WIP: reimplementing the adjacency list construction process using spark Datasets

This commit is contained in:
Claudio Atzori 2020-04-01 14:56:57 +02:00
parent 377e1ba840
commit adcdd2d05e
14 changed files with 652 additions and 664 deletions

View File

@ -1,291 +0,0 @@
package eu.dnetlib.dhp.oa.provision;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Iterables;
import com.google.common.collect.Maps;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import eu.dnetlib.dhp.oa.provision.model.*;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkContext;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import scala.Tuple2;
import java.io.IOException;
import java.io.Serializable;
import java.util.Map;
import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.asRelatedEntity;
/**
* Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
* The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
* and all the possible relationships (similarity links produced by the Dedup process are excluded).
*
* The operation is implemented creating the union between the entity types (E), joined by the relationships (R), and again
* by E, finally grouped by E.id;
*
* Different manipulations of the E and R sets are introduced to reduce the complexity of the operation
* 1) treat the object payload as string, extracting only the necessary information beforehand using json path,
* it seems that deserializing it with jackson's object mapper has higher memory footprint.
*
* 2) only consider rels that are not virtually deleted ($.dataInfo.deletedbyinference == false)
* 3) we only need a subset of fields from the related entities, so we introduce a distinction between E_source = S
* and E_target = T. Objects in T are heavily pruned by all the unnecessary information
*
* 4) perform the join as (((T.id join R.target) union S) groupby S.id) yield S -> [ <T, R> ]
*/
public class GraphJoiner implements Serializable {
private Map<String, LongAccumulator> accumulators = Maps.newHashMap();
public static final int MAX_RELS = 100;
public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd";
private SparkSession spark;
private ContextMapper contextMapper;
private String inputPath;
private String outPath;
private String otherDsTypeId;
public GraphJoiner(SparkSession spark, ContextMapper contextMapper, String otherDsTypeId, String inputPath, String outPath) {
this.spark = spark;
this.contextMapper = contextMapper;
this.otherDsTypeId = otherDsTypeId;
this.inputPath = inputPath;
this.outPath = outPath;
final SparkContext sc = spark.sparkContext();
prepareAccumulators(sc);
}
public GraphJoiner adjacencyLists() {
final JavaSparkContext jsc = new JavaSparkContext(getSpark().sparkContext());
// read each entity
JavaPairRDD<String, TypedRow> datasource = readPathEntity(jsc, getInputPath(), "datasource");
JavaPairRDD<String, TypedRow> organization = readPathEntity(jsc, getInputPath(), "organization");
JavaPairRDD<String, TypedRow> project = readPathEntity(jsc, getInputPath(), "project");
JavaPairRDD<String, TypedRow> dataset = readPathEntity(jsc, getInputPath(), "dataset");
JavaPairRDD<String, TypedRow> otherresearchproduct = readPathEntity(jsc, getInputPath(), "otherresearchproduct");
JavaPairRDD<String, TypedRow> software = readPathEntity(jsc, getInputPath(), "software");
JavaPairRDD<String, TypedRow> publication = readPathEntity(jsc, getInputPath(), "publication");
// create the union between all the entities
final String entitiesPath = getOutPath() + "/entities";
datasource
.union(organization)
.union(project)
.union(dataset)
.union(otherresearchproduct)
.union(software)
.union(publication)
.map(e -> new EntityRelEntity().setSource(e._2()))
.map(GraphMappingUtils::serialize)
.saveAsTextFile(entitiesPath, GzipCodec.class);
JavaPairRDD<String, EntityRelEntity> entities = jsc.textFile(entitiesPath)
.map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
.mapToPair(t -> new Tuple2<>(t.getSource().getSourceId(), t));
final String relationPath = getOutPath() + "/relation";
// reads the relationships
final JavaPairRDD<SortableRelationKey, EntityRelEntity> rels = readPathRelation(jsc, getInputPath())
.filter(rel -> !rel.getDeleted()) //only consider those that are not virtually deleted
.map(p -> new EntityRelEntity().setRelation(p))
.mapToPair(p -> new Tuple2<>(SortableRelationKey.from(p), p));
rels
.groupByKey(new RelationPartitioner(rels.getNumPartitions()))
.map(p -> Iterables.limit(p._2(), MAX_RELS))
.flatMap(p -> p.iterator())
.map(s -> new ObjectMapper().writeValueAsString(s))
.saveAsTextFile(relationPath, GzipCodec.class);
final JavaPairRDD<String, EntityRelEntity> relation = jsc.textFile(relationPath)
.map(s -> new ObjectMapper().readValue(s, EntityRelEntity.class))
.mapToPair(p -> new Tuple2<>(p.getRelation().getTargetId(), p));
final String bySourcePath = getOutPath() + "/join_by_source";
relation
.join(entities
.filter(e -> !e._2().getSource().getDeleted())
.mapToPair(e -> new Tuple2<>(e._1(), asRelatedEntity(e._2()))))
.map(s -> new EntityRelEntity()
.setRelation(s._2()._1().getRelation())
.setTarget(s._2()._2().getSource()))
.map(j -> new ObjectMapper().writeValueAsString(j))
.saveAsTextFile(bySourcePath, GzipCodec.class);
JavaPairRDD<String, EntityRelEntity> bySource = jsc.textFile(bySourcePath)
.map(e -> getObjectMapper().readValue(e, EntityRelEntity.class))
.mapToPair(t -> new Tuple2<>(t.getRelation().getSourceId(), t));
final XmlRecordFactory recordFactory = new XmlRecordFactory(accumulators, contextMapper, false, schemaLocation, otherDsTypeId);
entities
.union(bySource)
.groupByKey() // by source id
.map(l -> toJoinedEntity(l))
.mapToPair(je -> new Tuple2<>(
new Text(je.getEntity().getId()),
new Text(recordFactory.build(je))))
.saveAsHadoopFile(getOutPath() + "/xml", Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
return this;
}
public SparkSession getSpark() {
return spark;
}
public String getInputPath() {
return inputPath;
}
public String getOutPath() {
return outPath;
}
// HELPERS
private OafEntity parseOaf(final String json, final String type, final ObjectMapper mapper) {
try {
switch (GraphMappingUtils.EntityType.valueOf(type)) {
case publication:
return mapper.readValue(json, Publication.class);
case dataset:
return mapper.readValue(json, Dataset.class);
case otherresearchproduct:
return mapper.readValue(json, OtherResearchProduct.class);
case software:
return mapper.readValue(json, Software.class);
case datasource:
return mapper.readValue(json, Datasource.class);
case organization:
return mapper.readValue(json, Organization.class);
case project:
return mapper.readValue(json, Project.class);
default:
throw new IllegalArgumentException("invalid type: " + type);
}
} catch (IOException e) {
throw new IllegalArgumentException(e);
}
}
private JoinedEntity toJoinedEntity(Tuple2<String, Iterable<EntityRelEntity>> p) {
final ObjectMapper mapper = getObjectMapper();
final JoinedEntity j = new JoinedEntity();
final Links links = new Links();
for(EntityRelEntity rel : p._2()) {
if (rel.hasMainEntity() & j.getEntity() == null) {
j.setType(rel.getSource().getType());
j.setEntity(parseOaf(rel.getSource().getOaf(), rel.getSource().getType(), mapper));
}
if (rel.hasRelatedEntity()) {
try {
links.add(
new eu.dnetlib.dhp.oa.provision.model.Tuple2()
.setRelation(mapper.readValue(rel.getRelation().getOaf(), Relation.class))
.setRelatedEntity(mapper.readValue(rel.getTarget().getOaf(), RelatedEntity.class)));
} catch (IOException e) {
throw new IllegalArgumentException(e);
}
}
}
j.setLinks(links);
if (j.getEntity() == null) {
throw new IllegalStateException("missing main entity on '" + p._1() + "'");
}
return j;
}
/**
* Reads a set of eu.dnetlib.dhp.schema.oaf.OafEntity objects from a sequence file <className, entity json serialization>,
* extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
* @param sc
* @param inputPath
* @param type
* @return the JavaPairRDD<String, TypedRow> indexed by entity identifier
*/
private JavaPairRDD<String, TypedRow> readPathEntity(final JavaSparkContext sc, final String inputPath, final String type) {
return sc.textFile(inputPath + "/" + type)
.mapToPair((PairFunction<String, String, TypedRow>) s -> {
final DocumentContext json = JsonPath.parse(s);
final String id = json.read("$.id");
return new Tuple2<>(id, new TypedRow()
.setSourceId(id)
.setDeleted(json.read("$.dataInfo.deletedbyinference"))
.setType(type)
.setOaf(s));
});
}
/**
* Reads a set of eu.dnetlib.dhp.schema.oaf.Relation objects from a sequence file <className, relation json serialization>,
* extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
* @param sc
* @param inputPath
* @return the JavaRDD<TypedRow> containing all the relationships
*/
private JavaRDD<TypedRow> readPathRelation(final JavaSparkContext sc, final String inputPath) {
return sc.textFile(inputPath + "/relation")
.map(s -> {
final DocumentContext json = JsonPath.parse(s);
return new TypedRow()
.setSourceId(json.read("$.source"))
.setTargetId(json.read("$.target"))
.setDeleted(json.read("$.dataInfo.deletedbyinference"))
.setType("relation")
.setRelType("$.relType")
.setSubRelType("$.subRelType")
.setRelClass("$.relClass")
.setOaf(s);
});
}
private ObjectMapper getObjectMapper() {
return new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
}
private void prepareAccumulators(SparkContext sc) {
accumulators.put("resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments"));
accumulators.put("resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments"));
accumulators.put("resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo"));
accumulators.put("resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy"));
accumulators.put("resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn"));
accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges"));
accumulators.put("resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo"));
accumulators.put("resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo"));
accumulators.put("resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy"));
accumulators.put("resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces"));
accumulators.put("resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf"));
accumulators.put("resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution"));
accumulators.put("projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant"));
accumulators.put("projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant"));
accumulators.put("organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn"));
accumulators.put("organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces"));
accumulators.put("datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy"));
accumulators.put("datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides"));
}
}

View File

@ -0,0 +1,328 @@
package eu.dnetlib.dhp.oa.provision;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Iterators;
import com.google.common.collect.Maps;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.oa.provision.model.*;
import eu.dnetlib.dhp.oa.provision.utils.*;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.spark.SparkContext;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.*;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.types.*;
import org.apache.spark.util.LongAccumulator;
import scala.Tuple2;
import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.asRelatedEntity;
/**
* Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
* The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
* and all the possible relationships (similarity links produced by the Dedup process are excluded).
*
* The operation is implemented creating the union between the entity types (E), joined by the relationships (R), and again
* by E, finally grouped by E.id;
*
* Different manipulations of the E and R sets are introduced to reduce the complexity of the operation
* 1) treat the object payload as string, extracting only the necessary information beforehand using json path,
* it seems that deserializing it with jackson's object mapper has higher memory footprint.
*
* 2) only consider rels that are not virtually deleted ($.dataInfo.deletedbyinference == false)
* 3) we only need a subset of fields from the related entities, so we introduce a distinction between E_source = S
* and E_target = T. Objects in T are heavily pruned by all the unnecessary information
*
* 4) perform the join as (((T.id join R.target) union S) groupby S.id) yield S -> [ <T, R> ]
*/
public class GraphJoiner_v2 implements Serializable {
public static final int LIMIT = 1000000;
private Map<String, LongAccumulator> accumulators = Maps.newHashMap();
public static final int MAX_RELS = 100;
public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd";
private static final StructType KV_SCHEMA = StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())
));
private static final StructType TYPED_ROW_SCHEMA = StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("sourceId", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("targetId", DataTypes.StringType, true, Metadata.empty()),
StructField$.MODULE$.apply("deleted", DataTypes.BooleanType, false, Metadata.empty()),
StructField$.MODULE$.apply("type", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("relType", DataTypes.StringType, true, Metadata.empty()),
StructField$.MODULE$.apply("subRelType", DataTypes.StringType, true, Metadata.empty()),
StructField$.MODULE$.apply("relClass", DataTypes.StringType, true, Metadata.empty()),
StructField$.MODULE$.apply("oaf", DataTypes.BinaryType, false, Metadata.empty())
));
private static final StructType ENTITY_REL_ENTITY_SCHEMA = StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("source", TYPED_ROW_SCHEMA, false, Metadata.empty()),
StructField$.MODULE$.apply("relation", TYPED_ROW_SCHEMA, true, Metadata.empty()),
StructField$.MODULE$.apply("target", TYPED_ROW_SCHEMA, false, Metadata.empty())
));
private SparkSession spark;
private ContextMapper contextMapper;
private String inputPath;
private String outPath;
private String otherDsTypeId;
public GraphJoiner_v2(SparkSession spark, ContextMapper contextMapper, String otherDsTypeId, String inputPath, String outPath) {
this.spark = spark;
this.contextMapper = contextMapper;
this.otherDsTypeId = otherDsTypeId;
this.inputPath = inputPath;
this.outPath = outPath;
final SparkContext sc = spark.sparkContext();
prepareAccumulators(sc);
}
public GraphJoiner_v2 adjacencyLists() throws IOException {
final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(getSpark().sparkContext());
// read each entity
Dataset<TypedRow> datasource = readPathEntity(jsc, getInputPath(), "datasource");
Dataset<TypedRow> organization = readPathEntity(jsc, getInputPath(), "organization");
Dataset<TypedRow> project = readPathEntity(jsc, getInputPath(), "project");
Dataset<TypedRow> dataset = readPathEntity(jsc, getInputPath(), "dataset");
Dataset<TypedRow> otherresearchproduct = readPathEntity(jsc, getInputPath(), "otherresearchproduct");
Dataset<TypedRow> software = readPathEntity(jsc, getInputPath(), "software");
Dataset<TypedRow> publication = readPathEntity(jsc, getInputPath(), "publication");
// create the union between all the entities
Dataset<Tuple2<String, TypedRow>> entities =
datasource
.union(organization)
.union(project)
.union(dataset)
.union(otherresearchproduct)
.union(software)
.union(publication)
.map((MapFunction<TypedRow, Tuple2<String, TypedRow>>) value -> new Tuple2<>(
value.getId(),
value),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class)))
.limit(LIMIT)
.cache();
System.out.println("Entities schema:");
entities.printSchema();
// reads the relationships
Dataset<Relation> rels = readPathRelation(jsc, getInputPath())
.groupByKey((MapFunction<Relation, SortableRelationKey>) t -> SortableRelationKey.from(t), Encoders.kryo(SortableRelationKey.class))
.flatMapGroups((FlatMapGroupsFunction<SortableRelationKey, Relation, Relation>) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.bean(Relation.class))
.limit(LIMIT)
.cache();
System.out.println("Relation schema:");
rels.printSchema();
Dataset<Tuple2<String, Relation>> relsByTarget = rels
.map((MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(), r), Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)));
System.out.println("Relation by target schema:");
relsByTarget.printSchema();
Dataset<Tuple2<String, EntityRelEntity>> bySource = relsByTarget
.joinWith(entities, relsByTarget.col("_1").equalTo(entities.col("_1")), "inner")
.filter((FilterFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, TypedRow>>>) value -> value._2()._2().getDeleted() == false)
.map((MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, TypedRow>>, EntityRelEntity>) t -> {
EntityRelEntity e = new EntityRelEntity();
e.setRelation(t._1()._2());
e.setTarget(asRelatedEntity(t._2()._2()));
return e;
}, Encoders.bean(EntityRelEntity.class))
.map((MapFunction<EntityRelEntity, Tuple2<String, EntityRelEntity>>) e -> new Tuple2<>(e.getRelation().getSource(), e),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class)));
System.out.println("bySource schema");
bySource.printSchema();
Dataset<EntityRelEntity> joined = entities
.joinWith(bySource, entities.col("_1").equalTo(bySource.col("_1")), "left")
.map((MapFunction<Tuple2<Tuple2<String, TypedRow>, Tuple2<String, EntityRelEntity>>, EntityRelEntity>) value -> {
EntityRelEntity re = new EntityRelEntity();
re.setEntity(value._1()._2());
Optional<EntityRelEntity> related = Optional.ofNullable(value._2()).map(Tuple2::_2);
if (related.isPresent()) {
re.setRelation(related.get().getRelation());
re.setTarget(related.get().getTarget());
}
return re;
}, Encoders.kryo(EntityRelEntity.class));
System.out.println("joined schema");
joined.printSchema();
//joined.write().json(getOutPath() + "/joined");
final Dataset<JoinedEntity> grouped = joined
.groupByKey((MapFunction<EntityRelEntity, TypedRow>) e -> e.getEntity(), Encoders.kryo(TypedRow.class))
.mapGroups((MapGroupsFunction<TypedRow, EntityRelEntity, JoinedEntity>) (key, values) -> toJoinedEntity(key, values), Encoders.kryo(JoinedEntity.class));
System.out.println("grouped schema");
grouped.printSchema();
final XmlRecordFactory recordFactory = new XmlRecordFactory(accumulators, contextMapper, false, schemaLocation, otherDsTypeId);
grouped
.map((MapFunction<JoinedEntity, String>) value -> recordFactory.build(value), Encoders.STRING())
.limit(LIMIT)
.write()
.text(getOutPath() + "/xml");
/*
.javaRDD()
.mapToPair((PairFunction<Tuple2<String, String>, String, String>) t -> new Tuple2<>(t._1(), t._2()))
.saveAsHadoopFile(getOutPath() + "/xml", Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
*/
return this;
}
public SparkSession getSpark() {
return spark;
}
public String getInputPath() {
return inputPath;
}
public String getOutPath() {
return outPath;
}
// HELPERS
private JoinedEntity toJoinedEntity(TypedRow key, Iterator<EntityRelEntity> values) {
final ObjectMapper mapper = getObjectMapper();
final JoinedEntity j = new JoinedEntity();
j.setType(key.getType());
j.setEntity(parseOaf(key.getOaf(), key.getType(), mapper));
final Links links = new Links();
values.forEachRemaining(rel -> links.add(
new eu.dnetlib.dhp.oa.provision.model.Tuple2(
rel.getRelation(),
rel.getTarget()
)));
j.setLinks(links);
return j;
}
private OafEntity parseOaf(final String json, final String type, final ObjectMapper mapper) {
try {
switch (GraphMappingUtils.EntityType.valueOf(type)) {
case publication:
return mapper.readValue(json, Publication.class);
case dataset:
return mapper.readValue(json, eu.dnetlib.dhp.schema.oaf.Dataset.class);
case otherresearchproduct:
return mapper.readValue(json, OtherResearchProduct.class);
case software:
return mapper.readValue(json, Software.class);
case datasource:
return mapper.readValue(json, Datasource.class);
case organization:
return mapper.readValue(json, Organization.class);
case project:
return mapper.readValue(json, Project.class);
default:
throw new IllegalArgumentException("invalid type: " + type);
}
} catch (IOException e) {
throw new IllegalArgumentException(e);
}
}
/**
* Reads a set of eu.dnetlib.dhp.schema.oaf.OafEntity objects from a new line delimited json file,
* extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
* @param sc
* @param inputPath
* @param type
* @return the JavaPairRDD<String, TypedRow> indexed by entity identifier
*/
private Dataset<TypedRow> readPathEntity(final JavaSparkContext sc, final String inputPath, final String type) {
RDD<Row> rdd = sc.textFile(inputPath + "/" + type)
.map((Function<String, Row>) s -> RowFactory.create("", s))
.rdd();
return getSpark().createDataFrame(rdd, KV_SCHEMA)
.map((MapFunction<Row, TypedRow>) row -> {
final String s = row.getAs("value");
final DocumentContext json = JsonPath.parse(s);
final TypedRow t = new TypedRow();
t.setId(json.read("$.id"));
t.setDeleted(json.read("$.dataInfo.deletedbyinference"));
t.setType(type);
t.setOaf(s);
return t;
}, Encoders.bean(TypedRow.class));
}
/**
* Reads a set of eu.dnetlib.dhp.schema.oaf.Relation objects from a sequence file <className, relation json serialization>,
* extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
* @param sc
* @param inputPath
* @return the JavaRDD<TypedRow> containing all the relationships
*/
private Dataset<Relation> readPathRelation(final JavaSparkContext sc, final String inputPath) {
final RDD<Row> rdd = sc.textFile(inputPath + "/relation")
.map((Function<String, Row>) s -> RowFactory.create("", s))
.rdd();
return getSpark().createDataFrame(rdd, KV_SCHEMA)
.map((MapFunction<Row, Relation>) value -> new ObjectMapper().readValue(value.<String>getAs("value"), Relation.class), Encoders.bean(Relation.class));
}
private ObjectMapper getObjectMapper() {
return new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
}
private void prepareAccumulators(SparkContext sc) {
accumulators.put("resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments"));
accumulators.put("resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments"));
accumulators.put("resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo"));
accumulators.put("resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy"));
accumulators.put("resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn"));
accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges"));
accumulators.put("resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo"));
accumulators.put("resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo"));
accumulators.put("resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy"));
accumulators.put("resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces"));
accumulators.put("resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf"));
accumulators.put("resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution"));
accumulators.put("projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant"));
accumulators.put("projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant"));
accumulators.put("organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn"));
accumulators.put("organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces"));
accumulators.put("datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy"));
accumulators.put("datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides"));
}
}

View File

@ -84,7 +84,7 @@ public class SparkXmlIndexingJob {
return SparkSession return SparkSession
.builder() .builder()
.config(conf) .config(conf)
.appName(SparkXmlRecordBuilderJob.class.getSimpleName()) .appName(SparkXmlIndexingJob.class.getSimpleName())
.master(master) .master(master)
.getOrCreate(); .getOrCreate();
} }

View File

@ -1,47 +0,0 @@
package eu.dnetlib.dhp.oa.provision;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
public class SparkXmlRecordBuilderJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(
SparkXmlRecordBuilderJob.class.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
parser.parseArgument(args);
final String master = parser.get("master");
final SparkConf conf = new SparkConf()
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
try(SparkSession spark = getSession(conf, master)) {
final String inputPath = parser.get("sourcePath");
final String outputPath = parser.get("outputPath");
final String isLookupUrl = parser.get("isLookupUrl");
final String otherDsTypeId = parser.get("otherDsTypeId");
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
new GraphJoiner(spark, ContextMapper.fromIS(isLookupUrl), otherDsTypeId, inputPath, outputPath)
.adjacencyLists();
}
}
private static SparkSession getSession(SparkConf conf, String master) {
return SparkSession
.builder()
.config(conf)
.appName(SparkXmlRecordBuilderJob.class.getSimpleName())
.master(master)
.getOrCreate();
}
}

View File

@ -0,0 +1,81 @@
package eu.dnetlib.dhp.oa.provision;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.model.*;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
public class SparkXmlRecordBuilderJob_v2 {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(
SparkXmlRecordBuilderJob_v2.class.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
parser.parseArgument(args);
final String master = parser.get("master");
try(SparkSession spark = getSession(master)) {
final String inputPath = parser.get("sourcePath");
final String outputPath = parser.get("outputPath");
final String isLookupUrl = parser.get("isLookupUrl");
final String otherDsTypeId = parser.get("otherDsTypeId");
new GraphJoiner_v2(spark, ContextMapper.fromIS(isLookupUrl), otherDsTypeId, inputPath, outputPath)
.adjacencyLists();
}
}
private static SparkSession getSession(String master) {
final SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.set("spark.sql.shuffle.partitions", "500");
conf.registerKryoClasses(new Class[]{
Author.class,
Context.class,
Country.class,
DataInfo.class,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
Datasource.class,
ExternalReference.class,
ExtraInfo.class,
Field.class,
GeoLocation.class,
Instance.class,
Journal.class,
KeyValue.class,
Oaf.class,
OafEntity.class,
OAIProvenance.class,
Organization.class,
OriginDescription.class,
OtherResearchProduct.class,
Project.class,
Publication.class,
Qualifier.class,
Relation.class,
Result.class,
Software.class,
StructuredProperty.class,
TypedRow.class,
EntityRelEntity.class,
JoinedEntity.class,
SortableRelationKey.class,
Tuple2.class,
Links.class,
RelatedEntity.class
});
return SparkSession
.builder()
.config(conf)
.appName(SparkXmlRecordBuilderJob_v2.class.getSimpleName())
.master(master)
.getOrCreate();
}
}

View File

@ -1,54 +1,36 @@
package eu.dnetlib.dhp.oa.provision.model; package eu.dnetlib.dhp.oa.provision.model;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.Serializable; import java.io.Serializable;
public class EntityRelEntity implements Serializable { public class EntityRelEntity implements Serializable {
private TypedRow source; private TypedRow entity;
private TypedRow relation; private Relation relation;
private TypedRow target; private RelatedEntity target;
public EntityRelEntity() { public TypedRow getEntity() {
return entity;
} }
public EntityRelEntity(TypedRow source) { public void setEntity(TypedRow entity) {
this.source = source; this.entity = entity;
} }
//helpers public Relation getRelation() {
public Boolean hasMainEntity() {
return getSource() != null & getRelation() == null & getTarget() == null;
}
public Boolean hasRelatedEntity() {
return getSource() == null & getRelation() != null & getTarget() != null;
}
public TypedRow getSource() {
return source;
}
public EntityRelEntity setSource(TypedRow source) {
this.source = source;
return this;
}
public TypedRow getRelation() {
return relation; return relation;
} }
public EntityRelEntity setRelation(TypedRow relation) { public void setRelation(Relation relation) {
this.relation = relation; this.relation = relation;
return this;
} }
public TypedRow getTarget() { public RelatedEntity getTarget() {
return target; return target;
} }
public EntityRelEntity setTarget(TypedRow target) { public void setTarget(RelatedEntity target) {
this.target = target; this.target = target;
return this;
} }
} }

View File

@ -16,26 +16,23 @@ public class JoinedEntity implements Serializable {
return type; return type;
} }
public JoinedEntity setType(String type) { public void setType(String type) {
this.type = type; this.type = type;
return this;
} }
public OafEntity getEntity() { public OafEntity getEntity() {
return entity; return entity;
} }
public JoinedEntity setEntity(OafEntity entity) { public void setEntity(OafEntity entity) {
this.entity = entity; this.entity = entity;
return this;
} }
public Links getLinks() { public Links getLinks() {
return links; return links;
} }
public JoinedEntity setLinks(Links links) { public void setLinks(Links links) {
this.links = links; this.links = links;
return this;
} }
} }

View File

@ -49,207 +49,183 @@ public class RelatedEntity implements Serializable {
return id; return id;
} }
public RelatedEntity setId(String id) { public void setId(String id) {
this.id = id; this.id = id;
return this;
}
public StructuredProperty getTitle() {
return title;
}
public RelatedEntity setTitle(StructuredProperty title) {
this.title = title;
return this;
}
public String getDateofacceptance() {
return dateofacceptance;
}
public RelatedEntity setDateofacceptance(String dateofacceptance) {
this.dateofacceptance = dateofacceptance;
return this;
}
public String getPublisher() {
return publisher;
}
public RelatedEntity setPublisher(String publisher) {
this.publisher = publisher;
return this;
}
public List<StructuredProperty> getPid() {
return pid;
}
public RelatedEntity setPid(List<StructuredProperty> pid) {
this.pid = pid;
return this;
}
public String getCodeRepositoryUrl() {
return codeRepositoryUrl;
}
public RelatedEntity setCodeRepositoryUrl(String codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl;
return this;
}
public Qualifier getResulttype() {
return resulttype;
}
public RelatedEntity setResulttype(Qualifier resulttype) {
this.resulttype = resulttype;
return this;
}
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public RelatedEntity setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
return this;
}
public List<Instance> getInstances() {
return instances;
}
public RelatedEntity setInstances(List<Instance> instances) {
this.instances = instances;
return this;
}
public String getOfficialname() {
return officialname;
}
public RelatedEntity setOfficialname(String officialname) {
this.officialname = officialname;
return this;
}
public String getWebsiteurl() {
return websiteurl;
}
public RelatedEntity setWebsiteurl(String websiteurl) {
this.websiteurl = websiteurl;
return this;
}
public Qualifier getDatasourcetype() {
return datasourcetype;
}
public RelatedEntity setDatasourcetype(Qualifier datasourcetype) {
this.datasourcetype = datasourcetype;
return this;
}
public Qualifier getDatasourcetypeui() {
return datasourcetypeui;
}
public RelatedEntity setDatasourcetypeui(Qualifier datasourcetypeui) {
this.datasourcetypeui = datasourcetypeui;
return this;
}
public Qualifier getOpenairecompatibility() {
return openairecompatibility;
}
public RelatedEntity setOpenairecompatibility(Qualifier openairecompatibility) {
this.openairecompatibility = openairecompatibility;
return this;
}
public String getLegalname() {
return legalname;
}
public RelatedEntity setLegalname(String legalname) {
this.legalname = legalname;
return this;
}
public String getLegalshortname() {
return legalshortname;
}
public RelatedEntity setLegalshortname(String legalshortname) {
this.legalshortname = legalshortname;
return this;
}
public Qualifier getCountry() {
return country;
}
public RelatedEntity setCountry(Qualifier country) {
this.country = country;
return this;
}
public String getCode() {
return code;
}
public RelatedEntity setCode(String code) {
this.code = code;
return this;
}
public String getAcronym() {
return acronym;
}
public RelatedEntity setAcronym(String acronym) {
this.acronym = acronym;
return this;
}
public Qualifier getContracttype() {
return contracttype;
}
public RelatedEntity setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
return this;
}
public List<String> getFundingtree() {
return 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() { public String getType() {
return type; return type;
} }
public RelatedEntity setType(String type) { public void setType(String type) {
this.type = type; this.type = type;
return this;
} }
public StructuredProperty getTitle() {
return title;
}
public void setTitle(StructuredProperty title) {
this.title = title;
}
public String getWebsiteurl() {
return websiteurl;
}
public void setWebsiteurl(String websiteurl) {
this.websiteurl = websiteurl;
}
public String getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(String dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public String getPublisher() {
return publisher;
}
public void setPublisher(String publisher) {
this.publisher = publisher;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public String getCodeRepositoryUrl() {
return codeRepositoryUrl;
}
public void setCodeRepositoryUrl(String codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl;
}
public Qualifier getResulttype() {
return resulttype;
}
public void setResulttype(Qualifier resulttype) {
this.resulttype = resulttype;
}
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public List<Instance> getInstances() {
return instances;
}
public void setInstances(List<Instance> instances) {
this.instances = instances;
}
public String getOfficialname() {
return officialname;
}
public void setOfficialname(String officialname) {
this.officialname = officialname;
}
public Qualifier getDatasourcetype() {
return datasourcetype;
}
public void setDatasourcetype(Qualifier datasourcetype) {
this.datasourcetype = datasourcetype;
}
public Qualifier getDatasourcetypeui() {
return datasourcetypeui;
}
public void setDatasourcetypeui(Qualifier datasourcetypeui) {
this.datasourcetypeui = datasourcetypeui;
}
public Qualifier getOpenairecompatibility() {
return openairecompatibility;
}
public void setOpenairecompatibility(Qualifier openairecompatibility) {
this.openairecompatibility = openairecompatibility;
}
public String getLegalname() {
return legalname;
}
public void setLegalname(String legalname) {
this.legalname = legalname;
}
public String getLegalshortname() {
return legalshortname;
}
public void setLegalshortname(String legalshortname) {
this.legalshortname = legalshortname;
}
public Qualifier getCountry() {
return country;
}
public void setCountry(Qualifier country) {
this.country = country;
}
public String getProjectTitle() {
return projectTitle;
}
public void setProjectTitle(String projectTitle) {
this.projectTitle = projectTitle;
}
public String getCode() {
return code;
}
public void setCode(String code) {
this.code = code;
}
public String getAcronym() {
return acronym;
}
public void setAcronym(String acronym) {
this.acronym = acronym;
}
public Qualifier getContracttype() {
return contracttype;
}
public void setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
}
public List<String> getFundingtree() {
return fundingtree;
}
public void setFundingtree(List<String> fundingtree) {
this.fundingtree = fundingtree;
}
} }

View File

@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.provision.model;
import com.google.common.collect.ComparisonChain; import com.google.common.collect.ComparisonChain;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.Serializable; import java.io.Serializable;
import java.util.Map; import java.util.Map;
@ -33,58 +34,54 @@ public class SortableRelationKey implements Comparable<SortableRelationKey>, Ser
weights.put("dedup", 8); weights.put("dedup", 8);
} }
public static SortableRelationKey from(final EntityRelEntity e) { public static SortableRelationKey from(final Relation r) {
return new SortableRelationKey() final SortableRelationKey s = new SortableRelationKey();
.setSourceId(e.getRelation().getSourceId()) s.setSourceId(r.getSource());
.setTargetId(e.getRelation().getTargetId()) s.setTargetId(r.getTarget());
.setRelType(e.getRelation().getRelType()) s.setRelType(r.getRelType());
.setSubRelType(e.getRelation().getSubRelType()) s.setSubRelType(r.getSubRelType());
.setRelClass(e.getRelation().getRelClass()); s.setRelClass(r.getRelClass());
return s;
} }
public String getSourceId() { public String getSourceId() {
return sourceId; return sourceId;
} }
public SortableRelationKey setSourceId(String sourceId) { public void setSourceId(String sourceId) {
this.sourceId = sourceId; this.sourceId = sourceId;
return this;
} }
public String getTargetId() { public String getTargetId() {
return targetId; return targetId;
} }
public SortableRelationKey setTargetId(String targetId) { public void setTargetId(String targetId) {
this.targetId = targetId; this.targetId = targetId;
return this;
} }
public String getRelType() { public String getRelType() {
return relType; return relType;
} }
public SortableRelationKey setRelType(String relType) { public void setRelType(String relType) {
this.relType = relType; this.relType = relType;
return this;
} }
public String getSubRelType() { public String getSubRelType() {
return subRelType; return subRelType;
} }
public SortableRelationKey setSubRelType(String subRelType) { public void setSubRelType(String subRelType) {
this.subRelType = subRelType; this.subRelType = subRelType;
return this;
} }
public String getRelClass() { public String getRelClass() {
return relClass; return relClass;
} }
public SortableRelationKey setRelClass(String relClass) { public void setRelClass(String relClass) {
this.relClass = relClass; this.relClass = relClass;
return this;
} }
@Override @Override

View File

@ -8,21 +8,24 @@ public class Tuple2 {
private RelatedEntity relatedEntity; private RelatedEntity relatedEntity;
public Tuple2(Relation relation, RelatedEntity relatedEntity) {
this.relation = relation;
this.relatedEntity = relatedEntity;
}
public Relation getRelation() { public Relation getRelation() {
return relation; return relation;
} }
public Tuple2 setRelation(Relation relation) { public void setRelation(Relation relation) {
this.relation = relation; this.relation = relation;
return this;
} }
public RelatedEntity getRelatedEntity() { public RelatedEntity getRelatedEntity() {
return relatedEntity; return relatedEntity;
} }
public Tuple2 setRelatedEntity(RelatedEntity relatedEntity) { public void setRelatedEntity(RelatedEntity relatedEntity) {
this.relatedEntity = relatedEntity; this.relatedEntity = relatedEntity;
return this;
} }
} }

View File

@ -1,92 +1,61 @@
package eu.dnetlib.dhp.oa.provision.model; package eu.dnetlib.dhp.oa.provision.model;
import com.google.common.base.Objects;
import java.io.Serializable; import java.io.Serializable;
public class TypedRow implements Serializable { public class TypedRow implements Serializable {
private String sourceId; private String id;
private String targetId;
private Boolean deleted; private Boolean deleted;
private String type; private String type;
private String relType;
private String subRelType;
private String relClass;
private String oaf; private String oaf;
public String getSourceId() { public String getId() {
return sourceId; return id;
} }
public TypedRow setSourceId(String sourceId) { public void setId(String id) {
this.sourceId = sourceId; this.id = id;
return this;
}
public String getTargetId() {
return targetId;
}
public TypedRow setTargetId(String targetId) {
this.targetId = targetId;
return this;
} }
public Boolean getDeleted() { public Boolean getDeleted() {
return deleted; return deleted;
} }
public TypedRow setDeleted(Boolean deleted) { public void setDeleted(Boolean deleted) {
this.deleted = deleted; this.deleted = deleted;
return this;
} }
public String getType() { public String getType() {
return type; return type;
} }
public TypedRow setType(String type) { public void setType(String type) {
this.type = type; this.type = type;
return this;
}
public String getRelType() {
return relType;
}
public TypedRow setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubRelType() {
return subRelType;
}
public TypedRow setSubRelType(String subRelType) {
this.subRelType = subRelType;
return this;
}
public String getRelClass() {
return relClass;
}
public TypedRow setRelClass(String relClass) {
this.relClass = relClass;
return this;
} }
public String getOaf() { public String getOaf() {
return oaf; return oaf;
} }
public TypedRow setOaf(String oaf) { public void setOaf(String oaf) {
this.oaf = oaf; this.oaf = oaf;
return this; }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
TypedRow typedRow2 = (TypedRow) o;
return Objects.equal(id, typedRow2.id);
}
@Override
public int hashCode() {
return Objects.hashCode(id);
} }
} }

View File

@ -3,14 +3,11 @@ package eu.dnetlib.dhp.oa.provision.utils;
import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Predicate;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath; import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity; import eu.dnetlib.dhp.oa.provision.model.*;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.TypedRow;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import net.minidev.json.JSONArray; import net.minidev.json.JSONArray;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
@ -66,14 +63,14 @@ public class GraphMappingUtils {
return MainEntityType.result.name().equals(getMainType(type)); return MainEntityType.result.name().equals(getMainType(type));
} }
public static Predicate<String> instanceFilter = s -> instanceFieldFilter.contains(s); public static RelatedEntity asRelatedEntity(TypedRow e) {
public static EntityRelEntity asRelatedEntity(EntityRelEntity e) { final DocumentContext j = JsonPath.parse(e.getOaf());
final RelatedEntity re = new RelatedEntity();
re.setId(j.read("$.id"));
re.setType(e.getType());
final DocumentContext j = JsonPath.parse(e.getSource().getOaf()); switch (EntityType.valueOf(e.getType())) {
final RelatedEntity re = new RelatedEntity().setId(j.read("$.id")).setType(e.getSource().getType());
switch (EntityType.valueOf(e.getSource().getType())) {
case publication: case publication:
case dataset: case dataset:
case otherresearchproduct: case otherresearchproduct:
@ -147,14 +144,11 @@ public class GraphMappingUtils {
break; break;
} }
return new EntityRelEntity().setSource(
new TypedRow() return re;
.setSourceId(e.getSource().getSourceId())
.setDeleted(e.getSource().getDeleted())
.setType(e.getSource().getType())
.setOaf(serialize(re)));
} }
private static KeyValue asKV(LinkedHashMap<String, Object> j) { private static KeyValue asKV(LinkedHashMap<String, Object> j) {
final KeyValue kv = new KeyValue(); final KeyValue kv = new KeyValue();
kv.setKey((String) j.get("key")); kv.setKey((String) j.get("key"));

View File

@ -7,9 +7,7 @@ import com.google.common.collect.Maps;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import com.mycila.xmltool.XMLDoc; import com.mycila.xmltool.XMLDoc;
import com.mycila.xmltool.XMLTag; import com.mycila.xmltool.XMLTag;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.*;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.Tuple2;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;

View File

@ -65,7 +65,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>build_adjacency_lists</name> <name>build_adjacency_lists</name>
<class>eu.dnetlib.dhp.oa.provision.SparkXmlRecordBuilderJob</class> <class>eu.dnetlib.dhp.oa.provision.SparkXmlRecordBuilderJob_v2</class>
<jar>dhp-graph-provision-${projectVersion}.jar</jar> <jar>dhp-graph-provision-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores ${sparkExecutorCoresForJoining} --executor-cores ${sparkExecutorCoresForJoining}
@ -75,6 +75,7 @@
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.network.timeout=10000000
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn</arg> <arg>-mt</arg> <arg>yarn</arg>
<arg>-is</arg> <arg>${isLookupUrl}</arg> <arg>-is</arg> <arg>${isLookupUrl}</arg>