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Merge branch 'provision_indexing' of https://code-repo.d4science.org/D-Net/dnet-hadoop into HEAD

 Conflicts:
	dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/GraphJoiner.java
	dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/MappingUtils.java
	dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/RelatedEntity.java
	dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlRecordBuilderJob.java
This commit is contained in:
Claudio Atzori 2020-01-30 17:59:46 +01:00
commit 7bacd6812e
7 changed files with 184 additions and 9 deletions

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@ -0,0 +1,77 @@
package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import java.io.IOException;
import java.util.stream.Collectors;
public class GraphMapper {
public void map(final SparkSession spark, final String outPath) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
sc.textFile(outPath + "/linked_entities")
.map(LinkedEntityWrapper::parse)
.map(GraphMapper::asLinkedEntity)
.map(e -> new ObjectMapper().writeValueAsString(e))
.saveAsTextFile(outPath + "/linked_entities_types");
}
private static LinkedEntity asLinkedEntity(final LinkedEntityWrapper lw) throws JsonProcessingException {
final LinkedEntity le = new LinkedEntity();
try {
le.setType(lw.getEntity().getType());
le.setEntity(parseEntity(lw.getEntity().getOaf(), le.getType()));
le.setLinks(lw.getLinks()
.stream()
.map(l -> new Link()
.setRelation(parseRelation(l.getRelation().getOaf()))
.setRelatedEntity(RelatedEntity.parse(l.getTarget().getOaf())))
.collect(Collectors.toList()));
return le;
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException(new ObjectMapper().writeValueAsString(lw), e);
}
}
private static Relation parseRelation(final String s) {
try {
return new ObjectMapper().readValue(s, Relation.class);
} catch (IOException e) {
throw new IllegalArgumentException("unable to decode Relation: " + s);
}
}
private static OafEntity parseEntity(final String json, final String type) {
final ObjectMapper o = new ObjectMapper();
try {
switch (type) {
case "publication":
return o.readValue(json, Publication.class);
case "dataset":
return o.readValue(json, Dataset.class);
case "otherresearchproduct":
return o.readValue(json, OtherResearchProduct.class);
case "software":
return o.readValue(json, Software.class);
case "datasource":
return o.readValue(json, Datasource.class);
case "project":
return o.readValue(json, Project.class);
case "organization":
return o.readValue(json, Organization.class);
default:
throw new IllegalArgumentException("invalid entity type: " + type);
}
} catch (IOException e) {
throw new IllegalArgumentException("unable to decode oaf entity: " + json);
}
}
}

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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.graph;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.Serializable;
public class Link implements Serializable {
private Relation relation;
private RelatedEntity relatedEntity;
public Relation getRelation() {
return relation;
}
public Link setRelation(Relation relation) {
this.relation = relation;
return this;
}
public RelatedEntity getRelatedEntity() {
return relatedEntity;
}
public Link setRelatedEntity(RelatedEntity relatedEntity) {
this.relatedEntity = relatedEntity;
return this;
}
}

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@ -1,28 +1,41 @@
package eu.dnetlib.dhp.graph;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import java.io.Serializable;
import java.util.List;
public class LinkedEntity implements Serializable {
private TypedRow entity;
private String type;
private List<Tuple> links;
private OafEntity entity;
public TypedRow getEntity() {
private List<Link> links;
public String getType() {
return type;
}
public LinkedEntity setType(String type) {
this.type = type;
return this;
}
public OafEntity getEntity() {
return entity;
}
public LinkedEntity setEntity(TypedRow entity) {
public LinkedEntity setEntity(OafEntity entity) {
this.entity = entity;
return this;
}
public List<Tuple> getLinks() {
public List<Link> getLinks() {
return links;
}
public LinkedEntity setLinks(List<Tuple> links) {
public LinkedEntity setLinks(List<Link> links) {
this.links = links;
return this;
}

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@ -0,0 +1,40 @@
package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import java.io.Serializable;
import java.util.List;
public class LinkedEntityWrapper implements Serializable {
private TypedRow entity;
private List<TupleWrapper> links;
public static LinkedEntityWrapper parse(final String s) {
try {
return new ObjectMapper().readValue(s, LinkedEntityWrapper.class);
} catch (IOException e) {
throw new IllegalArgumentException("unable to decode LinkedEntityWrapper: " + s);
}
}
public TypedRow getEntity() {
return entity;
}
public LinkedEntityWrapper setEntity(TypedRow entity) {
this.entity = entity;
return this;
}
public List<TupleWrapper> getLinks() {
return links;
}
public LinkedEntityWrapper setLinks(List<TupleWrapper> links) {
this.links = links;
return this;
}
}

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@ -2,7 +2,7 @@ package eu.dnetlib.dhp.graph;
import java.io.Serializable;
public class Tuple implements Serializable {
public class TupleWrapper implements Serializable {
private TypedRow relation;
@ -13,7 +13,7 @@ public class Tuple implements Serializable {
return relation;
}
public Tuple setRelation(TypedRow relation) {
public TupleWrapper setRelation(TypedRow relation) {
this.relation = relation;
return this;
}
@ -22,7 +22,7 @@ public class Tuple implements Serializable {
return target;
}
public Tuple setTarget(TypedRow target) {
public TupleWrapper setTarget(TypedRow target) {
this.target = target;
return this;
}

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@ -39,4 +39,14 @@ public class MappingUtilsTest {
System.out.println(out);
}
@Test
public void testParseRelatedEntity() throws IOException {
final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json"));
final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class);
System.out.println(e);
}
}

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@ -0,0 +1,5 @@
{
"id": "20|nih_________::6b8108b6d6399f7163a6a7ccdd0efc2d",
"type": "organization",
"legalname": "MCGILL UNIVERSITY"
}