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test unit for propagation of result to organization from institutional repository

This commit is contained in:
Miriam Baglioni 2020-04-16 11:05:21 +02:00
parent b078710924
commit a97e915c24
1 changed files with 169 additions and 0 deletions
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169
dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/Result2OrganizationJobTest.java
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@ -1,4 +1,173 @@
package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.io.FileUtils;
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 java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
public class Result2OrganizationJobTest {
private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SparkResultToOrganizationFromIstRepoJob2.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(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
/**
* No modifications done to the sample sets, so that no possible updates are created
* @throws Exception
*/
@Test
public void NoUpdateTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(),
"-hive_metastore_uris", "",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/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());
}
/**
* Testing set with modified association between datasource and organization. Copied some hostedby collectedfrom
* from the software sample set. No intersection with the already linked (all the possible new relations, will became
* new relations)
* @throws Exception
*/
@Test
public void UpdateNoMixTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(),
"-hive_metastore_uris", "",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/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(20, tmp.count());
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(8, verificationDs.filter("target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2'").count());
Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091'").count());
Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::4429502fa1936b0941f4647b69b844c8'").count());
Assertions.assertEquals(2, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and " +
"(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' " +
"or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')").count());
}
@Test
public void UpdateMixTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix").getPath(),
"-hive_metastore_uris", "",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate", "false",
"-saveGraph", "true",
"-outputPath", workingDir.toString() + "/relation",
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization").getPath(),
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/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));
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(8, verificationDs.count());
Assertions.assertEquals(2, verificationDs.filter("source = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6'").count());
Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218'").count());
Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523'").count());
Assertions.assertEquals(1, verificationDs.filter("source = '20|wt__________::a72760363ca885e6bef165804770e00c'").count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and substring(source, 1,2) = '50'").count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and substring(source, 1,2) = '20'").count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and " +
"substring(source, 1,2) = '50' and substring(target, 1, 2) = '20'").count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and " +
"substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'").count());
}
}