diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 7a7a9a89c..79138d641 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -1,14 +1,25 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.List; import java.util.Objects; public abstract class Oaf implements Serializable { + protected List collectedfrom; + private DataInfo dataInfo; private Long lastupdatetimestamp; + public List getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + } + public DataInfo getDataInfo() { return dataInfo; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 86f4ff616..6db3b7f74 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -10,8 +10,6 @@ public abstract class OafEntity extends Oaf implements Serializable { private List originalId; - private List collectedfrom; - private List pid; private String dateofcollection; @@ -38,14 +36,6 @@ public abstract class OafEntity extends Oaf implements Serializable { this.originalId = originalId; } - public List getCollectedfrom() { - return collectedfrom; - } - - public void setCollectedfrom(List collectedfrom) { - this.collectedfrom = collectedfrom; - } - public List getPid() { return pid; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 9d211d058..aaeecb871 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -18,8 +18,6 @@ public class Relation extends Oaf { private String target; - private List collectedFrom = new ArrayList<>(); - public String getRelType() { return relType; } @@ -60,14 +58,6 @@ public class Relation extends Oaf { this.target = target; } - public List getCollectedFrom() { - return collectedFrom; - } - - public void setCollectedFrom(final List collectedFrom) { - this.collectedFrom = collectedFrom; - } - public void mergeFrom(final Relation r) { checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); @@ -77,12 +67,12 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedFrom( + setCollectedfrom( Stream.concat( - Optional.ofNullable(getCollectedFrom()) + Optional.ofNullable(getCollectedfrom()) .map(Collection::stream) .orElse(Stream.empty()), - Optional.ofNullable(r.getCollectedFrom()) + Optional.ofNullable(r.getCollectedfrom()) .map(Collection::stream) .orElse(Stream.empty())) .distinct() // relies on KeyValue.equals @@ -103,6 +93,6 @@ public class Relation extends Oaf { @Override public int hashCode() { - return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); + return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom); } } diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index aa2078be5..22ca7504d 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -47,6 +47,16 @@ jaxen + + org.apache.hadoop + hadoop-distcp + + + + eu.dnetlib + dnet-openaire-data-protos + + eu.dnetlib.dhp dhp-schemas @@ -57,6 +67,44 @@ eu.dnetlib dnet-actionmanager-api + + eu.dnetlib + dnet-actionmanager-common + + + eu.dnetlib + dnet-openaireplus-mapping-utils + + + saxonica + saxon + + + saxonica + saxon-dom + + + jgrapht + jgrapht + + + net.sf.ehcache + ehcache + + + org.springframework + spring-test + + + org.apache.* + * + + + apache + * + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java similarity index 96% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java index 126a97e39..8998a090d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; import java.util.Comparator; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java similarity index 88% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java index 680f7759c..db1bed48a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; import com.google.common.base.Splitter; import com.google.common.collect.Lists; @@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.io.File; import java.io.FileOutputStream; import java.io.OutputStream; -import java.util.*; +import java.util.ArrayList; +import java.util.LinkedList; +import java.util.List; +import java.util.Properties; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.tools.DistCp; import org.apache.hadoop.tools.DistCpOptions; import org.apache.hadoop.util.ToolRunner; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class MigrateActionSet { - private static final Log log = LogFactory.getLog(MigrateActionSet.class); + private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class); private static final String SEPARATOR = "/"; private static final String TARGET_PATHS = "target_paths"; private static final String RAWSET_PREFIX = "rawset_"; - private static Boolean DEFAULT_TRANSFORM_ONLY = false; - public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json"))); + "/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json"))); parser.parseArgument(args); new MigrateActionSet().run(parser); @@ -56,11 +57,11 @@ public class MigrateActionSet { final String transform_only_s = parser.get("transform_only"); - log.info("transform only param: " + transform_only_s); + log.info("transform only param: {}", transform_only_s); final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only")); - log.info("transform only: " + transformOnly); + log.info("transform only: {}", transformOnly); ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); @@ -79,22 +80,19 @@ public class MigrateActionSet { final List sourcePaths = getSourcePaths(sourceNN, isLookUp); log.info( - String.format( - "paths to process:\n%s", - sourcePaths.stream() - .map(p -> p.toString()) - .collect(Collectors.joining("\n")))); + "paths to process:\n{}", + sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n"))); for (Path source : sourcePaths) { if (!sourceFS.exists(source)) { - log.warn(String.format("skipping unexisting path: %s", source)); + log.warn("skipping unexisting path: {}", source); } else { LinkedList pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath())); final String rawSet = pathQ.pollLast(); - log.info(String.format("got RAWSET: %s", rawSet)); + log.info("got RAWSET: {}", rawSet); if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) { @@ -109,7 +107,7 @@ public class MigrateActionSet { + SEPARATOR + rawSet); - log.info(String.format("using TARGET PATH: %s", targetPath)); + log.info("using TARGET PATH: {}", targetPath); if (!transformOnly) { if (targetFS.exists(targetPath)) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index b5d027c03..adeffa9fc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -1,4 +1,9 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; + +import static eu.dnetlib.data.proto.KindProtos.Kind.entity; +import static eu.dnetlib.data.proto.KindProtos.Kind.relation; +import static eu.dnetlib.data.proto.TypeProtos.*; +import static eu.dnetlib.data.proto.TypeProtos.Type.*; import com.google.common.collect.Lists; import com.googlecode.protobuf.format.JsonFormat; @@ -41,7 +46,7 @@ public class ProtoConverter implements Serializable { rel.setRelType(r.getRelType().toString()); rel.setSubRelType(r.getSubRelType().toString()); rel.setRelClass(r.getRelClass()); - rel.setCollectedFrom( + rel.setCollectedfrom( r.getCollectedfromCount() > 0 ? r.getCollectedfromList().stream() .map(kv -> mapKV(kv)) diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java new file mode 100644 index 000000000..3226361cb --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java @@ -0,0 +1,179 @@ +package eu.dnetlib.dhp.actionmanager.migration; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.base.Splitter; +import com.google.common.collect.Lists; +import com.google.protobuf.InvalidProtocolBufferException; +import eu.dnetlib.data.proto.OafProtos; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.io.Serializable; +import java.util.LinkedList; +import java.util.Objects; +import java.util.Optional; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +public class TransformActions implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(TransformActions.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String SEPARATOR = "/"; + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateActionSet.class.getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json"))); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final String inputPaths = parser.get("inputPaths"); + + if (StringUtils.isBlank(inputPaths)) { + throw new RuntimeException("empty inputPaths"); + } + log.info("inputPaths: {}", inputPaths); + + final String targetBaseDir = getTargetBaseDir(isLookupUrl); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> transformActions(inputPaths, targetBaseDir, spark)); + } + + private static void transformActions( + String inputPaths, String targetBaseDir, SparkSession spark) throws IOException { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); + + for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { + + LinkedList pathQ = + Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); + + final String rawset = pathQ.pollLast(); + final String actionSetDirectory = pathQ.pollLast(); + + final Path targetDirectory = + new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset); + + if (fs.exists(targetDirectory)) { + log.info("found target directory '{}", targetDirectory); + fs.delete(targetDirectory, true); + log.info("deleted target directory '{}", targetDirectory); + } + + log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory); + + sc.sequenceFile(sourcePath, Text.class, Text.class) + .map( + a -> + eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( + a._2().toString())) + .map(TransformActions::doTransform) + .filter(Objects::nonNull) + .mapToPair( + a -> + new Tuple2<>( + a.getClazz().toString(), + OBJECT_MAPPER.writeValueAsString(a))) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + targetDirectory.toString(), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); + } + } + + private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) + throws InvalidProtocolBufferException { + + // dedup similarity relations had empty target value, don't migrate them + if (aa.getTargetValue().length == 0) { + return null; + } + final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); + final Oaf oaf = ProtoConverter.convert(proto_oaf); + switch (proto_oaf.getKind()) { + case entity: + switch (proto_oaf.getEntity().getType()) { + case datasource: + return new AtomicAction<>(Datasource.class, (Datasource) oaf); + case organization: + return new AtomicAction<>(Organization.class, (Organization) oaf); + case project: + return new AtomicAction<>(Project.class, (Project) oaf); + case result: + final String resulttypeid = + proto_oaf + .getEntity() + .getResult() + .getMetadata() + .getResulttype() + .getClassid(); + switch (resulttypeid) { + case "publication": + return new AtomicAction<>(Publication.class, (Publication) oaf); + case "software": + return new AtomicAction<>(Software.class, (Software) oaf); + case "other": + return new AtomicAction<>( + OtherResearchProduct.class, (OtherResearchProduct) oaf); + case "dataset": + return new AtomicAction<>(Dataset.class, (Dataset) oaf); + default: + // can be an update, where the resulttype is not specified + return new AtomicAction<>(Result.class, (Result) oaf); + } + default: + throw new IllegalArgumentException( + "invalid entity type: " + proto_oaf.getEntity().getType()); + } + case relation: + return new AtomicAction<>(Relation.class, (Relation) oaf); + default: + throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind()); + } + } + + private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException { + ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); + String XQUERY = + "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; + return isLookUp.getResourceProfileByQuery(XQUERY); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json new file mode 100644 index 000000000..c7b931c44 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json @@ -0,0 +1,56 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "sn", + "paramLongName": "sourceNameNode", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "tn", + "paramLongName": "targetNameNode", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDirectory", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "nm", + "paramLongName": "distcp_num_maps", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "mm", + "paramLongName": "distcp_memory_mb", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "tt", + "paramLongName": "distcp_task_timeout", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "tr", + "paramLongName": "transform_only", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json new file mode 100644 index 000000000..85c39c5b3 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "inputPaths", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/config-default.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/config-default.xml rename to dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml similarity index 63% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml rename to dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml index ed01c8de4..d8888de9d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml @@ -10,7 +10,6 @@ workingDirectory - /tmp/actionsets working directory @@ -44,6 +43,20 @@ 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 @@ -66,23 +79,27 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + - + - + - eu.dnetlib.dhp.migration.actions.MigrateActionSet + eu.dnetlib.dhp.actionmanager.migration.MigrateActionSet -Dmapred.task.timeout=${distcp_task_timeout} - -is${isLookupUrl} - -sn${sourceNN} - -tn${nameNode} - -w${workingDirectory} - -nm${distcp_num_maps} - -mm${distcp_memory_mb} - -tt${distcp_task_timeout} - -tr${transform_only} + --isLookupUrl${isLookupUrl} + --sourceNameNode${sourceNN} + --targetNameNode${nameNode} + --workingDirectory${workingDirectory} + --distcp_num_maps${distcp_num_maps} + --distcp_memory_mb${distcp_memory_mb} + --distcp_task_timeout${distcp_task_timeout} + --transform_only${transform_only} @@ -94,19 +111,18 @@ yarn cluster transform_actions - eu.dnetlib.dhp.migration.actions.TransformActions - dhp-aggregation-${projectVersion}.jar + eu.dnetlib.dhp.actionmanager.migration.TransformActions + dhp-actionmanager-${projectVersion}.jar - --executor-cores ${sparkExecutorCores} - --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -mtyarn - -is${isLookupUrl} + --isLookupUrl${isLookupUrl} --inputPaths${wf:actionData('migrate_actionsets')['target_paths']} diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json index bc65230a8..36d3fdd27 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json @@ -1,10 +1,10 @@ -{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java deleted file mode 100644 index 81c2e7705..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java +++ /dev/null @@ -1,213 +0,0 @@ -package eu.dnetlib.dhp.migration.actions; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.base.Splitter; -import com.google.common.collect.Lists; -import com.google.protobuf.InvalidProtocolBufferException; -import eu.dnetlib.data.proto.OafProtos; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import java.io.IOException; -import java.io.Serializable; -import java.util.LinkedList; -import java.util.Objects; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; - -public class TransformActions implements Serializable { - - private static final Log log = LogFactory.getLog(TransformActions.class); - private static final String SEPARATOR = "/"; - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json"))); - parser.parseArgument(args); - - new TransformActions().run(parser); - } - - private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException { - - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: " + isLookupUrl); - - final String inputPaths = parser.get("inputPaths"); - - if (StringUtils.isBlank(inputPaths)) { - throw new RuntimeException("empty inputPaths"); - } - log.info("inputPaths: " + inputPaths); - - final String targetBaseDir = getTargetBaseDir(isLookupUrl); - - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); - - for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { - - LinkedList pathQ = - Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); - - final String rawset = pathQ.pollLast(); - final String actionSetDirectory = pathQ.pollLast(); - - final Path targetDirectory = - new Path( - targetBaseDir - + SEPARATOR - + actionSetDirectory - + SEPARATOR - + rawset); - - if (fs.exists(targetDirectory)) { - log.info(String.format("found target directory '%s", targetDirectory)); - fs.delete(targetDirectory, true); - log.info(String.format("deleted target directory '%s", targetDirectory)); - } - - log.info( - String.format( - "transforming actions from '%s' to '%s'", - sourcePath, targetDirectory)); - - sc.sequenceFile(sourcePath, Text.class, Text.class) - .map( - a -> - eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( - a._2().toString())) - .map(a -> doTransform(a)) - .filter(Objects::isNull) - .filter(a -> a.getPayload() == null) - .map(a -> new ObjectMapper().writeValueAsString(a)) - .saveAsTextFile(targetDirectory.toString(), GzipCodec.class); - } - } - } - - private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa) - throws InvalidProtocolBufferException, JsonProcessingException { - final Text out = new Text(); - final ObjectMapper mapper = new ObjectMapper(); - if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) { - out.set(mapper.writeValueAsString(doTransform(aa))); - } - return out; - } - - private AtomicAction getRelationAtomicAction(String atomicaActionId) { - final String[] splitId = atomicaActionId.split("@"); - - String source = splitId[0]; - String target = splitId[2]; - - String[] relSemantic = splitId[1].split("_"); - - Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(relSemantic[0]); - rel.setSubRelType(relSemantic[1]); - rel.setRelClass(relSemantic[2]); - - DataInfo d = new DataInfo(); - d.setDeletedbyinference(false); - d.setInferenceprovenance("deduplication"); - d.setInferred(true); - d.setInvisible(false); - Qualifier provenanceaction = new Qualifier(); - - provenanceaction.setClassid("deduplication"); - provenanceaction.setClassname("deduplication"); - provenanceaction.setSchemeid("dnet:provenanceActions"); - provenanceaction.setSchemename("dnet:provenanceActions"); - - d.setProvenanceaction(provenanceaction); - - rel.setDataInfo(d); - - return new AtomicAction<>(Relation.class, rel); - } - - private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) - throws InvalidProtocolBufferException { - final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); - final Oaf oaf = ProtoConverter.convert(proto_oaf); - switch (proto_oaf.getKind()) { - case entity: - switch (proto_oaf.getEntity().getType()) { - case datasource: - return new AtomicAction<>(Datasource.class, (Datasource) oaf); - case organization: - return new AtomicAction<>(Organization.class, (Organization) oaf); - case project: - return new AtomicAction<>(Project.class, (Project) oaf); - case result: - final String resulttypeid = - proto_oaf - .getEntity() - .getResult() - .getMetadata() - .getResulttype() - .getClassid(); - switch (resulttypeid) { - case "publication": - return new AtomicAction<>(Publication.class, (Publication) oaf); - case "software": - return new AtomicAction<>(Software.class, (Software) oaf); - case "other": - return new AtomicAction<>( - OtherResearchProduct.class, (OtherResearchProduct) oaf); - case "dataset": - return new AtomicAction<>(Dataset.class, (Dataset) oaf); - default: - // can be an update, where the resulttype is not specified - return new AtomicAction<>(Result.class, (Result) oaf); - } - default: - throw new IllegalArgumentException( - "invalid entity type: " + proto_oaf.getEntity().getType()); - } - case relation: - return new AtomicAction<>(Relation.class, (Relation) oaf); - default: - throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind()); - } - } - - private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException { - ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - String XQUERY = - "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; - return isLookUp.getResourceProfileByQuery(XQUERY); - } - - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession.builder() - .appName(TransformActions.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json deleted file mode 100644 index c4910ec61..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json +++ /dev/null @@ -1,10 +0,0 @@ -[ - {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, - {"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true}, - {"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true}, - {"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true}, - {"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true}, - {"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true}, - {"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true} -] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json deleted file mode 100644 index ce72f53ca..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json +++ /dev/null @@ -1,5 +0,0 @@ -[ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, - {"paramName":"i", "paramLongName":"inputPaths", "paramDescription": "URL of the isLookUp Service", "paramRequired": true} -] diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 1cb04d02f..e5c8a4606 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.pace.config.DedupConfig; import java.util.Collection; import java.util.Iterator; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; public class DedupRecordFactory { + private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class); + protected static final ObjectMapper OBJECT_MAPPER = - new com.fasterxml.jackson.databind.ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static Dataset createDedupRecord( final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, - final Class clazz, - final DedupConfig dedupConf) { + final Class clazz) { long ts = System.currentTimeMillis(); @@ -54,40 +54,39 @@ public class DedupRecordFactory { r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - // return mergeRels - .joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") - .filter( - (FilterFunction, Tuple2>>) - value -> value._2() != null) + .joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner") .map( - (MapFunction, Tuple2>, T>) - value -> value._2()._2(), - Encoders.kryo(clazz)) - .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + (MapFunction< + Tuple2, Tuple2>, + Tuple2>) + value -> new Tuple2<>(value._1()._1(), value._2()._2()), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))) + .groupByKey( + (MapFunction, String>) entity -> entity._1(), + Encoders.STRING()) .mapGroups( - (MapGroupsFunction) + (MapGroupsFunction, T>) (key, values) -> entityMerger(key, values, ts, clazz), Encoders.bean(clazz)); } private static T entityMerger( - String id, Iterator entities, final long ts, Class clazz) { + String id, Iterator> entities, long ts, Class clazz) { try { T entity = clazz.newInstance(); entity.setId(id); - if (entity.getDataInfo() == null) { - entity.setDataInfo(new DataInfo()); - } + entity.setDataInfo(new DataInfo()); entity.getDataInfo().setTrust("0.9"); entity.setLastupdatetimestamp(ts); final Collection dates = Lists.newArrayList(); entities.forEachRemaining( - e -> { - entity.mergeFrom(e); - if (ModelSupport.isSubClass(e, Result.class)) { - Result r1 = (Result) e; + t -> { + T duplicate = t._2(); + entity.mergeFrom(duplicate); + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result r1 = (Result) duplicate; Result er = (Result) entity; er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 127a19139..c46464ffd 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -11,8 +11,6 @@ import eu.dnetlib.pace.config.DedupConfig; import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; @@ -71,13 +69,10 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) - .map( - (MapFunction) - value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(outputPath); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index fde5dd75f..ee13eff6b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -33,7 +33,7 @@ public class SparkUpdateEntity extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class); - final String IDJSONPATH = "$.id"; + private static final String IDJSONPATH = "$.id"; public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -65,27 +65,25 @@ public class SparkUpdateEntity extends AbstractSparkAction { log.info("workingPath: '{}'", workingPath); log.info("dedupGraphPath: '{}'", dedupGraphPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); // for each entity ModelSupport.entityTypes.forEach( - (entity, clazz) -> { - final String outputPath = dedupGraphPath + "/" + entity; + (type, clazz) -> { + final String outputPath = dedupGraphPath + "/" + type; removeOutputDir(spark, outputPath); JavaRDD sourceEntity = sc.textFile( - DedupUtility.createEntityPath( - graphBasePath, entity.toString())); + DedupUtility.createEntityPath(graphBasePath, type.toString())); - if (mergeRelExists(workingPath, entity.toString())) { + if (mergeRelExists(workingPath, type.toString())) { final String mergeRelPath = - DedupUtility.createMergeRelPath( - workingPath, "*", entity.toString()); + DedupUtility.createMergeRelPath(workingPath, "*", type.toString()); final String dedupRecordPath = DedupUtility.createDedupRecordPath( - workingPath, "*", entity.toString()); + workingPath, "*", type.toString()); final Dataset rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); @@ -107,7 +105,6 @@ public class SparkUpdateEntity extends AbstractSparkAction { MapDocumentUtil.getJPathString( IDJSONPATH, s), s)); - JavaRDD map = entitiesWithId .leftOuterJoin(mergedIds) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 7ad2f6d17..5979fc9b7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -8,6 +8,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.util.MapDocumentUtil; import java.io.File; import java.io.IOException; import java.io.Serializable; @@ -16,14 +17,20 @@ import java.nio.file.Paths; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import scala.Tuple2; @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @@ -41,7 +48,7 @@ public class SparkDedupTest implements Serializable { private static final String testActionSetId = "test-orchestrator"; @BeforeAll - private static void cleanUp() throws IOException, URISyntaxException { + public static void cleanUp() throws IOException, URISyntaxException { testGraphBasePath = Paths.get( @@ -65,7 +72,7 @@ public class SparkDedupTest implements Serializable { spark = SparkSession.builder() - .appName(SparkCreateSimRels.class.getSimpleName()) + .appName(SparkDedupTest.class.getSimpleName()) .master("local[*]") .config(new SparkConf()) .getOrCreate(); @@ -74,7 +81,7 @@ public class SparkDedupTest implements Serializable { } @BeforeEach - private void setUp() throws IOException, ISLookUpException { + public void setUp() throws IOException, ISLookUpException { lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) @@ -96,6 +103,13 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkDedupTest.class.getResourceAsStream( "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); } @Test @@ -109,7 +123,6 @@ public class SparkDedupTest implements Serializable { "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument( new String[] { - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -126,9 +139,14 @@ public class SparkDedupTest implements Serializable { spark.read() .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel") .count(); + long sw_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_simrel") + .count(); - assertEquals(3288, orgs_simrel); + assertEquals(3432, orgs_simrel); assertEquals(7260, pubs_simrel); + assertEquals(344, sw_simrel); } @Test @@ -142,7 +160,6 @@ public class SparkDedupTest implements Serializable { "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument( new String[] { - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -159,9 +176,14 @@ public class SparkDedupTest implements Serializable { spark.read() .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") .count(); + long sw_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .count(); - assertEquals(1244, orgs_mergerel); + assertEquals(1276, orgs_mergerel); assertEquals(1460, pubs_mergerel); + assertEquals(288, sw_mergerel); } @Test @@ -175,7 +197,6 @@ public class SparkDedupTest implements Serializable { "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); parser.parseArgument( new String[] { - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -198,9 +219,13 @@ public class SparkDedupTest implements Serializable { + testActionSetId + "/publication_deduprecord") .count(); + long sw_deduprecord = + jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") + .count(); assertEquals(82, orgs_deduprecord); assertEquals(66, pubs_deduprecord); + assertEquals(51, sw_deduprecord); } @Test @@ -214,7 +239,6 @@ public class SparkDedupTest implements Serializable { "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); parser.parseArgument( new String[] { - "-mt", "local[*]", "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath @@ -224,6 +248,9 @@ public class SparkDedupTest implements Serializable { long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); + long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); + long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); long mergedOrgs = spark.read() @@ -245,20 +272,40 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); + long mergedSw = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + assertEquals(897, publications); assertEquals(835, organizations); + assertEquals(100, projects); + assertEquals(100, datasource); + assertEquals(200, softwares); long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") .filter(this::isDeletedByInference) .count(); + long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication") .filter(this::isDeletedByInference) .count(); + long deletedSw = + jsc.textFile(testDedupGraphBasePath + "/software") + .filter(this::isDeletedByInference) + .count(); + assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); + assertEquals(mergedSw, deletedSw); } @Test @@ -272,7 +319,6 @@ public class SparkDedupTest implements Serializable { "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); parser.parseArgument( new String[] { - "-mt", "local[*]", "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath @@ -283,6 +329,43 @@ public class SparkDedupTest implements Serializable { long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); assertEquals(826, relations); + + // check deletedbyinference + final Dataset mergeRels = + spark.read() + .load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")) + .as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = + mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) + r -> new Tuple2(r.getString(0), "d")); + + JavaRDD toCheck = + jsc.textFile(testDedupGraphBasePath + "/relation") + .mapToPair( + json -> + new Tuple2<>( + MapDocumentUtil.getJPathString("$.source", json), + json)) + .join(mergedIds) + .map(t -> t._2()._1()) + .mapToPair( + json -> + new Tuple2<>( + MapDocumentUtil.getJPathString("$.target", json), + json)) + .join(mergedIds) + .map(t -> t._2()._1()); + + long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); + long updated = toCheck.count(); + + assertEquals(updated, deletedbyinference); } @AfterAll diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json new file mode 100644 index 000000000..532900506 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json @@ -0,0 +1,118 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "dataset", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } } + ], + "decisionTree" : { + "start" : { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid" + } + } + ], + "threshold": 0.5, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2" : { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "false" + }, + "layer3" : { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true" + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { + "name" : "doi", + "type" : "String", + "path" : "$.pid[@.qualifier.classid = 'doi'].value" + }, + { + "name" : "pid", + "type" : "JSON", + "path" : "$.pid", + "overrideMatch" : "true" + }, + { + "name" : "title", + "type" : "String", + "path" : "$.title[@.qualifier.classid = 'main title'].value", + "length" : 250, + "size" : 5 + }, + { + "name" : "authors", + "type" : "String", + "path" : "$.author[*].fullname", + "size" : 200 + }, + { + "name" : "resulttype", + "type" : "String", + "path" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms" : {} + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json new file mode 100644 index 000000000..76e656743 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json @@ -0,0 +1,118 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "otherresearchproduct", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } } + ], + "decisionTree" : { + "start" : { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid" + } + } + ], + "threshold": 0.5, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2" : { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "false" + }, + "layer3" : { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true" + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { + "name" : "doi", + "type" : "String", + "path" : "$.pid[@.qualifier.classid = 'doi'}].value" + }, + { + "name" : "pid", + "type" : "JSON", + "path" : "$.pid", + "overrideMatch" : "true" + }, + { + "name" : "title", + "type" : "String", + "path" : "$.title[@.qualifier.classid = 'main title'].value", + "length" : 250, + "size" : 5 + }, + { + "name" : "authors", + "type" : "String", + "path" : "$.author[*].fullname", + "size" : 200 + }, + { + "name" : "resulttype", + "type" : "String", + "path" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms" : {} + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json new file mode 100644 index 000000000..815dd7a57 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json @@ -0,0 +1,92 @@ + { + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "software", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "doi", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "url", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1, + "aggregation": "OR", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "false" + }, + "layer2": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitleIgnoreVersion", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + 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Merged PR from Ibai

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  • added numpy to install requires
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  • fixed issue with new f2py versions
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Fixes a py3 issue in installation.

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This release will allow Zendo to create a DOI for this project. No updates to the code have been made.

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    \\n
  • Now validates using Julia v0.6.3 against R package rdiversity v1.2
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Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************

\\n\\n


\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.

\\n\\n

The physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. "Simulation of entangled polymer solutions." The Journal of Chemical Physics 145.12 (2016): 124113.

\\n\\n

The extension for shear flow is described in this article: (also attached)
\\nAiridas Korolkovas, Philipp Gutfreund, and Maximilian Wolff. "Dynamical structure of entangled polymers simulated under shear flow." (in preparation)

\\n\\n


\\n--- System requirements ---
\\nThe code runs in Matlab, and was tested for the Matlab 2016a version. There is both a CPU and a GPU option (about 10-50x faster).
\\nTo run the GPU code effectively, a CUDA-enabled Nvidia card is required. Quadro M5000 model was tested to give acceptable performance.

\\n\\n

 

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Bug fix:

\\n\\n
    \\n
  • When creating the StarModel.samples attribute, there used to be a hard-coded cut on lnprob that only made sense in a very limited circumstance. This has been replaced with a cut to cull the top 99.5% (as ranked by lnprob) samples.
  • \\n
\\n\\n

Feature added:

\\n\\n
    \\n
  • \\nTripleStarModel, along the lines of BinaryStarModel but with three stars.
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A wrapper and CLI to evaluate a TMVA Machine Learning classifier with as little boilerplate code as possible.

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    \\n
  • new global packet structure
  • \\n
  • moved releases to repo sotorrent/releases
  • \\n
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This is a beta release of StaG-mwc v0.3.0.

\\n

Several known issues exist, check or report issues in the issue tracker on Github. \\nKnown issues using the available rules for downloading reference databases.

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"Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************\\n\\n
\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.\\n\\nThe physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. \"Simulation of entangled polymer solutions.\" The Journal of Chemical Physics 145.12 (2016): 124113.\\n\\nThe extension for shear flow is described in this article: (also attached)
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\\n--- System requirements ---
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Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************

\\n\\n


\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.

\\n\\n

The physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. \"Simulation of entangled polymer solutions.\" The Journal of Chemical Physics 145.12 (2016): 124113.

\\n\\n

The extension for shear flow is described in this article: (also attached)
\\nAiridas Korolkovas, Philipp Gutfreund, and Maximilian Wolff. \"Dynamical structure of entangled polymers simulated under shear flow.\" (in preparation)

\\n\\n


\\n--- System requirements ---
\\nThe code runs in Matlab, and was tested for the Matlab 2016a version. There is both a CPU and a GPU option (about 10-50x faster).
\\nTo run the GPU code effectively, a CUDA-enabled Nvidia card is required. Quadro M5000 model was tested to give acceptable performance.

\\n\\n

\\xa0

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This is a python software that looks into the reduction of crime by the Los Angeles Police Department (L.A.P.D). The crimes are those that were reported to the various police divisions from the years 2010 to 2017. The software shows the most occurring crimes, the weapons used in perpetuating the crimes and the victims of the crimes. Also, a map showing the locations with most crimes and the nature of crimes that occurs most is included in the software. Bar charts were used to display various victims of crimes as well as the weapons used. Again, a pie chart was used to show the total number of crimes recorded in the various years. Further more, line graphs portraying the trend of crimes from the various years and a scatter plot displaying the various age ranges of the victims of crimes.

\\n\\n

Last but not least, a heat map of the locations of all the crimes from the years 2010 to 2017, with places that recorded the most crimes having deeper colorization of the map.

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This is a python software that looks into the reduction of crime by the Los Angeles Police Department (L.A.P.D). The crimes are those that were reported to the various police divisions from the years 2010 to 2017. The\\xa0software shows the most occurring crimes, the weapons used in perpetuating the crimes and the victims of the crimes. Also, a map showing the locations\\xa0with most crimes and the nature of crimes that occurs most is included in the\\xa0software. Bar charts\\xa0were\\xa0used to display various victims of crimes as well as the weapons used. Again, a pie chart was used to show the total number of crimes recorded in the various years. Further more, line graphs portraying the trend of crimes from the various years and a scatter plot displaying the various age ranges of the victims of\\xa0crimes.

\\n\\n

Last but not least, a heat map of the locations of all the crimes from the years 2010 to 2017, with places that recorded\\xa0the most crimes having deeper colorization of the map.

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    \\n
  • introduced python3 compatibility
  • \\n
  • modernized cmake
  • \\n
  • improved CI
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  • Fixes writing of OpenDX files (issue #21)
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Release 0.12.0-rc1 (April 20, 2016)

\\n\\n
    \\n\\t
  • ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
  • \\n\\t
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
  • \\n\\t
  • FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
  • \\n\\t
  • FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
  • \\n\\t
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
  • \\n\\t
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography (https://github.com/nipy/nipype/pull/1090)
  • \\n\\t
  • ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360, https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
  • \\n\\t
  • ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
  • \\n\\t
  • ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
  • \\n\\t
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
  • \\n\\t
  • TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
  • \\n\\t
  • ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
  • \\n\\t
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
  • \\n\\t
  • FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
  • \\n\\t
  • FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
  • \\n\\t
  • ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
  • \\n\\t
  • FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
  • \\n\\t
  • ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
  • \\n\\t
  • ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
  • \\n\\t
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • \\n\\t
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
  • \\n\\t
  • ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
  • \\n\\t
  • FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
  • \\n\\t
  • FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
  • \\n\\t
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
  • \\n\\t
  • FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
  • \\n\\t
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
  • \\n
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This software is an implementation of the general error model described in the work entitled \"General error model for analysis of laser-induced incandescence
signals\" by T. A. Sipkens and coworkers, which simulates signals according to the described error model (sufficient for generating Figure 1 in the associated work) and demonstrates a fitting procedure to infer the error model parameters from the produced signals.

This software package was developed for use with MATLAB 2016a running on Windows. Users can execute the main script immediately, provided all attached files are located in the same directory and that directory is included in the MATLAB path. One must then enter \"main_simulate_C\" in the MATLAB command line.
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Updated Zenodo badge to point to v2.0 of the tutorial.

\\n\\n

Added updated citations and DOI (for PSA paper in PLOS Computational Biology):

\\n\\n

Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1004568 (also: arXiv:1505.04807 [q-bio.QM])

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A wrapper and CLI to evaluate a TMVA Machine Learning classifier with as little boilerplate code as possible.

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-import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.keyValue; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import eu.dnetlib.dhp.schema.oaf.*; -import java.util.*; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OAIProvenance; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +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.schema.oaf.StructuredProperty; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; @@ -29,6 +58,12 @@ public abstract class AbstractMdRecordToOafMapper { qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier REPOSITORY_QUALIFIER = + qualifier( + "sysimport:crosswalk:repository", + "sysimport:crosswalk:repository", + "dnet:provenanceActions", + "dnet:provenanceActions"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -55,13 +90,13 @@ public abstract class AbstractMdRecordToOafMapper { final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = keyValue( - doc.valueOf("//oaf:collectedFrom/@id"), + createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name")); final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : keyValue( - doc.valueOf("//oaf:hostedBy/@id"), + createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); final DataInfo info = prepareDataInfo(doc); @@ -154,7 +189,7 @@ public abstract class AbstractMdRecordToOafMapper { r1.setRelClass("isProducedBy"); r1.setSource(docId); r1.setTarget(projectId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setCollectedfrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -165,7 +200,7 @@ public abstract class AbstractMdRecordToOafMapper { r2.setRelClass("produces"); r2.setSource(projectId); r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setCollectedfrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); @@ -398,7 +433,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//oaf:datainfo"); if (n == null) { - return null; + return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 6de7303c3..476e617d7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,11 +1,35 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +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.schema.oaf.StructuredProperty; import java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -119,7 +143,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); ds.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); ds.setPid(new ArrayList<>()); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query @@ -185,7 +210,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication p.setOriginalId(Arrays.asList(rs.getString("projectid"))); p.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); p.setPid(new ArrayList<>()); p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -240,7 +266,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); o.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); o.setPid(new ArrayList<>()); o.setDateofcollection(asString(rs.getDate("dateofcollection"))); o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -285,7 +312,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final List collectedFrom = listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("datasourceOrganization"); @@ -293,7 +321,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isProvidedBy"); r1.setSource(dsId); r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); + r1.setCollectedfrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -303,7 +331,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("provides"); r2.setSource(orgId); r2.setTarget(dsId); - r2.setCollectedFrom(collectedFrom); + r2.setCollectedfrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -320,7 +348,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String projectId = createOpenaireId(40, rs.getString("project"), true); final List collectedFrom = listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("projectOrganization"); @@ -328,7 +357,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isParticipant"); r1.setSource(projectId); r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); + r1.setCollectedfrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -338,7 +367,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("hasParticipant"); r2.setSource(orgId); r2.setTarget(projectId); - r2.setCollectedFrom(collectedFrom); + r2.setCollectedfrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -363,6 +392,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication "dnet:provenanceActions"), "0.9"); + final List collectedFrom = + listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); + try { if (rs.getString("source_type").equals("context")) { @@ -381,6 +413,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r.setLastupdatetimestamp(lastUpdateTimestamp); r.setContext(prepareContext(rs.getString("source_id"), info)); r.setDataInfo(info); + r.setCollectedfrom(collectedFrom); return Arrays.asList(r); } else { @@ -395,18 +428,22 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final Relation r2 = new Relation(); if (rs.getString("source_type").equals("project")) { + r1.setCollectedfrom(collectedFrom); r1.setRelType("resultProject"); r1.setSubRelType("outcome"); r1.setRelClass("produces"); + r2.setCollectedfrom(collectedFrom); r2.setRelType("resultProject"); r2.setSubRelType("outcome"); r2.setRelClass("isProducedBy"); } else { + r1.setCollectedfrom(collectedFrom); r1.setRelType("resultResult"); r1.setSubRelType("relationship"); r1.setRelClass("isRelatedTo"); + r2.setCollectedfrom(collectedFrom); r2.setRelType("resultResult"); r2.setSubRelType("relationship"); r2.setRelClass("isRelatedTo"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index e77b1f87f..6b304c9b0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -232,7 +232,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r1.setRelClass("isRelatedTo"); r1.setSource(docId); r1.setTarget(otherId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setCollectedfrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -243,7 +243,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r2.setRelClass("isRelatedTo"); r2.setSource(otherId); r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setCollectedfrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 5e6462417..f6fab499b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -334,7 +334,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { r.setRelClass(relClass); r.setSource(source); r.setTarget(target); - r.setCollectedFrom(Arrays.asList(collectedFrom)); + r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); return r; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index bfd5d5c7f..4d3cb02d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -186,7 +186,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(targetId); r.setRelType(relationSemantic); r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setCollectedfrom(parsedObject.getCollectedfrom()); r.setDataInfo(di); rels.add(r); r = new DLIRelation(); @@ -195,7 +195,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(parsedObject.getId()); r.setRelType(inverseRelation); r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setCollectedfrom(parsedObject.getCollectedfrom()); r.setDateOfCollection(dateOfCollection); rels.add(r); if ("unknown".equalsIgnoreCase(relatedType)) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index 271c7040f..67ca6a64a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -21,6 +21,28 @@ 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 + @@ -35,6 +57,10 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + @@ -52,14 +78,15 @@ eu.dnetlib.dhp.oa.graph.GraphHiveImporterJob dhp-graph-mapper-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - -mt yarn-cluster --sourcePath${sourcePath} --hive_db_name${hive_db_name} --hive_metastore_uris${hive_metastore_uris} 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 6af314d76..b09c5d638 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 @@ -1,11 +1,16 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.when; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; import java.io.IOException; import java.util.List; import java.util.Map; @@ -43,6 +48,7 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(p.getAuthor().size() > 0); assertTrue(p.getSubject().size() > 0); @@ -50,13 +56,24 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); assertTrue(StringUtils.isNotBlank(r1.getRelClass())); assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); + + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); } @Test @@ -65,15 +82,35 @@ public class MappersTest { final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(1, list.size()); + assertEquals(3, list.size()); assertTrue(list.get(0) instanceof Dataset); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); final Dataset d = (Dataset) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); + assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); assertTrue(d.getSubject().size() > 0); + + assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); + assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); } @Test @@ -88,6 +125,7 @@ public class MappersTest { final Software s = (Software) list.get(0); assertValidId(s.getId()); + assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); assertTrue(s.getAuthor().size() > 0); assertTrue(s.getSubject().size() > 0); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 3c7bc684d..b88731ba2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,10 +1,17 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; import java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -13,6 +20,7 @@ import java.sql.SQLException; import java.util.List; import java.util.Objects; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -42,14 +50,13 @@ public class MigrateDbEntitiesApplicationTest { final Datasource ds = (Datasource) list.get(0); assertValidId(ds.getId()); + assertValidId(ds.getCollectedfrom().get(0).getKey()); assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields)); assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals( ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); - assertEquals( - ds.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -65,10 +72,9 @@ public class MigrateDbEntitiesApplicationTest { final Project p = (Project) list.get(0); assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); - assertEquals( - p.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -86,6 +92,7 @@ public class MigrateDbEntitiesApplicationTest { final Organization o = (Organization) list.get(0); assertValidId(o.getId()); + assertValidId(o.getCollectedfrom().get(0).getKey()); assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); @@ -98,8 +105,6 @@ public class MigrateDbEntitiesApplicationTest { assertEquals( o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); - assertEquals( - o.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -137,6 +142,8 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r2.getSource()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); } @Test @@ -146,7 +153,12 @@ public class MigrateDbEntitiesApplicationTest { final List list = app.processClaims(rs); assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Result); + final Result r = (Result) list.get(0); + verifyMocks(fields); + + assertValidId(r.getCollectedfrom().get(0).getKey()); } @Test @@ -157,6 +169,33 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(2, list.size()); verifyMocks(fields); + + assertTrue(list.get(0) instanceof Relation); + assertTrue(list.get(1) instanceof Relation); + + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + + assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); + assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); + + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); + + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); } private List prepareMocks(final String jsonFile) throws IOException, SQLException { 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 0c36e8686..94dc802fa 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 @@ -87,6 +87,7 @@ und + corda_______::226852 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedFrom().stream() + rel.getCollectedfrom().stream() .map( cf -> new ScholixEntityId( @@ -73,7 +73,7 @@ public class Scholix implements Serializable { if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedFrom().stream() + rel.getCollectedfrom().stream() .map( cf -> new ScholixEntityId( diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json index e029ddf62..3cca6e370 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json @@ -1 +1 @@ -{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedFrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file +{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedfrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index 6b1dd52ce..df5b8779a 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -11,11 +11,13 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.*; +import java.util.List; +import java.util.Objects; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -104,16 +106,12 @@ public class CreateRelatedEntitiesJob_phase1 { SparkSession spark, String inputRelationsPath, String inputEntityPath, - Class entityClazz, + Class clazz, String outputPath) { Dataset> relsByTarget = readPathRelation(spark, inputRelationsPath) - .filter( - (FilterFunction) - value -> - value.getDataInfo().getDeletedbyinference() - == false) + .filter("dataInfo.deletedbyinference == false") .map( (MapFunction>) r -> new Tuple2<>(r.getTarget(), r), @@ -122,10 +120,11 @@ public class CreateRelatedEntitiesJob_phase1 { .cache(); Dataset> entities = - readPathEntity(spark, inputEntityPath, entityClazz) + readPathEntity(spark, inputEntityPath, clazz) + .filter("dataInfo.invisible == false") .map( (MapFunction) - value -> asRelatedEntity(value, entityClazz), + value -> asRelatedEntity(value, clazz), Encoders.bean(RelatedEntity.class)) .map( (MapFunction>) @@ -146,7 +145,7 @@ public class CreateRelatedEntitiesJob_phase1 { Encoders.bean(EntityRelEntity.class)) .write() .mode(SaveMode.Overwrite) - .parquet(outputPath + "/" + EntityType.fromClass(entityClazz)); + .parquet(outputPath + "/" + EntityType.fromClass(clazz)); } private static Dataset readPathEntity( @@ -161,6 +160,81 @@ public class CreateRelatedEntitiesJob_phase1 { Encoders.bean(entityClazz)); } + public static RelatedEntity asRelatedEntity(E entity, Class clazz) { + + final RelatedEntity re = new RelatedEntity(); + re.setId(entity.getId()); + re.setType(EntityType.fromClass(clazz).name()); + + re.setPid(entity.getPid()); + re.setCollectedfrom(entity.getCollectedfrom()); + + switch (EntityType.fromClass(clazz)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + Result result = (Result) entity; + + if (result.getTitle() != null && !result.getTitle().isEmpty()) { + re.setTitle(result.getTitle().stream().findFirst().get()); + } + + re.setDateofacceptance(getValue(result.getDateofacceptance())); + re.setPublisher(getValue(result.getPublisher())); + re.setResulttype(result.getResulttype()); + re.setInstances(result.getInstance()); + + // TODO still to be mapped + // re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); + + break; + case datasource: + Datasource d = (Datasource) entity; + + re.setOfficialname(getValue(d.getOfficialname())); + re.setWebsiteurl(getValue(d.getWebsiteurl())); + re.setDatasourcetype(d.getDatasourcetype()); + re.setOpenairecompatibility(d.getOpenairecompatibility()); + + break; + case organization: + Organization o = (Organization) entity; + + re.setLegalname(getValue(o.getLegalname())); + re.setLegalshortname(getValue(o.getLegalshortname())); + re.setCountry(o.getCountry()); + re.setWebsiteurl(getValue(o.getWebsiteurl())); + break; + case project: + Project p = (Project) entity; + + re.setProjectTitle(getValue(p.getTitle())); + re.setCode(getValue(p.getCode())); + re.setAcronym(getValue(p.getAcronym())); + re.setContracttype(p.getContracttype()); + + List> f = p.getFundingtree(); + if (!f.isEmpty()) { + re.setFundingtree( + f.stream().map(s -> s.getValue()).collect(Collectors.toList())); + } + break; + } + return re; + } + + private static String getValue(Field field) { + return getFieldValueWithDefault(field, ""); + } + + private static T getFieldValueWithDefault(Field f, T defaultValue) { + return Optional.ofNullable(f) + .filter(Objects::nonNull) + .map(x -> x.getValue()) + .orElse(defaultValue); + } + /** * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline * delimited json text file, diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index a6c261ec7..87264df05 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -76,9 +76,6 @@ public class PrepareRelationsJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - int numPartitions = Integer.parseInt(parser.get("relPartitions")); - log.info("relPartitions: {}", numPartitions); - SparkConf conf = new SparkConf(); runWithSparkSession( @@ -86,16 +83,14 @@ public class PrepareRelationsJob { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareRelationsFromPaths(spark, inputRelationsPath, outputPath, numPartitions); + prepareRelationsFromPaths(spark, inputRelationsPath, outputPath); }); } private static void prepareRelationsFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + SparkSession spark, String inputRelationsPath, String outputPath) { readPathRelation(spark, inputRelationsPath) - .filter( - (FilterFunction) - value -> value.getDataInfo().getDeletedbyinference() == false) + .filter("dataInfo.deletedbyinference == false") .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) @@ -103,7 +98,6 @@ public class PrepareRelationsJob { (FlatMapGroupsFunction) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.bean(SortableRelation.class)) - .repartition(numPartitions) .write() .mode(SaveMode.Overwrite) .parquet(outputPath); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index cea3539bc..ebd33363b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -3,14 +3,8 @@ package eu.dnetlib.dhp.oa.provision.utils; import static org.apache.commons.lang3.StringUtils.substringAfter; import com.google.common.collect.Sets; -import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; -import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.oaf.*; -import java.util.List; -import java.util.Objects; -import java.util.Optional; import java.util.Set; -import java.util.stream.Collectors; public class GraphMappingUtils { @@ -18,81 +12,6 @@ public class GraphMappingUtils { public static Set authorPidTypes = Sets.newHashSet("orcid", "magidentifier"); - public static RelatedEntity asRelatedEntity(E entity, Class clazz) { - - final RelatedEntity re = new RelatedEntity(); - re.setId(entity.getId()); - re.setType(EntityType.fromClass(clazz).name()); - - re.setPid(entity.getPid()); - re.setCollectedfrom(entity.getCollectedfrom()); - - switch (EntityType.fromClass(clazz)) { - case publication: - case dataset: - case otherresearchproduct: - case software: - Result result = (Result) entity; - - if (result.getTitle() == null && !result.getTitle().isEmpty()) { - re.setTitle(result.getTitle().stream().findFirst().get()); - } - - re.setDateofacceptance(getValue(result.getDateofacceptance())); - re.setPublisher(getValue(result.getPublisher())); - re.setResulttype(result.getResulttype()); - re.setInstances(result.getInstance()); - - // TODO still to be mapped - // re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); - - break; - case datasource: - Datasource d = (Datasource) entity; - - re.setOfficialname(getValue(d.getOfficialname())); - re.setWebsiteurl(getValue(d.getWebsiteurl())); - re.setDatasourcetype(d.getDatasourcetype()); - re.setOpenairecompatibility(d.getOpenairecompatibility()); - - break; - case organization: - Organization o = (Organization) entity; - - re.setLegalname(getValue(o.getLegalname())); - re.setLegalshortname(getValue(o.getLegalshortname())); - re.setCountry(o.getCountry()); - re.setWebsiteurl(getValue(o.getWebsiteurl())); - break; - case project: - Project p = (Project) entity; - - re.setProjectTitle(getValue(p.getTitle())); - re.setCode(getValue(p.getCode())); - re.setAcronym(getValue(p.getAcronym())); - re.setContracttype(p.getContracttype()); - - List> f = p.getFundingtree(); - if (!f.isEmpty()) { - re.setFundingtree( - f.stream().map(s -> s.getValue()).collect(Collectors.toList())); - } - break; - } - return re; - } - - private static String getValue(Field field) { - return getFieldValueWithDefault(field, ""); - } - - private static T getFieldValueWithDefault(Field f, T defaultValue) { - return Optional.ofNullable(f) - .filter(Objects::nonNull) - .map(x -> x.getValue()) - .orElse(defaultValue); - } - public static String removePrefix(final String s) { if (s.contains("|")) return substringAfter(s, "|"); return s; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 3455cb5f3..874c34c09 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -22,6 +22,7 @@ import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; +import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.Set; @@ -41,6 +42,7 @@ import org.dom4j.io.XMLWriter; public class XmlRecordFactory implements Serializable { + public static final String REL_SUBTYPE_DEDUP = "dedup"; private Map accumulators; private Set specialDatasourceTypes; @@ -91,7 +93,14 @@ public class XmlRecordFactory implements Serializable { // rels has to be processed before the contexts because they enrich the contextMap with // the // funding info. - final List relations = listRelations(je, templateFactory, contexts); + final List relations = + je.getLinks().stream() + .filter( + t -> + !REL_SUBTYPE_DEDUP.equalsIgnoreCase( + t.getRelation().getSubRelType())) + .map(link -> mapRelation(link, templateFactory, contexts)) + .collect(Collectors.toCollection(ArrayList::new)); final String mainType = ModelSupport.getMainType(type); metadata.addAll(buildContexts(mainType, contexts)); @@ -102,7 +111,7 @@ public class XmlRecordFactory implements Serializable { mainType, metadata, relations, - listChildren(entity, je.getEntity().getType(), templateFactory), + listChildren(entity, je, templateFactory), listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); @@ -919,171 +928,149 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - private Qualifier getBestAccessright(final Result r) { - Qualifier bestAccessRight = new Qualifier(); - bestAccessRight.setClassid("UNKNOWN"); - bestAccessRight.setClassname("not available"); - bestAccessRight.setSchemeid("dnet:access_modes"); - bestAccessRight.setSchemename("dnet:access_modes"); + private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set contexts) { + final Relation rel = link.getRelation(); + final RelatedEntity re = link.getRelatedEntity(); + final String targetType = link.getRelatedEntity().getType(); - final LicenseComparator lc = new LicenseComparator(); - for (final Instance instance : r.getInstance()) { - if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) { - bestAccessRight = instance.getAccessright(); - } + final List metadata = Lists.newArrayList(); + switch (EntityType.valueOf(targetType)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { + metadata.add( + XmlSerializationUtils.mapStructuredProperty("title", re.getTitle())); + } + if (isNotBlank(re.getDateofacceptance())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", re.getDateofacceptance())); + } + if (isNotBlank(re.getPublisher())) { + metadata.add( + XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); + } + if (isNotBlank(re.getCodeRepositoryUrl())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "coderepositoryurl", re.getCodeRepositoryUrl())); + } + if (re.getResulttype() != null & re.getResulttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); + } + if (re.getCollectedfrom() != null) { + metadata.addAll( + re.getCollectedfrom().stream() + .map( + kv -> + XmlSerializationUtils.mapKeyValue( + "collectedfrom", kv)) + .collect(Collectors.toList())); + } + if (re.getPid() != null) { + metadata.addAll( + re.getPid().stream() + .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) + .collect(Collectors.toList())); + } + break; + case datasource: + if (isNotBlank(re.getOfficialname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "officialname", re.getOfficialname())); + } + if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { + mapDatasourceType(metadata, re.getDatasourcetype()); + } + if (re.getOpenairecompatibility() != null + & !re.getOpenairecompatibility().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "openairecompatibility", re.getOpenairecompatibility())); + } + break; + case organization: + if (isNotBlank(re.getLegalname())) { + metadata.add( + XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); + } + if (isNotBlank(re.getLegalshortname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalshortname", re.getLegalshortname())); + } + if (re.getCountry() != null & !re.getCountry().isBlank()) { + metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); + } + break; + case project: + if (isNotBlank(re.getProjectTitle())) { + metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); + } + if (isNotBlank(re.getCode())) { + metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); + } + if (isNotBlank(re.getAcronym())) { + metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); + } + if (re.getContracttype() != null & !re.getContracttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "contracttype", re.getContracttype())); + } + if (re.getFundingtree() != null & contexts != null) { + metadata.addAll( + re.getFundingtree().stream() + .peek(ft -> fillContextMap(ft, contexts)) + .map(ft -> getRelFundingTree(ft)) + .collect(Collectors.toList())); + } + break; + default: + throw new IllegalArgumentException("invalid target type: " + targetType); } - return bestAccessRight; - } + final DataInfo info = rel.getDataInfo(); + final String scheme = ModelSupport.getScheme(re.getType(), targetType); - private List listRelations( - final JoinedEntity je, TemplateFactory templateFactory, final Set contexts) { - final List rels = Lists.newArrayList(); - - for (final Tuple2 link : je.getLinks()) { - - final Relation rel = link.getRelation(); - final RelatedEntity re = link.getRelatedEntity(); - final String targetType = link.getRelatedEntity().getType(); - - final List metadata = Lists.newArrayList(); - switch (EntityType.valueOf(targetType)) { - case publication: - case dataset: - case otherresearchproduct: - case software: - if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { - metadata.add( - XmlSerializationUtils.mapStructuredProperty( - "title", re.getTitle())); - } - if (isNotBlank(re.getDateofacceptance())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "dateofacceptance", re.getDateofacceptance())); - } - if (isNotBlank(re.getPublisher())) { - metadata.add( - XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); - } - if (isNotBlank(re.getCodeRepositoryUrl())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "coderepositoryurl", re.getCodeRepositoryUrl())); - } - if (re.getResulttype() != null & re.getResulttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "resulttype", re.getResulttype())); - } - if (re.getCollectedfrom() != null) { - metadata.addAll( - re.getCollectedfrom().stream() - .map( - kv -> - XmlSerializationUtils.mapKeyValue( - "collectedfrom", kv)) - .collect(Collectors.toList())); - } - if (re.getPid() != null) { - metadata.addAll( - re.getPid().stream() - .map( - p -> - XmlSerializationUtils.mapStructuredProperty( - "pid", p)) - .collect(Collectors.toList())); - } - break; - case datasource: - if (isNotBlank(re.getOfficialname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "officialname", re.getOfficialname())); - } - if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { - mapDatasourceType(metadata, re.getDatasourcetype()); - } - if (re.getOpenairecompatibility() != null - & !re.getOpenairecompatibility().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "openairecompatibility", re.getOpenairecompatibility())); - } - break; - case organization: - if (isNotBlank(re.getLegalname())) { - metadata.add( - XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); - } - if (isNotBlank(re.getLegalshortname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "legalshortname", re.getLegalshortname())); - } - if (re.getCountry() != null & !re.getCountry().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier("country", re.getCountry())); - } - break; - case project: - if (isNotBlank(re.getProjectTitle())) { - metadata.add( - XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); - } - if (isNotBlank(re.getCode())) { - metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); - } - if (isNotBlank(re.getAcronym())) { - metadata.add( - XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); - } - if (re.getContracttype() != null & !re.getContracttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "contracttype", re.getContracttype())); - } - if (re.getFundingtree() != null) { - metadata.addAll( - re.getFundingtree().stream() - .peek(ft -> fillContextMap(ft, contexts)) - .map(ft -> getRelFundingTree(ft)) - .collect(Collectors.toList())); - } - break; - default: - throw new IllegalArgumentException("invalid target type: " + targetType); - } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); - - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); - } - - final String accumulatorName = - getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); - if (accumulators.containsKey(accumulatorName)) { - accumulators.get(accumulatorName).add(1); - } - - rels.add( - templateFactory.getRel( - targetType, - rel.getTarget(), - Sets.newHashSet(metadata), - rel.getRelClass(), - scheme, - info)); + if (StringUtils.isBlank(scheme)) { + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); } - return rels; + + final String accumulatorName = + getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); + if (accumulators.containsKey(accumulatorName)) { + accumulators.get(accumulatorName).add(1); + } + + return templateFactory.getRel( + targetType, + rel.getTarget(), + Sets.newHashSet(metadata), + rel.getRelClass(), + scheme, + info); } private List listChildren( - final OafEntity entity, String type, TemplateFactory templateFactory) { + final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); - EntityType entityType = EntityType.valueOf(type); + EntityType entityType = EntityType.valueOf(je.getEntity().getType()); + + children.addAll( + je.getLinks().stream() + .filter( + link -> + REL_SUBTYPE_DEDUP.equalsIgnoreCase( + link.getRelation().getSubRelType())) + .map(link -> mapRelation(link, templateFactory, null)) + .collect(Collectors.toCollection(ArrayList::new))); + if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); if (instances != null) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index e6587ef5e..923f6de69 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -98,6 +98,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 --inputRelationsPath${inputGraphRootPath}/relation --outputPath${workingDir}/relation diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 4b55c3433..5c4fc5131 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -262,7 +262,8 @@ sparkDriverMemory,sparkExecutorMemory,sparkExecutorCores, oozie.wf.application.path,projectVersion,oozie.use.system.libpath, oozieActionShareLibForSpark1,spark1YarnHistoryServerAddress,spark1EventLogDir, - oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir + oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir, + sparkSqlWarehouseDir true