From 8c079c7a49ce4c27b62445e2dedae3f25a461492 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 17 Apr 2020 16:53:03 +0200 Subject: [PATCH] unit test for orcid to result propagation from semrel --- .../OrcidPropagationJobTest.java | 191 ++++++++++++++++++ 1 file changed, 191 insertions(+) diff --git a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index a01b6d2dd..b666846ef 100644 --- a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -1,4 +1,195 @@ package eu.dnetlib.dhp.orcidtoresultfromsemrel; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.Result2OrganizationJobTest; +import eu.dnetlib.dhp.schema.oaf.Dataset; +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.Encoders; +import org.apache.spark.sql.Row; +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 OrcidPropagationJobTest { + + 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(OrcidPropagationJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(OrcidPropagationJobTest.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(OrcidPropagationJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + + @Test + public void noUpdateTest()throws Exception{ + SparkOrcidToResultFromSemRelJob3.main(new String[]{ + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate").getPath(), + "-hive_metastore_uris", "", + "-saveGraph","true", + "-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath",workingDir.toString() + "/dataset", + "-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc.textFile(workingDir.toString()+"/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + //tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); + + Assertions.assertEquals(10, tmp.count()); + + org.apache.spark.sql.Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id " + + "from dataset " + + "lateral view explode(author) a as MyT " + + "lateral view explode(MyT.pid) p as MyP " + + "where MyP.datainfo.inferenceprovenance = 'propagation'"; + + Assertions.assertEquals(0, spark.sql(query).count()); + } + + @Test + public void oneUpdateTest() throws Exception{ + SparkOrcidToResultFromSemRelJob3.main(new String[]{ + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate").getPath(), + "-hive_metastore_uris", "", + "-saveGraph","true", + "-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath",workingDir.toString() + "/dataset", + "-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc.textFile(workingDir.toString()+"/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + //tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); + + Assertions.assertEquals(10, tmp.count()); + + org.apache.spark.sql.Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " + + "from dataset " + + "lateral view explode(author) a as MyT " + + "lateral view explode(MyT.pid) p as MyP " + + "where MyP.datainfo.inferenceprovenance = 'propagation'"; + + org.apache.spark.sql.Dataset propagatedAuthors = spark.sql(query); + + Assertions.assertEquals(1, propagatedAuthors.count()); + + Assertions.assertEquals(1, propagatedAuthors.filter("id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' " + + "and name = 'Vajinder' and surname = 'Kumar' and pidType = 'ORCID'").count()); + + Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count()); + + } + + @Test + public void twoUpdatesTest() throws Exception{ + SparkOrcidToResultFromSemRelJob3.main(new String[]{ + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/twoupdates").getPath(), + "-hive_metastore_uris", "", + "-saveGraph","true", + "-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath",workingDir.toString() + "/dataset", + "-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc.textFile(workingDir.toString()+"/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + org.apache.spark.sql.Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " + + "from dataset " + + "lateral view explode(author) a as MyT " + + "lateral view explode(MyT.pid) p as MyP " + + "where MyP.datainfo.inferenceprovenance = 'propagation'"; + + org.apache.spark.sql.Dataset propagatedAuthors = spark.sql(query); + + Assertions.assertEquals(2, propagatedAuthors.count()); + + Assertions.assertEquals(1, propagatedAuthors.filter("name = 'Marc' and surname = 'Schmidtmann'").count()); + Assertions.assertEquals(1, propagatedAuthors.filter("name = 'Ruediger' and surname = 'Beckhaus'").count()); + + query = "select id, MyT.name name, MyT.surname surname, MyP.value pid ,MyP.qualifier.classid pidType " + + "from dataset " + + "lateral view explode(author) a as MyT " + + "lateral view explode(MyT.pid) p as MyP "; + + org.apache.spark.sql.Dataset authorsExplodedPids = spark.sql(query); + + Assertions.assertEquals(2, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann'").count()); + Assertions.assertEquals(1, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann' and pidType = 'MAG Identifier'").count()); + + } + }