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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 ;
@ExtendWith ( MockitoExtension . class )
public class DumpJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper ( ) ;
private static SparkSession spark ;
private static Path workingDir ;
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private static String MOCK_IS_LOOK_UP_URL = " BASEURL:8280/is/services/isLookUp " ;
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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 " ) ;
}
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@Mock
private SparkDumpCommunityProducts dumpCommunityProducts ;
private QueryInformationSystem queryInformationSystem ;
@Mock
private ISLookUpService isLookUpService ;
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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 \" /> " ) ;
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 {
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lenient ( ) . when ( isLookUpService . quickSearchProfile ( XQUERY ) ) . thenReturn ( communityMap ) ;
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lenient ( ) . when ( dumpCommunityProducts . getIsLookUpService ( MOCK_IS_LOOK_UP_URL ) ) . thenReturn ( isLookUpService ) ;
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}
@AfterAll
public static void afterAll ( ) throws IOException {
FileUtils . deleteDirectory ( workingDir . toFile ( ) ) ;
spark . stop ( ) ;
}
@Test
public void test1 ( ) throws Exception {
final String sourcePath = getClass ( )
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. getResource ( " /eu/dnetlib/dhp/oa/graph/dump/dataset.json " )
. getPath ( ) ;
dumpCommunityProducts . exec ( MOCK_IS_LOOK_UP_URL , Boolean . FALSE , workingDir . toString ( ) + " /dataset " , sourcePath , " eu.dnetlib.dhp.schema.oaf.Dataset " , " eu.dnetlib.dhp.schema.dump.oaf.Dataset " ) ;
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final JavaSparkContext sc = JavaSparkContext . fromSparkContext ( spark . sparkContext ( ) ) ;
JavaRDD < eu . dnetlib . dhp . schema . dump . oaf . Dataset > tmp = sc
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. textFile ( workingDir . toString ( ) + " /dataset " )
. map ( item - > OBJECT_MAPPER . readValue ( item , eu . dnetlib . dhp . schema . dump . oaf . Dataset . class ) ) ;
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org . apache . spark . sql . Dataset < eu . dnetlib . dhp . schema . dump . oaf . Dataset > verificationDataset = spark
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. createDataset ( tmp . rdd ( ) , Encoders . bean ( eu . dnetlib . dhp . schema . dump . oaf . Dataset . class ) ) ;
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verificationDataset . show ( false ) ;
}
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@Test
public void test0 ( ) throws ISLookUpException {
System . out . println ( new Gson ( ) . toJson ( queryInformationSystem . getCommunityMap ( ) ) ) ;
}
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// @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());
// }
}