From a97e915c24f4943af5fa1323d30cc10778384d90 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 16 Apr 2020 11:05:21 +0200 Subject: [PATCH] test unit for propagation of result to organization from institutional repository --- .../Result2OrganizationJobTest.java | 169 ++++++++++++++++++ 1 file changed, 169 insertions(+) diff --git a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/Result2OrganizationJobTest.java b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/Result2OrganizationJobTest.java index bc21423143..61366b6d73 100644 --- a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/Result2OrganizationJobTest.java +++ b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/Result2OrganizationJobTest.java @@ -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 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 tmp = sc.textFile(workingDir.toString()+"/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + Assertions.assertEquals(20, tmp.count()); + + Dataset 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 tmp = sc.textFile(workingDir.toString()+"/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + Dataset 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()); + } + + }