forked from D-Net/dnet-hadoop
joining entities using T x R x S, WIP: last representation based on LinkedEntity type
This commit is contained in:
parent
fcbc4ccd70
commit
8c2aff99b0
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@ -1,11 +1,14 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.jayway.jsonpath.DocumentContext;
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import com.jayway.jsonpath.JsonPath;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.*;
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import net.minidev.json.JSONArray;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.api.java.JavaPairRDD;
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@ -15,8 +18,10 @@ import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.List;
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import java.util.stream.Collectors;
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/**
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* Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
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@ -38,7 +43,7 @@ import java.util.List;
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*/
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public class GraphJoiner implements Serializable {
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public static final int MAX_RELS = 10;
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public static final int MAX_RELS = 100;
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public void join(final SparkSession spark, final String inputPath, final String hiveDbName, final String outPath) {
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@ -63,7 +68,7 @@ public class GraphJoiner implements Serializable {
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.union(software)
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.union(publication)
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.map(e -> new EntityRelEntity().setSource(e._2()))
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.map(MappingUtils::serialize)
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.saveAsTextFile(entitiesPath, GzipCodec.class);
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JavaPairRDD<String, EntityRelEntity> entities = sc.textFile(entitiesPath)
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@ -84,41 +89,24 @@ public class GraphJoiner implements Serializable {
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relation
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.join(entities
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.filter(e -> !e._2().getSource().getDeleted())
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/*.mapToPair(e -> new Tuple2<>(e._1(), new MappingUtils().pruneModel(e._2())))*/)
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.mapToPair(e -> new Tuple2<>(e._1(), MappingUtils.pruneModel(e._2()))))
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.map(s -> new EntityRelEntity()
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.setRelation(s._2()._1().getRelation())
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.setTarget(s._2()._2().getSource()))
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.map(MappingUtils::serialize)
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.saveAsTextFile(joinByTargetPath, GzipCodec.class);
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JavaPairRDD<String, EntityRelEntity> bySource = sc.textFile(joinByTargetPath)
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.map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
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.mapToPair(t -> new Tuple2<>(t.getRelation().getSourceId(), t));
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final String linkedEntitiesPath = outPath + "/linked_entities";
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entities
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.union(bySource)
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.groupByKey() // by source id
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.map(p -> {
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final LinkedEntity e = new LinkedEntity();
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final List<Tuple> links = Lists.newArrayList();
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for(EntityRelEntity rel : p._2()) {
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if (rel.hasMainEntity() & e.getEntity() == null) {
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e.setEntity(rel.getSource());
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}
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if (rel.hasRelatedEntity()) {
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links.add(new Tuple()
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.setRelation(rel.getRelation())
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.setTarget(rel.getTarget()));
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}
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}
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e.setLinks(links);
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if (e.getEntity() == null) {
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throw new IllegalStateException("missing main entity on '" + p._1() + "'");
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}
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return e;
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})
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.saveAsTextFile(outPath + "/linked_entities", GzipCodec.class);
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.map(GraphJoiner::asLinkedEntityWrapper)
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.map(MappingUtils::serialize)
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.saveAsTextFile(linkedEntitiesPath, GzipCodec.class);
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}
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/**
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@ -153,14 +141,35 @@ public class GraphJoiner implements Serializable {
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private JavaRDD<TypedRow> readPathRelation(final JavaSparkContext sc, final String inputPath) {
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return sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> {
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final String json = item._2().toString();
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final String s = item._2().toString();
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final DocumentContext json = JsonPath.parse(s);
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return new TypedRow()
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.setSourceId(JsonPath.read(json, "$.source"))
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.setTargetId(JsonPath.read(json, "$.target"))
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.setDeleted(JsonPath.read(json, "$.dataInfo.deletedbyinference"))
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.setSourceId(json.read("$.source"))
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.setTargetId(json.read("$.target"))
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.setDeleted(json.read("$.dataInfo.deletedbyinference"))
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.setType("relation")
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.setOaf(json);
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.setOaf(s);
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});
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}
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private static LinkedEntityWrapper asLinkedEntityWrapper(Tuple2<String, Iterable<EntityRelEntity>> p) {
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final LinkedEntityWrapper e = new LinkedEntityWrapper();
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final List<TupleWrapper> links = Lists.newArrayList();
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for (EntityRelEntity rel : p._2()) {
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if (rel.hasMainEntity() & e.getEntity() == null) {
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e.setEntity(rel.getSource());
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}
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if (rel.hasRelatedEntity()) {
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links.add(new TupleWrapper()
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.setRelation(rel.getRelation())
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.setTarget(rel.getTarget()));
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}
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}
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e.setLinks(links);
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if (e.getEntity() == null) {
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throw new IllegalStateException("missing main entity on '" + p._1() + "'");
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}
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return e;
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}
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}
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@ -0,0 +1,77 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.SparkSession;
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import java.io.IOException;
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import java.util.stream.Collectors;
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public class GraphMapper {
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public void map(final SparkSession spark, final String outPath) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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sc.textFile(outPath + "/linked_entities")
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.map(LinkedEntityWrapper::parse)
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.map(GraphMapper::asLinkedEntity)
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.saveAsTextFile(outPath + "/linked_entities_types");
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}
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private static LinkedEntity asLinkedEntity(final LinkedEntityWrapper lw) throws JsonProcessingException {
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final LinkedEntity le = new LinkedEntity();
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try {
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le.setType(lw.getEntity().getType());
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le.setEntity(parseEntity(lw.getEntity().getOaf(), le.getType()));
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le.setLinks(lw.getLinks()
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.stream()
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.map(l -> new Link()
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.setRelation(parseRelation(l.getRelation().getOaf()))
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.setRelatedEntity(RelatedEntity.parse(l.getTarget().getOaf())))
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.collect(Collectors.toList()));
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return le;
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(new ObjectMapper().writeValueAsString(lw), e);
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}
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}
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private static Relation parseRelation(final String s) {
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try {
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return new ObjectMapper().readValue(s, Relation.class);
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} catch (IOException e) {
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throw new IllegalArgumentException("unable to decode Relation: " + s);
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}
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}
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private static OafEntity parseEntity(final String json, final String type) {
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final ObjectMapper o = new ObjectMapper();
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try {
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switch (type) {
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case "publication":
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return o.readValue(json, Publication.class);
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case "dataset":
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return o.readValue(json, Dataset.class);
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case "otherresearchproduct":
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return o.readValue(json, OtherResearchProduct.class);
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case "software":
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return o.readValue(json, Software.class);
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case "datasource":
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return o.readValue(json, Datasource.class);
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case "project":
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return o.readValue(json, Project.class);
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case "organization":
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return o.readValue(json, Organization.class);
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default:
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throw new IllegalArgumentException("invalid entity type: " + type);
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}
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} catch (IOException e) {
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throw new IllegalArgumentException("unable to decode oaf entity: " + json);
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}
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}
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}
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@ -0,0 +1,30 @@
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package eu.dnetlib.dhp.graph;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.io.Serializable;
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public class Link implements Serializable {
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private Relation relation;
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private RelatedEntity relatedEntity;
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public Relation getRelation() {
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return relation;
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}
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public Link setRelation(Relation relation) {
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this.relation = relation;
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return this;
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}
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public RelatedEntity getRelatedEntity() {
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return relatedEntity;
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}
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public Link setRelatedEntity(RelatedEntity relatedEntity) {
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this.relatedEntity = relatedEntity;
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return this;
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}
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}
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package eu.dnetlib.dhp.graph;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import java.io.Serializable;
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import java.util.List;
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public class LinkedEntity implements Serializable {
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private TypedRow entity;
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private String type;
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private List<Tuple> links;
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private OafEntity entity;
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public TypedRow getEntity() {
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private List<Link> links;
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public String getType() {
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return type;
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}
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public LinkedEntity setType(String type) {
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this.type = type;
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return this;
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}
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public OafEntity getEntity() {
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return entity;
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}
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public LinkedEntity setEntity(TypedRow entity) {
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public LinkedEntity setEntity(OafEntity entity) {
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this.entity = entity;
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return this;
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}
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public List<Tuple> getLinks() {
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public List<Link> getLinks() {
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return links;
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}
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public LinkedEntity setLinks(List<Tuple> links) {
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public LinkedEntity setLinks(List<Link> links) {
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this.links = links;
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return this;
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}
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@ -0,0 +1,40 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.List;
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public class LinkedEntityWrapper implements Serializable {
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private TypedRow entity;
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private List<TupleWrapper> links;
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public static LinkedEntityWrapper parse(final String s) {
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try {
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return new ObjectMapper().readValue(s, LinkedEntityWrapper.class);
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} catch (IOException e) {
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throw new IllegalArgumentException("unable to decode LinkedEntityWrapper: " + s);
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}
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}
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public TypedRow getEntity() {
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return entity;
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}
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public LinkedEntityWrapper setEntity(TypedRow entity) {
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this.entity = entity;
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return this;
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}
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public List<TupleWrapper> getLinks() {
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return links;
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}
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public LinkedEntityWrapper setLinks(List<TupleWrapper> links) {
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this.links = links;
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return this;
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}
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}
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@ -1,5 +1,6 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.jayway.jsonpath.DocumentContext;
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public class MappingUtils {
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public EntityRelEntity pruneModel(EntityRelEntity e) throws JsonProcessingException {
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public static EntityRelEntity pruneModel(EntityRelEntity e) {
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final DocumentContext j = JsonPath.parse(e.getSource().getOaf());
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final RelatedEntity re = new RelatedEntity();
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final RelatedEntity re = new RelatedEntity().setId(j.read("$.id")).setType(e.getSource().getType());
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switch (e.getSource().getType()) {
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case "publication":
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case "dataset":
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case "otherresearchproduct":
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case "software":
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mapTitle(j, re);
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re.setDateofacceptance(j.read("$.dateofacceptance.value"));
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re.setPublisher(j.read("$.publisher.value"));
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case "datasource":
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re.setOfficialname(j.read("$.officialname.value"));
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re.setWebsiteurl(j.read("$.websiteurl.value"));
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re.setDatasourcetype(asQualifier(j.read("$.datasourcetype")));
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re.setOpenairecompatibility(asQualifier(j.read("$.openairecompatibility")));
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break;
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case "organization":
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re.setLegalname(j.read("$.legalname.value"));
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re.setLegalshortname(j.read("$.legalshortname.value"));
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re.setCountry(asQualifier(j.read("$.country")));
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break;
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case "project":
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mapTitle(j, re);
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re.setProjectTitle(j.read("$.title.value"));
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re.setCode(j.read("$.code.value"));
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re.setAcronym(j.read("$.acronym.value"));
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re.setContracttype(asQualifier(j.read("$.contracttype")));
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JSONArray f = j.read("$.fundingtree");
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if (!f.isEmpty()) {
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re.setFundingtree(f.stream()
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.map(s -> s.toString())
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.collect(Collectors.toList()));
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}
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break;
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}
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return new EntityRelEntity().setSource(
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new TypedRow()
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.setSourceId(e.getSource().getSourceId())
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.setDeleted(e.getSource().getDeleted())
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.setType(e.getSource().getType())
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.setOaf(new ObjectMapper().writeValueAsString(re)));
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.setOaf(serialize(re)));
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}
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private KeyValue asKV(LinkedHashMap<String, Object> j) {
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private static KeyValue asKV(LinkedHashMap<String, Object> j) {
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final KeyValue kv = new KeyValue();
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kv.setKey((String) j.get("key"));
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kv.setValue((String) j.get("value"));
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return kv;
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}
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private void mapTitle(DocumentContext j, RelatedEntity re) {
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JSONArray a = j.read("$.title");
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private static void mapTitle(DocumentContext j, RelatedEntity re) {
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final JSONArray a = j.read("$.title");
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if (!a.isEmpty()) {
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re.setTitle(asStructuredProperty((LinkedHashMap<String, Object>) a.get(0)));
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}
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}
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private StructuredProperty asStructuredProperty(LinkedHashMap<String, Object> j) {
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private static StructuredProperty asStructuredProperty(LinkedHashMap<String, Object> j) {
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final StructuredProperty sp = new StructuredProperty();
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sp.setValue((String) j.get("value"));
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sp.setQualifier(asQualifier((LinkedHashMap<String, String>) j.get("qualifier")));
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return sp;
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}
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public Qualifier asQualifier(LinkedHashMap<String, String> j) {
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Qualifier q = new Qualifier();
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public static Qualifier asQualifier(LinkedHashMap<String, String> j) {
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final Qualifier q = new Qualifier();
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q.setClassid(j.get("classid"));
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q.setClassname(j.get("classname"));
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q.setSchemeid(j.get("schemeid"));
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@ -100,4 +111,14 @@ public class MappingUtils {
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return q;
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}
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public static String serialize(final Object o) {
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try {
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return new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL)
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.writeValueAsString(o);
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} catch (JsonProcessingException e) {
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throw new IllegalArgumentException("unable to serialize: " + o.toString(), e);
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}
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}
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}
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@ -3,14 +3,22 @@ package eu.dnetlib.dhp.graph;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import org.codehaus.jackson.map.ObjectMapper;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.List;
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public class RelatedEntity implements Serializable {
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private String id;
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private String type;
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// common fields
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private StructuredProperty title;
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private String websiteurl; // datasource, organizations, projects
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// results
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private StructuredProperty title; // also for projects
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private String dateofacceptance;
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private String publisher;
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private List<StructuredProperty> pid;
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|
@ -20,11 +28,10 @@ public class RelatedEntity implements Serializable {
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// datasource
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private String officialname;
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private String websiteurl; // also for organizations, projects
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private Qualifier datasourcetype;
|
||||
private Qualifier datasourcetypeui;
|
||||
//private String aggregatortype;
|
||||
private Qualifier openairecompatibility;
|
||||
//private String aggregatortype;
|
||||
|
||||
// organization
|
||||
private String legalname;
|
||||
|
@ -32,10 +39,28 @@ public class RelatedEntity implements Serializable {
|
|||
private Qualifier country;
|
||||
|
||||
// project
|
||||
private String projectTitle;
|
||||
private String code;
|
||||
private String acronym;
|
||||
private Qualifier contracttype;
|
||||
private String fundingtree;
|
||||
private List<String> fundingtree;
|
||||
|
||||
public static RelatedEntity parse(final String json) {
|
||||
try {
|
||||
return new ObjectMapper().readValue(json, RelatedEntity.class);
|
||||
} catch (IOException e) {
|
||||
throw new IllegalArgumentException("invalid RelatedEntity, cannot parse: " + json);
|
||||
}
|
||||
}
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public RelatedEntity setId(String id) {
|
||||
this.id = id;
|
||||
return this;
|
||||
}
|
||||
|
||||
public StructuredProperty getTitle() {
|
||||
return title;
|
||||
|
@ -199,12 +224,30 @@ public class RelatedEntity implements Serializable {
|
|||
return this;
|
||||
}
|
||||
|
||||
public String getFundingtree() {
|
||||
public List<String> getFundingtree() {
|
||||
return fundingtree;
|
||||
}
|
||||
|
||||
public RelatedEntity setFundingtree(String fundingtree) {
|
||||
public RelatedEntity setFundingtree(List<String> fundingtree) {
|
||||
this.fundingtree = fundingtree;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getProjectTitle() {
|
||||
return projectTitle;
|
||||
}
|
||||
|
||||
public RelatedEntity setProjectTitle(String projectTitle) {
|
||||
this.projectTitle = projectTitle;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public RelatedEntity setType(String type) {
|
||||
this.type = type;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
|
@ -38,6 +38,7 @@ public class SparkGraphIndexingJob {
|
|||
}
|
||||
|
||||
new GraphJoiner().join(spark, inputPath, hiveDbName, OUTPUT_BASE_PATH);
|
||||
new GraphMapper().map(spark, OUTPUT_BASE_PATH);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -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;
|
||||
}
|
|
@ -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);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
@ -0,0 +1,5 @@
|
|||
{
|
||||
"id": "20|nih_________::6b8108b6d6399f7163a6a7ccdd0efc2d",
|
||||
"type": "organization",
|
||||
"legalname": "MCGILL UNIVERSITY"
|
||||
}
|
Loading…
Reference in New Issue