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collectedfrom field moved in common parent class Oaf.java

This commit is contained in:
Claudio Atzori 2020-04-20 12:25:19 +02:00
parent 8ff7facfa3
commit d714bfb4d4
23 changed files with 1873 additions and 1774 deletions
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11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
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@ -1,14 +1,25 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
import java.util.Objects; import java.util.Objects;
public abstract class Oaf implements Serializable { public abstract class Oaf implements Serializable {
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo; private DataInfo dataInfo;
private Long lastupdatetimestamp; private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; 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<String> originalId;
private List<KeyValue> collectedfrom;
private List<StructuredProperty> pid; private List<StructuredProperty> pid;
private String dateofcollection; private String dateofcollection;
@ -38,14 +36,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.originalId = originalId; this.originalId = originalId;
} }
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; 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 String target;
private List<KeyValue> collectedFrom = new ArrayList<>();
public String getRelType() { public String getRelType() {
return relType; return relType;
} }
@ -60,14 +58,6 @@ public class Relation extends Oaf {
this.target = target; 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) { public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); 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"); Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setCollectedFrom( setCollectedfrom(
Stream.concat( Stream.concat(
Optional.ofNullable(getCollectedFrom()) Optional.ofNullable(getCollectedfrom())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty()), .orElse(Stream.empty()),
Optional.ofNullable(r.getCollectedFrom()) Optional.ofNullable(r.getCollectedfrom())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty())) .orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals .distinct() // relies on KeyValue.equals
@ -103,6 +93,6 @@ public class Relation extends Oaf {
@Override @Override
public int hashCode() { 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":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|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":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":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":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|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|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":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":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":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.setRelType(r.getRelType().toString());
rel.setSubRelType(r.getSubRelType().toString()); rel.setSubRelType(r.getSubRelType().toString());
rel.setRelClass(r.getRelClass()); rel.setRelClass(r.getRelClass());
rel.setCollectedFrom( rel.setCollectedfrom(
r.getCollectedfromCount() > 0 r.getCollectedfromCount() > 0
? r.getCollectedfromList().stream() ? r.getCollectedfromList().stream()
.map(kv -> mapKV(kv)) .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.ArrayList;
import java.util.List; import java.util.List;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.Document; import org.dom4j.Document;
@ -24,6 +26,9 @@ import org.dom4j.io.SAXReader;
abstract class AbstractSparkAction implements Serializable { 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 = protected static final ObjectMapper OBJECT_MAPPER =
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@ -84,8 +89,29 @@ abstract class AbstractSparkAction implements Serializable {
return SparkSession.builder().config(conf).getOrCreate(); return SparkSession.builder().config(conf).getOrCreate();
} }
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) { protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath); 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) { 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 java.io.IOException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; 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.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -71,14 +69,11 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) save(
.map( DedupRecordFactory.createDedupRecord(
(MapFunction<OafEntity, String>) spark, mergeRelPath, entityPath, clazz, dedupConf),
value -> OBJECT_MAPPER.writeValueAsString(value), outputPath,
Encoders.STRING()) SaveMode.Overwrite);
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
} }
} }
} }

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.oa.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo; 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.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -35,9 +34,7 @@ import scala.Tuple2;
public class SparkCreateMergeRels extends AbstractSparkAction { public class SparkCreateMergeRels extends AbstractSparkAction {
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark); super(parser, spark);
@ -148,22 +145,13 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
r.setRelClass(relClass); r.setRelClass(relClass);
r.setSubRelType("dedup"); r.setSubRelType("dedup");
DataInfo info = new DataInfo(); DataInfo info = getDataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId()); 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 // TODO calculate the trust value based on the similarity score of the elements in the CC
// info.setTrust(); // info.setTrust();
r.setDataInfo(info); r.setDataInfo(getDataInfo());
return r; 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.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block; 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.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -115,7 +114,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
r.setTarget(target); r.setTarget(target);
r.setSubRelType("dedupSimilarity"); r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo"); r.setRelClass("isSimilarTo");
r.setDataInfo(new DataInfo()); r.setDataInfo(getDataInfo());
switch (entity) { switch (entity) {
case "result": 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.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport; 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.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -125,7 +124,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
return value -> { return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
if (rel.getDataInfo() == null) { if (rel.getDataInfo() == null) {
rel.setDataInfo(new DataInfo()); rel.setDataInfo(getDataInfo());
} }
return rel; return rel;
}; };
@ -149,7 +148,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
Relation r = value._1()._2(); Relation r = value._1()._2();
String id = value._2()._2(); String id = value._2()._2();
if (r.getDataInfo() == null) { if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo()); r.setDataInfo(getDataInfo());
} }
r.getDataInfo().setDeletedbyinference(false); r.getDataInfo().setDeletedbyinference(false);
switch (type) { switch (type) {
@ -173,7 +172,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
if (value._2() != null) { if (value._2() != null) {
Relation r = value._1()._2(); Relation r = value._1()._2();
if (r.getDataInfo() == null) { if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo()); r.setDataInfo(getDataInfo());
} }
r.getDataInfo().setDeletedbyinference(true); r.getDataInfo().setDeletedbyinference(true);
return r; return r;

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

@ -98,305 +98,305 @@
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{"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": 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"} {"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": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f42cac35d9e8dd17b1a175afa512c13a", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f42cac35d9e8dd17b1a175afa512c13a", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f6cf64f0efe65afec422b282218514b5", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f6cf64f0efe65afec422b282218514b5", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f7f3b7f8caf2520e2fcaa7f3a704ec03", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f7f3b7f8caf2520e2fcaa7f3a704ec03", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::fcc8d792603a72774ecbd9fe4504b3da", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::fcc8d792603a72774ecbd9fe4504b3da", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"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_________::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|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"} {"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"}

166
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -10,19 +10,6 @@ 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.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.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;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -40,6 +27,17 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; 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;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
public abstract class AbstractMdRecordToOafMapper { public abstract class AbstractMdRecordToOafMapper {
@ -49,7 +47,11 @@ public abstract class AbstractMdRecordToOafMapper {
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); qualifier(
"publication",
"publication",
"dnet:result_typologies",
"dnet:result_typologies");
protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
@ -57,7 +59,11 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier REPOSITORY_QUALIFIER = protected static final Qualifier REPOSITORY_QUALIFIER =
qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions"); qualifier(
"sysimport:crosswalk:repository",
"sysimport:crosswalk:repository",
"dnet:provenanceActions",
"dnet:provenanceActions");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) { protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name; this.code2name = code2name;
@ -76,15 +82,22 @@ public abstract class AbstractMdRecordToOafMapper {
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final Document doc = final Document doc =
DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); DocumentHelper.parseText(
xml.replaceAll(
"http://datacite.org/schema/kernel-4",
"http://datacite.org/schema/kernel-3"));
final String type = doc.valueOf("//dr:CobjCategory/@type"); final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom = final KeyValue collectedFrom =
keyValue(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name")); keyValue(
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy = final KeyValue hostedBy =
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom ? collectedFrom
: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); : keyValue(
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
doc.valueOf("//oaf:hostedBy/@name"));
final DataInfo info = prepareDataInfo(doc); final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime(); final long lastUpdateTimestamp = new Date().getTime();
@ -176,7 +189,7 @@ public abstract class AbstractMdRecordToOafMapper {
r1.setRelClass("isProducedBy"); r1.setRelClass("isProducedBy");
r1.setSource(docId); r1.setSource(docId);
r1.setTarget(projectId); r1.setTarget(projectId);
r1.setCollectedFrom(Arrays.asList(collectedFrom)); r1.setCollectedfrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info); r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r1); res.add(r1);
@ -187,7 +200,7 @@ public abstract class AbstractMdRecordToOafMapper {
r2.setRelClass("produces"); r2.setRelClass("produces");
r2.setSource(projectId); r2.setSource(projectId);
r2.setTarget(docId); r2.setTarget(docId);
r2.setCollectedFrom(Arrays.asList(collectedFrom)); r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info); r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp); r2.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r2); res.add(r2);
@ -214,7 +227,14 @@ public abstract class AbstractMdRecordToOafMapper {
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); r.setPid(
prepareListStructProps(
doc,
"//oaf:identifier",
"@identifierType",
"dnet:pid_types",
"dnet:pid_types",
info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@ -243,10 +263,7 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Instance> prepareInstances( protected abstract List<Instance> prepareInstances(
Document doc, Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
DataInfo info,
KeyValue collectedfrom,
KeyValue hostedby);
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info); protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
@ -271,34 +288,28 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info); protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools( protected abstract List<Field<String>> prepareOtherResearchProductTools(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups( protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons( protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSoftwareLicenses( protected abstract List<StructuredProperty> prepareSoftwareLicenses(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls( protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info); protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetMetadataVersionNumber( protected abstract Field<String> prepareDatasetMetadataVersionNumber(
Document doc, Document doc, DataInfo info);
DataInfo info);
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
@ -322,16 +333,27 @@ public abstract class AbstractMdRecordToOafMapper {
final String sp = n.valueOf("@sp"); final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol"); final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition"); final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } if (StringUtils.isNotBlank(name)) {
return journal(
name,
issnPrinted,
issnOnline,
issnLinking,
ep,
iss,
sp,
vol,
edition,
null,
null,
info);
}
} }
return null; return null;
} }
protected Qualifier prepareQualifier( protected Qualifier prepareQualifier(
final Node node, final Node node, final String xpath, final String schemeId, final String schemeName) {
final String xpath,
final String schemeId,
final String schemeName) {
final String classId = node.valueOf(xpath); final String classId = node.valueOf(xpath);
final String className = code2name.get(classId); final String className = code2name.get(classId);
return qualifier(classId, className, schemeId, schemeName); return qualifier(classId, className, schemeId, schemeName);
@ -349,16 +371,15 @@ public abstract class AbstractMdRecordToOafMapper {
final Node n = (Node) o; final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId); final String classId = n.valueOf(xpathClassId);
final String className = code2name.get(classId); final String className = code2name.get(classId);
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); res.add(
structuredProperty(
n.getText(), classId, className, schemeId, schemeName, info));
} }
return res; return res;
} }
protected List<StructuredProperty> prepareListStructProps( protected List<StructuredProperty> prepareListStructProps(
final Node node, final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
final String xpath,
final Qualifier qualifier,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>(); final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) { for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o; final Node n = (Node) o;
@ -368,37 +389,52 @@ public abstract class AbstractMdRecordToOafMapper {
} }
protected List<StructuredProperty> prepareListStructProps( protected List<StructuredProperty> prepareListStructProps(
final Node node, final Node node, final String xpath, final DataInfo info) {
final String xpath,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>(); final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) { for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o; final Node n = (Node) o;
res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); res.add(
structuredProperty(
n.getText(),
n.valueOf("@classid"),
n.valueOf("@classname"),
n.valueOf("@schemeid"),
n.valueOf("@schemename"),
info));
} }
return res; return res;
} }
protected OAIProvenance prepareOAIprovenance(final Document doc) { protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n = final Node n =
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); doc.selectSingleNode(
"//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) { return null; } if (n == null) {
return null;
}
final String identifier = n.valueOf("./*[local-name()='identifier']"); final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");; final String baseURL = n.valueOf("./*[local-name()='baseURL']");
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; ;
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
;
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
final String datestamp = n.valueOf("./*[local-name()='datestamp']");; final String datestamp = n.valueOf("./*[local-name()='datestamp']");
final String harvestDate = n.valueOf("@harvestDate");; ;
final String harvestDate = n.valueOf("@harvestDate");
;
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); return oaiIProvenance(
identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
} }
protected DataInfo prepareDataInfo(final Document doc) { protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo"); final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); } if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@ -411,7 +447,13 @@ public abstract class AbstractMdRecordToOafMapper {
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf:trust"); final String trust = n.valueOf("./oaf:trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); return dataInfo(
deletedbyinference,
inferenceprovenance,
inferred,
false,
qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
trust);
} }
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) { protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
@ -419,9 +461,7 @@ public abstract class AbstractMdRecordToOafMapper {
} }
protected List<Field<String>> prepareListFields( protected List<Field<String>> prepareListFields(
final Node node, final Node node, final String xpath, final DataInfo info) {
final String xpath,
final DataInfo info) {
return listFields(info, prepareListString(node, xpath)); return listFields(info, prepareListString(node, xpath));
} }

169
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -10,23 +10,6 @@ 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.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import java.io.Closeable;
import java.io.IOException;
import java.sql.Array;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
@ -47,12 +30,31 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.io.Closeable;
import java.io.IOException;
import java.sql.Array;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
implements Closeable { implements Closeable {
private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions"); qualifier(
"sysimport:crosswalk:entityregistry",
"sysimport:crosswalk:entityregistry",
"dnet:provenance_actions",
"dnet:provenance_actions");
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
@ -63,8 +65,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
IOUtils.toString(MigrateDbEntitiesApplication.class IOUtils.toString(
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); MigrateDbEntitiesApplication.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
@ -93,7 +96,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing relations ds <-> orgs ..."); log.info("Processing relations ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); smdbe.execute(
"queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ..."); log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
@ -119,7 +123,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer) public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
throws Exception { throws Exception {
final String sql = final String sql =
IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); IOUtils.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
@ -136,14 +141,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true));
ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
ds.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"))); ds.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
ds.setPid(new ArrayList<>()); ds.setPid(new ArrayList<>());
ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
ds.setDateoftransformation(null); // Value not returned by the SQL query ds.setDateoftransformation(null); // Value not returned by the SQL query
ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
ds.setOaiprovenance(null); // Values not present in the DB ds.setOaiprovenance(null); // Values not present in the DB
ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); ds.setOpenairecompatibility(
prepareQualifierSplitting(rs.getString("openairecompatibility")));
ds.setOfficialname(field(rs.getString("officialname"), info)); ds.setOfficialname(field(rs.getString("officialname"), info));
ds.setEnglishname(field(rs.getString("englishname"), info)); ds.setEnglishname(field(rs.getString("englishname"), info));
ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
@ -176,7 +185,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
ds.setPidsystems(field(rs.getString("pidsystems"), info)); ds.setPidsystems(field(rs.getString("pidsystems"), info));
ds.setCertificates(field(rs.getString("certificates"), info)); ds.setCertificates(field(rs.getString("certificates"), info));
ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal ds.setJournal(
prepareJournal(
rs.getString("officialname"),
rs.getString("journal"),
info)); // Journal
ds.setDataInfo(info); ds.setDataInfo(info);
ds.setLastupdatetimestamp(lastUpdateTimestamp); ds.setLastupdatetimestamp(lastUpdateTimestamp);
@ -195,7 +208,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
p.setId(createOpenaireId(40, rs.getString("projectid"), true)); p.setId(createOpenaireId(40, rs.getString("projectid"), true));
p.setOriginalId(Arrays.asList(rs.getString("projectid"))); p.setOriginalId(Arrays.asList(rs.getString("projectid")));
p.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"))); p.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
p.setPid(new ArrayList<>()); p.setPid(new ArrayList<>());
p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateofcollection(asString(rs.getDate("dateofcollection")));
p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
@ -211,7 +227,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
p.setKeywords(field(rs.getString("keywords"), info)); p.setKeywords(field(rs.getString("keywords"), info));
p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); p.setOamandatepublications(
field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info));
@ -247,7 +264,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); o.setId(createOpenaireId(20, rs.getString("organizationid"), true));
o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
o.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"))); o.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
o.setPid(new ArrayList<>()); o.setPid(new ArrayList<>());
o.setDateofcollection(asString(rs.getDate("dateofcollection"))); o.setDateofcollection(asString(rs.getDate("dateofcollection")));
o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
@ -261,10 +281,17 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); o.setEcresearchorganization(
o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info)); field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info)); o.setEchighereducation(
o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); field(Boolean.toString(rs.getBoolean("echighereducation")), info));
o.setEcinternationalorganizationeurinterests(
field(
Boolean.toString(
rs.getBoolean("ecinternationalorganizationeurinterests")),
info));
o.setEcinternationalorganization(
field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
@ -284,7 +311,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final String orgId = createOpenaireId(20, rs.getString("organization"), true); final String orgId = createOpenaireId(20, rs.getString("organization"), true);
final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final String dsId = createOpenaireId(10, rs.getString("datasource"), true);
final List<KeyValue> collectedFrom = final List<KeyValue> collectedFrom =
listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname"));
final Relation r1 = new Relation(); final Relation r1 = new Relation();
r1.setRelType("datasourceOrganization"); r1.setRelType("datasourceOrganization");
@ -292,7 +321,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
r1.setRelClass("isProvidedBy"); r1.setRelClass("isProvidedBy");
r1.setSource(dsId); r1.setSource(dsId);
r1.setTarget(orgId); r1.setTarget(orgId);
r1.setCollectedFrom(collectedFrom); r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info); r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setLastupdatetimestamp(lastUpdateTimestamp);
@ -302,7 +331,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
r2.setRelClass("provides"); r2.setRelClass("provides");
r2.setSource(orgId); r2.setSource(orgId);
r2.setTarget(dsId); r2.setTarget(dsId);
r2.setCollectedFrom(collectedFrom); r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info); r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp); r2.setLastupdatetimestamp(lastUpdateTimestamp);
@ -318,7 +347,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); final String orgId = createOpenaireId(20, rs.getString("resporganization"), true);
final String projectId = createOpenaireId(40, rs.getString("project"), true); final String projectId = createOpenaireId(40, rs.getString("project"), true);
final List<KeyValue> collectedFrom = final List<KeyValue> collectedFrom =
listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname"));
final Relation r1 = new Relation(); final Relation r1 = new Relation();
r1.setRelType("projectOrganization"); r1.setRelType("projectOrganization");
@ -326,7 +357,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
r1.setRelClass("isParticipant"); r1.setRelClass("isParticipant");
r1.setSource(projectId); r1.setSource(projectId);
r1.setTarget(orgId); r1.setTarget(orgId);
r1.setCollectedFrom(collectedFrom); r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info); r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setLastupdatetimestamp(lastUpdateTimestamp);
@ -336,7 +367,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
r2.setRelClass("hasParticipant"); r2.setRelClass("hasParticipant");
r2.setSource(orgId); r2.setSource(orgId);
r2.setTarget(projectId); r2.setTarget(projectId);
r2.setCollectedFrom(collectedFrom); r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info); r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp); r2.setLastupdatetimestamp(lastUpdateTimestamp);
@ -349,9 +380,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
public List<Oaf> processClaims(final ResultSet rs) { public List<Oaf> processClaims(final ResultSet rs) {
final DataInfo info = final DataInfo info =
dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9"); dataInfo(
false,
null,
false,
false,
qualifier(
"user:claim",
"user:claim",
"dnet:provenanceActions",
"dnet:provenanceActions"),
"0.9");
final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); final List<KeyValue> collectedFrom =
listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
try { try {
@ -376,30 +418,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
return Arrays.asList(r); return Arrays.asList(r);
} else { } else {
final String sourceId = final String sourceId =
createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false); createOpenaireId(
rs.getString("source_type"), rs.getString("source_id"), false);
final String targetId = final String targetId =
createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false); createOpenaireId(
rs.getString("target_type"), rs.getString("target_id"), false);
final Relation r1 = new Relation(); final Relation r1 = new Relation();
final Relation r2 = new Relation(); final Relation r2 = new Relation();
if (rs.getString("source_type").equals("project")) { if (rs.getString("source_type").equals("project")) {
r1.setCollectedFrom(collectedFrom); r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultProject"); r1.setRelType("resultProject");
r1.setSubRelType("outcome"); r1.setSubRelType("outcome");
r1.setRelClass("produces"); r1.setRelClass("produces");
r2.setCollectedFrom(collectedFrom); r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultProject"); r2.setRelType("resultProject");
r2.setSubRelType("outcome"); r2.setSubRelType("outcome");
r2.setRelClass("isProducedBy"); r2.setRelClass("isProducedBy");
} else { } else {
r1.setCollectedFrom(collectedFrom); r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultResult"); r1.setRelType("resultResult");
r1.setSubRelType("relationship"); r1.setSubRelType("relationship");
r1.setRelClass("isRelatedTo"); r1.setRelClass("isRelatedTo");
r2.setCollectedFrom(collectedFrom); r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultResult"); r2.setRelType("resultResult");
r2.setSubRelType("relationship"); r2.setSubRelType("relationship");
r2.setRelClass("isRelatedTo"); r2.setRelClass("isRelatedTo");
@ -435,11 +479,19 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final String inferenceprovenance = rs.getString("inferenceprovenance"); final String inferenceprovenance = rs.getString("inferenceprovenance");
final Boolean inferred = rs.getBoolean("inferred"); final Boolean inferred = rs.getBoolean("inferred");
final String trust = rs.getString("trust"); final String trust = rs.getString("trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); return dataInfo(
deletedbyinference,
inferenceprovenance,
inferred,
false,
ENTITYREGISTRY_PROVENANCE_ACTION,
trust);
} }
private Qualifier prepareQualifierSplitting(final String s) { private Qualifier prepareQualifierSplitting(final String s) {
if (StringUtils.isBlank(s)) { return null; } if (StringUtils.isBlank(s)) {
return null;
}
final String[] arr = s.split("@@@"); final String[] arr = s.split("@@@");
return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
} }
@ -455,19 +507,22 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
} }
private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
if (StringUtils.isBlank(s)) { return null; } if (StringUtils.isBlank(s)) {
return null;
}
final String[] parts = s.split("###"); final String[] parts = s.split("###");
if (parts.length == 2) { if (parts.length == 2) {
final String value = parts[0]; final String value = parts[0];
final String[] arr = parts[1].split("@@@"); final String[] arr = parts[1].split("@@@");
if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); } if (arr.length == 4) {
return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo);
}
} }
return null; return null;
} }
private List<StructuredProperty> prepareListOfStructProps( private List<StructuredProperty> prepareListOfStructProps(
final Array array, final Array array, final DataInfo dataInfo) throws SQLException {
final DataInfo dataInfo) throws SQLException {
final List<StructuredProperty> res = new ArrayList<>(); final List<StructuredProperty> res = new ArrayList<>();
if (array != null) { if (array != null) {
for (final String s : (String[]) array.getArray()) { for (final String s : (String[]) array.getArray()) {
@ -486,10 +541,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final String[] arr = sj.split("@@@"); final String[] arr = sj.split("@@@");
if (arr.length == 3) { if (arr.length == 3) {
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;; final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;; ;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;
;
if (issn != null || eissn != null || lissn != null) { if (issn != null || eissn != null || lissn != null) {
return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); return journal(
name, issn, eissn, eissn, null, null, null, null, null, null, null,
info);
} }
} }
} }

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.setRelClass("isRelatedTo");
r1.setSource(docId); r1.setSource(docId);
r1.setTarget(otherId); r1.setTarget(otherId);
r1.setCollectedFrom(Arrays.asList(collectedFrom)); r1.setCollectedfrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info); r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp); r1.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r1); res.add(r1);
@ -243,7 +243,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
r2.setRelClass("isRelatedTo"); r2.setRelClass("isRelatedTo");
r2.setSource(otherId); r2.setSource(otherId);
r2.setTarget(docId); r2.setTarget(docId);
r2.setCollectedFrom(Arrays.asList(collectedFrom)); r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info); r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp); r2.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r2); 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.setRelClass(relClass);
r.setSource(source); r.setSource(source);
r.setTarget(target); r.setTarget(target);
r.setCollectedFrom(Arrays.asList(collectedFrom)); r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setDataInfo(info); r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp); r.setLastupdatetimestamp(lastUpdateTimestamp);
return r; 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.setTarget(targetId);
r.setRelType(relationSemantic); r.setRelType(relationSemantic);
r.setRelClass("datacite"); r.setRelClass("datacite");
r.setCollectedFrom(parsedObject.getCollectedfrom()); r.setCollectedfrom(parsedObject.getCollectedfrom());
r.setDataInfo(di); r.setDataInfo(di);
rels.add(r); rels.add(r);
r = new DLIRelation(); r = new DLIRelation();
@ -195,7 +195,7 @@ public abstract class AbstractScholexplorerParser {
r.setTarget(parsedObject.getId()); r.setTarget(parsedObject.getId());
r.setRelType(inverseRelation); r.setRelType(inverseRelation);
r.setRelClass("datacite"); r.setRelClass("datacite");
r.setCollectedFrom(parsedObject.getCollectedfrom()); r.setCollectedfrom(parsedObject.getCollectedfrom());
r.setDateOfCollection(dateOfCollection); r.setDateOfCollection(dateOfCollection);
rels.add(r); rels.add(r);
if ("unknown".equalsIgnoreCase(relatedType)) if ("unknown".equalsIgnoreCase(relatedType))

19
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -6,10 +6,14 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.when; 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 java.io.IOException; import java.io.IOException;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
@ -18,17 +22,10 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
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;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class MappersTest { public class MappersTest {
@Mock @Mock private Map<String, String> code2name;
private Map<String, String> code2name;
@BeforeEach @BeforeEach
public void setUp() throws Exception { public void setUp() throws Exception {
@ -62,8 +59,8 @@ public class MappersTest {
assertValidId(r1.getTarget()); assertValidId(r1.getTarget());
assertValidId(r2.getSource()); assertValidId(r2.getSource());
assertValidId(r2.getTarget()); assertValidId(r2.getTarget());
assertValidId(r1.getCollectedFrom().get(0).getKey()); assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey());
assertNotNull(r1.getDataInfo()); assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo()); assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust()); assertNotNull(r1.getDataInfo().getTrust());

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

@ -4,6 +4,14 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue; 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 java.io.IOException; import java.io.IOException;
import java.sql.Array; import java.sql.Array;
import java.sql.Date; import java.sql.Date;
@ -11,7 +19,6 @@ import java.sql.ResultSet;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.List; import java.util.List;
import java.util.Objects; import java.util.Objects;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
@ -21,23 +28,12 @@ import org.mockito.Mock;
import org.mockito.Mockito; import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
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;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class MigrateDbEntitiesApplicationTest { public class MigrateDbEntitiesApplicationTest {
private MigrateDbEntitiesApplication app; private MigrateDbEntitiesApplication app;
@Mock @Mock private ResultSet rs;
private ResultSet rs;
@BeforeEach @BeforeEach
public void setUp() { public void setUp() {
@ -59,8 +55,11 @@ public class MigrateDbEntitiesApplicationTest {
assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields));
assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields));
assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); assertEquals(
assertEquals(ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields));
assertEquals(
ds.getCollectedfrom().get(0).getValue(),
getValueAsString("collectedfromname", fields));
} }
@Test @Test
@ -76,8 +75,9 @@ public class MigrateDbEntitiesApplicationTest {
assertValidId(p.getCollectedfrom().get(0).getKey()); assertValidId(p.getCollectedfrom().get(0).getKey());
assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields));
assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); assertEquals(p.getTitle().getValue(), getValueAsString("title", fields));
assertEquals(p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); assertEquals(
p.getCollectedfrom().get(0).getValue(),
getValueAsString("collectedfromname", fields));
} }
@Test @Test
@ -96,11 +96,18 @@ public class MigrateDbEntitiesApplicationTest {
assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields));
assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields));
assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); assertEquals(
assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]);
assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); assertEquals(
assertEquals(o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]);
assertEquals(o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); assertEquals(
o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]);
assertEquals(
o.getCountry().getSchemename(),
getValueAsString("country", fields).split("@@@")[3]);
assertEquals(
o.getCollectedfrom().get(0).getValue(),
getValueAsString("collectedfromname", fields));
} }
@Test @Test
@ -135,8 +142,8 @@ public class MigrateDbEntitiesApplicationTest {
assertValidId(r2.getSource()); assertValidId(r2.getSource());
assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget()); assertEquals(r2.getSource(), r1.getTarget());
assertValidId(r1.getCollectedFrom().get(0).getKey()); assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey());
} }
@Test @Test
@ -184,8 +191,8 @@ public class MigrateDbEntitiesApplicationTest {
assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertValidId(r1.getCollectedFrom().get(0).getKey()); assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey());
// System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2)); // System.out.println(new ObjectMapper().writeValueAsString(r2));

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

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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) if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0)
s.setPublicationDate(scholixSummary.getDate().get(0)); s.setPublicationDate(scholixSummary.getDate().get(0));
s.setLinkprovider( s.setLinkprovider(
rel.getCollectedFrom().stream() rel.getCollectedfrom().stream()
.map( .map(
cf -> cf ->
new ScholixEntityId( new ScholixEntityId(
@ -73,7 +73,7 @@ public class Scholix implements Serializable {
if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0)
s.setPublicationDate(scholixSummary.getDate().get(0)); s.setPublicationDate(scholixSummary.getDate().get(0));
s.setLinkprovider( s.setLinkprovider(
rel.getCollectedFrom().stream() rel.getCollectedfrom().stream()
.map( .map(
cf -> cf ->
new ScholixEntityId( 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) readPathRelation(spark, inputRelationsPath)
.filter( .filter(
(FilterFunction<SortableRelation>) (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( .groupByKey(
(MapFunction<SortableRelation, String>) value -> value.getSource(), (MapFunction<SortableRelation, String>) value -> value.getSource(),
Encoders.STRING()) Encoders.STRING())

79
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.Serializable;
import java.io.StringReader; import java.io.StringReader;
import java.io.StringWriter; import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Set; import java.util.Set;
@ -41,6 +42,7 @@ import org.dom4j.io.XMLWriter;
public class XmlRecordFactory implements Serializable { public class XmlRecordFactory implements Serializable {
public static final String REL_SUBTYPE_DEDUP = "dedup";
private Map<String, LongAccumulator> accumulators; private Map<String, LongAccumulator> accumulators;
private Set<String> specialDatasourceTypes; 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 // rels has to be processed before the contexts because they enrich the contextMap with
// the // the
// funding info. // 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); final String mainType = ModelSupport.getMainType(type);
metadata.addAll(buildContexts(mainType, contexts)); metadata.addAll(buildContexts(mainType, contexts));
@ -102,7 +111,7 @@ public class XmlRecordFactory implements Serializable {
mainType, mainType,
metadata, metadata,
relations, relations,
listChildren(entity, je.getEntity().getType(), templateFactory), listChildren(entity, je, templateFactory),
listExtraInfo(entity)); listExtraInfo(entity));
return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent);
@ -919,28 +928,7 @@ public class XmlRecordFactory implements Serializable {
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType));
} }
private Qualifier getBestAccessright(final Result r) { private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set<String> contexts) {
Qualifier bestAccessRight = new Qualifier();
bestAccessRight.setClassid("UNKNOWN");
bestAccessRight.setClassname("not available");
bestAccessRight.setSchemeid("dnet:access_modes");
bestAccessRight.setSchemename("dnet:access_modes");
final LicenseComparator lc = new LicenseComparator();
for (final Instance instance : r.getInstance()) {
if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) {
bestAccessRight = instance.getAccessright();
}
}
return bestAccessRight;
}
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 Relation rel = link.getRelation();
final RelatedEntity re = link.getRelatedEntity(); final RelatedEntity re = link.getRelatedEntity();
final String targetType = link.getRelatedEntity().getType(); final String targetType = link.getRelatedEntity().getType();
@ -953,8 +941,7 @@ public class XmlRecordFactory implements Serializable {
case software: case software:
if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) {
metadata.add( metadata.add(
XmlSerializationUtils.mapStructuredProperty( XmlSerializationUtils.mapStructuredProperty("title", re.getTitle()));
"title", re.getTitle()));
} }
if (isNotBlank(re.getDateofacceptance())) { if (isNotBlank(re.getDateofacceptance())) {
metadata.add( metadata.add(
@ -972,8 +959,7 @@ public class XmlRecordFactory implements Serializable {
} }
if (re.getResulttype() != null & re.getResulttype().isBlank()) { if (re.getResulttype() != null & re.getResulttype().isBlank()) {
metadata.add( metadata.add(
XmlSerializationUtils.mapQualifier( XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype()));
"resulttype", re.getResulttype()));
} }
if (re.getCollectedfrom() != null) { if (re.getCollectedfrom() != null) {
metadata.addAll( metadata.addAll(
@ -987,10 +973,7 @@ public class XmlRecordFactory implements Serializable {
if (re.getPid() != null) { if (re.getPid() != null) {
metadata.addAll( metadata.addAll(
re.getPid().stream() re.getPid().stream()
.map( .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p))
p ->
XmlSerializationUtils.mapStructuredProperty(
"pid", p))
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
break; break;
@ -1021,28 +1004,25 @@ public class XmlRecordFactory implements Serializable {
"legalshortname", re.getLegalshortname())); "legalshortname", re.getLegalshortname()));
} }
if (re.getCountry() != null & !re.getCountry().isBlank()) { if (re.getCountry() != null & !re.getCountry().isBlank()) {
metadata.add( metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry()));
XmlSerializationUtils.mapQualifier("country", re.getCountry()));
} }
break; break;
case project: case project:
if (isNotBlank(re.getProjectTitle())) { if (isNotBlank(re.getProjectTitle())) {
metadata.add( metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle()));
XmlSerializationUtils.asXmlElement("title", re.getProjectTitle()));
} }
if (isNotBlank(re.getCode())) { if (isNotBlank(re.getCode())) {
metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode()));
} }
if (isNotBlank(re.getAcronym())) { if (isNotBlank(re.getAcronym())) {
metadata.add( metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym()));
XmlSerializationUtils.asXmlElement("acronym", re.getAcronym()));
} }
if (re.getContracttype() != null & !re.getContracttype().isBlank()) { if (re.getContracttype() != null & !re.getContracttype().isBlank()) {
metadata.add( metadata.add(
XmlSerializationUtils.mapQualifier( XmlSerializationUtils.mapQualifier(
"contracttype", re.getContracttype())); "contracttype", re.getContracttype()));
} }
if (re.getFundingtree() != null) { if (re.getFundingtree() != null & contexts != null) {
metadata.addAll( metadata.addAll(
re.getFundingtree().stream() re.getFundingtree().stream()
.peek(ft -> fillContextMap(ft, contexts)) .peek(ft -> fillContextMap(ft, contexts))
@ -1067,23 +1047,30 @@ public class XmlRecordFactory implements Serializable {
accumulators.get(accumulatorName).add(1); accumulators.get(accumulatorName).add(1);
} }
rels.add( return templateFactory.getRel(
templateFactory.getRel(
targetType, targetType,
rel.getTarget(), rel.getTarget(),
Sets.newHashSet(metadata), Sets.newHashSet(metadata),
rel.getRelClass(), rel.getRelClass(),
scheme, scheme,
info)); info);
}
return rels;
} }
private List<String> listChildren( private List<String> listChildren(
final OafEntity entity, String type, TemplateFactory templateFactory) { final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) {
final List<String> children = Lists.newArrayList(); 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))) { if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
final List<Instance> instances = ((Result) entity).getInstance(); final List<Instance> instances = ((Result) entity).getInstance();
if (instances != null) { if (instances != null) {