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Merge branch 'master' into deduptesting

This commit is contained in:
miconis 2020-04-20 14:50:12 +02:00
parent 5f45f2c77f d714bfb4d4
commit 772f75d167
24 changed files with 707 additions and 561 deletions
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11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -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<KeyValue> collectedfrom;
private DataInfo dataInfo;
private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() {
return dataInfo;
}

10
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -10,8 +10,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
private List<String> originalId;
private List<KeyValue> collectedfrom;
private List<StructuredProperty> pid;
private String dateofcollection;
@ -38,14 +36,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.originalId = originalId;
}
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public List<StructuredProperty> getPid() {
return pid;
}

18
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -18,8 +18,6 @@ public class Relation extends Oaf {
private String target;
private List<KeyValue> collectedFrom = new ArrayList<>();
public String getRelType() {
return relType;
}
@ -60,14 +58,6 @@ public class Relation extends Oaf {
this.target = target;
}
public List<KeyValue> getCollectedFrom() {
return collectedFrom;
}
public void setCollectedFrom(final List<KeyValue> 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);
}
}

20
dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json
View File

@ -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"}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java
View File

@ -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))

30
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java
View File

@ -14,7 +14,9 @@ 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;
@ -24,6 +26,9 @@ 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);
@ -84,8 +89,29 @@ abstract class AbstractSparkAction implements Serializable {
return SparkSession.builder().config(conf).getOrCreate();
}
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath);
protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.map(
(MapFunction<T, String>) 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 removeOutputDir(SparkSession spark, String path) {

15
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
View File

@ -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;
@ -71,14 +69,11 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf)
.map(
(MapFunction<OafEntity, String>)
value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
save(
DedupRecordFactory.createDedupRecord(
spark, mergeRelPath, entityPath, clazz, dedupConf),
outputPath,
SaveMode.Overwrite);
}
}
}

16
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
View File

@ -6,7 +6,6 @@ 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;
@ -35,9 +34,7 @@ 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);
@ -148,22 +145,13 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
r.setRelClass(relClass);
r.setSubRelType("dedup");
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
DataInfo info = getDataInfo();
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(info);
r.setDataInfo(getDataInfo());
return r;
}

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
View File

@ -2,7 +2,6 @@ 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;
@ -115,7 +114,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
r.setTarget(target);
r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo");
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
switch (entity) {
case "result":

7
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -4,7 +4,6 @@ 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;
@ -125,7 +124,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
if (rel.getDataInfo() == null) {
rel.setDataInfo(new DataInfo());
rel.setDataInfo(getDataInfo());
}
return rel;
};
@ -149,7 +148,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
Relation r = value._1()._2();
String id = value._2()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
}
r.getDataInfo().setDeletedbyinference(false);
switch (type) {
@ -173,7 +172,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
if (value._2() != null) {
Relation r = value._1()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
}
r.getDataInfo().setDeletedbyinference(true);
return r;

598
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation
View File

@ -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": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
{"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": "20|doajarticles::c3534dbd02b4a4aa35f235671f7631aa", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
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{"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|erc_________::8511e17e153877fecd5a9a4ea8eb0969", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::07c370987d51b8273071fedf5931acf6"}
{"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|erc_________::67b1c4d6876a12e265e965c1451a7f36", "lastupdatetimestamp": 0, "relType": "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"}

51
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -1,9 +1,38 @@
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.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<String, String> 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");

59
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -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<KeyValue> 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<KeyValue> 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<KeyValue> 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");

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -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);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -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;

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java
View File

@ -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))

42
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -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<Oaf> 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);

53
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -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<Oaf> 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<TypedField> prepareMocks(final String jsonFile) throws IOException, SQLException {

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml
View File

@ -87,6 +87,7 @@
<oaf:language>und</oaf:language>
<oaf:concept id="https://zenodo.org/communities/epfl"/>
<oaf:hostedBy id="re3data_____::r3d100010468" name="Zenodo"/>
<oaf:projectid>corda_______::226852</oaf:projectid>
<oaf:collectedFrom id="re3data_____::r3d100010468" name="Zenodo"/>
</metadata>
<about xmlns:dc="http://purl.org/dc/elements/1.1/"

BIN
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/relation/relation_100.json.gz
View File

Binary file not shown.

4
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java
View File

@ -48,7 +48,7 @@ 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(
@ -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(

2
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json
View File

@ -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}]}
{"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}]}

13
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java
View File

@ -95,7 +95,18 @@ public class PrepareRelationsJob {
readPathRelation(spark, inputRelationsPath)
.filter(
(FilterFunction<SortableRelation>)
value -> value.getDataInfo().getDeletedbyinference() == false)
r -> {
try {
return r != null
&& r.getDataInfo() != null
&& !r.getDataInfo().getDeletedbyinference();
} catch (NullPointerException e) {
log.info(
"invalid NPE '{}'",
OBJECT_MAPPER.writeValueAsString(r));
throw e;
}
})
.groupByKey(
(MapFunction<SortableRelation, String>) value -> value.getSource(),
Encoders.STRING())

303
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -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<String, LongAccumulator> accumulators;
private Set<String> 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<String> relations = listRelations(je, templateFactory, contexts);
final List<String> 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<String> 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<String> 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<String> listRelations(
final JoinedEntity je, TemplateFactory templateFactory, final Set<String> contexts) {
final List<String> 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<String> 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<String> listChildren(
final OafEntity entity, String type, TemplateFactory templateFactory) {
final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) {
final List<String> 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<Instance> instances = ((Result) entity).getInstance();
if (instances != null) {