test unit for result to project propagation

This commit is contained in:
Miriam Baglioni 2020-04-14 15:28:00 +02:00
parent 8f12292daa
commit 4b01dc60e6
2 changed files with 194 additions and 0 deletions

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package eu.dnetlib.dhp.projecttoresult;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
import eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
public class ProjectPropagationJobTest {
private static final Logger log = LoggerFactory.getLogger(ProjectPropagationJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = ProjectPropagationJobTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(ProjectPropagationJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(ProjectPropagationJobTest.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(ProjectPropagationJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
/**
* There are no new relations to be added. All the possible relations have already been linked with the project in the graph
* @throws Exception
*/
@Test
public void NoUpdateTest() throws Exception {
SparkResultToProjectThroughSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/sample/relation").getPath(),
"-hive_metastore_uris", "",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-potentialUpdatePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/noupdates/potentialUpdates").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(0, tmp.count());
}
/**
* All the possible updates will produce a new relation. No relations are already linked in the grpha
* @throws Exception
*/
@Test
public void UpdateTenTest() throws Exception{
SparkResultToProjectThroughSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/sample/relation").getPath(),
"-hive_metastore_uris", "",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-potentialUpdatePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/tenupdates/potentialUpdates").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
//got 20 new relations because "produces" and "isProducedBy" are added
Assertions.assertEquals(20, tmp.count());
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(10, verificationDs.filter("relClass = 'produces'").count());
Assertions.assertEquals(10, verificationDs.filter("relClass = 'isProducedBy'").count());
Assertions.assertEquals(10, verificationDs.filter(r -> r.getSource().substring(0, 2). equals("50") &&
r.getTarget().substring(0,2).equals("40") &&
r.getRelClass().equals("isProducedBy")).count());
Assertions.assertEquals(10, verificationDs.filter(r -> r.getSource().substring(0, 2). equals("40") &&
r.getTarget().substring(0,2).equals("50") &&
r.getRelClass().equals("produces")).count());
verificationDs.createOrReplaceTempView("temporary");
Assertions.assertEquals(20, spark.sql("Select * from temporary where datainfo.inferenceprovenance = 'propagation'").count());
}
/**
* One of the relations in the possible updates is already linked to the project in the graph.
* All the others are not. There will be 9 new associations leading to 18 new relations
* @throws Exception
*/
@Test
public void UpdateMixTest() throws Exception{
SparkResultToProjectThroughSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/sample/relation").getPath(),
"-hive_metastore_uris", "",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-potentialUpdatePath", getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/updatesmixed/potentialUpdates").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
// JavaRDD<Relation> tmp = sc.textFile("/tmp/relation")
// .map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
//got 20 new relations because "produces" and "isProducedBy" are added
Assertions.assertEquals(18, tmp.count());
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(9, verificationDs.filter("relClass = 'produces'").count());
Assertions.assertEquals(9, verificationDs.filter("relClass = 'isProducedBy'").count());
Assertions.assertEquals(9, verificationDs.filter(r -> r.getSource().substring(0, 2). equals("50") &&
r.getTarget().substring(0,2).equals("40") &&
r.getRelClass().equals("isProducedBy")).count());
Assertions.assertEquals(9, verificationDs.filter(r -> r.getSource().substring(0, 2). equals("40") &&
r.getTarget().substring(0,2).equals("50") &&
r.getRelClass().equals("produces")).count());
verificationDs.createOrReplaceTempView("temporary");
Assertions.assertEquals(18, spark.sql("Select * from temporary where datainfo.inferenceprovenance = 'propagation'").count());
}
}