b..2a01188a9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -7,12 +7,12 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; -import eu.dnetlib.broker.objects.Author; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerAuthor; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMissingAuthorOrcid extends UpdateMatcher { +public class EnrichMissingAuthorOrcid extends UpdateMatcher { public EnrichMissingAuthorOrcid() { super(true, @@ -22,13 +22,13 @@ public class EnrichMissingAuthorOrcid extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingOrcids = target .getCreators() .stream() - .map(Author::getOrcid) + .map(OaBrokerAuthor::getOrcid) .filter(StringUtils::isNotBlank) .collect(Collectors.toSet()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index e870cf1fa..487382957 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -5,28 +5,28 @@ import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerInstance; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; -public class EnrichMissingOpenAccess extends UpdateMatcher { +public class EnrichMissingOpenAccess extends UpdateMatcher { public EnrichMissingOpenAccess() { super(true, i -> Topic.ENRICH_MISSING_OA_VERSION, (p, i) -> p.getInstances().add(i), - Instance::getUrl); + OaBrokerInstance::getUrl); } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final long count = target .getInstances() .stream() - .map(Instance::getLicense) + .map(OaBrokerInstance::getLicense) .filter(right -> right.equals(BrokerConstants.OPEN_ACCESS)) .count(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java index cc72d9fa9..ee1617b1e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java @@ -5,12 +5,12 @@ import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.TypedValue; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMissingPid extends UpdateMatcher { +public class EnrichMissingPid extends UpdateMatcher { public EnrichMissingPid() { super(true, @@ -20,8 +20,8 @@ public class EnrichMissingPid extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final long count = target.getPids().size(); if (count > 0) { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java index ed8c26b5a..2c0533fa3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java @@ -5,7 +5,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; @@ -19,8 +19,8 @@ public class EnrichMissingPublicationDate extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { if (isMissing(target.getPublicationdate()) && !isMissing(source.getPublicationdate())) { return Arrays.asList(source.getPublicationdate()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index 07b1fa41a..9ab9fce48 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.TypedValue; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMissingSubject extends UpdateMatcher { +public class EnrichMissingSubject extends UpdateMatcher { public EnrichMissingSubject() { super(true, @@ -20,8 +20,8 @@ public class EnrichMissingSubject extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingSubject = target .getSubjects() .stream() @@ -35,7 +35,7 @@ public class EnrichMissingSubject extends UpdateMatcher { .collect(Collectors.toList()); } - private static String subjectAsString(final TypedValue s) { + private static String subjectAsString(final OaBrokerTypedValue s) { return s.getType() + "::" + s.getValue(); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index bfef3ee4f..e90a8f201 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -5,24 +5,24 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerInstance; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; -public class EnrichMoreOpenAccess extends UpdateMatcher { +public class EnrichMoreOpenAccess extends UpdateMatcher { public EnrichMoreOpenAccess() { super(true, i -> Topic.ENRICH_MORE_OA_VERSION, (p, i) -> p.getInstances().add(i), - Instance::getUrl); + OaBrokerInstance::getUrl); } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set urls = target .getInstances() .stream() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java index d1f2e6022..43b4f0628 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.TypedValue; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMorePid extends UpdateMatcher { +public class EnrichMorePid extends UpdateMatcher { public EnrichMorePid() { super(true, @@ -20,8 +20,8 @@ public class EnrichMorePid extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingPids = target .getPids() .stream() @@ -35,7 +35,7 @@ public class EnrichMorePid extends UpdateMatcher { .collect(Collectors.toList()); } - private static String pidAsString(final TypedValue pid) { + private static String pidAsString(final OaBrokerTypedValue pid) { return pid.getType() + "::" + pid.getValue(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index 39225e8ab..04fb494ef 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -5,12 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.TypedValue; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -public class EnrichMoreSubject extends UpdateMatcher { +public class EnrichMoreSubject extends UpdateMatcher { public EnrichMoreSubject() { super(true, @@ -20,8 +20,8 @@ public class EnrichMoreSubject extends UpdateMatcher { } @Override - protected List findDifferences(final OpenaireBrokerResult source, - final OpenaireBrokerResult target) { + protected List findDifferences(final OaBrokerMainEntity source, + final OaBrokerMainEntity target) { final Set existingSubjects = target .getSubjects() .stream() @@ -35,7 +35,7 @@ public class EnrichMoreSubject extends UpdateMatcher { .collect(Collectors.toList()); } - private static String subjectAsString(final TypedValue s) { + private static String subjectAsString(final OaBrokerTypedValue s) { return s.getType() + "::" + s.getValue(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java new file mode 100644 index 000000000..8bcea5e6e --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.common.HdfsSupport; + +public class ClusterUtils { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void removeDir(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + final SparkSession spark, + final String inputPath, + final Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 730d06519..b61d5e7cc 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -15,8 +15,16 @@ import org.slf4j.LoggerFactory; import com.google.common.base.Function; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.TypedValue; +import eu.dnetlib.broker.objects.OaBrokerAuthor; +import eu.dnetlib.broker.objects.OaBrokerExternalReference; +import eu.dnetlib.broker.objects.OaBrokerInstance; +import eu.dnetlib.broker.objects.OaBrokerJournal; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerProject; +import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; +import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; +import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; +import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.ExternalReference; @@ -35,13 +43,13 @@ public class ConversionUtils { private static final Logger log = LoggerFactory.getLogger(ConversionUtils.class); - public static List oafInstanceToBrokerInstances(final Instance i) { + public static List oafInstanceToBrokerInstances(final Instance i) { if (i == null) { return new ArrayList<>(); } return mappedList(i.getUrl(), url -> { - final eu.dnetlib.broker.objects.Instance res = new eu.dnetlib.broker.objects.Instance(); + final OaBrokerInstance res = new OaBrokerInstance(); res.setUrl(url); res.setInstancetype(classId(i.getInstancetype())); res.setLicense(BrokerConstants.OPEN_ACCESS); @@ -50,20 +58,21 @@ public class ConversionUtils { }); } - public static TypedValue oafPidToBrokerPid(final StructuredProperty sp) { + public static OaBrokerTypedValue oafPidToBrokerPid(final StructuredProperty sp) { return oafStructPropToBrokerTypedValue(sp); } - public static TypedValue oafStructPropToBrokerTypedValue(final StructuredProperty sp) { - return sp != null ? new TypedValue(classId(sp.getQualifier()), sp.getValue()) : null; + public static OaBrokerTypedValue oafStructPropToBrokerTypedValue(final StructuredProperty sp) { + return sp != null ? new OaBrokerTypedValue(classId(sp.getQualifier()), sp.getValue()) : null; } - public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) { + public static final OaBrokerRelatedDataset oafDatasetToBrokerDataset(final Dataset d) { if (d == null) { return null; } - final eu.dnetlib.broker.objects.Dataset res = new eu.dnetlib.broker.objects.Dataset(); + final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset(); + res.setOpenaireId(d.getId()); res.setOriginalId(first(d.getOriginalId())); res.setTitle(structPropValue(d.getTitle())); res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -72,12 +81,13 @@ public class ConversionUtils { return res; } - public static eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication p) { + public static OaBrokerRelatedPublication oafPublicationToBrokerPublication(final Publication p) { if (p == null) { return null; } - final eu.dnetlib.broker.objects.Publication res = new eu.dnetlib.broker.objects.Publication(); + final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication(); + res.setOpenaireId(p.getId()); res.setOriginalId(first(p.getOriginalId())); res.setTitle(structPropValue(p.getTitle())); res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -87,12 +97,12 @@ public class ConversionUtils { return res; } - public static final OpenaireBrokerResult oafResultToBrokerResult(final Result result) { + public static final OaBrokerMainEntity oafResultToBrokerResult(final Result result) { if (result == null) { return null; } - final OpenaireBrokerResult res = new OpenaireBrokerResult(); + final OaBrokerMainEntity res = new OaBrokerMainEntity(); res.setOpenaireId(result.getId()); res.setOriginalId(first(result.getOriginalId())); @@ -118,7 +128,7 @@ public class ConversionUtils { return res; } - private static eu.dnetlib.broker.objects.Author oafAuthorToBrokerAuthor(final Author author) { + private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) { if (author == null) { return null; } @@ -135,15 +145,15 @@ public class ConversionUtils { .findFirst() .orElse(null) : null; - return new eu.dnetlib.broker.objects.Author(author.getFullname(), pids); + return new OaBrokerAuthor(author.getFullname(), pids); } - private static eu.dnetlib.broker.objects.Journal oafJournalToBrokerJournal(final Journal journal) { + private static OaBrokerJournal oafJournalToBrokerJournal(final Journal journal) { if (journal == null) { return null; } - final eu.dnetlib.broker.objects.Journal res = new eu.dnetlib.broker.objects.Journal(); + final OaBrokerJournal res = new OaBrokerJournal(); res.setName(journal.getName()); res.setIssn(journal.getIssnPrinted()); res.setEissn(journal.getIssnOnline()); @@ -152,12 +162,12 @@ public class ConversionUtils { return res; } - private static eu.dnetlib.broker.objects.ExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) { + private static OaBrokerExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) { if (ref == null) { return null; } - final eu.dnetlib.broker.objects.ExternalReference res = new eu.dnetlib.broker.objects.ExternalReference(); + final OaBrokerExternalReference res = new OaBrokerExternalReference(); res.setRefidentifier(ref.getRefidentifier()); res.setSitename(ref.getSitename()); res.setType(classId(ref.getQualifier())); @@ -165,12 +175,13 @@ public class ConversionUtils { return res; } - public static final eu.dnetlib.broker.objects.Project oafProjectToBrokerProject(final Project p) { + public static final OaBrokerProject oafProjectToBrokerProject(final Project p) { if (p == null) { return null; } - final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project(); + final OaBrokerProject res = new OaBrokerProject(); + res.setOpenaireId(p.getId()); res.setTitle(fieldValue(p.getTitle())); res.setAcronym(fieldValue(p.getAcronym())); res.setCode(fieldValue(p.getCode())); @@ -190,12 +201,13 @@ public class ConversionUtils { return res; } - public static final eu.dnetlib.broker.objects.Software oafSoftwareToBrokerSoftware(final Software sw) { + public static final OaBrokerRelatedSoftware oafSoftwareToBrokerSoftware(final Software sw) { if (sw == null) { return null; } - final eu.dnetlib.broker.objects.Software res = new eu.dnetlib.broker.objects.Software(); + final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware(); + res.setOpenaireId(sw.getId()); res.setName(structPropValue(sw.getTitle())); res.setDescription(fieldValue(sw.getDescription())); res.setRepository(fieldValue(sw.getCodeRepositoryUrl())); @@ -247,7 +259,7 @@ public class ConversionUtils { : new ArrayList<>(); } - private static List structPropTypedList(final List list) { + private static List structPropTypedList(final List list) { if (list == null) { return new ArrayList<>(); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java index 4c20ac5ca..7451e5891 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java @@ -4,7 +4,7 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.broker.model.EventFactory; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy; @@ -68,7 +68,7 @@ public class EventFinder { public static EventGroup generateEvents(final ResultGroup results, final DedupConfig dedupConfig) { final List> list = new ArrayList<>(); - for (final OpenaireBrokerResult target : results.getData()) { + for (final OaBrokerMainEntity target : results.getData()) { for (final UpdateMatcher matcher : matchers) { list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), dedupConfig)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index 2c4bda53d..25d0d2bca 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -9,10 +9,10 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.broker.objects.OpenAireEventPayload; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; -import eu.dnetlib.broker.objects.Provenance; +import eu.dnetlib.broker.objects.OaBrokerEventPayload; +import eu.dnetlib.broker.objects.OaBrokerInstance; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.broker.objects.OaBrokerProvenance; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; @@ -25,11 +25,11 @@ public final class UpdateInfo { private final T highlightValue; - private final OpenaireBrokerResult source; + private final OaBrokerMainEntity source; - private final OpenaireBrokerResult target; + private final OaBrokerMainEntity target; - private final BiConsumer compileHighlight; + private final BiConsumer compileHighlight; private final Function highlightToString; @@ -37,9 +37,9 @@ public final class UpdateInfo { private static final Logger log = LoggerFactory.getLogger(UpdateInfo.class); - public UpdateInfo(final Topic topic, final T highlightValue, final OpenaireBrokerResult source, - final OpenaireBrokerResult target, - final BiConsumer compileHighlight, + public UpdateInfo(final Topic topic, final T highlightValue, final OaBrokerMainEntity source, + final OaBrokerMainEntity target, + final BiConsumer compileHighlight, final Function highlightToString, final DedupConfig dedupConfig) { this.topic = topic; @@ -55,17 +55,17 @@ public final class UpdateInfo { return highlightValue; } - public OpenaireBrokerResult getSource() { + public OaBrokerMainEntity getSource() { return source; } - public OpenaireBrokerResult getTarget() { + public OaBrokerMainEntity getTarget() { return target; } private float calculateTrust(final DedupConfig dedupConfig, - final OpenaireBrokerResult r1, - final OpenaireBrokerResult r2) { + final OaBrokerMainEntity r1, + final OaBrokerMainEntity r2) { if (dedupConfig == null) { return BrokerConstants.MIN_TRUST; @@ -104,11 +104,11 @@ public final class UpdateInfo { return highlightToString.apply(getHighlightValue()); } - public OpenAireEventPayload asBrokerPayload() { + public OaBrokerEventPayload asBrokerPayload() { compileHighlight.accept(target, getHighlightValue()); - final OpenaireBrokerResult hl = new OpenaireBrokerResult(); + final OaBrokerMainEntity hl = new OaBrokerMainEntity(); compileHighlight.accept(hl, getHighlightValue()); final String provId = getSource().getOriginalId(); @@ -117,14 +117,14 @@ public final class UpdateInfo { final String provUrl = getSource() .getInstances() .stream() - .map(Instance::getUrl) + .map(OaBrokerInstance::getUrl) .findFirst() .orElse(null); ; - final Provenance provenance = new Provenance(provId, provRepo, provUrl); + final OaBrokerProvenance provenance = new OaBrokerProvenance(provId, provRepo, provUrl); - final OpenAireEventPayload res = new OpenAireEventPayload(); + final OaBrokerEventPayload res = new OaBrokerEventPayload(); res.setResult(target); res.setHighlight(hl); res.setTrust(trust); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java index a46fde445..ee1c8963e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java @@ -5,11 +5,11 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.expressions.Aggregator; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; -public class ResultAggregator extends Aggregator, ResultGroup, ResultGroup> { +public class ResultAggregator extends Aggregator, ResultGroup, ResultGroup> { /** * @@ -22,7 +22,7 @@ public class ResultAggregator extends Aggregator t) { + public ResultGroup reduce(final ResultGroup group, final Tuple2 t) { group.getData().add(t._1); return group; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java index 3f9dbe8af..e718e0f1c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java @@ -5,7 +5,7 @@ import java.io.Serializable; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; public class ResultGroup implements Serializable { @@ -14,13 +14,13 @@ public class ResultGroup implements Serializable { */ private static final long serialVersionUID = -3360828477088669296L; - private List data = new ArrayList<>(); + private List data = new ArrayList<>(); - public List getData() { + public List getData() { return data; } - public void setData(final List data) { + public void setData(final List data) { this.data = data; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java similarity index 59% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java index e72dcb988..6a2d9b06d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java @@ -5,11 +5,11 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.expressions.Aggregator; -import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.OaBrokerMainEntity; import scala.Tuple2; -public class OpenaireBrokerResultAggregator - extends Aggregator, OpenaireBrokerResult, OpenaireBrokerResult> { +public class OaBrokerMainEntityAggregator + extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { /** * @@ -17,17 +17,17 @@ public class OpenaireBrokerResultAggregator private static final long serialVersionUID = -3687878788861013488L; @Override - public OpenaireBrokerResult zero() { - return new OpenaireBrokerResult(); + public OaBrokerMainEntity zero() { + return new OaBrokerMainEntity(); } @Override - public OpenaireBrokerResult finish(final OpenaireBrokerResult g) { + public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { return g; } @Override - public OpenaireBrokerResult reduce(final OpenaireBrokerResult g, final Tuple2 t) { + public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { if (g.getOriginalId() == null) { return t._1; } else if (t._2 instanceof RelatedSoftware) { @@ -38,13 +38,15 @@ public class OpenaireBrokerResultAggregator g.getPublications().add(((RelatedPublication) t._2).getRelPublication()); } else if (t._2 instanceof RelatedProject) { g.getProjects().add(((RelatedProject) t._2).getRelProject()); + } else { + throw new RuntimeException("Invalid Object: " + t._2.getClass()); } return g; } @Override - public OpenaireBrokerResult merge(final OpenaireBrokerResult g1, final OpenaireBrokerResult g2) { + public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { if (g1.getOriginalId() != null) { g1.getSoftwares().addAll(g2.getSoftwares()); g1.getDatasets().addAll(g2.getDatasets()); @@ -57,13 +59,13 @@ public class OpenaireBrokerResultAggregator } @Override - public Encoder bufferEncoder() { - return Encoders.bean(OpenaireBrokerResult.class); + public Encoder bufferEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); } @Override - public Encoder outputEncoder() { - return Encoders.bean(OpenaireBrokerResult.class); + public Encoder outputEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java index 6a5fb258c..daf75ea2e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; import java.io.Serializable; -import eu.dnetlib.broker.objects.Dataset; +import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; public class RelatedDataset implements Serializable { @@ -13,12 +13,12 @@ public class RelatedDataset implements Serializable { private static final long serialVersionUID = 774487705184038324L; private String source; private String relType; - private Dataset relDataset; + private OaBrokerRelatedDataset relDataset; public RelatedDataset() { } - public RelatedDataset(final String source, final String relType, final Dataset relDataset) { + public RelatedDataset(final String source, final String relType, final OaBrokerRelatedDataset relDataset) { this.source = source; this.relType = relType; this.relDataset = relDataset; @@ -40,11 +40,11 @@ public class RelatedDataset implements Serializable { this.relType = relType; } - public Dataset getRelDataset() { + public OaBrokerRelatedDataset getRelDataset() { return relDataset; } - public void setRelDataset(final Dataset relDataset) { + public void setRelDataset(final OaBrokerRelatedDataset relDataset) { this.relDataset = relDataset; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java index fafec1e19..4116c8c77 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; import java.io.Serializable; -import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.broker.objects.OaBrokerProject; public class RelatedProject implements Serializable { @@ -14,12 +14,12 @@ public class RelatedProject implements Serializable { private String source; private String relType; - private Project relProject; + private OaBrokerProject relProject; public RelatedProject() { } - public RelatedProject(final String source, final String relType, final Project relProject) { + public RelatedProject(final String source, final String relType, final OaBrokerProject relProject) { this.source = source; this.relType = relType; this.relProject = relProject; @@ -41,11 +41,11 @@ public class RelatedProject implements Serializable { this.relType = relType; } - public Project getRelProject() { + public OaBrokerProject getRelProject() { return relProject; } - public void setRelProject(final Project relProject) { + public void setRelProject(final OaBrokerProject relProject) { this.relProject = relProject; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java index 8a31ddf7e..9e222a952 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; import java.io.Serializable; -import eu.dnetlib.broker.objects.Publication; +import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; public class RelatedPublication implements Serializable { @@ -14,12 +14,13 @@ public class RelatedPublication implements Serializable { private String source; private String relType; - private Publication relPublication; + private OaBrokerRelatedPublication relPublication; public RelatedPublication() { } - public RelatedPublication(final String source, final String relType, final Publication relPublication) { + public RelatedPublication(final String source, final String relType, + final OaBrokerRelatedPublication relPublication) { this.source = source; this.relType = relType; this.relPublication = relPublication; @@ -41,11 +42,11 @@ public class RelatedPublication implements Serializable { this.relType = relType; } - public Publication getRelPublication() { + public OaBrokerRelatedPublication getRelPublication() { return relPublication; } - public void setRelPublication(final Publication relPublication) { + public void setRelPublication(final OaBrokerRelatedPublication relPublication) { this.relPublication = relPublication; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java index 319387469..2f3b8668c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; import java.io.Serializable; -import eu.dnetlib.broker.objects.Software; +import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; public class RelatedSoftware implements Serializable { @@ -13,12 +13,12 @@ public class RelatedSoftware implements Serializable { private static final long serialVersionUID = 7573383356943300157L; private String source; private String relType; - private Software relSoftware; + private OaBrokerRelatedSoftware relSoftware; public RelatedSoftware() { } - public RelatedSoftware(final String source, final String relType, final Software relSoftware) { + public RelatedSoftware(final String source, final String relType, final OaBrokerRelatedSoftware relSoftware) { this.source = source; this.relType = relType; this.relSoftware = relSoftware; @@ -40,11 +40,11 @@ public class RelatedSoftware implements Serializable { this.relType = relType; } - public Software getRelSoftware() { + public OaBrokerRelatedSoftware getRelSoftware() { return relSoftware; } - public void setRelSoftware(final Software relSoftware) { + public void setRelSoftware(final OaBrokerRelatedSoftware relSoftware) { this.relSoftware = relSoftware; } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json new file mode 100644 index 000000000..32fd1d8f3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the path where there the graph is stored", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "relsPath", + "paramDescription": "the path where the generated relations will be stored", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json new file mode 100644 index 000000000..6f5e330f6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the path where there the graph is stored", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "simpleEntitiesPath", + "paramDescription": "the path where the generated simple entities (without relations) will be stored", + "paramRequired": true + } +] From 7d416f08d8838d33e2d37b24d520e11d97aada1f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Jun 2020 09:50:43 +0200 Subject: [PATCH 03/16] graph cleaning workflow: set hostedby to unknown repository when defined as NULL --- .../dnetlib/dhp/schema/common/ModelConstants.java | 15 +++++++++++++++ .../dhp/oa/graph/clean/CleanGraphSparkJob.java | 3 +++ 2 files changed, 18 insertions(+) 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 a3c1610db..c5905e45b 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 @@ -1,6 +1,10 @@ package eu.dnetlib.dhp.schema.common; +import java.security.Key; + +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Qualifier; public class ModelConstants { @@ -95,6 +99,9 @@ public class ModelConstants { SYSIMPORT_CROSSWALK_ENTITYREGISTRY, SYSIMPORT_CROSSWALK_ENTITYREGISTRY, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + public static final KeyValue UNKNOWN_REPOSITORY = keyValue( + "10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository"); + private static Qualifier qualifier( final String classid, final String classname, @@ -107,4 +114,12 @@ public class ModelConstants { q.setSchemename(schemename); return q; } + + private static KeyValue keyValue(String key, String value) { + KeyValue kv = new KeyValue(); + kv.setKey(key); + kv.setValue(value); + kv.setDataInfo(new DataInfo()); + return kv; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index c90898814..8f43ab1cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -144,6 +144,9 @@ public class CleanGraphSparkJob { if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) { i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); } + if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) { + i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY); + } } } From 961a0d0b4952a51aaf27fb10c3a6a2bcba018710 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Jun 2020 10:20:45 +0200 Subject: [PATCH 04/16] [actionset promotion] log debugging info in case of error in the action payload extraction or parsing the data --- .../PromoteActionPayloadForGraphTableJob.java | 29 +++++++++++++++---- 1 file changed, 23 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java index 17bfc4af3..5fa9e6723 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.promote; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; +import java.io.IOException; import java.util.Objects; import java.util.Optional; import java.util.function.BiFunction; @@ -20,6 +21,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; @@ -134,24 +136,39 @@ public class PromoteActionPayloadForGraphTableJob { .map( (MapFunction) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz)); - - /* - * return spark .read() .parquet(path) .as(Encoders.bean(rowClazz)); - */ } private static Dataset readActionPayload( SparkSession spark, String path, Class actionPayloadClazz) { logger.info("Reading action payload from path: {}", path); + return spark .read() .parquet(path) + .map((MapFunction) value -> extractPayload(value), Encoders.STRING()) .map( - (MapFunction) value -> OBJECT_MAPPER - .readValue(value. getAs("payload"), actionPayloadClazz), + (MapFunction) value -> decodePayload(actionPayloadClazz, value), Encoders.bean(actionPayloadClazz)); } + private static String extractPayload(Row value) { + try { + return value. getAs("payload"); + } catch (IllegalArgumentException | ClassCastException e) { + logger.error("cannot extract payload from action: {}", value.toString()); + throw e; + } + } + + private static A decodePayload(Class actionPayloadClazz, String payload) throws IOException { + try { + return OBJECT_MAPPER.readValue(payload, actionPayloadClazz); + } catch (UnrecognizedPropertyException e) { + logger.error("error decoding payload: {}", payload); + throw e; + } + } + private static Dataset promoteActionPayloadForGraphTable( Dataset rowDS, Dataset actionPayloadDS, From 1e3dab06318516b1eda81fe42dd370aa2c726d0b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Jun 2020 11:27:39 +0200 Subject: [PATCH 05/16] [maven-release-plugin] prepare release dhp-1.2.3 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-schemas/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-dedup-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 2 +- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-worfklow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 23 insertions(+), 23 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 2a89a26fd..2eb7e76c6 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 - 1.2.3-SNAPSHOT + 1.2.3 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 5be114e3c..6696f2f53 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 - 1.2.3-SNAPSHOT + 1.2.3 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 515ed35ce..40a5df58d 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.3-SNAPSHOT + 1.2.3 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index d2dcbc36e..a787b2fb5 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.3-SNAPSHOT + 1.2.3 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 0e7652dd3..c79662380 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.3-SNAPSHOT + 1.2.3 ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index 56fb8ead2..a770ab6b1 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.3-SNAPSHOT + 1.2.3 ../ diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index b50c6705b..d978b4e1e 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.3-SNAPSHOT + 1.2.3 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c04910a58..da05f16bd 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.3-SNAPSHOT + 1.2.3 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 04d334cd7..14bc6bc98 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 8d7d3b88c..3ebebc579 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 1f5f2620e..ec5ff7308 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml index e9e11b417..4aa3ebced 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 5707ddfc5..5e2995340 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 39bb81ec1..40fc62c2d 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index e71a72f3e..43ad12e0c 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index f650f1c17..b4f7a4059 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index 2466ca8e2..c27c1b1b8 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index b0aec1e5d..69dcd249e 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 397bd8d08..148e93ae7 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 - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index e03362034..34c622b1a 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3-SNAPSHOT + 1.2.3 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 8d8d57c84..1a1082ba2 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.3-SNAPSHOT + 1.2.3 ../ diff --git a/pom.xml b/pom.xml index 06e2b7aaf..6ec6bfb3a 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.3-SNAPSHOT + 1.2.3 pom @@ -38,7 +38,7 @@ 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 + dhp-1.2.3 This module is the root descriptor for the dnet-hadoop project From 9cd27183b6738e2bddbf1890bb37547bde054bca Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Jun 2020 11:27:44 +0200 Subject: [PATCH 06/16] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-schemas/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-dedup-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 2 +- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-worfklow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 23 insertions(+), 23 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 2eb7e76c6..012ff89a3 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 - 1.2.3 + 1.2.4-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 6696f2f53..256017e2c 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 - 1.2.3 + 1.2.4-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 40a5df58d..e60e8076e 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.3 + 1.2.4-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a787b2fb5..12b999b9c 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.3 + 1.2.4-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c79662380..0819a8bd2 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.3 + 1.2.4-SNAPSHOT ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index a770ab6b1..2e5652b43 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.3 + 1.2.4-SNAPSHOT ../ diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index d978b4e1e..0b4d25700 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.3 + 1.2.4-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index da05f16bd..a1bc1c483 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.3 + 1.2.4-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 14bc6bc98..9c25f7b29 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 3ebebc579..424015a3c 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index ec5ff7308..03ddbcf4c 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml index 4aa3ebced..aa4070b01 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 5e2995340..8c10538c0 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 40fc62c2d..3299c1496 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 43ad12e0c..d0ab77cc5 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index b4f7a4059..0439c2ba3 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index c27c1b1b8..05ca7d4ce 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 69dcd249e..fa1964773 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 148e93ae7..52f35ff07 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 - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index 34c622b1a..34996a021 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.3 + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 1a1082ba2..9fbc6d714 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.3 + 1.2.4-SNAPSHOT ../ diff --git a/pom.xml b/pom.xml index 6ec6bfb3a..89b7e8829 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.3 + 1.2.4-SNAPSHOT pom @@ -38,7 +38,7 @@ 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/ - dhp-1.2.3 + HEAD This module is the root descriptor for the dnet-hadoop project From ed787398b37d2276765c6ca5b3e57a628ca2b6bd Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 22 Jun 2020 11:45:14 +0200 Subject: [PATCH 07/16] refactoring wf --- .../broker/oa/GenerateEventsApplication.java | 190 ---------------- .../dhp/broker/oa/GenerateEventsJob.java | 106 +++++++++ .../dhp/broker/oa/JoinEntitiesJob.java | 94 ++++++++ .../dhp/broker/oa/PrepareGroupsJob.java | 88 ++++++++ ...ts.java => PrepareRelatedDatasetsJob.java} | 13 +- ...ts.java => PrepareRelatedProjectsJob.java} | 13 +- ...ava => PrepareRelatedPublicationsJob.java} | 13 +- ...s.java => PrepareRelatedSoftwaresJob.java} | 14 +- ...s.java => PrepareSimpleEntititiesJob.java} | 34 ++- .../dhp/broker/oa/util/ClusterUtils.java | 4 + ...rate_relations.json => common_params.json} | 4 +- .../oa/generate_all/oozie_app/workflow.xml | 210 +++++++++++++++++- ...roker_events.json => generate_events.json} | 2 +- .../broker/oa/generate_simple_entities.json | 14 -- 14 files changed, 546 insertions(+), 253 deletions(-) delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{GenerateRelatedDatasets.java => PrepareRelatedDatasetsJob.java} (82%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{GenerateRelatedProjects.java => PrepareRelatedProjectsJob.java} (84%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{GenerateRelatedPublications.java => PrepareRelatedPublicationsJob.java} (83%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{GenerateRelatedSoftwares.java => PrepareRelatedSoftwaresJob.java} (83%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{GenerateSimpleEntitities.java => PrepareSimpleEntititiesJob.java} (68%) rename dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/{generate_relations.json => common_params.json} (64%) rename dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/{generate_broker_events.json => generate_events.json} (94%) delete mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json 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 deleted file mode 100644 index db5992010..000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ /dev/null @@ -1,190 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.apache.spark.sql.TypedColumn; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.broker.objects.OaBrokerMainEntity; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.broker.model.Event; -import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; -import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.EventFinder; -import eu.dnetlib.dhp.broker.oa.util.EventGroup; -import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; -import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OaBrokerMainEntityAggregator; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.config.DedupConfig; -import scala.Tuple2; - -public class GenerateEventsApplication { - - private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class); - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.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 String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); - - final String dedupConfigProfileId = parser.get("dedupConfProfile"); - log.info("dedupConfigProfileId: {}", dedupConfigProfileId); - - final SparkConf conf = new SparkConf(); - // conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - // conf.registerKryoClasses(BrokerConstants.getModelClasses()); - - // TODO UNCOMMENT - // final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId); - final DedupConfig dedupConfig = null; - - runWithSparkSession(conf, isSparkSessionManaged, spark -> { - - ClusterUtils.removeDir(spark, eventsPath); - - // TODO REMOVE THIS - - expandResultsWithRelations(spark, graphPath, Publication.class) - .write() - .mode(SaveMode.Overwrite) - .json(eventsPath); - - // TODO UNCOMMENT THIS - // spark - // .emptyDataset(Encoders.bean(Event.class)) - // .union(generateEvents(spark, graphPath, Publication.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, Software.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig)) - // .write() - // .mode(SaveMode.Overwrite) - // .option("compression", "gzip") - // .json(eventsPath); - }); - - } - - private static Dataset generateEvents( - final SparkSession spark, - final String graphPath, - final Class sourceClass, - final DedupConfig dedupConfig) { - - final Dataset results = expandResultsWithRelations(spark, graphPath, sourceClass); - - final Dataset mergedRels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - - final TypedColumn, ResultGroup> aggr = new ResultAggregator() - .toColumn(); - - return results - .joinWith(mergedRels, results.col("openaireId").equalTo(mergedRels.col("source")), "inner") - .groupByKey( - (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) - .agg(aggr) - .map((MapFunction, ResultGroup>) t -> t._2, Encoders.bean(ResultGroup.class)) - .filter(rg -> rg.getData().size() > 1) - .map( - (MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), - Encoders.bean(EventGroup.class)) - .flatMap(group -> group.getData().iterator(), Encoders.bean(Event.class)); - } - - private static Dataset expandResultsWithRelations( - final SparkSession spark, - final String graphPath, - final Class sourceClass) { - - // final Dataset datasets = readPath( - // spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - // final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); - // final Dataset publications = readPath(spark, graphPath + "/publication", Publication.class); - - final Dataset r0 = ClusterUtils - .readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) - .filter(r -> r.getDataInfo().getDeletedbyinference()) - .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OaBrokerMainEntity.class)); - - // TODO UNCOMMENT THIS - // final Dataset r1 = join(r0, relatedProjects(spark, graphPath)); - // final Dataset r2 = join(r1, relatedDataset(spark, graphPath)); - // final Dataset r3 = join(r2, relatedPublications(spark, graphPath)); - // final Dataset r4 = join(r3, relatedSoftwares(spark, graphPath)); - - return r0; // TODO it should be r4 - } - - private static Dataset join(final Dataset sources, - final Dataset typedRels) { - - final TypedColumn, OaBrokerMainEntity> aggr = new OaBrokerMainEntityAggregator() - .toColumn(); - - return sources - .joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer") - .groupByKey( - (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) - .agg(aggr) - .map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class)); - - } - - private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception { - - final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); - - final String conf = isLookUpService - .getResourceProfileByQuery( - String - .format( - "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", - profId)); - - final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); - dedupConfig.getPace().initModel(); - dedupConfig.getPace().initTranslationMap(); - // dedupConfig.getWf().setConfigurationId("???"); - - return dedupConfig; - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java new file mode 100644 index 000000000..3ea0086ff --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -0,0 +1,106 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +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.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.EventFinder; +import eu.dnetlib.dhp.broker.oa.util.EventGroup; +import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.config.DedupConfig; + +public class GenerateEventsJob { + + private static final Logger log = LoggerFactory.getLogger(GenerateEventsJob.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenerateEventsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.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 workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final String dedupConfigProfileId = parser.get("dedupConfProfile"); + log.info("dedupConfigProfileId: {}", dedupConfigProfileId); + + final String eventsPath = workingPath + "/eventsPath"; + log.info("eventsPath: {}", eventsPath); + + final SparkConf conf = new SparkConf(); + + // TODO UNCOMMENT + // final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId); + final DedupConfig dedupConfig = null; + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, eventsPath); + + final Dataset groups = ClusterUtils + .readPath(spark, graphPath + "/relation", ResultGroup.class); + + final Dataset events = groups + .map( + (MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), + Encoders.bean(EventGroup.class)) + .flatMap(group -> group.getData().iterator(), Encoders.bean(Event.class)); + + events.write().mode(SaveMode.Overwrite).json(eventsPath); + + }); + + } + + private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception { + + final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + final String conf = isLookUpService + .getResourceProfileByQuery( + String + .format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + profId)); + + final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); + dedupConfig.getPace().initModel(); + dedupConfig.getPace().initTranslationMap(); + // dedupConfig.getWf().setConfigurationId("???"); + + return dedupConfig; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java new file mode 100644 index 000000000..dac308f36 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java @@ -0,0 +1,94 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.TypedColumn; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OaBrokerMainEntityAggregator; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; +import scala.Tuple2; + +public class JoinEntitiesJob { + + private static final Logger log = LoggerFactory.getLogger(JoinEntitiesJob.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + JoinEntitiesJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.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 workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String joinedEntitiesPath = workingPath + "/joinedEntities"; + log.info("joinedEntitiesPath: {}", joinedEntitiesPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, joinedEntitiesPath); + + final Dataset r0 = ClusterUtils + .readPath(spark, graphPath + "/simpleEntities", OaBrokerMainEntity.class); + + final Dataset r1 = join( + r0, ClusterUtils.readPath(spark, graphPath + "/relatedProjects", RelatedProject.class)); + final Dataset r2 = join( + r1, ClusterUtils.readPath(spark, graphPath + "/relatedDatasets", RelatedDataset.class)); + final Dataset r3 = join( + r2, ClusterUtils.readPath(spark, graphPath + "/relatedPublications", RelatedPublication.class)); + final Dataset r4 = join( + r3, ClusterUtils.readPath(spark, graphPath + "/relatedSoftwares", RelatedSoftware.class)); + + r4.write().mode(SaveMode.Overwrite).json(joinedEntitiesPath); + + }); + + } + + private static Dataset join(final Dataset sources, + final Dataset typedRels) { + + final TypedColumn, OaBrokerMainEntity> aggr = new OaBrokerMainEntityAggregator() + .toColumn(); + + return sources + .joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer") + .groupByKey( + (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) + .agg(aggr) + .map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class)); + + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java new file mode 100644 index 000000000..aa057eee8 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.TypedColumn; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; +import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +public class PrepareGroupsJob { + + private static final Logger log = LoggerFactory.getLogger(PrepareGroupsJob.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + JoinEntitiesJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.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 workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String groupsPath = workingPath + "/groups"; + log.info("groupsPath: {}", groupsPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + + ClusterUtils.removeDir(spark, groupsPath); + + final Dataset results = ClusterUtils + .readPath(spark, graphPath + "/joinedEntities", OaBrokerMainEntity.class); + + final Dataset mergedRels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); + + final TypedColumn, ResultGroup> aggr = new ResultAggregator() + .toColumn(); + + final Dataset groups = results + .joinWith(mergedRels, results.col("openaireId").equalTo(mergedRels.col("source")), "inner") + .groupByKey( + (MapFunction, String>) t -> t._2.getTarget(), + Encoders.STRING()) + .agg(aggr) + .map( + (MapFunction, ResultGroup>) t -> t._2, Encoders.bean(ResultGroup.class)) + .filter(rg -> rg.getData().size() > 1); + + groups + .write() + .mode(SaveMode.Overwrite) + .json(groupsPath); + + }); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java similarity index 82% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 4a10fbabf..edf9b9a7e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedDatasets.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -19,16 +19,16 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; import eu.dnetlib.dhp.schema.oaf.Relation; -public class GenerateRelatedDatasets { +public class PrepareRelatedDatasetsJob { - private static final Logger log = LoggerFactory.getLogger(GenerateRelatedDatasets.class); + private static final Logger log = LoggerFactory.getLogger(PrepareRelatedDatasetsJob.class); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - GenerateRelatedDatasets.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.json"))); + PrepareRelatedDatasetsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -40,7 +40,10 @@ public class GenerateRelatedDatasets { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String relsPath = parser.get("relsPath"); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String relsPath = workingPath + "/relatedDatasets"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java similarity index 84% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index 59ed388e7..00957972a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedProjects.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -23,9 +23,9 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; -public class GenerateRelatedProjects { +public class PrepareRelatedProjectsJob { - private static final Logger log = LoggerFactory.getLogger(GenerateRelatedProjects.class); + private static final Logger log = LoggerFactory.getLogger(PrepareRelatedProjectsJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -33,8 +33,8 @@ public class GenerateRelatedProjects { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - GenerateRelatedProjects.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.json"))); + PrepareRelatedProjectsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -46,7 +46,10 @@ public class GenerateRelatedProjects { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String relsPath = parser.get("relsPath"); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String relsPath = workingPath + "/relatedProjects"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java similarity index 83% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 0c20081dc..945fd9ed7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedPublications.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -22,9 +22,9 @@ import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; -public class GenerateRelatedPublications { +public class PrepareRelatedPublicationsJob { - private static final Logger log = LoggerFactory.getLogger(GenerateRelatedPublications.class); + private static final Logger log = LoggerFactory.getLogger(PrepareRelatedPublicationsJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -32,8 +32,8 @@ public class GenerateRelatedPublications { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - GenerateRelatedPublications.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.json"))); + PrepareRelatedPublicationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -45,7 +45,10 @@ public class GenerateRelatedPublications { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String relsPath = parser.get("relsPath"); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String relsPath = workingPath + "/relatedPublications"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java similarity index 83% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index b95788846..edb8dc1c3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateRelatedSoftwares.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -22,9 +22,9 @@ import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Software; -public class GenerateRelatedSoftwares { +public class PrepareRelatedSoftwaresJob { - private static final Logger log = LoggerFactory.getLogger(GenerateRelatedSoftwares.class); + private static final Logger log = LoggerFactory.getLogger(PrepareRelatedSoftwaresJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -32,8 +32,8 @@ public class GenerateRelatedSoftwares { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - GenerateRelatedSoftwares.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_relations.json"))); + PrepareRelatedSoftwaresJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -45,7 +45,10 @@ public class GenerateRelatedSoftwares { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String relsPath = parser.get("relsPath"); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String relsPath = workingPath + "/relatedSoftwares"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); @@ -53,6 +56,7 @@ public class GenerateRelatedSoftwares { runWithSparkSession(conf, isSparkSessionManaged, spark -> { ClusterUtils.removeDir(spark, relsPath); + final Dataset softwares = ClusterUtils.readPath(spark, graphPath + "/software", Software.class); final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java similarity index 68% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java index 59485d5cf..213003db2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateSimpleEntitities.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java @@ -18,19 +18,21 @@ import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; -public class GenerateSimpleEntitities { +public class PrepareSimpleEntititiesJob { - private static final Logger log = LoggerFactory.getLogger(GenerateSimpleEntitities.class); + private static final Logger log = LoggerFactory.getLogger(PrepareSimpleEntititiesJob.class); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - GenerateSimpleEntitities.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json"))); + PrepareSimpleEntititiesJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -42,7 +44,10 @@ public class GenerateSimpleEntitities { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String simpleEntitiesPath = parser.get("simpleEntitiesPath"); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + final String simpleEntitiesPath = workingPath + "/simpleEntities"; log.info("simpleEntitiesPath: {}", simpleEntitiesPath); final SparkConf conf = new SparkConf(); @@ -51,27 +56,18 @@ public class GenerateSimpleEntitities { ClusterUtils.removeDir(spark, simpleEntitiesPath); - expandResultsWithRelations(spark, graphPath, Publication.class) + prepareSimpleEntities(spark, graphPath, Publication.class) + .union(prepareSimpleEntities(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class)) + .union(prepareSimpleEntities(spark, graphPath, Software.class)) + .union(prepareSimpleEntities(spark, graphPath, OtherResearchProduct.class)) .write() .mode(SaveMode.Overwrite) .json(simpleEntitiesPath); - - // TODO UNCOMMENT THIS - // spark - // .emptyDataset(Encoders.bean(Event.class)) - // .union(generateEvents(spark, graphPath, Publication.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, Software.class, dedupConfig)) - // .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig)) - // .write() - // .mode(SaveMode.Overwrite) - // .option("compression", "gzip") - // .json(eventsPath); }); } - private static Dataset expandResultsWithRelations( + private static Dataset prepareSimpleEntities( final SparkSession spark, final String graphPath, final Class sourceClass) { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index 8bcea5e6e..15a1ddd88 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -14,6 +14,10 @@ public class ClusterUtils { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static void createDirIfMissing(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + public static void removeDir(final SparkSession spark, final String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json similarity index 64% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json index 32fd1d8f3..adee1888a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_relations.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json @@ -7,8 +7,8 @@ }, { "paramName": "o", - "paramLongName": "relsPath", - "paramDescription": "the path where the generated relations will be stored", + "paramLongName": "workingPath", + "paramDescription": "the path where the temporary data will be stored", "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea9aabcfc..74abcd268 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -6,8 +6,8 @@ the path where the graph is stored - eventsOutputPath - the path where the the events will be stored + workingPath + the path where the the generated data will be stored isLookupUrl @@ -73,18 +73,35 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + + + + + + + + + + + + + + + + + + yarn cluster - GenerateEvents - eu.dnetlib.dhp.broker.oa.GenerateEventsApplication + PrepareSimpleEntititiesJob + eu.dnetlib.dhp.broker.oa.PrepareSimpleEntititiesJob dhp-broker-events-${projectVersion}.jar --executor-cores=${sparkExecutorCores} @@ -97,7 +114,183 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --eventsPath${eventsOutputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareRelatedDatasetsJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedDatasetsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareRelatedProjectsJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedProjectsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareRelatedPublicationsJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedPublicationsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareRelatedSoftwaresJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedSoftwaresJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + + yarn + cluster + JoinEntitiesJob + eu.dnetlib.dhp.broker.oa.JoinEntitiesJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareGroupsJob + eu.dnetlib.dhp.broker.oa.PrepareGroupsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + GenerateEventsJob + eu.dnetlib.dhp.broker.oa.GenerateEventsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} --isLookupUrl${isLookupUrl} --dedupConfProfile${dedupConfProfId} @@ -105,6 +298,9 @@ + + + diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_broker_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json similarity index 94% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_broker_events.json rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index 6ab6d9a2d..d185bc73d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_broker_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -7,7 +7,7 @@ }, { "paramName": "o", - "paramLongName": "eventsPath", + "paramLongName": "workingPath", "paramDescription": "the path where the generated events will be stored", "paramRequired": true }, diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json deleted file mode 100644 index 6f5e330f6..000000000 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_simple_entities.json +++ /dev/null @@ -1,14 +0,0 @@ -[ - { - "paramName": "g", - "paramLongName": "graphPath", - "paramDescription": "the path where there the graph is stored", - "paramRequired": true - }, - { - "paramName": "o", - "paramLongName": "simpleEntitiesPath", - "paramDescription": "the path where the generated simple entities (without relations) will be stored", - "paramRequired": true - } -] From 3ce20c198ebd38b8c66c162bd4884986d4fc4e78 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 22 Jun 2020 12:14:25 +0200 Subject: [PATCH 08/16] reformatting --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 74abcd268..9783fcab6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -79,7 +79,6 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - @@ -120,7 +119,6 @@ - yarn @@ -145,7 +143,6 @@ - yarn @@ -170,7 +167,6 @@ - yarn @@ -195,7 +191,6 @@ - yarn @@ -246,7 +241,6 @@ - yarn @@ -271,7 +265,6 @@ - yarn @@ -297,10 +290,6 @@ - - - - From e162ba5075e43b09b784000f513266e4c479549c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Jun 2020 14:12:28 +0200 Subject: [PATCH 09/16] added dnet workflows to orchestrate the execution of graph2hive, updateSolr and updateStats oozie wfs --- .../{provision.xml => graph_construction.xml} | 2 +- .../dhp/wf/profiles/graph_to_hiveDB.xml | 73 ++++++++++++++ .../dnetlib/dhp/wf/profiles/update_solr.xml | 98 +++++++++++++++++++ .../dnetlib/dhp/wf/profiles/update_stats.xml | 74 ++++++++++++++ 4 files changed, 246 insertions(+), 1 deletion(-) rename dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/{provision.xml => graph_construction.xml} (99%) create mode 100644 dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_to_hiveDB.xml create mode 100644 dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_solr.xml create mode 100644 dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_stats.xml diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_construction.xml similarity index 99% rename from dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml rename to dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_construction.xml index 28cbde70d..819b3e12d 100644 --- a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_construction.xml @@ -7,7 +7,7 @@ - Data Provision [OCEAN] + Graph Construction [OCEAN] Data Provision 30 diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_to_hiveDB.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_to_hiveDB.xml new file mode 100644 index 000000000..0ace12ea3 --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_to_hiveDB.xml @@ -0,0 +1,73 @@ + +
+ + + + + +
+ + Graph to HiveDB [OCEAN] + Data Provision + 30 + + + Set the path containing the AGGREGATOR graph + + inputPath + + + + + + + + Set the target path to store the RAW graph + + hiveDbName + + + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'inputPath' : 'inputPath', + 'hiveDbName' : 'hiveDbName' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/graph/hive/oozie_app' + } + + build-report + + + + + + + + + wf_20200615_163630_609 + 2020-06-15T17:08:00+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_solr.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_solr.xml new file mode 100644 index 000000000..8a7738bcf --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_solr.xml @@ -0,0 +1,98 @@ + +
+ + + + + +
+ + Update Solr [OCEAN] + Data Provision + 30 + + + Set the path containing the AGGREGATOR graph + + inputGraphRootPath + + + + + + + + Set the target path to store the RAW graph + + format + TMF + + + + + + + Set the lookup address + + isLookupUrl + http://beta.services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'inputGraphRootPath' : 'inputGraphRootPath', + 'isLookupUrl' : 'isLookupUrl', + 'format' : 'format' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/provision/oozie_app', + 'maxRelations' : '100', + 'relPartitions' : '3000', + 'batchSize' : '2000', + 'relationFilter' : 'isAuthorInstitutionOf,produces,hasAmongTopNSimilarDocuments', + 'otherDsTypeId' : 'scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource', + 'resumeFrom' : 'prepare_relations', + 'sparkDriverMemoryForJoining' : '3G', + 'sparkExecutorMemoryForJoining' : '7G', + 'sparkExecutorCoresForJoining' : '4', + 'sparkDriverMemoryForIndexing' : '2G', + 'sparkExecutorMemoryForIndexing' : '2G', + 'sparkExecutorCoresForIndexing' : '64', + 'sparkNetworkTimeout' : '600', + 'workingDir' : '/tmp/beta_provision/working_dir/update_solr' + } + + build-report + + + + + + + + + wf_20200615_163630_609 + 2020-06-15T17:08:00+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_stats.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_stats.xml new file mode 100644 index 000000000..a91b6302e --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/update_stats.xml @@ -0,0 +1,74 @@ + +
+ + + + + +
+ + Update Stats [OCEAN] + Data Provision + 30 + + + Set the path containing the AGGREGATOR graph + + openaire_db_name + + + + + + + + Set the target path to store the RAW graph + + stats_db_name + + + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'openaire_db_name' : 'openaire_db_name', + 'stats_db_name' : 'stats_db_name' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/graph/stats/oozie_app', + 'hive_timeout' : '3000' + } + + build-report + + + + + + + + + wf_20200615_163630_609 + 2020-06-15T17:08:00+00:00 + SUCCESS + + + + \ No newline at end of file From af2f7705fc631c7dbd7d0f7918f21e525e507ab2 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 23 Jun 2020 08:37:35 +0200 Subject: [PATCH 10/16] partial refactoring of some joins --- .../broker/oa/PrepareRelatedDatasetsJob.java | 16 +- .../broker/oa/PrepareRelatedProjectsJob.java | 4 +- .../oa/PrepareRelatedPublicationsJob.java | 29 +-- .../broker/oa/PrepareRelatedSoftwaresJob.java | 28 ++- .../broker/oa/PrepareSimpleEntititiesJob.java | 1 + .../dhp/broker/oa/util/ClusterUtils.java | 4 + .../oa/generate_all/oozie_app/workflow.xml | 9 +- .../oa/partial/oozie_app/config-default.xml | 18 ++ .../broker/oa/partial/oozie_app/workflow.xml | 215 ++++++++++++++++++ 9 files changed, 289 insertions(+), 35 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index edf9b9a7e..bcd333d56 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -13,6 +13,7 @@ import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; @@ -52,18 +53,23 @@ public class PrepareRelatedDatasetsJob { ClusterUtils.removeDir(spark, relsPath); - final Dataset datasets = ClusterUtils - .readPath(spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + final Dataset datasets = ClusterUtils + .readPath(spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class) + .filter(d -> !ClusterUtils.isDedupRoot(d.getId())) + .map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class)); - final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + final Dataset rels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) + .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels - .joinWith(datasets, datasets.col("id").equalTo(rels.col("target")), "inner") + .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") .map( t -> new RelatedDataset( t._1.getSource(), t._1.getRelType(), - ConversionUtils.oafDatasetToBrokerDataset(t._2)), + t._2), Encoders.bean(RelatedDataset.class)) .write() .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index 00957972a..0460bfabb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -62,7 +62,9 @@ public class PrepareRelatedProjectsJob { final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)); + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) + .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) + .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels .joinWith(projects, projects.col("id").equalTo(rels.col("target")), "inner") diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 945fd9ed7..f3db509bb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -15,6 +15,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; @@ -31,9 +32,8 @@ public class PrepareRelatedPublicationsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - PrepareRelatedPublicationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString(PrepareRelatedPublicationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -57,19 +57,22 @@ public class PrepareRelatedPublicationsJob { ClusterUtils.removeDir(spark, relsPath); - final Dataset pubs = ClusterUtils - .readPath(spark, graphPath + "/publication", Publication.class); + final Dataset pubs = ClusterUtils + .readPath(spark, graphPath + "/publication", Publication.class) + .filter(p -> !ClusterUtils.isDedupRoot(p.getId())) + .map(ConversionUtils::oafPublicationToBrokerPublication, Encoders.bean(OaBrokerRelatedPublication.class)); - final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + final Dataset rels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) + .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels - .joinWith(pubs, pubs.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedPublication( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafPublicationToBrokerPublication(t._2)), - Encoders.bean(RelatedPublication.class)) + .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") + .map(t -> new RelatedPublication( + t._1.getSource(), + t._1.getRelType(), + t._2), Encoders.bean(RelatedPublication.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index edb8dc1c3..ffc3a8c65 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -15,6 +15,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; @@ -31,9 +32,8 @@ public class PrepareRelatedSoftwaresJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - PrepareRelatedSoftwaresJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString(PrepareRelatedSoftwaresJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -57,18 +57,22 @@ public class PrepareRelatedSoftwaresJob { ClusterUtils.removeDir(spark, relsPath); - final Dataset softwares = ClusterUtils.readPath(spark, graphPath + "/software", Software.class); + final Dataset softwares = ClusterUtils + .readPath(spark, graphPath + "/software", Software.class) + .filter(sw -> !ClusterUtils.isDedupRoot(sw.getId())) + .map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class)); - final Dataset rels = ClusterUtils.readPath(spark, graphPath + "/relation", Relation.class); + final Dataset rels = ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) + .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels - .joinWith(softwares, softwares.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedSoftware( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafSoftwareToBrokerSoftware(t._2)), - Encoders.bean(RelatedSoftware.class)) + .joinWith(softwares, softwares.col("openaireId").equalTo(rels.col("target")), "inner") + .map(t -> new RelatedSoftware( + t._1.getSource(), + t._1.getRelType(), + t._2), Encoders.bean(RelatedSoftware.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java index 213003db2..1b9c279fd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java @@ -74,6 +74,7 @@ public class PrepareSimpleEntititiesJob { return ClusterUtils .readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass) + .filter(r -> !ClusterUtils.isDedupRoot(r.getId())) .filter(r -> r.getDataInfo().getDeletedbyinference()) .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OaBrokerMainEntity.class)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index 15a1ddd88..968bde881 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -32,4 +32,8 @@ public class ClusterUtils { .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } + public static boolean isDedupRoot(final String id) { + return id.contains("dedup_wf_"); + } + } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 9783fcab6..bec6f221d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -88,11 +88,11 @@ - + + - @@ -119,6 +119,7 @@ + yarn @@ -190,7 +191,7 @@ - + yarn @@ -214,7 +215,7 @@ - + diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml new file mode 100644 index 000000000..2e0ed9aee --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml new file mode 100644 index 000000000..253910595 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml @@ -0,0 +1,215 @@ + + + + + graphInputPath + the path where the graph is stored + + + workingPath + the path where the the generated data will be stored + + + isLookupUrl + the address of the lookUp service + + + dedupConfProfId + the id of a valid Dedup Configuration Profile + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + yarn + cluster + PrepareRelatedPublicationsJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedPublicationsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + + yarn + cluster + PrepareRelatedDatasetsJob + eu.dnetlib.dhp.broker.oa.PrepareRelatedDatasetsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + yarn + cluster + JoinEntitiesJob + eu.dnetlib.dhp.broker.oa.JoinEntitiesJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + yarn + cluster + PrepareGroupsJob + eu.dnetlib.dhp.broker.oa.PrepareGroupsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + + + + + + + + yarn + cluster + GenerateEventsJob + eu.dnetlib.dhp.broker.oa.GenerateEventsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --graphPath${graphInputPath} + --workingPath${workingPath} + --isLookupUrl${isLookupUrl} + --dedupConfProfile${dedupConfProfId} + + + + + + + + \ No newline at end of file From c3286f4c37d8e828ae00240a45e933fc03d9fabc Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 23 Jun 2020 09:32:32 +0200 Subject: [PATCH 11/16] fixed relType --- .../broker/oa/PrepareRelatedDatasetsJob.java | 15 ++++++++----- .../broker/oa/PrepareRelatedProjectsJob.java | 17 +++++++------- .../oa/PrepareRelatedPublicationsJob.java | 22 +++++++++++++------ .../broker/oa/PrepareRelatedSoftwaresJob.java | 14 +++++++----- .../aggregators/withRels/RelatedDataset.java | 13 ++--------- .../aggregators/withRels/RelatedProject.java | 12 +--------- .../withRels/RelatedPublication.java | 13 +---------- .../aggregators/withRels/RelatedSoftware.java | 13 ++--------- 8 files changed, 47 insertions(+), 72 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index bcd333d56..110f5f317 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -15,9 +15,11 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; public class PrepareRelatedDatasetsJob { @@ -60,17 +62,18 @@ public class PrepareRelatedDatasetsJob { final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedDataset( - t._1.getSource(), - t._1.getRelType(), - t._2), - Encoders.bean(RelatedDataset.class)) + .map(t -> { + final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2); + rel.getRelDataset().setRelType(t._1.getRelClass()); + return rel; + }, Encoders.bean(RelatedDataset.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index 0460bfabb..3ae240982 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -15,7 +15,9 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.broker.objects.OaBrokerProject; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; @@ -58,22 +60,21 @@ public class PrepareRelatedProjectsJob { ClusterUtils.removeDir(spark, relsPath); - final Dataset projects = ClusterUtils.readPath(spark, graphPath + "/project", Project.class); + final Dataset projects = ClusterUtils + .readPath(spark, graphPath + "/project", Project.class) + .filter(p -> !ClusterUtils.isDedupRoot(p.getId())) + .map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class)); final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels - .joinWith(projects, projects.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> new RelatedProject( - t._1.getSource(), - t._1.getRelType(), - ConversionUtils.oafProjectToBrokerProject(t._2)), - Encoders.bean(RelatedProject.class)) + .joinWith(projects, projects.col("openaireId").equalTo(rels.col("target")), "inner") + .map(t -> new RelatedProject(t._1.getSource(), t._2), Encoders.bean(RelatedProject.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index f3db509bb..17e078c2c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -17,9 +17,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -32,8 +34,9 @@ public class PrepareRelatedPublicationsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PrepareRelatedPublicationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString( + PrepareRelatedPublicationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -60,19 +63,24 @@ public class PrepareRelatedPublicationsJob { final Dataset pubs = ClusterUtils .readPath(spark, graphPath + "/publication", Publication.class) .filter(p -> !ClusterUtils.isDedupRoot(p.getId())) - .map(ConversionUtils::oafPublicationToBrokerPublication, Encoders.bean(OaBrokerRelatedPublication.class)); + .map( + ConversionUtils::oafPublicationToBrokerPublication, + Encoders.bean(OaBrokerRelatedPublication.class)); final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") - .map(t -> new RelatedPublication( - t._1.getSource(), - t._1.getRelType(), - t._2), Encoders.bean(RelatedPublication.class)) + .map(t -> { + final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2); + rel.getRelPublication().setRelType(t._1.getRelClass()); + return rel; + }, Encoders.bean(RelatedPublication.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index ffc3a8c65..0704fb44a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -17,9 +17,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Software; @@ -32,8 +34,9 @@ public class PrepareRelatedSoftwaresJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PrepareRelatedSoftwaresJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString( + PrepareRelatedSoftwaresJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -64,15 +67,14 @@ public class PrepareRelatedSoftwaresJob { final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); rels .joinWith(softwares, softwares.col("openaireId").equalTo(rels.col("target")), "inner") - .map(t -> new RelatedSoftware( - t._1.getSource(), - t._1.getRelType(), - t._2), Encoders.bean(RelatedSoftware.class)) + .map(t -> new RelatedSoftware(t._1.getSource(), t._2), Encoders.bean(RelatedSoftware.class)) .write() .mode(SaveMode.Overwrite) .json(relsPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java index daf75ea2e..0925e3291 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java @@ -11,16 +11,15 @@ public class RelatedDataset implements Serializable { * */ private static final long serialVersionUID = 774487705184038324L; + private String source; - private String relType; private OaBrokerRelatedDataset relDataset; public RelatedDataset() { } - public RelatedDataset(final String source, final String relType, final OaBrokerRelatedDataset relDataset) { + public RelatedDataset(final String source, final OaBrokerRelatedDataset relDataset) { this.source = source; - this.relType = relType; this.relDataset = relDataset; } @@ -32,14 +31,6 @@ public class RelatedDataset implements Serializable { this.source = source; } - public String getRelType() { - return relType; - } - - public void setRelType(final String relType) { - this.relType = relType; - } - public OaBrokerRelatedDataset getRelDataset() { return relDataset; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java index 4116c8c77..74d19fe9d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java @@ -13,15 +13,13 @@ public class RelatedProject implements Serializable { private static final long serialVersionUID = 4941437626549329870L; private String source; - private String relType; private OaBrokerProject relProject; public RelatedProject() { } - public RelatedProject(final String source, final String relType, final OaBrokerProject relProject) { + public RelatedProject(final String source, final OaBrokerProject relProject) { this.source = source; - this.relType = relType; this.relProject = relProject; } @@ -33,14 +31,6 @@ public class RelatedProject implements Serializable { this.source = source; } - public String getRelType() { - return relType; - } - - public void setRelType(final String relType) { - this.relType = relType; - } - public OaBrokerProject getRelProject() { return relProject; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java index 9e222a952..ed6aeeab1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java @@ -13,16 +13,13 @@ public class RelatedPublication implements Serializable { private static final long serialVersionUID = 9021609640411395128L; private String source; - private String relType; private OaBrokerRelatedPublication relPublication; public RelatedPublication() { } - public RelatedPublication(final String source, final String relType, - final OaBrokerRelatedPublication relPublication) { + public RelatedPublication(final String source, final OaBrokerRelatedPublication relPublication) { this.source = source; - this.relType = relType; this.relPublication = relPublication; } @@ -34,14 +31,6 @@ public class RelatedPublication implements Serializable { this.source = source; } - public String getRelType() { - return relType; - } - - public void setRelType(final String relType) { - this.relType = relType; - } - public OaBrokerRelatedPublication getRelPublication() { return relPublication; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java index 2f3b8668c..0aa3a4045 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java @@ -11,16 +11,15 @@ public class RelatedSoftware implements Serializable { * */ private static final long serialVersionUID = 7573383356943300157L; + private String source; - private String relType; private OaBrokerRelatedSoftware relSoftware; public RelatedSoftware() { } - public RelatedSoftware(final String source, final String relType, final OaBrokerRelatedSoftware relSoftware) { + public RelatedSoftware(final String source, final OaBrokerRelatedSoftware relSoftware) { this.source = source; - this.relType = relType; this.relSoftware = relSoftware; } @@ -32,14 +31,6 @@ public class RelatedSoftware implements Serializable { this.source = source; } - public String getRelType() { - return relType; - } - - public void setRelType(final String relType) { - this.relType = relType; - } - public OaBrokerRelatedSoftware getRelSoftware() { return relSoftware; } From 38bb45d0b6cd28cc8c73f89b681b7def19877c47 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 23 Jun 2020 10:14:39 +0200 Subject: [PATCH 12/16] test osf:refereed --- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 ++ .../test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml | 1 + .../test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 + 3 files changed, 4 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 9bd20303f..b1f0ecf0d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -111,6 +111,7 @@ public class MappersTest { assertNotNull(i.getAccessright()); assertEquals("OPEN", i.getAccessright().getClassid()); }); + assertEquals("0001", p.getInstance().get(0).getRefereed().getClassid()); assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); @@ -217,6 +218,7 @@ public class MappersTest { assertNotNull(i.getAccessright()); assertEquals("OPEN", i.getAccessright().getClassid()); }); + assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid()); assertValidId(r1.getSource()); assertValidId(r1.getTarget()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 2cb0ba1c7..ead22aa96 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -57,6 +57,7 @@ 10.3897/oneeco.2.e13718 https://oneecosystem.pensoft.net/article/13718/ One Ecosystem + 0001 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 88ae9d106..5525a2753 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -90,6 +90,7 @@ corda_______::226852 + 0001s Date: Tue, 23 Jun 2020 10:24:15 +0200 Subject: [PATCH 13/16] filter of valid resultResult relations --- .../dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java | 3 +-- .../dhp/broker/oa/PrepareRelatedPublicationsJob.java | 3 +-- .../java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java | 8 ++++++++ 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 110f5f317..fe9c87e87 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -15,7 +15,6 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.broker.objects.OaBrokerRelatedDataset; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; @@ -63,7 +62,7 @@ public class PrepareRelatedDatasetsJob { final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) - .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) + .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 17e078c2c..8814ef3e0 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -17,7 +17,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; @@ -70,7 +69,7 @@ public class PrepareRelatedPublicationsJob { final Dataset rels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) - .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) + .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) .filter(r -> !ClusterUtils.isDedupRoot(r.getSource())) .filter(r -> !ClusterUtils.isDedupRoot(r.getTarget())); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index 968bde881..de9b901d0 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -36,4 +36,12 @@ public class ClusterUtils { return id.contains("dedup_wf_"); } + public static final boolean isValidResultResultClass(final String s) { + return s.equals("isReferencedBy") + || s.equals("isRelatedTo") + || s.equals("references") + || s.equals("isSupplementedBy") + || s.equals("isSupplementedTo"); + } + } From d13e3d3f6896efc23ecac430e629e163cb4615c6 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 23 Jun 2020 11:01:42 +0200 Subject: [PATCH 14/16] fixed paths --- .../dhp/broker/oa/GenerateEventsJob.java | 5 +- .../dhp/broker/oa/JoinEntitiesJob.java | 13 ++-- .../dhp/broker/oa/PrepareGroupsJob.java | 2 +- .../oa/generate_all/oozie_app/workflow.xml | 1 - .../dhp/broker/oa/generate_events.json | 6 -- .../broker/oa/partial/oozie_app/workflow.xml | 59 +------------------ 6 files changed, 8 insertions(+), 78 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 3ea0086ff..089fbf6d4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -44,9 +44,6 @@ public class GenerateEventsJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); @@ -70,7 +67,7 @@ public class GenerateEventsJob { ClusterUtils.removeDir(spark, eventsPath); final Dataset groups = ClusterUtils - .readPath(spark, graphPath + "/relation", ResultGroup.class); + .readPath(spark, workingPath + "/relation", ResultGroup.class); final Dataset events = groups .map( diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java index dac308f36..da77a4673 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java @@ -43,9 +43,6 @@ public class JoinEntitiesJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); @@ -59,16 +56,16 @@ public class JoinEntitiesJob { ClusterUtils.removeDir(spark, joinedEntitiesPath); final Dataset r0 = ClusterUtils - .readPath(spark, graphPath + "/simpleEntities", OaBrokerMainEntity.class); + .readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class); final Dataset r1 = join( - r0, ClusterUtils.readPath(spark, graphPath + "/relatedProjects", RelatedProject.class)); + r0, ClusterUtils.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class)); final Dataset r2 = join( - r1, ClusterUtils.readPath(spark, graphPath + "/relatedDatasets", RelatedDataset.class)); + r1, ClusterUtils.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class)); final Dataset r3 = join( - r2, ClusterUtils.readPath(spark, graphPath + "/relatedPublications", RelatedPublication.class)); + r2, ClusterUtils.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class)); final Dataset r4 = join( - r3, ClusterUtils.readPath(spark, graphPath + "/relatedSoftwares", RelatedSoftware.class)); + r3, ClusterUtils.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class)); r4.write().mode(SaveMode.Overwrite).json(joinedEntitiesPath); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index aa057eee8..159047dad 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -58,7 +58,7 @@ public class PrepareGroupsJob { ClusterUtils.removeDir(spark, groupsPath); final Dataset results = ClusterUtils - .readPath(spark, graphPath + "/joinedEntities", OaBrokerMainEntity.class); + .readPath(spark, workingPath + "/joinedEntities", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index bec6f221d..18e2eedca 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -283,7 +283,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --graphPath${graphInputPath} --workingPath${workingPath} --isLookupUrl${isLookupUrl} --dedupConfProfile${dedupConfProfId} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index d185bc73d..7ae076159 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -1,10 +1,4 @@ [ - { - "paramName": "g", - "paramLongName": "graphPath", - "paramDescription": "the path where there the graph is stored", - "paramRequired": true - }, { "paramName": "o", "paramLongName": "workingPath", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml index 253910595..1ccdef929 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml @@ -73,68 +73,12 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - yarn - cluster - PrepareRelatedPublicationsJob - eu.dnetlib.dhp.broker.oa.PrepareRelatedPublicationsJob - dhp-broker-events-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - --graphPath${graphInputPath} - --workingPath${workingPath} - - - - - - - - - yarn - cluster - PrepareRelatedDatasetsJob - eu.dnetlib.dhp.broker.oa.PrepareRelatedDatasetsJob - dhp-broker-events-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - --graphPath${graphInputPath} - --workingPath${workingPath} - - - - @@ -201,7 +145,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --graphPath${graphInputPath} --workingPath${workingPath} --isLookupUrl${isLookupUrl} --dedupConfProfile${dedupConfProfId} From 8b9933b934eac804d50f126411a3f27ee2384182 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 24 Jun 2020 08:57:13 +0200 Subject: [PATCH 15/16] refactoring aggregators --- .../dhp/broker/oa/GenerateEventsJob.java | 2 +- .../dhp/broker/oa/JoinEntitiesJob.java | 35 +++++---- .../dhp/broker/oa/PrepareGroupsJob.java | 2 +- .../OaBrokerMainEntityAggregator.java | 71 ------------------- .../withRels/RelatedDatasetAggregator.java | 58 +++++++++++++++ .../withRels/RelatedProjectAggregator.java | 58 +++++++++++++++ .../RelatedPublicationAggregator.java | 59 +++++++++++++++ .../withRels/RelatedSoftwareAggregator.java | 58 +++++++++++++++ 8 files changed, 252 insertions(+), 91 deletions(-) delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 089fbf6d4..eaeb6d271 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -67,7 +67,7 @@ public class GenerateEventsJob { ClusterUtils.removeDir(spark, eventsPath); final Dataset groups = ClusterUtils - .readPath(spark, workingPath + "/relation", ResultGroup.class); + .readPath(spark, workingPath + "/duplicates", ResultGroup.class); final Dataset events = groups .map( diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java index da77a4673..868faa8f5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinEntitiesJob.java @@ -11,18 +11,15 @@ import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.TypedColumn; +import org.apache.spark.sql.expressions.Aggregator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OaBrokerMainEntityAggregator; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProjectAggregator; import scala.Tuple2; public class JoinEntitiesJob { @@ -59,31 +56,33 @@ public class JoinEntitiesJob { .readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class); final Dataset r1 = join( - r0, ClusterUtils.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class)); - final Dataset r2 = join( - r1, ClusterUtils.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class)); - final Dataset r3 = join( - r2, ClusterUtils.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class)); - final Dataset r4 = join( - r3, ClusterUtils.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class)); + r0, ClusterUtils.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class), + new RelatedProjectAggregator()); + // final Dataset r2 = join( + // r1, ClusterUtils.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class), new + // RelatedDatasetAggregator()); + // final Dataset r3 = join( + // r2, ClusterUtils.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class), new + // RelatedPublicationAggregator()); + // final Dataset r4 = join( + // r3, ClusterUtils.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class), new + // RelatedSoftwareAggregator()); - r4.write().mode(SaveMode.Overwrite).json(joinedEntitiesPath); + r1.write().mode(SaveMode.Overwrite).json(joinedEntitiesPath); }); } private static Dataset join(final Dataset sources, - final Dataset typedRels) { - - final TypedColumn, OaBrokerMainEntity> aggr = new OaBrokerMainEntityAggregator() - .toColumn(); + final Dataset typedRels, + final Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> aggr) { return sources .joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer") .groupByKey( (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) - .agg(aggr) + .agg(aggr.toColumn()) .map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index 159047dad..934ddff59 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -48,7 +48,7 @@ public class PrepareGroupsJob { final String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); - final String groupsPath = workingPath + "/groups"; + final String groupsPath = workingPath + "/duplicates"; log.info("groupsPath: {}", groupsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java deleted file mode 100644 index 6a2d9b06d..000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OaBrokerMainEntityAggregator.java +++ /dev/null @@ -1,71 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; - -import org.apache.spark.sql.Encoder; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.expressions.Aggregator; - -import eu.dnetlib.broker.objects.OaBrokerMainEntity; -import scala.Tuple2; - -public class OaBrokerMainEntityAggregator - extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { - - /** - * - */ - private static final long serialVersionUID = -3687878788861013488L; - - @Override - public OaBrokerMainEntity zero() { - return new OaBrokerMainEntity(); - } - - @Override - public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { - return g; - } - - @Override - public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { - if (g.getOriginalId() == null) { - return t._1; - } else if (t._2 instanceof RelatedSoftware) { - g.getSoftwares().add(((RelatedSoftware) t._2).getRelSoftware()); - } else if (t._2 instanceof RelatedDataset) { - g.getDatasets().add(((RelatedDataset) t._2).getRelDataset()); - } else if (t._2 instanceof RelatedPublication) { - g.getPublications().add(((RelatedPublication) t._2).getRelPublication()); - } else if (t._2 instanceof RelatedProject) { - g.getProjects().add(((RelatedProject) t._2).getRelProject()); - } else { - throw new RuntimeException("Invalid Object: " + t._2.getClass()); - } - return g; - - } - - @Override - public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { - if (g1.getOriginalId() != null) { - g1.getSoftwares().addAll(g2.getSoftwares()); - g1.getDatasets().addAll(g2.getDatasets()); - g1.getPublications().addAll(g2.getPublications()); - g1.getProjects().addAll(g2.getProjects()); - return g1; - } else { - return g2; - } - } - - @Override - public Encoder bufferEncoder() { - return Encoders.bean(OaBrokerMainEntity.class); - } - - @Override - public Encoder outputEncoder() { - return Encoders.bean(OaBrokerMainEntity.class); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java new file mode 100644 index 000000000..04840afe9 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; + +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import scala.Tuple2; + +public class RelatedDatasetAggregator + extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { + + /** + * + */ + private static final long serialVersionUID = 6969761680131482557L; + + @Override + public OaBrokerMainEntity zero() { + return new OaBrokerMainEntity(); + } + + @Override + public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { + return g; + } + + @Override + public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; + res.getDatasets().add(t._2.getRelDataset()); + return res; + + } + + @Override + public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { + if (StringUtils.isNotBlank(g1.getOriginalId())) { + g1.getDatasets().addAll(g2.getDatasets()); + return g1; + } else { + return g2; + } + } + + @Override + public Encoder bufferEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + + @Override + public Encoder outputEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java new file mode 100644 index 000000000..025cc413a --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; + +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import scala.Tuple2; + +public class RelatedProjectAggregator + extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { + + /** + * + */ + private static final long serialVersionUID = 8559808519152275763L; + + @Override + public OaBrokerMainEntity zero() { + return new OaBrokerMainEntity(); + } + + @Override + public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { + return g; + } + + @Override + public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; + res.getProjects().add(t._2.getRelProject()); + return res; + + } + + @Override + public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { + if (StringUtils.isNotBlank(g1.getOriginalId())) { + g1.getProjects().addAll(g2.getProjects()); + return g1; + } else { + return g2; + } + } + + @Override + public Encoder bufferEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + + @Override + public Encoder outputEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java new file mode 100644 index 000000000..1b54d4a12 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java @@ -0,0 +1,59 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; + +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import scala.Tuple2; + +public class RelatedPublicationAggregator + extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { + + /** + * + */ + private static final long serialVersionUID = 4656934981558135919L; + + @Override + public OaBrokerMainEntity zero() { + return new OaBrokerMainEntity(); + } + + @Override + public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { + return g; + } + + @Override + public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, + final Tuple2 t) { + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; + res.getPublications().add(t._2.getRelPublication()); + return res; + + } + + @Override + public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { + if (StringUtils.isNotBlank(g1.getOriginalId())) { + g1.getPublications().addAll(g2.getPublications()); + return g1; + } else { + return g2; + } + } + + @Override + public Encoder bufferEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + + @Override + public Encoder outputEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java new file mode 100644 index 000000000..871cc4f06 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; + +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.broker.objects.OaBrokerMainEntity; +import scala.Tuple2; + +public class RelatedSoftwareAggregator + extends Aggregator, OaBrokerMainEntity, OaBrokerMainEntity> { + + /** + * + */ + private static final long serialVersionUID = -8987959389106443702L; + + @Override + public OaBrokerMainEntity zero() { + return new OaBrokerMainEntity(); + } + + @Override + public OaBrokerMainEntity finish(final OaBrokerMainEntity g) { + return g; + } + + @Override + public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; + res.getSoftwares().add(t._2.getRelSoftware()); + return res; + + } + + @Override + public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { + if (StringUtils.isNotBlank(g1.getOriginalId())) { + g1.getSoftwares().addAll(g2.getSoftwares()); + return g1; + } else { + return g2; + } + } + + @Override + public Encoder bufferEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + + @Override + public Encoder outputEncoder() { + return Encoders.bean(OaBrokerMainEntity.class); + } + +} From e53dd62e879dfe7645ca8f0a4e681f7e126fe090 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 24 Jun 2020 09:24:45 +0200 Subject: [PATCH 16/16] minot changes --- .../java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java | 2 +- .../aggregators/withRels/RelatedDatasetAggregator.java | 8 +++++--- .../aggregators/withRels/RelatedProjectAggregator.java | 8 +++++--- .../withRels/RelatedPublicationAggregator.java | 8 +++++--- .../aggregators/withRels/RelatedSoftwareAggregator.java | 8 +++++--- 5 files changed, 21 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index eaeb6d271..dbe2fdd47 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -53,7 +53,7 @@ public class GenerateEventsJob { final String dedupConfigProfileId = parser.get("dedupConfProfile"); log.info("dedupConfigProfileId: {}", dedupConfigProfileId); - final String eventsPath = workingPath + "/eventsPath"; + final String eventsPath = workingPath + "/events"; log.info("eventsPath: {}", eventsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java index 04840afe9..a963f073d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDatasetAggregator.java @@ -29,15 +29,17 @@ public class RelatedDatasetAggregator @Override public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { - final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; - res.getDatasets().add(t._2.getRelDataset()); + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1; + if (t._2 != null) { + res.getDatasets().add(t._2.getRelDataset()); + } return res; } @Override public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { - if (StringUtils.isNotBlank(g1.getOriginalId())) { + if (StringUtils.isNotBlank(g1.getOpenaireId())) { g1.getDatasets().addAll(g2.getDatasets()); return g1; } else { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java index 025cc413a..3fedb1a32 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProjectAggregator.java @@ -29,15 +29,17 @@ public class RelatedProjectAggregator @Override public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { - final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; - res.getProjects().add(t._2.getRelProject()); + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1; + if (t._2 != null) { + res.getProjects().add(t._2.getRelProject()); + } return res; } @Override public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { - if (StringUtils.isNotBlank(g1.getOriginalId())) { + if (StringUtils.isNotBlank(g1.getOpenaireId())) { g1.getProjects().addAll(g2.getProjects()); return g1; } else { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java index 1b54d4a12..b331599ad 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublicationAggregator.java @@ -30,15 +30,17 @@ public class RelatedPublicationAggregator @Override public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { - final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; - res.getPublications().add(t._2.getRelPublication()); + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1; + if (t._2 != null) { + res.getPublications().add(t._2.getRelPublication()); + } return res; } @Override public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { - if (StringUtils.isNotBlank(g1.getOriginalId())) { + if (StringUtils.isNotBlank(g1.getOpenaireId())) { g1.getPublications().addAll(g2.getPublications()); return g1; } else { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java index 871cc4f06..d3b1c3407 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftwareAggregator.java @@ -29,15 +29,17 @@ public class RelatedSoftwareAggregator @Override public OaBrokerMainEntity reduce(final OaBrokerMainEntity g, final Tuple2 t) { - final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOriginalId()) ? g : t._1; - res.getSoftwares().add(t._2.getRelSoftware()); + final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1; + if (t._2 != null) { + res.getSoftwares().add(t._2.getRelSoftware()); + } return res; } @Override public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) { - if (StringUtils.isNotBlank(g1.getOriginalId())) { + if (StringUtils.isNotBlank(g1.getOpenaireId())) { g1.getSoftwares().addAll(g2.getSoftwares()); return g1; } else {