From 6135096ef119c9fc399f38f143a41ca863442c3c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Apr 2020 10:57:50 +0200 Subject: [PATCH] refactoring --- .../CountryPropagationJobTest.java | 270 +++++++++++------ .../OrcidPropagationJobTest.java | 233 +++++++++------ .../Result2OrganizationJobTest.java | 274 +++++++++++++----- 3 files changed, 517 insertions(+), 260 deletions(-) diff --git a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java index db8e3fd99f..675bb39179 100644 --- a/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java +++ b/dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java @@ -1,10 +1,13 @@ package eu.dnetlib.dhp.countrypropagation; -import com.google.gson.Gson; -import eu.dnetlib.dhp.schema.common.ModelSupport; +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Software; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.List; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -16,18 +19,8 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import scala.Array; 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; -import java.util.stream.Collectors; - public class CountryPropagationJobTest { private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class); @@ -54,13 +47,11 @@ public class CountryPropagationJobTest { conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(CountryPropagationJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - - + spark = + SparkSession.builder() + .appName(CountryPropagationJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -69,95 +60,190 @@ public class CountryPropagationJobTest { spark.stop(); } - @Test + @Test public void testCountryPropagationSoftware() throws Exception { - SparkCountryPropagationJob2.main(new String[]{ - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/countrypropagation/sample/software").getPath(), - "-hive_metastore_uris", "", - "-writeUpdate","false", - "-saveGraph","true", - "-resultTableName","eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath",workingDir.toString() + "/software", - "-preparedInfoPath", getClass().getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo").getPath(), - }); + SparkCountryPropagationJob2.main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software") + .getPath(), + "-hive_metastore_uris", + "", + "-saveGraph", + "true", + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Software", + "-outputPath", + workingDir.toString() + "/software", + "-preparedInfoPath", + getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo") + .getPath(), + }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc.textFile(workingDir.toString()+"/software") - .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + JavaRDD tmp = + sc.textFile(workingDir.toString() + "/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); - //tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); + // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); Assertions.assertEquals(10, tmp.count()); - Dataset verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); + Dataset verificationDs = + spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); - Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count()); - Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count()); - Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count()); - Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count()); + Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count()); + Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count()); + Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count()); + Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count()); + Dataset countryExploded = + verificationDs + .flatMap(row -> row.getCountry().iterator(), Encoders.bean(Country.class)) + .map(c -> c.getClassid(), Encoders.STRING()); - Dataset countryExploded = verificationDs - .flatMap(row -> row.getCountry().iterator(), Encoders.bean(Country.class)) - .map(c -> c.getClassid(), Encoders.STRING()); + Assertions.assertEquals(9, countryExploded.count()); - Assertions.assertEquals(9, countryExploded.count()); + Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count()); + Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count()); + Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count()); + Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count()); + Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count()); + Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count()); + Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count()); - Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count()); - Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count()); - Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count()); - Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count()); - Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count()); - Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count()); - Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count()); + Dataset> countryExplodedWithCountryclassid = + verificationDs.flatMap( + row -> { + List> prova = new ArrayList(); + List country_list = row.getCountry(); + country_list.stream() + .forEach( + c -> + prova.add( + new Tuple2<>( + row.getId(), c.getClassid()))); + return prova.iterator(); + }, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - Dataset> countryExplodedWithCountryclassid = verificationDs - .flatMap(row -> { - List> prova = new ArrayList(); - List country_list = row.getCountry(); - country_list.stream().forEach(c -> prova.add(new Tuple2<>(row.getId(), c.getClassid()))); - return prova.iterator(); - }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + Assertions.assertEquals(9, countryExplodedWithCountryclassid.count()); - Assertions.assertEquals(9, countryExplodedWithCountryclassid.count()); + countryExplodedWithCountryclassid.show(false); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ") + .count()); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ") + .count()); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassid + .filter( + "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ") + .count()); - countryExplodedWithCountryclassid.show(false); - Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ").count()); - Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ").count()); - Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ").count()); + Dataset> countryExplodedWithCountryclassname = + verificationDs.flatMap( + row -> { + List> prova = new ArrayList(); + List country_list = row.getCountry(); + country_list.stream() + .forEach( + c -> + prova.add( + new Tuple2<>( + row.getId(), + c.getClassname()))); + return prova.iterator(); + }, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - Dataset> countryExplodedWithCountryclassname = verificationDs - .flatMap(row -> { - List> prova = new ArrayList(); - List country_list = row.getCountry(); - country_list.stream().forEach(c -> prova.add(new Tuple2<>(row.getId(), c.getClassname()))); - return prova.iterator(); - }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + countryExplodedWithCountryclassname.show(false); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ") + .count()); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ") + .count()); + Assertions.assertEquals( + 1, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ") + .count()); + Assertions.assertEquals( + 2, + countryExplodedWithCountryclassname + .filter( + "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ") + .count()); - countryExplodedWithCountryclassname.show(false); - Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ").count()); - Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ").count()); - Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ").count()); - Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ").count()); - - Dataset> countryExplodedWithCountryProvenance = verificationDs - .flatMap(row -> { - List> prova = new ArrayList(); - List country_list = row.getCountry(); - country_list.stream().forEach(c -> prova.add(new Tuple2<>(row.getId(), c.getDataInfo().getInferenceprovenance()))); - return prova.iterator(); - }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - - Assertions.assertEquals(7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count()); - } + Dataset> countryExplodedWithCountryProvenance = + verificationDs.flatMap( + row -> { + List> prova = new ArrayList(); + List country_list = row.getCountry(); + country_list.stream() + .forEach( + c -> + prova.add( + new Tuple2<>( + row.getId(), + c.getDataInfo() + .getInferenceprovenance()))); + return prova.iterator(); + }, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + Assertions.assertEquals( + 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count()); + } } - - 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 b666846ef7..4292f3b057 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 @@ -1,8 +1,10 @@ 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 java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -17,23 +19,18 @@ 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 Logger log = LoggerFactory.getLogger(OrcidPropagationJobTest.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader(); + private static final ClassLoader cl = OrcidPropagationJobTest.class.getClassLoader(); private static SparkSession spark; private static Path workingDir; - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files.createTempDirectory(OrcidPropagationJobTest.class.getSimpleName()); @@ -49,13 +46,11 @@ public class OrcidPropagationJobTest { 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(); - + spark = + SparkSession.builder() + .appName(OrcidPropagationJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -64,132 +59,194 @@ public class OrcidPropagationJobTest { 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() - }); + 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)); + 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)); + // 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)); + 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'"; + 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() - }); + 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)); + 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)); + // 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)); + 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'"; + 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( + "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() - }); + 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)); + 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)); + 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'"; + 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()); + 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 "; + 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()); - + 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()); } - } 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 61366b6d73..2b2f64a333 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 @@ -2,6 +2,9 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Relation; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -16,10 +19,6 @@ 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); @@ -32,10 +31,11 @@ public class Result2OrganizationJobTest { private static Path workingDir; - @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName()); + workingDir = + Files.createTempDirectory( + SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -48,13 +48,11 @@ public class Result2OrganizationJobTest { 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(); - + spark = + SparkSession.builder() + .appName(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -65,109 +63,225 @@ public class Result2OrganizationJobTest { /** * 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(), - }); + 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)); + 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) + * 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(), - }); + 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)); + 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()); + 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()); + 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(), - }); + 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)); + 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)); + 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( + 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( + 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'") + .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()); + 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()); } - - }