job test for class producing first step of results dump
This commit is contained in:
parent
206abba48c
commit
bb9f21d0e7
|
|
@ -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<String,String> 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<String> communityMap = Arrays.asList("<community id=\"egi\" label=\"EGI Federation\"/>",
|
||||
"<community id=\"fet-fp7\" label=\"FET FP7\"/>" ,
|
||||
"<community id=\"fet-h2020\" label=\"FET H2020\"/>" ,
|
||||
"<community id=\"clarin\" label=\"CLARIN\"/>",
|
||||
"<community id=\"rda\" label=\"Research Data Alliance\"/>",
|
||||
"<community id=\"ee\" label=\"SDSN - Greece\"/>",
|
||||
"<community id=\"dh-ch\" label=\"Digital Humanities and Cultural Heritage\"/>" ,
|
||||
"<community id=\"fam\" label=\"Fisheries and Aquaculture Management\"/>",
|
||||
"<community id=\"ni\" label=\"Neuroinformatics\"/>",
|
||||
"<community id=\"mes\" label=\"European Marine Science\"/>",
|
||||
"<community id=\"instruct\" label=\"Instruct-ERIC\"/>",
|
||||
"<community id=\"elixir-gr\" label=\"ELIXIR GR\"/>" ,
|
||||
"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
|
||||
"<community id=\"dariah\" label=\"DARIAH EU\"/>",
|
||||
"<community id=\"risis\" label=\"RISIS\"/>",
|
||||
"<community id=\"epos\" label=\"EPOS\"/>",
|
||||
"<community id=\"beopen\" label=\"Transport Research\"/>",
|
||||
"<community id=\"euromarine\" label=\"EuroMarine\"/>",
|
||||
"<community id=\"ifremer\" label=\"Ifremer\"/>",
|
||||
"<community id=\"oa-pg\" label=\"EC Post-Grant Open Access Pilot\"/>",
|
||||
"<community id=\"science-innovation-policy\" label=\"Science and Innovation Policy Studies\"/>",
|
||||
"<community id=\"covid-19\" label=\"COVID-19\"/>",
|
||||
"<community id=\"enermaps\" label=\"Energy Research\"/>");
|
||||
|
||||
@Mock
|
||||
private SparkDumpCommunityProducts dumpCommunityProducts;
|
||||
|
||||
|
||||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " +
|
||||
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
||||
" return " +
|
||||
"<community> " +
|
||||
"{$x//CONFIGURATION/context/@id}" +
|
||||
"{$x//CONFIGURATION/context/@label}" +
|
||||
"</community>";
|
||||
|
||||
@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<eu.dnetlib.dhp.schema.dump.oaf.Dataset> 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<eu.dnetlib.dhp.schema.dump.oaf.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<Dataset> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/dataset")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<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<Row> 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<Dataset> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/dataset")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<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<Row> 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<Publication> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/publication")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<Publication> 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<Row> 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<OtherResearchProduct> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/orp")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<OtherResearchProduct> 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<Row> 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<Row> 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<Dataset> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/dataset")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<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<Row> 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<Row> 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<Software> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/software")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<Software> 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<Row> 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<Row> 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<Dataset> tmp = sc
|
||||
// .textFile(workingDir.toString() + "/dataset")
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
//
|
||||
// Assertions.assertEquals(10, tmp.count());
|
||||
// org.apache.spark.sql.Dataset<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<Row> idExplodeCommunity = spark.sql(query);
|
||||
//
|
||||
// idExplodeCommunity.show(false);
|
||||
// Assertions.assertEquals(3, idExplodeCommunity.count());
|
||||
//
|
||||
// Assertions
|
||||
// .assertEquals(
|
||||
// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||
// }
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue