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This commit is contained in:
Miriam Baglioni 2021-12-13 15:01:40 +01:00
parent 4bb1d43afc
commit 8d755cca80
9 changed files with 94 additions and 76 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java
View File

@ -41,7 +41,7 @@ public class CreateContextEntities implements Serializable {
.toString(
CreateContextEntities.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java
View File

@ -48,7 +48,7 @@ public class CreateContextRelation implements Serializable {
.requireNonNull(
CreateContextRelation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")));
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java
View File

@ -31,7 +31,7 @@ public class SparkCollectAndSave implements Serializable {
.toString(
SparkCollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java
View File

@ -22,7 +22,7 @@ public class SparkDumpEntitiesJob implements Serializable {
.toString(
SparkDumpEntitiesJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/wf/input_parameters.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java
View File

@ -38,7 +38,7 @@ public class SparkDumpRelationJob implements Serializable {
.toString(
SparkDumpRelationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
@ -55,13 +55,12 @@ public class SparkDumpRelationJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
Optional<String> rs = Optional.ofNullable(parser.get("removeSet"));
Optional<String> rs = Optional.ofNullable(parser.get("removeSet"));
final Set<String> removeSet = new HashSet<>();
if(rs.isPresent()){
if (rs.isPresent()) {
Collections.addAll(removeSet, rs.get().split(";"));
}
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -78,7 +77,7 @@ public class SparkDumpRelationJob implements Serializable {
private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set<String> removeSet) {
Dataset<Relation> relations = Utils.readPath(spark, inputPath, Relation.class);
relations
.filter((FilterFunction<Relation>)r -> !removeSet.contains(r.getRelClass()))
.filter((FilterFunction<Relation>) r -> !removeSet.contains(r.getRelClass()))
.map((MapFunction<Relation, eu.dnetlib.dhp.schema.dump.oaf.graph.Relation>) relation -> {
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
relNew

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java
View File

@ -39,7 +39,7 @@ public class SparkOrganizationRelation implements Serializable {
.toString(
SparkOrganizationRelation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java
View File

@ -35,7 +35,7 @@ public class SparkSelectValidRelationsJob implements Serializable {
.toString(
SparkSelectValidRelationsJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

49
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -917,7 +917,7 @@ public class DumpJobTest {
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -949,18 +949,45 @@ public class DumpJobTest {
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
temp = spark
.sql(
"select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " +
"from check " +
"lateral view explode (instance) i as inst " +
"where inst.articleprocessingcharge is not null");
.sql(
"select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " +
"from check " +
"lateral view explode (instance) i as inst " +
"where inst.articleprocessingcharge is not null");
Assertions
.assertEquals(
"3131.64",
temp
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
.collectAsList()
.get(0)
.getString(1));
Assertions
.assertEquals(
"EUR",
temp
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
.collectAsList()
.get(0)
.getString(2));
Assertions.assertEquals("3131.64", temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").collectAsList().get(0).getString(1));
Assertions.assertEquals("EUR", temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").collectAsList().get(0).getString(2));
Assertions.assertEquals("2578.35", temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").collectAsList().get(0).getString(1));
Assertions.assertEquals("EUR", temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").collectAsList().get(0).getString(2));
Assertions
.assertEquals(
"2578.35",
temp
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
.collectAsList()
.get(0)
.getString(1));
Assertions
.assertEquals(
"EUR",
temp
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
.collectAsList()
.get(0)
.getString(2));
}
}

100
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java
View File

@ -4,10 +4,8 @@ package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -83,7 +81,6 @@ public class DumpRelationTest {
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
@ -145,7 +142,6 @@ public class DumpRelationTest {
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
@ -207,105 +203,101 @@ public class DumpRelationTest {
@Test
public void test3() throws Exception {//
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
.getPath();
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
.getPath();
SparkDumpRelationJob.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-removeSet", "isParticipant"
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-removeSet", "isParticipant"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
verificationDataset.createOrReplaceTempView("table");
verificationDataset
.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
Dataset<Row> check = spark
.sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
+
"from table ");
.sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
+
"from table ");
Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count());
Assertions
.assertEquals(
22, check
.filter(
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
"provenance = 'Harvested'")
.count());
.assertEquals(
22, check
.filter(
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
"provenance = 'Harvested'")
.count());
Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count());
Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count());
Assertions
.assertEquals(
1, check
.filter(
"name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " +
"and provenance = 'Inferred by OpenAIRE'")
.count());
.assertEquals(
1, check
.filter(
"name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " +
"and provenance = 'Inferred by OpenAIRE'")
.count());
}
@Test
public void test4() throws Exception {//
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
.getPath();
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
.getPath();
SparkDumpRelationJob.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-removeSet", "isParticipant;isAuthorInstitutionOf"
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-removeSet", "isParticipant;isAuthorInstitutionOf"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
verificationDataset.createOrReplaceTempView("table");
verificationDataset
.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
Dataset<Row> check = spark
.sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
+
"from table ");
.sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
+
"from table ");
Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count());
Assertions
.assertEquals(
22, check
.filter(
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
"provenance = 'Harvested'")
.count());
.assertEquals(
22, check
.filter(
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
"provenance = 'Harvested'")
.count());
Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count());
Assertions.assertEquals(0, check.filter("name = 'isAuthorInstitutionOf'").count());
}