forked from D-Net/dnet-hadoop
test unit for propagation of result to organization from institutional repository
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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public class Result2OrganizationJobTest {
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public class Result2OrganizationJobTest {
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private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader();
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private static SparkSession spark;
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private static Path workingDir;
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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/**
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* No modifications done to the sample sets, so that no possible updates are created
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* @throws Exception
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*/
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@Test
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public void NoUpdateTest() throws Exception {
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SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
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"-isTest", Boolean.TRUE.toString(),
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(),
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"-hive_metastore_uris", "",
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"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
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"-writeUpdate", "false",
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"-saveGraph", "true",
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"-outputPath", workingDir.toString() + "/relation",
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"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization").getPath(),
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"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked").getPath(),
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
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Assertions.assertEquals(0, tmp.count());
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}
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/**
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* Testing set with modified association between datasource and organization. Copied some hostedby collectedfrom
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* from the software sample set. No intersection with the already linked (all the possible new relations, will became
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* new relations)
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* @throws Exception
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*/
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@Test
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public void UpdateNoMixTest() throws Exception {
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SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
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"-isTest", Boolean.TRUE.toString(),
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(),
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"-hive_metastore_uris", "",
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"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
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"-writeUpdate", "false",
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"-saveGraph", "true",
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"-outputPath", workingDir.toString() + "/relation",
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"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization").getPath(),
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"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked").getPath(),
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
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Assertions.assertEquals(20, tmp.count());
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Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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Assertions.assertEquals(8, verificationDs.filter("target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2'").count());
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Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091'").count());
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Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::4429502fa1936b0941f4647b69b844c8'").count());
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Assertions.assertEquals(2, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and " +
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"(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' " +
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"or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')").count());
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}
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@Test
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public void UpdateMixTest() throws Exception {
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SparkResultToOrganizationFromIstRepoJob2.main(new String[]{
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"-isTest", Boolean.TRUE.toString(),
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix").getPath(),
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"-hive_metastore_uris", "",
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"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software",
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"-writeUpdate", "false",
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"-saveGraph", "true",
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"-outputPath", workingDir.toString() + "/relation",
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"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization").getPath(),
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"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked").getPath(),
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
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Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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Assertions.assertEquals(8, verificationDs.count());
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Assertions.assertEquals(2, verificationDs.filter("source = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6'").count());
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Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218'").count());
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Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523'").count());
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Assertions.assertEquals(1, verificationDs.filter("source = '20|wt__________::a72760363ca885e6bef165804770e00c'").count());
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Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and substring(source, 1,2) = '50'").count());
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Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and substring(source, 1,2) = '20'").count());
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Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and " +
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"substring(source, 1,2) = '50' and substring(target, 1, 2) = '20'").count());
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Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and " +
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"substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'").count());
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}
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}
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}
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