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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
View File

@ -1,14 +1,25 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.List;
import java.util.Objects;
public abstract class Oaf implements Serializable {
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo;
private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() {
return dataInfo;
}

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

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

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

@ -18,8 +18,6 @@ public class Relation extends Oaf {
private String target;
private List<KeyValue> collectedFrom = new ArrayList<>();
public String getRelType() {
return relType;
}
@ -60,14 +58,6 @@ public class Relation extends Oaf {
this.target = target;
}
public List<KeyValue> getCollectedFrom() {
return collectedFrom;
}
public void setCollectedFrom(final List<KeyValue> collectedFrom) {
this.collectedFrom = collectedFrom;
}
public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");
@ -77,12 +67,12 @@ public class Relation extends Oaf {
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setCollectedFrom(
setCollectedfrom(
Stream.concat(
Optional.ofNullable(getCollectedFrom())
Optional.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional.ofNullable(r.getCollectedFrom())
Optional.ofNullable(r.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
@ -103,6 +93,6 @@ public class Relation extends Oaf {
@Override
public int hashCode() {
return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom);
return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom);
}
}

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

@ -1,10 +1,10 @@
{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"}
{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"}

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

@ -41,7 +41,7 @@ public class ProtoConverter implements Serializable {
rel.setRelType(r.getRelType().toString());
rel.setSubRelType(r.getSubRelType().toString());
rel.setRelClass(r.getRelClass());
rel.setCollectedFrom(
rel.setCollectedfrom(
r.getCollectedfromCount() > 0
? r.getCollectedfromList().stream()
.map(kv -> mapKV(kv))

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

@ -14,7 +14,9 @@ import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
@ -24,6 +26,9 @@ import org.dom4j.io.SAXReader;
abstract class AbstractSparkAction implements Serializable {
protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
protected static final ObjectMapper OBJECT_MAPPER =
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@ -84,8 +89,29 @@ abstract class AbstractSparkAction implements Serializable {
return SparkSession.builder().config(conf).getOrCreate();
}
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath);
protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.map(
(MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(mode)
.text(outPath);
}
protected static DataInfo getDataInfo() {
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
return info;
}
protected static void removeOutputDir(SparkSession spark, String path) {

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

@ -11,8 +11,6 @@ import eu.dnetlib.pace.config.DedupConfig;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
@ -71,14 +69,11 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf)
.map(
(MapFunction<OafEntity, String>)
value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
save(
DedupRecordFactory.createDedupRecord(
spark, mergeRelPath, entityPath, clazz, dedupConf),
outputPath,
SaveMode.Overwrite);
}
}
}

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

@ -6,7 +6,6 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -35,9 +34,7 @@ import scala.Tuple2;
public class SparkCreateMergeRels extends AbstractSparkAction {
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
@ -148,22 +145,13 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
r.setRelClass(relClass);
r.setSubRelType("dedup");
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
DataInfo info = getDataInfo();
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
// TODO calculate the trust value based on the similarity score of the elements in the CC
// info.setTrust();
r.setDataInfo(info);
r.setDataInfo(getDataInfo());
return r;
}

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

@ -2,7 +2,6 @@ package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -115,7 +114,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
r.setTarget(target);
r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo");
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
switch (entity) {
case "result":

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

@ -4,7 +4,6 @@ import static org.apache.spark.sql.functions.col;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -125,7 +124,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
if (rel.getDataInfo() == null) {
rel.setDataInfo(new DataInfo());
rel.setDataInfo(getDataInfo());
}
return rel;
};
@ -149,7 +148,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
Relation r = value._1()._2();
String id = value._2()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
}
r.getDataInfo().setDeletedbyinference(false);
switch (type) {
@ -173,7 +172,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
if (value._2() != null) {
Relation r = value._1()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(new DataInfo());
r.setDataInfo(getDataInfo());
}
r.getDataInfo().setDeletedbyinference(true);
return r;

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

@ -98,305 +98,305 @@
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::c3534dbd02b4a4aa35f235671f7631aa", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
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{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::8511e17e153877fecd5a9a4ea8eb0969", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::07c370987d51b8273071fedf5931acf6"}
{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::67b1c4d6876a12e265e965c1451a7f36", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}
{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|od______1106::aabdb9c07beef7bdf7a93b6455f75e06", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}

850
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.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.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -40,399 +27,452 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
public abstract class AbstractMdRecordToOafMapper {
protected final Map<String, String> code2name;
protected static final Qualifier MAIN_TITLE_QUALIFIER =
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier REPOSITORY_QUALIFIER =
qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
}
public List<Oaf> processMdRecord(final String xml) {
try {
final Map<String, String> nsContext = new HashMap<>();
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final Document doc =
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 KeyValue collectedFrom =
keyValue(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy =
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name"));
final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
protected List<Oaf> createOafs(
final Document doc,
final String type,
final KeyValue collectedFrom,
final KeyValue hostedBy,
final DataInfo info,
final long lastUpdateTimestamp) {
final List<Oaf> oafs = new ArrayList<>();
switch (type.toLowerCase()) {
case "":
case "publication":
final Publication p = new Publication();
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER);
p.setJournal(prepareJournal(doc, info));
oafs.add(p);
break;
case "dataset":
final Dataset d = new Dataset();
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setResulttype(DATASET_RESULTTYPE_QUALIFIER);
d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info));
d.setVersion(prepareDatasetVersion(doc, info));
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
oafs.add(d);
break;
case "software":
final Software s = new Software();
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
oafs.add(s);
break;
case "otherresearchproducts":
default:
final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
o.setResulttype(OTHER_RESULTTYPE_QUALIFIER);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info));
oafs.add(o);
break;
}
if (!oafs.isEmpty()) {
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
}
return oafs;
}
private List<Oaf> addProjectRels(
final Document doc,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final List<Oaf> res = new ArrayList<>();
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
for (final Object o : doc.selectNodes("//oaf:projectid")) {
final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
final Relation r1 = new Relation();
r1.setRelType("resultProject");
r1.setSubRelType("outcome");
r1.setRelClass("isProducedBy");
r1.setSource(docId);
r1.setTarget(projectId);
r1.setCollectedFrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r1);
final Relation r2 = new Relation();
r2.setRelType("resultProject");
r2.setSubRelType("outcome");
r2.setRelClass("produces");
r2.setSource(projectId);
r2.setTarget(docId);
r2.setCollectedFrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r2);
}
return res;
}
protected abstract List<Oaf> addOtherResultRels(
final Document doc,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp);
private void populateResultFields(
final Result r,
final Document doc,
final KeyValue collectedFrom,
final KeyValue hostedBy,
final DataInfo info,
final long lastUpdateTimestamp) {
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setOaiprovenance(prepareOAIprovenance(doc));
r.setAuthor(prepareAuthors(doc, info));
r.setLanguage(prepareLanguages(doc));
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setSubject(prepareSubjects(doc, info));
r.setTitle(prepareTitles(doc, info));
r.setRelevantdate(prepareRelevantDates(doc, info));
r.setDescription(prepareDescriptions(doc, info));
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
r.setPublisher(preparePublisher(doc, info));
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
r.setSource(prepareSources(doc, info));
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setFormat(prepareFormats(doc, info));
r.setContributor(prepareContributors(doc, info));
r.setResourcetype(prepareResourceType(doc, info));
r.setCoverage(prepareCoverages(doc, info));
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
}
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Instance> prepareInstances(
Document doc,
DataInfo info,
KeyValue collectedfrom,
KeyValue hostedby);
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
protected abstract Qualifier prepareLanguages(Document doc);
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools(
Document doc,
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc,
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
Document doc,
DataInfo info);
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
Document doc,
DataInfo info);
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
Document doc,
DataInfo info);
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
Document doc,
DataInfo info);
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
private Journal prepareJournal(final Document doc, final DataInfo info) {
final Node n = doc.selectSingleNode("//oaf:journal");
if (n != null) {
final String name = n.getText();
final String issnPrinted = n.valueOf("@issn");
final String issnOnline = n.valueOf("@eissn");
final String issnLinking = n.valueOf("@lissn");
final String ep = n.valueOf("@ep");
final String iss = n.valueOf("@iss");
final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
}
return null;
}
protected Qualifier prepareQualifier(
final Node node,
final String xpath,
final String schemeId,
final String schemeName) {
final String classId = node.valueOf(xpath);
final String className = code2name.get(classId);
return qualifier(classId, className, schemeId, schemeName);
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final String xpathClassId,
final String schemeId,
final String schemeName,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId);
final String className = code2name.get(classId);
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
}
return res;
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final Qualifier qualifier,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res.add(structuredProperty(n.getText(), qualifier, info));
}
return res;
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
}
return res;
}
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n =
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) { return null; }
final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
final String harvestDate = n.valueOf("@harvestDate");;
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
}
protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); }
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
final boolean deletedbyinference =
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf: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) {
return field(node.valueOf(xpath), info);
}
protected List<Field<String>> prepareListFields(
final Node node,
final String xpath,
final DataInfo info) {
return listFields(info, prepareListString(node, xpath));
}
protected List<String> prepareListString(final Node node, final String xpath) {
final List<String> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final String s = ((Node) o).getText().trim();
if (StringUtils.isNotBlank(s)) {
res.add(s);
}
}
return res;
}
protected final Map<String, String> code2name;
protected static final Qualifier MAIN_TITLE_QUALIFIER =
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier(
"publication",
"publication",
"dnet:result_typologies",
"dnet:result_typologies");
protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier REPOSITORY_QUALIFIER =
qualifier(
"sysimport:crosswalk:repository",
"sysimport:crosswalk:repository",
"dnet:provenanceActions",
"dnet:provenanceActions");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
}
public List<Oaf> processMdRecord(final String xml) {
try {
final Map<String, String> nsContext = new HashMap<>();
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final Document doc =
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 KeyValue collectedFrom =
keyValue(
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy =
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: keyValue(
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
doc.valueOf("//oaf:hostedBy/@name"));
final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
protected List<Oaf> createOafs(
final Document doc,
final String type,
final KeyValue collectedFrom,
final KeyValue hostedBy,
final DataInfo info,
final long lastUpdateTimestamp) {
final List<Oaf> oafs = new ArrayList<>();
switch (type.toLowerCase()) {
case "":
case "publication":
final Publication p = new Publication();
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER);
p.setJournal(prepareJournal(doc, info));
oafs.add(p);
break;
case "dataset":
final Dataset d = new Dataset();
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setResulttype(DATASET_RESULTTYPE_QUALIFIER);
d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info));
d.setVersion(prepareDatasetVersion(doc, info));
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
oafs.add(d);
break;
case "software":
final Software s = new Software();
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
oafs.add(s);
break;
case "otherresearchproducts":
default:
final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
o.setResulttype(OTHER_RESULTTYPE_QUALIFIER);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info));
oafs.add(o);
break;
}
if (!oafs.isEmpty()) {
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
}
return oafs;
}
private List<Oaf> addProjectRels(
final Document doc,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final List<Oaf> res = new ArrayList<>();
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
for (final Object o : doc.selectNodes("//oaf:projectid")) {
final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
final Relation r1 = new Relation();
r1.setRelType("resultProject");
r1.setSubRelType("outcome");
r1.setRelClass("isProducedBy");
r1.setSource(docId);
r1.setTarget(projectId);
r1.setCollectedfrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r1);
final Relation r2 = new Relation();
r2.setRelType("resultProject");
r2.setSubRelType("outcome");
r2.setRelClass("produces");
r2.setSource(projectId);
r2.setTarget(docId);
r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r2);
}
return res;
}
protected abstract List<Oaf> addOtherResultRels(
final Document doc,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp);
private void populateResultFields(
final Result r,
final Document doc,
final KeyValue collectedFrom,
final KeyValue hostedBy,
final DataInfo info,
final long lastUpdateTimestamp) {
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(
prepareListStructProps(
doc,
"//oaf:identifier",
"@identifierType",
"dnet:pid_types",
"dnet:pid_types",
info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setOaiprovenance(prepareOAIprovenance(doc));
r.setAuthor(prepareAuthors(doc, info));
r.setLanguage(prepareLanguages(doc));
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setSubject(prepareSubjects(doc, info));
r.setTitle(prepareTitles(doc, info));
r.setRelevantdate(prepareRelevantDates(doc, info));
r.setDescription(prepareDescriptions(doc, info));
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
r.setPublisher(preparePublisher(doc, info));
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
r.setSource(prepareSources(doc, info));
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setFormat(prepareFormats(doc, info));
r.setContributor(prepareContributors(doc, info));
r.setResourcetype(prepareResourceType(doc, info));
r.setCoverage(prepareCoverages(doc, info));
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
}
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Instance> prepareInstances(
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
protected abstract Qualifier prepareLanguages(Document doc);
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools(
Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
Document doc, DataInfo info);
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
Document doc, DataInfo info);
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
Document doc, DataInfo info);
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
private Journal prepareJournal(final Document doc, final DataInfo info) {
final Node n = doc.selectSingleNode("//oaf:journal");
if (n != null) {
final String name = n.getText();
final String issnPrinted = n.valueOf("@issn");
final String issnOnline = n.valueOf("@eissn");
final String issnLinking = n.valueOf("@lissn");
final String ep = n.valueOf("@ep");
final String iss = n.valueOf("@iss");
final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) {
return journal(
name,
issnPrinted,
issnOnline,
issnLinking,
ep,
iss,
sp,
vol,
edition,
null,
null,
info);
}
}
return null;
}
protected Qualifier prepareQualifier(
final Node node, final String xpath, final String schemeId, final String schemeName) {
final String classId = node.valueOf(xpath);
final String className = code2name.get(classId);
return qualifier(classId, className, schemeId, schemeName);
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final String xpathClassId,
final String schemeId,
final String schemeName,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId);
final String className = code2name.get(classId);
res.add(
structuredProperty(
n.getText(), classId, className, schemeId, schemeName, info));
}
return res;
}
protected List<StructuredProperty> prepareListStructProps(
final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res.add(structuredProperty(n.getText(), qualifier, info));
}
return res;
}
protected List<StructuredProperty> prepareListStructProps(
final Node node, final String xpath, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res.add(
structuredProperty(
n.getText(),
n.valueOf("@classid"),
n.valueOf("@classname"),
n.valueOf("@schemeid"),
n.valueOf("@schemename"),
info));
}
return res;
}
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n =
doc.selectSingleNode(
"//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) {
return null;
}
final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
;
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
;
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
;
final String harvestDate = n.valueOf("@harvestDate");
;
return oaiIProvenance(
identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
}
protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
final boolean deletedbyinference =
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf: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) {
return field(node.valueOf(xpath), info);
}
protected List<Field<String>> prepareListFields(
final Node node, final String xpath, final DataInfo info) {
return listFields(info, prepareListString(node, xpath));
}
protected List<String> prepareListString(final Node node, final String xpath) {
final List<String> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final String s = ((Node) o).getText().trim();
if (StringUtils.isNotBlank(s)) {
res.add(s);
}
}
return res;
}
}

997
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
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4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -232,7 +232,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
r1.setRelClass("isRelatedTo");
r1.setSource(docId);
r1.setTarget(otherId);
r1.setCollectedFrom(Arrays.asList(collectedFrom));
r1.setCollectedfrom(Arrays.asList(collectedFrom));
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r1);
@ -243,7 +243,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
r2.setRelClass("isRelatedTo");
r2.setSource(otherId);
r2.setTarget(docId);
r2.setCollectedFrom(Arrays.asList(collectedFrom));
r2.setCollectedfrom(Arrays.asList(collectedFrom));
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
res.add(r2);

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

@ -334,7 +334,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
r.setRelClass(relClass);
r.setSource(source);
r.setTarget(target);
r.setCollectedFrom(Arrays.asList(collectedFrom));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
return r;

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

@ -186,7 +186,7 @@ public abstract class AbstractScholexplorerParser {
r.setTarget(targetId);
r.setRelType(relationSemantic);
r.setRelClass("datacite");
r.setCollectedFrom(parsedObject.getCollectedfrom());
r.setCollectedfrom(parsedObject.getCollectedfrom());
r.setDataInfo(di);
rels.add(r);
r = new DLIRelation();
@ -195,7 +195,7 @@ public abstract class AbstractScholexplorerParser {
r.setTarget(parsedObject.getId());
r.setRelType(inverseRelation);
r.setRelClass("datacite");
r.setCollectedFrom(parsedObject.getCollectedfrom());
r.setCollectedfrom(parsedObject.getCollectedfrom());
r.setDateOfCollection(dateOfCollection);
rels.add(r);
if ("unknown".equalsIgnoreCase(relatedType))

197
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.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.util.List;
import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach;
@ -18,126 +22,119 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
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)
public class MappersTest {
@Mock
private Map<String, String> code2name;
@Mock private Map<String, String> code2name;
@BeforeEach
public void setUp() throws Exception {
when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0));
}
@BeforeEach
public void setUp() throws Exception {
when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0));
}
@Test
void testPublication() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
@Test
void testPublication() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
final List<Oaf> list = new OafToOafMapper(code2name).processMdRecord(xml);
final List<Oaf> list = new OafToOafMapper(code2name).processMdRecord(xml);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Publication);
assertTrue(list.get(1) instanceof Relation);
assertTrue(list.get(2) instanceof Relation);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Publication);
assertTrue(list.get(1) instanceof Relation);
assertTrue(list.get(2) instanceof Relation);
final Publication p = (Publication) list.get(0);
final Relation r1 = (Relation) list.get(1);
final Relation r2 = (Relation) list.get(2);
final Publication p = (Publication) list.get(0);
final Relation r1 = (Relation) list.get(1);
final Relation r2 = (Relation) list.get(2);
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
assertTrue(p.getAuthor().size() > 0);
assertTrue(p.getSubject().size() > 0);
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
assertTrue(p.getAuthor().size() > 0);
assertTrue(p.getSubject().size() > 0);
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertValidId(r1.getCollectedFrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
@Test
void testDataset() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml"));
@Test
void testDataset() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml"));
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml);
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Dataset);
assertTrue(list.get(1) instanceof Relation);
assertTrue(list.get(2) instanceof Relation);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Dataset);
assertTrue(list.get(1) instanceof Relation);
assertTrue(list.get(2) instanceof Relation);
final Dataset d = (Dataset) list.get(0);
final Relation r1 = (Relation) list.get(1);
final Relation r2 = (Relation) list.get(2);
final Dataset d = (Dataset) list.get(0);
final Relation r1 = (Relation) list.get(1);
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0);
assertTrue(d.getSubject().size() > 0);
assertValidId(d.getId());
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0);
assertTrue(d.getSubject().size() > 0);
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
}
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
}
@Test
void testSoftware() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));
@Test
void testSoftware() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml);
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Software);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Software);
final Software s = (Software) list.get(0);
final Software s = (Software) list.get(0);
assertValidId(s.getId());
assertValidId(s.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
assertTrue(s.getAuthor().size() > 0);
assertTrue(s.getSubject().size() > 0);
}
assertValidId(s.getId());
assertValidId(s.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
assertTrue(s.getAuthor().size() > 0);
assertTrue(s.getSubject().size() > 0);
}
private void assertValidId(final String id) {
assertEquals(49, id.length());
assertEquals('|', id.charAt(2));
assertEquals(':', id.charAt(15));
assertEquals(':', id.charAt(16));
}
private void assertValidId(final String id) {
assertEquals(49, id.length());
assertEquals('|', id.charAt(2));
assertEquals(':', id.charAt(15));
assertEquals(':', id.charAt(16));
}
}

541
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.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.sql.Array;
import java.sql.Date;
@ -11,7 +19,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;
import java.util.Objects;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach;
@ -21,325 +28,325 @@ import org.mockito.Mock;
import org.mockito.Mockito;
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)
public class MigrateDbEntitiesApplicationTest {
private MigrateDbEntitiesApplication app;
private MigrateDbEntitiesApplication app;
@Mock
private ResultSet rs;
@Mock private ResultSet rs;
@BeforeEach
public void setUp() {
this.app = new MigrateDbEntitiesApplication();
}
@BeforeEach
public void setUp() {
this.app = new MigrateDbEntitiesApplication();
}
@Test
public void testProcessDatasource() throws Exception {
final List<TypedField> fields = prepareMocks("datasources_resultset_entry.json");
@Test
public void testProcessDatasource() throws Exception {
final List<TypedField> fields = prepareMocks("datasources_resultset_entry.json");
final List<Oaf> list = app.processDatasource(rs);
assertEquals(1, list.size());
verifyMocks(fields);
final List<Oaf> list = app.processDatasource(rs);
assertEquals(1, list.size());
verifyMocks(fields);
final Datasource ds = (Datasource) list.get(0);
assertValidId(ds.getId());
assertValidId(ds.getCollectedfrom().get(0).getKey());
assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields));
assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields));
assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields));
assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields));
assertEquals(ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields));
}
final Datasource ds = (Datasource) list.get(0);
assertValidId(ds.getId());
assertValidId(ds.getCollectedfrom().get(0).getKey());
assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields));
assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields));
assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields));
assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(
ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields));
assertEquals(
ds.getCollectedfrom().get(0).getValue(),
getValueAsString("collectedfromname", fields));
}
@Test
public void testProcessProject() throws Exception {
final List<TypedField> fields = prepareMocks("projects_resultset_entry.json");
@Test
public void testProcessProject() throws Exception {
final List<TypedField> fields = prepareMocks("projects_resultset_entry.json");
final List<Oaf> list = app.processProject(rs);
assertEquals(1, list.size());
verifyMocks(fields);
final List<Oaf> list = app.processProject(rs);
assertEquals(1, list.size());
verifyMocks(fields);
final Project p = (Project) list.get(0);
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields));
assertEquals(p.getTitle().getValue(), getValueAsString("title", fields));
assertEquals(p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields));
final Project p = (Project) list.get(0);
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields));
assertEquals(p.getTitle().getValue(), getValueAsString("title", fields));
assertEquals(
p.getCollectedfrom().get(0).getValue(),
getValueAsString("collectedfromname", fields));
}
}
@Test
public void testProcessOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("organizations_resultset_entry.json");
@Test
public void testProcessOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("organizations_resultset_entry.json");
final List<Oaf> list = app.processOrganization(rs);
final List<Oaf> list = app.processOrganization(rs);
assertEquals(1, list.size());
assertEquals(1, list.size());
verifyMocks(fields);
verifyMocks(fields);
final Organization o = (Organization) list.get(0);
assertValidId(o.getId());
assertValidId(o.getCollectedfrom().get(0).getKey());
assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields));
assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields));
assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(
o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]);
assertEquals(
o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]);
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));
}
final Organization o = (Organization) list.get(0);
assertValidId(o.getId());
assertValidId(o.getCollectedfrom().get(0).getKey());
assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields));
assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields));
assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields));
assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]);
assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]);
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
public void testProcessDatasourceOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("datasourceorganization_resultset_entry.json");
@Test
public void testProcessDatasourceOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("datasourceorganization_resultset_entry.json");
final List<Oaf> list = app.processDatasourceOrganization(rs);
final List<Oaf> list = app.processDatasourceOrganization(rs);
assertEquals(2, list.size());
verifyMocks(fields);
assertEquals(2, list.size());
verifyMocks(fields);
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
assertValidId(r1.getSource());
assertValidId(r2.getSource());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
}
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
assertValidId(r1.getSource());
assertValidId(r2.getSource());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
}
@Test
public void testProcessProjectOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("projectorganization_resultset_entry.json");
@Test
public void testProcessProjectOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("projectorganization_resultset_entry.json");
final List<Oaf> list = app.processProjectOrganization(rs);
final List<Oaf> list = app.processProjectOrganization(rs);
assertEquals(2, list.size());
verifyMocks(fields);
assertEquals(2, list.size());
verifyMocks(fields);
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
assertValidId(r1.getSource());
assertValidId(r2.getSource());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
}
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
assertValidId(r1.getSource());
assertValidId(r2.getSource());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertValidId(r1.getCollectedFrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey());
}
@Test
public void testProcessClaims_context() throws Exception {
final List<TypedField> fields = prepareMocks("claimscontext_resultset_entry.json");
@Test
public void testProcessClaims_context() throws Exception {
final List<TypedField> fields = prepareMocks("claimscontext_resultset_entry.json");
final List<Oaf> list = app.processClaims(rs);
final List<Oaf> list = app.processClaims(rs);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Result);
final Result r = (Result) list.get(0);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Result);
final Result r = (Result) list.get(0);
verifyMocks(fields);
verifyMocks(fields);
assertValidId(r.getCollectedfrom().get(0).getKey());
}
assertValidId(r.getCollectedfrom().get(0).getKey());
}
@Test
public void testProcessClaims_rels() throws Exception {
final List<TypedField> fields = prepareMocks("claimsrel_resultset_entry.json");
@Test
public void testProcessClaims_rels() throws Exception {
final List<TypedField> fields = prepareMocks("claimsrel_resultset_entry.json");
final List<Oaf> list = app.processClaims(rs);
final List<Oaf> list = app.processClaims(rs);
assertEquals(2, list.size());
verifyMocks(fields);
assertEquals(2, list.size());
verifyMocks(fields);
assertTrue(list.get(0) instanceof Relation);
assertTrue(list.get(1) instanceof Relation);
assertTrue(list.get(0) instanceof Relation);
assertTrue(list.get(1) instanceof Relation);
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
final Relation r1 = (Relation) list.get(0);
final Relation r2 = (Relation) list.get(1);
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
assertValidId(r1.getCollectedFrom().get(0).getKey());
assertValidId(r2.getCollectedFrom().get(0).getKey());
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
private List<TypedField> prepareMocks(final String jsonFile) throws IOException, SQLException {
final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile));
final ObjectMapper mapper = new ObjectMapper();
final List<TypedField> list =
mapper.readValue(json, new TypeReference<List<TypedField>>() {});
private List<TypedField> prepareMocks(final String jsonFile) throws IOException, SQLException {
final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile));
final ObjectMapper mapper = new ObjectMapper();
final List<TypedField> list =
mapper.readValue(json, new TypeReference<List<TypedField>>() {});
for (final TypedField tf : list) {
if (tf.getValue() == null) {
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false);
break;
case "date":
Mockito.when(rs.getDate(tf.getField())).thenReturn(null);
break;
case "int":
Mockito.when(rs.getInt(tf.getField())).thenReturn(0);
break;
case "double":
Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0);
break;
case "array":
Mockito.when(rs.getArray(tf.getField())).thenReturn(null);
break;
case "string":
default:
Mockito.when(rs.getString(tf.getField())).thenReturn(null);
break;
}
} else {
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.when(rs.getBoolean(tf.getField()))
.thenReturn(Boolean.parseBoolean(tf.getValue().toString()));
break;
case "date":
Mockito.when(rs.getDate(tf.getField()))
.thenReturn(Date.valueOf(tf.getValue().toString()));
break;
case "int":
Mockito.when(rs.getInt(tf.getField()))
.thenReturn(new Integer(tf.getValue().toString()));
break;
case "double":
Mockito.when(rs.getDouble(tf.getField()))
.thenReturn(new Double(tf.getValue().toString()));
break;
case "array":
final Array arr = Mockito.mock(Array.class);
final String[] values =
((List<?>) tf.getValue())
.stream()
.filter(Objects::nonNull)
.map(o -> o.toString())
.toArray(String[]::new);
for (final TypedField tf : list) {
if (tf.getValue() == null) {
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false);
break;
case "date":
Mockito.when(rs.getDate(tf.getField())).thenReturn(null);
break;
case "int":
Mockito.when(rs.getInt(tf.getField())).thenReturn(0);
break;
case "double":
Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0);
break;
case "array":
Mockito.when(rs.getArray(tf.getField())).thenReturn(null);
break;
case "string":
default:
Mockito.when(rs.getString(tf.getField())).thenReturn(null);
break;
}
} else {
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.when(rs.getBoolean(tf.getField()))
.thenReturn(Boolean.parseBoolean(tf.getValue().toString()));
break;
case "date":
Mockito.when(rs.getDate(tf.getField()))
.thenReturn(Date.valueOf(tf.getValue().toString()));
break;
case "int":
Mockito.when(rs.getInt(tf.getField()))
.thenReturn(new Integer(tf.getValue().toString()));
break;
case "double":
Mockito.when(rs.getDouble(tf.getField()))
.thenReturn(new Double(tf.getValue().toString()));
break;
case "array":
final Array arr = Mockito.mock(Array.class);
final String[] values =
((List<?>) tf.getValue())
.stream()
.filter(Objects::nonNull)
.map(o -> o.toString())
.toArray(String[]::new);
Mockito.when(arr.getArray()).thenReturn(values);
Mockito.when(rs.getArray(tf.getField())).thenReturn(arr);
break;
case "string":
default:
Mockito.when(rs.getString(tf.getField()))
.thenReturn(tf.getValue().toString());
break;
}
}
}
Mockito.when(arr.getArray()).thenReturn(values);
Mockito.when(rs.getArray(tf.getField())).thenReturn(arr);
break;
case "string":
default:
Mockito.when(rs.getString(tf.getField()))
.thenReturn(tf.getValue().toString());
break;
}
}
}
return list;
}
return list;
}
private void verifyMocks(final List<TypedField> list) throws SQLException {
for (final TypedField tf : list) {
private void verifyMocks(final List<TypedField> list) throws SQLException {
for (final TypedField tf : list) {
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField());
break;
case "date":
Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField());
break;
case "int":
Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField());
break;
case "double":
Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField());
break;
case "array":
Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField());
break;
case "string":
default:
Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField());
break;
}
}
}
switch (tf.getType()) {
case "not_used":
break;
case "boolean":
Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField());
break;
case "date":
Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField());
break;
case "int":
Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField());
break;
case "double":
Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField());
break;
case "array":
Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField());
break;
case "string":
default:
Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField());
break;
}
}
}
private void assertValidId(final String id) {
assertEquals(49, id.length());
assertEquals('|', id.charAt(2));
assertEquals(':', id.charAt(15));
assertEquals(':', id.charAt(16));
}
private void assertValidId(final String id) {
assertEquals(49, id.length());
assertEquals('|', id.charAt(2));
assertEquals(':', id.charAt(15));
assertEquals(':', id.charAt(16));
}
private String getValueAsString(final String name, final List<TypedField> fields) {
return fields.stream()
.filter(f -> f.getField().equals(name))
.map(TypedField::getValue)
.filter(Objects::nonNull)
.map(o -> o.toString())
.findFirst()
.get();
}
private String getValueAsString(final String name, final List<TypedField> fields) {
return fields.stream()
.filter(f -> f.getField().equals(name))
.map(TypedField::getValue)
.filter(Objects::nonNull)
.map(o -> o.toString())
.findFirst()
.get();
}
}
class TypedField {
private String field;
private String type;
private Object value;
private String field;
private String type;
private Object value;
public String getField() {
return field;
}
public String getField() {
return field;
}
public void setField(final String field) {
this.field = field;
}
public void setField(final String field) {
this.field = field;
}
public String getType() {
return type;
}
public String getType() {
return type;
}
public void setType(final String type) {
this.type = type;
}
public void setType(final String type) {
this.type = type;
}
public Object getValue() {
return value;
}
public Object getValue() {
return value;
}
public void setValue(final Object value) {
this.value = value;
}
public void setValue(final Object value) {
this.value = value;
}
}

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)
s.setPublicationDate(scholixSummary.getDate().get(0));
s.setLinkprovider(
rel.getCollectedFrom().stream()
rel.getCollectedfrom().stream()
.map(
cf ->
new ScholixEntityId(
@ -73,7 +73,7 @@ public class Scholix implements Serializable {
if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0)
s.setPublicationDate(scholixSummary.getDate().get(0));
s.setLinkprovider(
rel.getCollectedFrom().stream()
rel.getCollectedfrom().stream()
.map(
cf ->
new ScholixEntityId(

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

@ -1 +1 @@
{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedFrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]}
{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedfrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]}

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

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

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

@ -22,6 +22,7 @@ import java.io.IOException;
import java.io.Serializable;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
@ -41,6 +42,7 @@ import org.dom4j.io.XMLWriter;
public class XmlRecordFactory implements Serializable {
public static final String REL_SUBTYPE_DEDUP = "dedup";
private Map<String, LongAccumulator> accumulators;
private Set<String> specialDatasourceTypes;
@ -91,7 +93,14 @@ public class XmlRecordFactory implements Serializable {
// rels has to be processed before the contexts because they enrich the contextMap with
// the
// funding info.
final List<String> relations = listRelations(je, templateFactory, contexts);
final List<String> relations =
je.getLinks().stream()
.filter(
t ->
!REL_SUBTYPE_DEDUP.equalsIgnoreCase(
t.getRelation().getSubRelType()))
.map(link -> mapRelation(link, templateFactory, contexts))
.collect(Collectors.toCollection(ArrayList::new));
final String mainType = ModelSupport.getMainType(type);
metadata.addAll(buildContexts(mainType, contexts));
@ -102,7 +111,7 @@ public class XmlRecordFactory implements Serializable {
mainType,
metadata,
relations,
listChildren(entity, je.getEntity().getType(), templateFactory),
listChildren(entity, je, templateFactory),
listExtraInfo(entity));
return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent);
@ -919,171 +928,149 @@ public class XmlRecordFactory implements Serializable {
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType));
}
private Qualifier getBestAccessright(final Result r) {
Qualifier bestAccessRight = new Qualifier();
bestAccessRight.setClassid("UNKNOWN");
bestAccessRight.setClassname("not available");
bestAccessRight.setSchemeid("dnet:access_modes");
bestAccessRight.setSchemename("dnet:access_modes");
private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set<String> contexts) {
final Relation rel = link.getRelation();
final RelatedEntity re = link.getRelatedEntity();
final String targetType = link.getRelatedEntity().getType();
final LicenseComparator lc = new LicenseComparator();
for (final Instance instance : r.getInstance()) {
if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) {
bestAccessRight = instance.getAccessright();
}
final List<String> metadata = Lists.newArrayList();
switch (EntityType.valueOf(targetType)) {
case publication:
case dataset:
case otherresearchproduct:
case software:
if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) {
metadata.add(
XmlSerializationUtils.mapStructuredProperty("title", re.getTitle()));
}
if (isNotBlank(re.getDateofacceptance())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"dateofacceptance", re.getDateofacceptance()));
}
if (isNotBlank(re.getPublisher())) {
metadata.add(
XmlSerializationUtils.asXmlElement("publisher", re.getPublisher()));
}
if (isNotBlank(re.getCodeRepositoryUrl())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"coderepositoryurl", re.getCodeRepositoryUrl()));
}
if (re.getResulttype() != null & re.getResulttype().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype()));
}
if (re.getCollectedfrom() != null) {
metadata.addAll(
re.getCollectedfrom().stream()
.map(
kv ->
XmlSerializationUtils.mapKeyValue(
"collectedfrom", kv))
.collect(Collectors.toList()));
}
if (re.getPid() != null) {
metadata.addAll(
re.getPid().stream()
.map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p))
.collect(Collectors.toList()));
}
break;
case datasource:
if (isNotBlank(re.getOfficialname())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"officialname", re.getOfficialname()));
}
if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) {
mapDatasourceType(metadata, re.getDatasourcetype());
}
if (re.getOpenairecompatibility() != null
& !re.getOpenairecompatibility().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier(
"openairecompatibility", re.getOpenairecompatibility()));
}
break;
case organization:
if (isNotBlank(re.getLegalname())) {
metadata.add(
XmlSerializationUtils.asXmlElement("legalname", re.getLegalname()));
}
if (isNotBlank(re.getLegalshortname())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"legalshortname", re.getLegalshortname()));
}
if (re.getCountry() != null & !re.getCountry().isBlank()) {
metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry()));
}
break;
case project:
if (isNotBlank(re.getProjectTitle())) {
metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle()));
}
if (isNotBlank(re.getCode())) {
metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode()));
}
if (isNotBlank(re.getAcronym())) {
metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym()));
}
if (re.getContracttype() != null & !re.getContracttype().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier(
"contracttype", re.getContracttype()));
}
if (re.getFundingtree() != null & contexts != null) {
metadata.addAll(
re.getFundingtree().stream()
.peek(ft -> fillContextMap(ft, contexts))
.map(ft -> getRelFundingTree(ft))
.collect(Collectors.toList()));
}
break;
default:
throw new IllegalArgumentException("invalid target type: " + targetType);
}
return bestAccessRight;
}
final DataInfo info = rel.getDataInfo();
final String scheme = ModelSupport.getScheme(re.getType(), targetType);
private List<String> listRelations(
final JoinedEntity je, TemplateFactory templateFactory, final Set<String> contexts) {
final List<String> rels = Lists.newArrayList();
for (final Tuple2 link : je.getLinks()) {
final Relation rel = link.getRelation();
final RelatedEntity re = link.getRelatedEntity();
final String targetType = link.getRelatedEntity().getType();
final List<String> metadata = Lists.newArrayList();
switch (EntityType.valueOf(targetType)) {
case publication:
case dataset:
case otherresearchproduct:
case software:
if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) {
metadata.add(
XmlSerializationUtils.mapStructuredProperty(
"title", re.getTitle()));
}
if (isNotBlank(re.getDateofacceptance())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"dateofacceptance", re.getDateofacceptance()));
}
if (isNotBlank(re.getPublisher())) {
metadata.add(
XmlSerializationUtils.asXmlElement("publisher", re.getPublisher()));
}
if (isNotBlank(re.getCodeRepositoryUrl())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"coderepositoryurl", re.getCodeRepositoryUrl()));
}
if (re.getResulttype() != null & re.getResulttype().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier(
"resulttype", re.getResulttype()));
}
if (re.getCollectedfrom() != null) {
metadata.addAll(
re.getCollectedfrom().stream()
.map(
kv ->
XmlSerializationUtils.mapKeyValue(
"collectedfrom", kv))
.collect(Collectors.toList()));
}
if (re.getPid() != null) {
metadata.addAll(
re.getPid().stream()
.map(
p ->
XmlSerializationUtils.mapStructuredProperty(
"pid", p))
.collect(Collectors.toList()));
}
break;
case datasource:
if (isNotBlank(re.getOfficialname())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"officialname", re.getOfficialname()));
}
if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) {
mapDatasourceType(metadata, re.getDatasourcetype());
}
if (re.getOpenairecompatibility() != null
& !re.getOpenairecompatibility().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier(
"openairecompatibility", re.getOpenairecompatibility()));
}
break;
case organization:
if (isNotBlank(re.getLegalname())) {
metadata.add(
XmlSerializationUtils.asXmlElement("legalname", re.getLegalname()));
}
if (isNotBlank(re.getLegalshortname())) {
metadata.add(
XmlSerializationUtils.asXmlElement(
"legalshortname", re.getLegalshortname()));
}
if (re.getCountry() != null & !re.getCountry().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier("country", re.getCountry()));
}
break;
case project:
if (isNotBlank(re.getProjectTitle())) {
metadata.add(
XmlSerializationUtils.asXmlElement("title", re.getProjectTitle()));
}
if (isNotBlank(re.getCode())) {
metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode()));
}
if (isNotBlank(re.getAcronym())) {
metadata.add(
XmlSerializationUtils.asXmlElement("acronym", re.getAcronym()));
}
if (re.getContracttype() != null & !re.getContracttype().isBlank()) {
metadata.add(
XmlSerializationUtils.mapQualifier(
"contracttype", re.getContracttype()));
}
if (re.getFundingtree() != null) {
metadata.addAll(
re.getFundingtree().stream()
.peek(ft -> fillContextMap(ft, contexts))
.map(ft -> getRelFundingTree(ft))
.collect(Collectors.toList()));
}
break;
default:
throw new IllegalArgumentException("invalid target type: " + targetType);
}
final DataInfo info = rel.getDataInfo();
final String scheme = ModelSupport.getScheme(re.getType(), targetType);
if (StringUtils.isBlank(scheme)) {
throw new IllegalArgumentException(
String.format("missing scheme for: <%s - %s>", re.getType(), targetType));
}
final String accumulatorName =
getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass());
if (accumulators.containsKey(accumulatorName)) {
accumulators.get(accumulatorName).add(1);
}
rels.add(
templateFactory.getRel(
targetType,
rel.getTarget(),
Sets.newHashSet(metadata),
rel.getRelClass(),
scheme,
info));
if (StringUtils.isBlank(scheme)) {
throw new IllegalArgumentException(
String.format("missing scheme for: <%s - %s>", re.getType(), targetType));
}
return rels;
final String accumulatorName =
getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass());
if (accumulators.containsKey(accumulatorName)) {
accumulators.get(accumulatorName).add(1);
}
return templateFactory.getRel(
targetType,
rel.getTarget(),
Sets.newHashSet(metadata),
rel.getRelClass(),
scheme,
info);
}
private List<String> listChildren(
final OafEntity entity, String type, TemplateFactory templateFactory) {
final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) {
final List<String> children = Lists.newArrayList();
EntityType entityType = EntityType.valueOf(type);
EntityType entityType = EntityType.valueOf(je.getEntity().getType());
children.addAll(
je.getLinks().stream()
.filter(
link ->
REL_SUBTYPE_DEDUP.equalsIgnoreCase(
link.getRelation().getSubRelType()))
.map(link -> mapRelation(link, templateFactory, null))
.collect(Collectors.toCollection(ArrayList::new)));
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
final List<Instance> instances = ((Result) entity).getInstance();
if (instances != null) {