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Patch the identifiers (source/target) in the relations, refinements #131

Merged
claudio.atzori merged 6 commits from fct_project_id_replacement into master 2021-07-30 11:07:54 +02:00
Conversation 0 Commits 6 Files Changed 5 +198 -162
4 changed files with 198 additions and 162 deletions
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Showing only changes of commit a6a38cca9e - Show all commits

53
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
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@ -1,10 +1,12 @@
package eu.dnetlib.dhp.oa.graph.raw;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
import eu.dnetlib.dhp.schema.oaf.Relation;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.FileNotFoundException;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -15,14 +17,15 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
import java.io.FileNotFoundException;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class PatchRelationsApplication {
private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
@ -33,12 +36,12 @@ public class PatchRelationsApplication {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Optional.ofNullable(
Optional
.ofNullable(
PatchRelationsApplication.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
.orElseThrow(FileNotFoundException::new)
));
.orElseThrow(FileNotFoundException::new)));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
@ -72,7 +75,8 @@ public class PatchRelationsApplication {
* @param workingDir intermediate storage location
* @param idMappingPath dataset providing the old -> new identifier mapping
*/
private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) {
private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir,
final String idMappingPath) {
final String relationPath = graphBasePath + "/relation";
@ -82,19 +86,23 @@ public class PatchRelationsApplication {
log.info("relations: {}", rels.count());
log.info("idMapping: {}", idMapping.count());
rels
final Dataset<Relation> bySource = rels
.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
final Relation r = t._1();
Optional.ofNullable(t._2())
Optional
.ofNullable(t._2())
.map(RelationIdMapping::getNewId)
.ifPresent(r::setSource);
return r;
}, Encoders.bean(Relation.class))
.joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left")
}, Encoders.bean(Relation.class));
bySource
.joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left")
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
final Relation r = t._1();
Optional.ofNullable(t._2())
Optional
.ofNullable(t._2())
.map(RelationIdMapping::getNewId)
.ifPresent(r::setTarget);
return r;
@ -107,12 +115,13 @@ public class PatchRelationsApplication {
.option("compression", "gzip")
.text(workingDir);
spark.read().textFile(workingDir)
spark
.read()
.textFile(workingDir)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(relationPath);
}
}

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
public class RelationIdMapping {

76
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java
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@ -1,21 +1,27 @@
package eu.dnetlib.dhp.oa.graph.raw;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Optional;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PatchRelationApplicationTest {
@ -50,21 +56,15 @@ public class PatchRelationApplicationTest {
.config(conf)
.getOrCreate();
FileUtils.copyInputStreamToFile(
FileUtils
.copyInputStreamToFile(
PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
workingDir.resolve(ID_MAPPING_PATH).toFile()
);
workingDir.resolve(ID_MAPPING_PATH).toFile());
FileUtils.copyInputStreamToFile(
FileUtils
.copyInputStreamToFile(
PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
workingDir.resolve("graphBasePath/relation/rels.json").toFile()
);
}
@BeforeEach
public void setUp() throws IOException {
workingDir.resolve("graphBasePath/relation/rels.json").toFile());
}
@ -77,13 +77,39 @@ public class PatchRelationApplicationTest {
@Test
public void testPatchRelationApplication() throws Exception {
final String graphBasePath = workingDir.toString() + "/graphBasePath";
PatchRelationsApplication.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphBasePath", workingDir.toString() + "/graphBasePath",
"-graphBasePath", graphBasePath,
"-workingDir", workingDir.toString() + "/workingDir",
"-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
});
final List<Relation> rels = spark
.read()
.textFile(graphBasePath + "/relation")
.map(
(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
Encoders.bean(Relation.class))
.collectAsList();
assertEquals(6, rels.size());
assertEquals(0, getCount(rels, "1a"), "should be patched to 1b");
assertEquals(0, getCount(rels, "2a"), "should be patched to 2b");
assertEquals(2, getCount(rels, "10a"), "not included in patching");
assertEquals(2, getCount(rels, "20a"), "not included in patching");
assertEquals(2, getCount(rels, "15a"), "not included in patching");
assertEquals(2, getCount(rels, "25a"), "not included in patching");
assertEquals(2, getCount(rels, "1b"), "patched from 1a");
assertEquals(2, getCount(rels, "2b"), "patched from 2a");
}
private long getCount(List<Relation> rels, final String id) {
return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count();
}
}