From bb9f21d0e7ff48191f2dc4987557756ff739942b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 11 Jun 2020 10:20:05 +0200 Subject: [PATCH] job test for class producing first step of results dump --- .../dhp/oa/graph/dump/DumpJobTest.java | 812 ++++++++++++++++++ .../eu/dnetlib/dhp/oa/graph/dump/dataset.json | 136 +++ 2 files changed, 948 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/dataset.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java new file mode 100644 index 000000000..73c302b06 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -0,0 +1,812 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +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.dom4j.DocumentException; +import org.junit.jupiter.api.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; + +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import static org.mockito.Mockito.lenient; +import static org.mockito.Mockito.when; + +@ExtendWith(MockitoExtension.class) +public class DumpJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static String MOCK_IS_LOOK_UP_URL = "https://beta.services.openaire.eu/is/services/isLookUp"; + + private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); + + private static HashMap map = new HashMap<>(); + + static{ + map.put("egi", "EGI Federation"); + map.put("fet-fp7", "FET FP7"); + map.put("fet-h2020", "FET H2020"); + map.put("clarin", "CLARIN");map.put("fam", "Fisheries and Aquaculture Management");map.put("ni", "Neuroinformatics");map.put("mes", "European Marine Scinece");map.put("instruct", "Instruct-Eric"); + map.put("rda", "Research Data Alliance");map.put("elixir-gr", "ELIXIR GR");map.put("aginfra", "Agricultural and Food Sciences");map.put("dariah", "DARIAH EU");map.put("risis", "RISI"); + map.put("ee", "SDSN - Greece");map.put("oa-pg", "EC Post-Grant Open Access Pilot");map.put("beopen", "Transport Research");map.put("euromarine", "Euromarine");map.put("ifremer", "Ifremer"); + map.put("dh-ch", "Digital Humanities and Cultural Heritage");map.put("science-innovation-policy", "Science and Innovation Policy Studies");map.put("covid-19", "COVID-19");map.put("enrmaps", "Energy Research");map.put("epos", "EPOS"); + + + } + + List communityMap = Arrays.asList("", + "" , + "" , + "", + "", + "", + "" , + "", + "", + "", + "", + "" , + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + ""); + + @Mock + private SparkDumpCommunityProducts dumpCommunityProducts; + + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.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(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws ISLookUpException { + lenient().when(dumpCommunityProducts.getCommunityMap(MOCK_IS_LOOK_UP_URL)).thenReturn(map); + + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/dataset.json") + .getPath(); + dumpCommunityProducts + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-resultType","dataset", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-dumpTableName","eu.dnetlib.dhp.schema.dump.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.Dataset.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Dataset.class)); + + verificationDataset.show(false); + + + } + +// @Test +// public void bulktagBySubjectNoPreviousContextTest() throws Exception { +// final String sourcePath = getClass() +// .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") +// .getPath(); +// final String pathMap = DumpJobTest.pathMap; +// DumpJobTest +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", +// "-outputPath", workingDir.toString() + "/dataset", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// Assertions.assertEquals(5, spark.sql(query).count()); +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// Assertions +// .assertEquals( +// 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); +// Assertions +// .assertEquals( +// 5, +// idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count()); +// +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); +// +// Assertions +// .assertEquals( +// 1, +// idExplodeCommunity +// .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") +// .count()); +// Assertions +// .assertEquals( +// 1, +// idExplodeCommunity +// .filter( +// "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") +// .count()); +// +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") +// .count()); +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter( +// "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") +// .count()); +// +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") +// .count()); +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter( +// "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") +// .count()); +// } +// +// @Test +// public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { +// final String sourcePath = getClass() +// .getResource( +// "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") +// .getPath(); +// final String pathMap = BulkTagJobTest.pathMap; +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", +// "-outputPath", workingDir.toString() + "/dataset", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// 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.id community, MyD.provenanceaction.classid provenance " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyT.id = 'covid-19' "; +// +// Assertions.assertEquals(3, spark.sql(query).count()); +// +// org.apache.spark.sql.Dataset communityContext = spark.sql(query); +// +// Assertions +// .assertEquals( +// 2, +// communityContext +// .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") +// .count()); +// Assertions +// .assertEquals( +// 1, +// communityContext +// .filter( +// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'") +// .count()); +// Assertions +// .assertEquals( +// 1, +// communityContext +// .filter( +// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'") +// .count()); +// +// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " +// + "from dataset " +// + "lateral view explode (context) as MyT " +// + "where size(MyT.datainfo) > 0"; +// +// Assertions +// .assertEquals( +// 2, +// spark +// .sql(query) +// .select("datainfosize") +// .where( +// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a" +// + "nd community = 'covid-19'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// } +// +// @Test +// public void bulktagByDatasourceTest() throws Exception { +// final String sourcePath = getClass() +// .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") +// .getPath(); +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", +// "-outputPath", workingDir.toString() + "/publication", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); +// +// JavaRDD tmp = sc +// .textFile(workingDir.toString() + "/publication") +// .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); +// +// Assertions.assertEquals(10, tmp.count()); +// org.apache.spark.sql.Dataset verificationDataset = spark +// .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); +// +// verificationDataset.createOrReplaceTempView("publication"); +// +// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from publication " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// +// Assertions.assertEquals(5, idExplodeCommunity.count()); +// Assertions +// .assertEquals( +// 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); +// Assertions +// .assertEquals( +// 5, +// idExplodeCommunity +// .filter("name = 'Bulktagging for Community - Datasource'") +// .count()); +// +// Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); +// +// Assertions +// .assertEquals( +// 3, +// idExplodeCommunity +// .filter( +// "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' " +// + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' " +// + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") +// .count()); +// +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter( +// "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' " +// + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") +// .count()); +// } +// +// @Test +// public void bulktagByZenodoCommunityTest() throws Exception { +// final String sourcePath = getClass() +// .getResource( +// "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") +// .getPath(); +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", +// "-outputPath", workingDir.toString() + "/orp", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); +// +// JavaRDD tmp = sc +// .textFile(workingDir.toString() + "/orp") +// .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); +// +// Assertions.assertEquals(10, tmp.count()); +// org.apache.spark.sql.Dataset verificationDataset = spark +// .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class)); +// +// verificationDataset.createOrReplaceTempView("orp"); +// +// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from orp " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// Assertions.assertEquals(8, idExplodeCommunity.count()); +// +// Assertions +// .assertEquals( +// 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); +// Assertions +// .assertEquals( +// 8, +// idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count()); +// +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count()); +// +// Assertions +// .assertEquals( +// 1, +// idExplodeCommunity +// .filter( +// "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' " +// + "and community = 'covid-19'") +// .count()); +// Assertions +// .assertEquals( +// 3, +// idExplodeCommunity +// .filter( +// "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and " +// + "(community = 'aginfra' or community = 'mes' or community = 'fam')") +// .count()); +// Assertions +// .assertEquals( +// 1, +// idExplodeCommunity +// .filter( +// "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' " +// + "and community = 'beopen'") +// .count()); +// Assertions +// .assertEquals( +// 3, +// idExplodeCommunity +// .filter( +// "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and " +// + "(community = 'beopen' or community = 'fam' or community = 'mes')") +// .count()); +// +// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " +// + "from orp " +// + "lateral view explode (context) as MyT " +// + "where size(MyT.datainfo) > 0"; +// +// Assertions +// .assertEquals( +// 2, +// spark +// .sql(query) +// .select("datainfosize") +// .where( +// "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a" +// + "nd community = 'beopen'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// +// // verify the zenodo community context is not present anymore in the records +// query = "select id, MyT.id community " +// + "from orp " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD "; +// +// org.apache.spark.sql.Dataset tmp2 = spark.sql(query); +// +// Assertions +// .assertEquals( +// 0, +// tmp2 +// .select("community") +// .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR)) +// .count()); +// } +// +// @Test +// public void bulktagBySubjectDatasourceTest() throws Exception { +// final String sourcePath = getClass() +// .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") +// .getPath(); +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", +// "-outputPath", workingDir.toString() + "/dataset", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// Assertions.assertEquals(7, idExplodeCommunity.count()); +// +// Assertions +// .assertEquals( +// 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); +// Assertions +// .assertEquals( +// 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); +// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); +// +// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " +// + "from dataset " +// + "lateral view explode (context) as MyT " +// + "where size(MyT.datainfo) > 0"; +// +// org.apache.spark.sql.Dataset tmp2 = spark.sql(query); +// +// Assertions +// .assertEquals( +// 2, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " +// + "community = 'aginfra'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// +// Assertions +// .assertEquals( +// 1, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " +// + "community = 'covid-19'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// +// Assertions +// .assertEquals( +// 2, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " +// + "community = 'fam'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// Assertions +// .assertEquals( +// 2, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " +// + "community = 'covid-19'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// +// Assertions +// .assertEquals( +// 1, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " +// + "community = 'fam'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// Assertions +// .assertEquals( +// 1, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " +// + "community = 'mes'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// } +// +// @Test +// public void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception { +// +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", +// "-outputPath", workingDir.toString() + "/software", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); +// +// JavaRDD tmp = sc +// .textFile(workingDir.toString() + "/software") +// .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); +// +// Assertions.assertEquals(10, tmp.count()); +// org.apache.spark.sql.Dataset verificationDataset = spark +// .createDataset(tmp.rdd(), Encoders.bean(Software.class)); +// +// verificationDataset.createOrReplaceTempView("software"); +// +// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from software " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// Assertions.assertEquals(10, idExplodeCommunity.count()); +// +// idExplodeCommunity.show(false); +// Assertions +// .assertEquals( +// 3, idExplodeCommunity.filter("provenance = 'community:subject'").count()); +// Assertions +// .assertEquals( +// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); +// Assertions +// .assertEquals( +// 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); +// +// Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count()); +// Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count()); +// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); +// +// Assertions +// .assertEquals( +// 2, +// idExplodeCommunity +// .filter( +// "provenance = 'community:zenodocommunity' and " +// + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and (" +// + "community = 'dh-ch' or community = 'dariah')") +// .count()); +// +// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " +// + "from software " +// + "lateral view explode (context) as MyT " +// + "where size(MyT.datainfo) > 0"; +// +// org.apache.spark.sql.Dataset tmp2 = spark.sql(query); +// +// Assertions +// .assertEquals( +// 2, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and " +// + "community = 'covid-19'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// +// Assertions +// .assertEquals( +// 3, +// tmp2 +// .select("datainfosize") +// .where( +// "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and " +// + "community = 'aginfra'") +// .collectAsList() +// .get(0) +// .getInt(0)); +// } +// +// @Test +// public void bulktagDatasourcewithConstraintsTest() throws Exception { +// +// final String sourcePath = getClass() +// .getResource( +// "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") +// .getPath(); +// SparkBulkTagJob +// .main( +// new String[] { +// "-isTest", Boolean.TRUE.toString(), +// "-isSparkSessionManaged", Boolean.FALSE.toString(), +// "-sourcePath", sourcePath, +// "-taggingConf", taggingConf, +// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", +// "-outputPath", workingDir.toString() + "/dataset", +// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, +// "-pathMap", pathMap +// }); +// +// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'bulktagging'"; +// +// org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); +// +// idExplodeCommunity.show(false); +// Assertions.assertEquals(3, idExplodeCommunity.count()); +// +// Assertions +// .assertEquals( +// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); +// } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/dataset.json new file mode 100644 index 000000000..2b26d33f2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/dataset.json @@ -0,0 +1,136 @@ +entry +{"author":[{"affiliation":[],"fullname":"Kooi, M.","name":"M.","pid":[],"rank":1,"surname":"Kooi"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"datainfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"datainfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for Community - 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Aanleiding voor de bureaustudie is de voorgenomen dijkversterking in het plangebied van het deelproject Salmsteke. Het plangebied omvat in beginsel de Lekdijk met de direct omgeving. Mogelijk wordt de aangrenzende uiterwaard ook heringericht. Waar mogelijk zijn de potentiele gevolgen van deze maatregelen in deze bureaustudie benoemd.Het project bevindt zich op moment van schrijven in de verkenningsfase met betrekking tot het ontwikkelen van alternatieven, welke uiteindelijk moet eindigen met een voorkeursalternatief. Voordat de werkzaamheden kunnen plaatsvinden, zal hiervoor een omgevingsvergunning worden aangevraagd. "}],"device":null,"embargoenddate":null,"externalreference":null,"extrainfo":null,"format":null,"fulltext":null,"geolocation":null,"id":null,"instance":null,"language":null,"lastmetadataupdate":null,"lastupdatetimestamp":null,"metadataversionnumber":null,"oiaprovenance":null,"originalid":null,"pid":null,"publisher":null,"relevantdate":null,"resourcetype":null,"resulttype":null,"size":null,"source":null,"storagedate":null,"subject":null,"title":null,"version":null} +{"author":[{"affiliation":[],"fullname":"Holl, J.","name":"J.","pid":[],"rank":1,"surname":"Holl"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"datainfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"datainfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for Community - Subject","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null}],"id":"dh-ch"}],"contributor":[],"country":[],"coverage":[],"datainfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":null,"dateofcollection":"","dateoftransformation":"2020-05-25T12:26:05.372Z","description":[{"datainfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"ADC ArcheoProjecten heeft in mei 2018 een bureauonderzoek en inventariserend veldonderzoek uitgevoerd op de locatie Jordaniëstraat 107 te Delft, gemeente Delft. De aanleiding van het onderzoek is de voorgenomen sloop van de huidige bebouwing en nieuwbouw van een appartementencomplex."}],"device":null,"embargoenddate":null,"externalreference":null,"extrainfo":null,"format":null,"fulltext":null,"geolocation":null,"id":null,"instance":null,"language":null,"lastmetadataupdate":null,"lastupdatetimestamp":null,"metadataversionnumber":null,"oiaprovenance":null,"originalid":null,"pid":null,"publisher":null,"relevantdate":null,"resourcetype":null,"resulttype":null,"size":null,"source":null,"storagedate":null,"subject":null,"title":null,"version":null} +{"author":[{"affiliation":[],"fullname":"Beckers, I.S.J.","name":"I.S.J.","pid":[],"rank":1,"surname":"Beckers"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"datainfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"datainfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for Community - Subject","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null}],"id":"dh-ch"}],"contributor":[],"country":[],"coverage":[],"datainfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":null,"dateofcollection":"","dateoftransformation":"2020-05-25T12:30:12.903Z","description":[{"datainfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"In april 2016 is een archeologisch vooronderzoek uitgevoerd in een gepland leidingtracé langs de Schaapsdrift in De Bilt (gemeente De Bilt). De aanleiding voor het onderzoek vormt de aanleg van een nieuwe waterleiding en een beluchtingstoren op het pompstation Beerschoten. In het kader van deze ontwikkeling dient een omgevingsvergunning te worden aangevraagd. Het plangebied bestaat uit het deel van het leidingtracé waar op basis van het vigerend bestemmingsplan een dubbelbestemming ‘Waarde Archeologie’ geldt. Op basis van het bureauonderzoek werd in het plangebied een podzolgrond in de top van het dekzand verwacht, waar bovenop mogelijk een circa één-meter dikke laag stuifzand ligt. Het archeologisch niveau bevindt zich hierbij direct onder de bouwvoor c.q. humeuze bovengrond of in de top van een al dan niet begraven podzolbodem. De resten, die hierin te verwachten zijn, dateren naar verwachting in het Laat-Paleolithicum tot en met de Middeleeuwen en betreffen sporen van nederzetting en/of landgebruik uit die periode. De verwachting hierop is middelhoog. Voor wat betreft resten uit de Nieuwe tijd is de verwachting laag. 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Qualitative research was employed through face to face semi-structured in-depth interviews of 18 people which can be categorized into four groups as 1) Five existing organic farmers, 2) Five traditional farmers that are making the transition to organic, 3) Six traditional farmers who do not wish to become organic and 4) Two government agencies.Variables of this study are 1) Farmers’ characteristic such as age, educational, and income 2) Internal and external factors which affect farmers’ decision making. The example of internal factors are their past experiences, their characteristics, and their motivations. 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