fixed implementation of PatchRelationsApplication, refined the relative unit test
This commit is contained in:
parent
081fe92a21
commit
a6a38cca9e
|
|
@ -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;
|
||||
|
|
@ -15,104 +17,111 @@ 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);
|
||||
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 {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
Optional.ofNullable(
|
||||
PatchRelationsApplication.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
|
||||
.orElseThrow(FileNotFoundException::new)
|
||||
));
|
||||
parser.parseArgument(args);
|
||||
public static void main(final String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
Optional
|
||||
.ofNullable(
|
||||
PatchRelationsApplication.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
|
||||
.orElseThrow(FileNotFoundException::new)));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
log.info("graphBasePath: {}", graphBasePath);
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
log.info("graphBasePath: {}", graphBasePath);
|
||||
|
||||
final String workingDir = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingDir);
|
||||
final String workingDir = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingDir);
|
||||
|
||||
final String idMappingPath = parser.get("idMappingPath");
|
||||
log.info("idMappingPath: {}", idMappingPath);
|
||||
final String idMappingPath = parser.get("idMappingPath");
|
||||
log.info("idMappingPath: {}", idMappingPath);
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
|
||||
}
|
||||
final SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
|
||||
}
|
||||
|
||||
/**
|
||||
* 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.
|
||||
*
|
||||
* @param spark the SparkSession
|
||||
* @param graphBasePath base graph path providing the set of relations to patch
|
||||
* @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) {
|
||||
/**
|
||||
* 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.
|
||||
*
|
||||
* @param spark the SparkSession
|
||||
* @param graphBasePath base graph path providing the set of relations to patch
|
||||
* @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) {
|
||||
|
||||
final String relationPath = graphBasePath + "/relation";
|
||||
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);
|
||||
final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
|
||||
final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
|
||||
|
||||
log.info("relations: {}", rels.count());
|
||||
log.info("idMapping: {}", idMapping.count());
|
||||
log.info("relations: {}", rels.count());
|
||||
log.info("idMapping: {}", idMapping.count());
|
||||
|
||||
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())
|
||||
.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);
|
||||
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())
|
||||
.map(RelationIdMapping::getNewId)
|
||||
.ifPresent(r::setSource);
|
||||
return r;
|
||||
}, Encoders.bean(Relation.class));
|
||||
|
||||
spark.read().textFile(workingDir)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.text(relationPath);
|
||||
}
|
||||
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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,24 +1,25 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw.common;
|
||||
|
||||
public class RelationIdMapping {
|
||||
|
||||
private String oldId;
|
||||
private String oldId;
|
||||
|
||||
private String newId;
|
||||
private String newId;
|
||||
|
||||
public String getOldId() {
|
||||
return oldId;
|
||||
}
|
||||
public String getOldId() {
|
||||
return oldId;
|
||||
}
|
||||
|
||||
public void setOldId(final String oldId) {
|
||||
this.oldId = oldId;
|
||||
}
|
||||
public void setOldId(final String oldId) {
|
||||
this.oldId = oldId;
|
||||
}
|
||||
|
||||
public String getNewId() {
|
||||
return newId;
|
||||
}
|
||||
public String getNewId() {
|
||||
return newId;
|
||||
}
|
||||
|
||||
public void setNewId(final String newId) {
|
||||
this.newId = newId;
|
||||
}
|
||||
public void setNewId(final String newId) {
|
||||
this.newId = newId;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,89 +1,115 @@
|
|||
|
||||
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 {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
public static final String ID_MAPPING_PATH = "map/id_mapping.json";
|
||||
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 SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
|
||||
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);
|
||||
@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());
|
||||
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());
|
||||
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();
|
||||
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("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()
|
||||
);
|
||||
FileUtils
|
||||
.copyInputStreamToFile(
|
||||
PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
|
||||
workingDir.resolve("graphBasePath/relation/rels.json").toFile());
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException {
|
||||
@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
|
||||
});
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
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();
|
||||
|
||||
@Test
|
||||
public void testPatchRelationApplication() throws Exception {
|
||||
assertEquals(6, rels.size());
|
||||
|
||||
PatchRelationsApplication.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-graphBasePath", workingDir.toString() + "/graphBasePath",
|
||||
"-workingDir", workingDir.toString() + "/workingDir",
|
||||
"-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
|
||||
});
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,4 +3,4 @@
|
|||
{"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":[]}
|
||||
{"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":[]}
|
||||
Loading…
Reference in New Issue