forked from D-Net/dnet-hadoop
fixed implementation of PatchRelationsApplication, refined the relative unit test
This commit is contained in:
parent
081fe92a21
commit
a6a38cca9e
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@ -1,10 +1,12 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.FileNotFoundException;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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@ -15,104 +17,111 @@ import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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import java.io.FileNotFoundException;
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import java.util.Objects;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class PatchRelationsApplication {
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private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
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private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Optional.ofNullable(
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PatchRelationsApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
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.orElseThrow(FileNotFoundException::new)
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));
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parser.parseArgument(args);
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Optional
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.ofNullable(
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PatchRelationsApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
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.orElseThrow(FileNotFoundException::new)));
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String graphBasePath = parser.get("graphBasePath");
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log.info("graphBasePath: {}", graphBasePath);
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final String graphBasePath = parser.get("graphBasePath");
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log.info("graphBasePath: {}", graphBasePath);
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final String workingDir = parser.get("workingDir");
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log.info("workingDir: {}", workingDir);
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final String workingDir = parser.get("workingDir");
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log.info("workingDir: {}", workingDir);
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final String idMappingPath = parser.get("idMappingPath");
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log.info("idMappingPath: {}", idMappingPath);
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final String idMappingPath = parser.get("idMappingPath");
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log.info("idMappingPath: {}", idMappingPath);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
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}
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final SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
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}
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/**
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* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
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* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
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*
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* @param spark the SparkSession
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* @param graphBasePath base graph path providing the set of relations to patch
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* @param workingDir intermediate storage location
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* @param idMappingPath dataset providing the old -> new identifier mapping
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*/
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private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) {
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/**
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* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
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* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
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*
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* @param spark the SparkSession
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* @param graphBasePath base graph path providing the set of relations to patch
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* @param workingDir intermediate storage location
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* @param idMappingPath dataset providing the old -> new identifier mapping
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*/
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private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir,
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final String idMappingPath) {
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final String relationPath = graphBasePath + "/relation";
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final String relationPath = graphBasePath + "/relation";
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final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
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final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
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final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
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final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
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log.info("relations: {}", rels.count());
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log.info("idMapping: {}", idMapping.count());
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log.info("relations: {}", rels.count());
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log.info("idMapping: {}", idMapping.count());
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rels
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.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setSource);
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return r;
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}, Encoders.bean(Relation.class))
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.joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setTarget);
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return r;
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}, Encoders.bean(Relation.class))
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.map(
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(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
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Encoders.STRING())
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(workingDir);
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final Dataset<Relation> bySource = rels
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.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional
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.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setSource);
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return r;
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}, Encoders.bean(Relation.class));
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spark.read().textFile(workingDir)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(relationPath);
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}
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bySource
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.joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional
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.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setTarget);
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return r;
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}, Encoders.bean(Relation.class))
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.map(
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(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
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Encoders.STRING())
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(workingDir);
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spark
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.read()
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.textFile(workingDir)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(relationPath);
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}
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}
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@ -1,24 +1,25 @@
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package eu.dnetlib.dhp.oa.graph.raw.common;
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public class RelationIdMapping {
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private String oldId;
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private String oldId;
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private String newId;
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private String newId;
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public String getOldId() {
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return oldId;
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}
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public String getOldId() {
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return oldId;
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}
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public void setOldId(final String oldId) {
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this.oldId = oldId;
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}
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public void setOldId(final String oldId) {
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this.oldId = oldId;
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}
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public String getNewId() {
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return newId;
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}
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public String getNewId() {
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return newId;
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}
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public void setNewId(final String newId) {
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this.newId = newId;
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}
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public void setNewId(final String newId) {
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this.newId = newId;
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}
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}
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@ -1,89 +1,115 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.Optional;
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class PatchRelationApplicationTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static final String ID_MAPPING_PATH = "map/id_mapping.json";
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static final String ID_MAPPING_PATH = "map/id_mapping.json";
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private static SparkSession spark;
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private static SparkSession spark;
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private static Path workingDir;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
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private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(PatchRelationApplicationTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(PatchRelationApplicationTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(PatchRelationApplicationTest.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(PatchRelationApplicationTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(PatchRelationApplicationTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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spark = SparkSession
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.builder()
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.appName(PatchRelationApplicationTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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FileUtils.copyInputStreamToFile(
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PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
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workingDir.resolve(ID_MAPPING_PATH).toFile()
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);
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FileUtils
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.copyInputStreamToFile(
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PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
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workingDir.resolve(ID_MAPPING_PATH).toFile());
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FileUtils.copyInputStreamToFile(
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PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
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workingDir.resolve("graphBasePath/relation/rels.json").toFile()
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);
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FileUtils
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.copyInputStreamToFile(
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PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
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workingDir.resolve("graphBasePath/relation/rels.json").toFile());
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}
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}
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@BeforeEach
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public void setUp() throws IOException {
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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public void testPatchRelationApplication() throws Exception {
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}
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final String graphBasePath = workingDir.toString() + "/graphBasePath";
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PatchRelationsApplication.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-graphBasePath", graphBasePath,
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"-workingDir", workingDir.toString() + "/workingDir",
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"-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
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});
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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final List<Relation> rels = spark
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.read()
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.textFile(graphBasePath + "/relation")
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.map(
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(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
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Encoders.bean(Relation.class))
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.collectAsList();
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@Test
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public void testPatchRelationApplication() throws Exception {
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assertEquals(6, rels.size());
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PatchRelationsApplication.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-graphBasePath", workingDir.toString() + "/graphBasePath",
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"-workingDir", workingDir.toString() + "/workingDir",
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"-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
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});
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assertEquals(0, getCount(rels, "1a"), "should be patched to 1b");
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assertEquals(0, getCount(rels, "2a"), "should be patched to 2b");
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}
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assertEquals(2, getCount(rels, "10a"), "not included in patching");
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assertEquals(2, getCount(rels, "20a"), "not included in patching");
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assertEquals(2, getCount(rels, "15a"), "not included in patching");
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assertEquals(2, getCount(rels, "25a"), "not included in patching");
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assertEquals(2, getCount(rels, "1b"), "patched from 1a");
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assertEquals(2, getCount(rels, "2b"), "patched from 2a");
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}
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private long getCount(List<Relation> rels, final String id) {
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return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count();
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}
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}
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