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

Reviewed-on: #131
This commit is contained in:
Claudio Atzori 2021-07-30 11:07:54 +02:00
parent 6e3554a45e 4f78565c04
commit 5219d56be5
5 changed files with 237 additions and 98 deletions
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180
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; 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.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FilterFunction;
@ -15,101 +17,111 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; 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 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 { public class PatchRelationsApplication {
private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class); private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser( final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils IOUtils
.toString( .toString(
Optional.ofNullable( Optional
PatchRelationsApplication.class .ofNullable(
.getResourceAsStream( PatchRelationsApplication.class
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json")) .getResourceAsStream(
.orElseThrow(FileNotFoundException::new) "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
)); .orElseThrow(FileNotFoundException::new)));
parser.parseArgument(args); parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional final Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged")) .ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String graphBasePath = parser.get("graphBasePath"); final String graphBasePath = parser.get("graphBasePath");
log.info("graphBasePath: {}", graphBasePath); log.info("graphBasePath: {}", graphBasePath);
final String workingDir = parser.get("workingDir"); final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir); log.info("workingDir: {}", workingDir);
final String idMappingPath = parser.get("idMappingPath"); final String idMappingPath = parser.get("idMappingPath");
log.info("idMappingPath: {}", idMappingPath); log.info("idMappingPath: {}", idMappingPath);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath)); spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
} }
/** /**
* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location. * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
* *
* @param spark the SparkSession * @param spark the SparkSession
* @param graphBasePath base graph path providing the set of relations to patch * @param graphBasePath base graph path providing the set of relations to patch
* @param workingDir intermediate storage location * @param workingDir intermediate storage location
* @param idMappingPath dataset providing the old -> new identifier mapping * @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 String relationPath = graphBasePath + "/relation";
final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class); final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
rels log.info("relations: {}", rels.count());
.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") log.info("idMapping: {}", idMapping.count());
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
final Relation r = t._1();
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")
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
final Relation r = t._1();
Optional.ofNullable(t._2())
.map(RelationIdMapping::getNewId)
.ifPresent(r::setTarget);
return r;
}, Encoders.bean(Relation.class))
.map(
(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(workingDir);
spark.read().textFile(workingDir) final Dataset<Relation> bySource = rels
.write() .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
.mode(SaveMode.Overwrite) .map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
.option("compression", "gzip") final Relation r = t._1();
.text(relationPath); Optional
} .ofNullable(t._2())
.map(RelationIdMapping::getNewId)
.ifPresent(r::setSource);
return r;
}, 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())
.map(RelationIdMapping::getNewId)
.ifPresent(r::setTarget);
return r;
}, Encoders.bean(Relation.class))
.map(
(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(workingDir);
spark
.read()
.textFile(workingDir)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(relationPath);
}
} }

29
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java
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@ -1,24 +1,25 @@
package eu.dnetlib.dhp.oa.graph.raw.common; package eu.dnetlib.dhp.oa.graph.raw.common;
public class RelationIdMapping { public class RelationIdMapping {
private String oldId; private String oldId;
private String newId; private String newId;
public String getOldId() { public String getOldId() {
return oldId; return oldId;
} }
public void setOldId(final String oldId) { public void setOldId(final String oldId) {
this.oldId = oldId; this.oldId = oldId;
} }
public String getNewId() { public String getNewId() {
return newId; return newId;
} }
public void setNewId(final String newId) { public void setNewId(final String newId) {
this.newId = newId; this.newId = newId;
} }
} }

115
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java Normal file
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@ -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();
}
}

5
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json Normal file
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@ -0,0 +1,5 @@
{"oldId": "1a", "newId": "1b"}
{"oldId": "2a", "newId": "2b"}
{"oldId": "3a", "newId": "3b"}
{"oldId": "4a", "newId": "4b"}
{"oldId": "5a", "newId": "5b"}

6
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json Normal file
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@ -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":[]}