Merge pull request 'Patch the identifiers (source/target) in the relations, refinements' (#131) from fct_project_id_replacement into master

Reviewed-on: D-Net/dnet-hadoop#131

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java

@@ -1,10 +1,12 @@
+
 package eu.dnetlib.dhp.oa.graph.raw;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
-import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import java.io.FileNotFoundException;
-import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
+import java.util.Objects;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+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
@@ -72,26 +75,34 @@ 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";
 
 		final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
 		final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
 
-        rels
+		log.info("relations: {}", rels.count());
+		log.info("idMapping: {}", idMapping.count());
+
+		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))
+			}, Encoders.bean(Relation.class));
-                .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left")
+
+		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;
@@ -104,12 +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);
 	}
 
-
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.oa.graph.raw.common;
 
 public class RelationIdMapping {

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java

@@ -0,0 +1,115 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+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.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 {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	public static final String ID_MAPPING_PATH = "map/id_mapping.json";
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+
+	private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(PatchRelationApplicationTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(PatchRelationApplicationTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(PatchRelationApplicationTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+
+		FileUtils
+			.copyInputStreamToFile(
+				PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
+				workingDir.resolve(ID_MAPPING_PATH).toFile());
+
+		FileUtils
+			.copyInputStreamToFile(
+				PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
+				workingDir.resolve("graphBasePath/relation/rels.json").toFile());
+
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	public void testPatchRelationApplication() throws Exception {
+
+		final String graphBasePath = workingDir.toString() + "/graphBasePath";
+		PatchRelationsApplication.main(new String[] {
+			"-isSparkSessionManaged", Boolean.FALSE.toString(),
+			"-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();
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json

@@ -0,0 +1,5 @@
+{"oldId": "1a", "newId": "1b"}
+{"oldId": "2a", "newId": "2b"}
+{"oldId": "3a", "newId": "3b"}
+{"oldId": "4a", "newId": "4b"}
+{"oldId": "5a", "newId": "5b"}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json

@@ -0,0 +1,6 @@
+{"source":"1a","target":"10a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"10a","target":"1a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}