From 4da13e457040ca406ca00cf2605c055ba3ab080e Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 20 Apr 2020 16:04:49 +0200 Subject: [PATCH] Revert "Merge branch 'master' into deduptesting" This reverts commit 772f75d167fda38dfb68ee7a353f0e04a11cab11, reversing changes made to 5f45f2c77f49eeae144628a414dae9149f3cec5b. --- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 11 - .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 10 + .../eu/dnetlib/dhp/schema/oaf/Relation.java | 18 +- .../relation_action_payload/result.json | 20 +- .../dhp/migration/actions/ProtoConverter.java | 2 +- .../dhp/oa/dedup/AbstractSparkAction.java | 30 +- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 15 +- .../dhp/oa/dedup/SparkCreateMergeRels.java | 16 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 3 +- .../dhp/oa/dedup/SparkPropagateRelation.java | 7 +- .../eu/dnetlib/dhp/dedup/entities/relation | 598 +++++++++--------- .../raw/AbstractMdRecordToOafMapper.java | 51 +- .../raw/MigrateDbEntitiesApplication.java | 59 +- .../dhp/oa/graph/raw/OafToOafMapper.java | 4 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- .../parser/AbstractScholexplorerParser.java | 4 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 42 +- .../raw/MigrateDbEntitiesApplicationTest.java | 53 +- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 - .../sample/relation/relation_100.json.gz | Bin 3637 -> 3639 bytes .../dhp/provision/scholix/Scholix.java | 4 +- .../eu/dnetlib/dhp/provision/relation.json | 2 +- .../dhp/oa/provision/PrepareRelationsJob.java | 13 +- .../oa/provision/utils/XmlRecordFactory.java | 303 ++++----- 24 files changed, 561 insertions(+), 707 deletions(-) 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 79138d641e..7a7a9a89cd 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 @@ -1,25 +1,14 @@ 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 6db3b7f745..86f4ff616f 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 @@ -10,6 +10,8 @@ public abstract class OafEntity extends Oaf implements Serializable { private List originalId; + private List collectedfrom; + private List pid; private String dateofcollection; @@ -36,6 +38,14 @@ 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 aaeecb8716..9d211d0586 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 @@ -18,6 +18,8 @@ public class Relation extends Oaf { private String target; + private List collectedFrom = new ArrayList<>(); + public String getRelType() { return relType; } @@ -58,6 +60,14 @@ 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"); @@ -67,12 +77,12 @@ 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 @@ -93,6 +103,6 @@ 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/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 36d3fdd272..bc65230a84 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/ProtoConverter.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java index 5188cf55a2..b5d027c03a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java @@ -41,7 +41,7 @@ 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-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 3c3a63ca49..bb310050ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -14,9 +14,7 @@ import java.io.StringReader; import java.util.ArrayList; import java.util.List; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.Document; @@ -26,9 +24,6 @@ import org.dom4j.io.SAXReader; abstract class AbstractSparkAction implements Serializable { - protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup"; - protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; - protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); @@ -89,29 +84,8 @@ abstract class AbstractSparkAction implements Serializable { return SparkSession.builder().config(conf).getOrCreate(); } - protected static void save(Dataset dataset, String outPath, SaveMode mode) { - dataset.map( - (MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(mode) - .text(outPath); - } - - protected static DataInfo getDataInfo() { - DataInfo info = new DataInfo(); - info.setDeletedbyinference(false); - info.setInferred(true); - info.setInvisible(false); - - Qualifier provenanceAction = new Qualifier(); - provenanceAction.setClassid(PROVENANCE_ACTION_CLASS); - provenanceAction.setClassname(PROVENANCE_ACTION_CLASS); - provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS); - provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); - info.setProvenanceaction(provenanceAction); - return info; + protected static void save(Dataset dataset, String outPath, SaveMode mode) { + dataset.write().option("compression", "gzip").mode(mode).json(outPath); } protected static void removeOutputDir(SparkSession spark, String path) { 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 a4e69e6db1..127a19139e 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 @@ -11,6 +11,8 @@ 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; @@ -69,11 +71,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - save( - DedupRecordFactory.createDedupRecord( - spark, mergeRelPath, entityPath, clazz, dedupConf), - outputPath, - SaveMode.Overwrite); + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) + .map( + (MapFunction) + value -> OBJECT_MAPPER.writeValueAsString(value), + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .json(outputPath); } } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index cfd541f297..ca6d04d496 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -6,6 +6,7 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -34,7 +35,9 @@ import scala.Tuple2; public class SparkCreateMergeRels extends AbstractSparkAction { + public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup"; private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); + public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -145,13 +148,22 @@ public class SparkCreateMergeRels extends AbstractSparkAction { r.setRelClass(relClass); r.setSubRelType("dedup"); - DataInfo info = getDataInfo(); + DataInfo info = new DataInfo(); + info.setDeletedbyinference(false); + info.setInferred(true); + info.setInvisible(false); info.setInferenceprovenance(dedupConf.getWf().getConfigurationId()); + Qualifier provenanceAction = new Qualifier(); + provenanceAction.setClassid(PROVENANCE_ACTION_CLASS); + provenanceAction.setClassname(PROVENANCE_ACTION_CLASS); + provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS); + provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); + info.setProvenanceaction(provenanceAction); // TODO calculate the trust value based on the similarity score of the elements in the CC // info.setTrust(); - r.setDataInfo(getDataInfo()); + r.setDataInfo(info); return r; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index 186b21ef2c..2fd807ccb2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.model.Block; +import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -114,7 +115,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { r.setTarget(target); r.setSubRelType("dedupSimilarity"); r.setRelClass("isSimilarTo"); - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); switch (entity) { case "result": diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index b983f5a297..17c99c0023 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -4,6 +4,7 @@ import static org.apache.spark.sql.functions.col; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -124,7 +125,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { return value -> { final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); if (rel.getDataInfo() == null) { - rel.setDataInfo(getDataInfo()); + rel.setDataInfo(new DataInfo()); } return rel; }; @@ -148,7 +149,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { Relation r = value._1()._2(); String id = value._2()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); } r.getDataInfo().setDeletedbyinference(false); switch (type) { @@ -172,7 +173,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { if (value._2() != null) { Relation r = value._1()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); } r.getDataInfo().setDeletedbyinference(true); return r; diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation index b9b9c22ba3..50e71c3662 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation @@ -98,305 +98,305 @@ {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": 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"resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"} {"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|od______1106::aabdb9c07beef7bdf7a93b6455f75e06", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index a7aa600cff..f1058db385 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,38 +1,9 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.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 static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; -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 eu.dnetlib.dhp.schema.oaf.*; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; @@ -58,12 +29,6 @@ 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; @@ -90,13 +55,13 @@ public abstract class AbstractMdRecordToOafMapper { final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = keyValue( - createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), + doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : keyValue( - createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), + doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name")); final DataInfo info = prepareDataInfo(doc); @@ -189,7 +154,7 @@ 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); @@ -200,7 +165,7 @@ 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); @@ -433,7 +398,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//oaf:datainfo"); if (n == null) { - return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); + return null; } 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 476e617d78..6de7303c35 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 @@ -1,35 +1,11 @@ package eu.dnetlib.dhp.oa.graph.raw; -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 static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; 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.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 eu.dnetlib.dhp.schema.oaf.*; import java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -143,8 +119,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); ds.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); ds.setPid(new ArrayList<>()); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query @@ -210,8 +185,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication p.setOriginalId(Arrays.asList(rs.getString("projectid"))); p.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); p.setPid(new ArrayList<>()); p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -266,8 +240,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); o.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); o.setPid(new ArrayList<>()); o.setDateofcollection(asString(rs.getDate("dateofcollection"))); o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -312,8 +285,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final List collectedFrom = listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname")); + rs.getString("collectedfromid"), rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("datasourceOrganization"); @@ -321,7 +293,7 @@ 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); @@ -331,7 +303,7 @@ 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); @@ -348,8 +320,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String projectId = createOpenaireId(40, rs.getString("project"), true); final List collectedFrom = listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname")); + rs.getString("collectedfromid"), rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("projectOrganization"); @@ -357,7 +328,7 @@ 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); @@ -367,7 +338,7 @@ 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); @@ -392,9 +363,6 @@ 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")) { @@ -413,7 +381,6 @@ 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 { @@ -428,22 +395,18 @@ 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 6b304c9b0b..e77b1f87fe 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 f6fab499bf..5e64624170 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 4d3cb02d68..bfd5d5c7f4 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/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 b09c5d6385..6af314d76e 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 @@ -1,16 +1,11 @@ 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.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 eu.dnetlib.dhp.schema.oaf.*; import java.io.IOException; import java.util.List; import java.util.Map; @@ -48,7 +43,6 @@ 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); @@ -56,24 +50,13 @@ 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 @@ -82,35 +65,15 @@ public class MappersTest { final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); + assertEquals(1, 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 @@ -125,7 +88,6 @@ 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 b88731ba24..3c7bc684d3 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 @@ -1,17 +1,10 @@ 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.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 eu.dnetlib.dhp.schema.oaf.*; import java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -20,7 +13,6 @@ 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; @@ -50,13 +42,14 @@ 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)); @@ -72,9 +65,10 @@ 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)); @@ -92,7 +86,6 @@ 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)); @@ -105,6 +98,8 @@ 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)); @@ -142,8 +137,6 @@ 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 @@ -153,12 +146,7 @@ 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 @@ -169,33 +157,6 @@ 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 94dc802fac..0c36e8686f 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 @@ -87,7 +87,6 @@ und - corda_______::226852 &2J-DpY^S#Y3pZoM_ZWd z(=|BXypplZ9V^4h>SD{i{SEDu`{Un_h=s$iT2VFA@fb%?r8m5F%3-I$!H(bF=U@#U zzv5D~@mV0tVa-UOt??vr?pw^srgGJ1R6K@>QgyIkk0Da3ls{{(G0)EKkq!JX$7~+1RXIBD>k?YvID*=&eaqO!D~Hym zFZ+o3cG_)`u_{^R;4?=bhgre$HuUr~USN1jMRTMdcRn&(v6)24$~zCJA{HE@!YJ`` zhtou^!?#tR&Kpk)-A_KF@VCVKJSfg4PJwt)C}|hP7KM;ZpJz0WcMBOoIUiNKOe=5&~Wt) zL3G5*(iS~Vv0RY48PViXpahtPiMQGuA14=WR3MHXqv2GA5<6E$O=$o$l!5viV=noEfk>*=oRGz zK-86x3bW?R?$^Iw$fO%VQ(rnzzE__jO!4OGO6#t?QT`&lMNwKt(Z8W7z9Hq2Bm&W)9E0JBJf7i?d5{KmC7OdY4PHBX};ymK^#K}Yp726SdK;*MI_YU(@`D& zaYP4xyvll}aaQ{9^K`}R#w@+!6L^p^Yg8Nk=<)4Sb>0I%ReKGuef(%bKPtMJO@fM6 zZj*tU{<=QMqeOVbobIS=c}shdEmZ0cukK7n-OFj_i7mxCPehofL&GLoqMLJL?&SR% zqSRss{n4ZlkA~i6S77ds?joT^GcW{m?pvO~ti<+ipc*W9_JFxRraPJ`pMeyS9G5Bj z70z2dQp;$BATvFcIA;D~9SiRv8ikT$eZ-ERpLBkfoeQ&fFq^*_Ckg)WD%uce#W`Zd zk^aEa^=B~42+Gk9WV&yuz#U^DdFYK&wzpM9j@~kkm>j|q5UEMdGm+1YoQ#nZ5Yg$M z_k0pt3`O5@>y9^T`$;N*U#inf^oNgeAL0>|KGPI)Ml@GaDo%+(3%a8i$kP(?uoc|wF5)Cht0ULnO*qowF~HmpLu#M~0)E~BzhJwk>$$yN~Wt#8d#O$HKjehsXK~HXluw!3b zn?$6BR0yyhsK%;4cIx!+Z%K;MXx&n~H9b5P{!2`j4%LX3ZJB2kTv68(-Qg0zI5NJ?0wq(eMbYr+dmO&W%L ztaIq2yk-Md0|#aJiqroH&iZOL$@%Of2|iGt-8fVb)P4aOnTq~D8>G5k#L!-r_YJsjfVB`2ans%0+L8{-1P9enx z($c@t=TTdlLDM|Lf952KxZ7*i{gH9&q1U=PmCGTi`hGflS~IEk(^il4X4n)UWgc`pm6*lObo@q7xD@`HHlU{Cr!|@)!120%8FDUQ<8xW^VSV)* zeO?34y0BcZF~2$sz_z?Y)hJ{&TTOE@j@3irkwq|>kQ$3nN=*BRtm5vpIn7pByAaC_ z?TQ$;+d+af4Z3r%g*s0`k6=z6N_wKwe-vxV&$V48oORnE__?E!lW{8LrUrLkB&erk zm5%1gw-+RYv=4qy2+{gY;tSn`p-}XLmV&`y3l2M zzzWHc8O5(fz6u*9IqN3S)Uzb<(wi7(j1n(iCbb}ZQGRZ$7TE1_&6gp_%Z8=H@-rU| z#Y!Bt)@HBq6+&7MLPPEuDGoXF44a*EXijrm(FwQ>d)9SZ_+Ll&ROGw|W9kAG^0|=f z&=arO-jB2$77-k%=*q)=VGWuTlY*!0x|ixXU6xdtG@^6A=qLczxB2`3wR9P{Wz^6I zHCL;2@hhGWI0kcz_5#8lQjG1mB?Qpp;F6&?s(WUw-A0iQh4!XG7deAT;Ftw6pt^Gh zhBzEk_0Q$jw2e1o9wLtfZ`mnPG<(C#ctuss{+_#SDRrgs9-&bD8t#=+w{*C>1K$%y zb>Gt<;KcVIs#?E>WNf?R3nGr^M_4AAroPzhBwc)eQed_c|?7-dH5rKF}L+8^Mk1ln>4%g ze3i3}iRScK)U^d-H4i2JW!ur_k&t-1Ec-l!_9XHY*!rpyF%!FWXD4y1rn^$_nv*Ac zGM_efRZ0))puUyFyQPvo)d!Va;HOg1@=DLCw>s7wx;$Q~qheg}>=#Z1zU{i&o+;md zaT?6fw-;s6u=e;m7Aq^pnFO>Ols~K*Yf!oJ<~`=0<#efF9ci2$sDMK1Gm*l!Se5ka z4$5CGZAg_B(p9%N%E%LQDVe!%{*v1U^ipix1=lkV?t4@CR=Kplr}D8->2JANxV!x|#dOf$?!iFgv-Ba$+V!9m zl=xRKw;R4%y=U7Lt-RM0<~Nk@9AnrT7Ul4T9Z<7~U>fO6K^Mgd!j4mw@1P4*GU1BJ ziGi?@Wk}#h4QFmU)auCkJHSAWT(T zkEHmwlcV%*OVQ5Y%8wGs zu}EQz()XG|;+!Uj_V9;!`xKj7RgMh0jHvl|R*wkv3NydSYmtM@5dHrzznII_--Au+ zAEkZG$KbKf){yoXA1Yenk(JRGcMxQR&$ec2UibD$KZ9EJQkM5PHtGb5;UG@ zK(QCtJ;nwBe`_m@0Yy*jrgBDP0QslkYgd`+IfO1cQTRtfQYhiBm?qx%H zaiyBg{IC 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zYb;*zK{=S4AFf<4ib_8SVdlbCoZ7Xsa{>RCnT__Ht}BK)jH_(lBb7w)C+8xf--g^{c!3F346w{l{ z%v4*9%0JhN7oFSZf7xz={Bs1WM9Lp!D&9Pj9=yW`Go&Wz+VD#aboM^(vYK`E*nyj~ zR65^BS#u-uPuXexdjcVw+QuK;tfGPT_cw6b((eBgKNjEp_plX#4R;m9v}4cb)mE;g z$KfrFx6SP;G z!okzPFjf*ZHh8VjMoFzIgl4siHz9As`6{8tnVCV8c*@FX5#jbrFdH2E0vwm04J_*V zV$Hv&)r{j2hA)?eY~T!mT_N%Ctpm_DdN!NAU6gDVk3)Qm;;p#m7a!6+3qtYxt0`k{ zzScWRKO26|zXAM+8j}TCW>37Xut}({wCx6|5<*(YJ3D^fOmmllY~Dk~7V?krSW!W> z1+$G=#u!u1DO-nmZ_SAONz7Q(y4ofkH3VmWFXkDqSnxR$rFkN`Q(AZ~-PKXSQ{$S` zg&gH!_}i{t)a945W#OH`D$`UB(P)dj 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 3cca6e370f..e029ddf625 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/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index b663a8082e..a6c261ec72 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 @@ -95,18 +95,7 @@ public class PrepareRelationsJob { readPathRelation(spark, inputRelationsPath) .filter( (FilterFunction) - r -> { - try { - return r != null - && r.getDataInfo() != null - && !r.getDataInfo().getDeletedbyinference(); - } catch (NullPointerException e) { - log.info( - "invalid NPE '{}'", - OBJECT_MAPPER.writeValueAsString(r)); - throw e; - } - }) + value -> value.getDataInfo().getDeletedbyinference() == false) .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) 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 874c34c090..3455cb5f3b 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 @@ -22,7 +22,6 @@ 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; @@ -42,7 +41,6 @@ import org.dom4j.io.XMLWriter; public class XmlRecordFactory implements Serializable { - public static final String REL_SUBTYPE_DEDUP = "dedup"; private Map accumulators; private Set specialDatasourceTypes; @@ -93,14 +91,7 @@ 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 = - je.getLinks().stream() - .filter( - t -> - !REL_SUBTYPE_DEDUP.equalsIgnoreCase( - t.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, contexts)) - .collect(Collectors.toCollection(ArrayList::new)); + final List relations = listRelations(je, templateFactory, contexts); final String mainType = ModelSupport.getMainType(type); metadata.addAll(buildContexts(mainType, contexts)); @@ -111,7 +102,7 @@ public class XmlRecordFactory implements Serializable { mainType, metadata, relations, - listChildren(entity, je, templateFactory), + listChildren(entity, je.getEntity().getType(), templateFactory), listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); @@ -928,149 +919,171 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - 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(); + 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"); - 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); + final LicenseComparator lc = new LicenseComparator(); + for (final Instance instance : r.getInstance()) { + if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) { + bestAccessRight = instance.getAccessright(); + } } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); + return bestAccessRight; + } - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", 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)); } - - 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); + return rels; } private List listChildren( - final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { + final OafEntity entity, String type, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); - EntityType entityType = EntityType.valueOf(je.getEntity().getType()); - - children.addAll( - je.getLinks().stream() - .filter( - link -> - REL_SUBTYPE_DEDUP.equalsIgnoreCase( - link.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, null)) - .collect(Collectors.toCollection(ArrayList::new))); - + EntityType entityType = EntityType.valueOf(type); if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); if (instances != null) {