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test for graph dump

This commit is contained in:
Miriam Baglioni 2020-06-15 11:13:51 +02:00
parent e43eedb5b0
commit 0467145ae3
5 changed files with 900 additions and 710 deletions
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920
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -1,29 +1,6 @@
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;
@ -31,13 +8,20 @@ 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 org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.mockito.Mockito.lenient;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
@ExtendWith(MockitoExtension.class)
//@ExtendWith(MockitoExtension.class)
public class DumpJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -50,41 +34,57 @@ public class DumpJobTest {
private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class);
private static HashMap<String,String> map = new HashMap<>();
private static HashMap<String, String> map = new HashMap<>();
static{
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");
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");
}
@Mock
private SparkDumpCommunityProducts dumpCommunityProducts;
// @Mock
// private SparkDumpCommunityProducts dumpCommunityProducts;
private QueryInformationSystem queryInformationSystem;
// private QueryInformationSystem queryInformationSystem;
@Mock
private ISLookUpService isLookUpService;
// @Mock
// private ISLookUpService isLookUpService;
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\"/>" ,
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=\"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=\"elixir-gr\" label=\"ELIXIR GR\"/>",
"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
"<community id=\"dariah\" label=\"DARIAH EU\"/>",
"<community id=\"risis\" label=\"RISIS\"/>",
@ -97,13 +97,14 @@ public class DumpJobTest {
"<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>";
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 {
@ -127,12 +128,12 @@ public class DumpJobTest {
.getOrCreate();
}
@BeforeEach
public void setUp() throws ISLookUpException {
lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
lenient().when(dumpCommunityProducts.getIsLookUpService(MOCK_IS_LOOK_UP_URL)).thenReturn(isLookUpService);
}
// @BeforeEach
// public void setUp() throws ISLookUpException {
// lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
// lenient().when(dumpCommunityProducts.getIsLookUpService(MOCK_IS_LOOK_UP_URL)).thenReturn(isLookUpService);
//
// }
@AfterAll
public static void afterAll() throws IOException {
@ -141,672 +142,171 @@ public class DumpJobTest {
}
@Test
public void test1() throws Exception {
public void testDataset() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/dataset.json")
.getPath();
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/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");
SparkDumpCommunityProducts.main(new String[] {
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/dataset",
"-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-dumpTableName", "eu.dnetlib.dhp.schema.dump.oaf.Dataset",
"-communityMap", new Gson().toJson(map)
});
// 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");
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));
.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));
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Dataset.class));
Assertions.assertEquals(90, verificationDataset.count());
// verificationDataset.show(false);
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
.filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset
.filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset
.filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset
.filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'")
.count());
Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90);
verificationDataset.select("instance.type").show(false);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
@Test
public void testPublication() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json")
.getPath();
SparkDumpCommunityProducts.main(new String[] {
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/publication",
"-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
"-dumpTableName", "eu.dnetlib.dhp.schema.dump.oaf.Publication",
"-communityMap", new Gson().toJson(map)
});
// 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");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.Publication.class));
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.Publication> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Publication.class));
Assertions.assertEquals(76, verificationDataset.count());
verificationDataset.show(false);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
@Test
public void test0() throws ISLookUpException {
System.out.println(new Gson().toJson(queryInformationSystem.getCommunityMap()));
public void testSoftware() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json")
.getPath();
SparkDumpCommunityProducts.main(new String[] {
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/software",
"-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-dumpTableName", "eu.dnetlib.dhp.schema.dump.oaf.Software",
"-communityMap", new Gson().toJson(map)
});
// 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");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Software> tmp = sc
.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.Software.class));
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.Software> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Software.class));
Assertions.assertEquals(6, verificationDataset.count());
verificationDataset.show(false);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
@Test
public void testORP() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json")
.getPath();
SparkDumpCommunityProducts.main(new String[] {
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/orp",
"-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-dumpTableName", "eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct",
"-communityMap", new Gson().toJson(map)
});
// 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");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct> tmp = sc
.textFile(workingDir.toString() + "/orp")
.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct.class));
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct.class));
Assertions.assertEquals(3, verificationDataset.count());
verificationDataset.show(false);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
// @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());
// }
}

220
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java
View File

@ -1,4 +1,224 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
public class PrepareResultProjectJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class);
private static HashMap<String, String> map = new HashMap<>();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.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(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void testNoMatch() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
// 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");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
Assertions.assertEquals(0, verificationDataset.count());
}
@Test
public void testMatchOne() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
// 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");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
Assertions.assertTrue(verificationDataset.count() == 1);
Assertions
.assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
}
@Test
public void testMatch() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
Assertions.assertTrue(verificationDataset.count() == 2);
Assertions
.assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
Assertions
.assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym "
+ "from dataset "
+ "lateral view explode(projectsList) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(3, resultExplodedProvenance.count());
Assertions
.assertEquals(
2,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
Assertions
.assertEquals(
2,
resultExplodedProvenance
.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
resultExplodedProvenance.show(false);
}
}

112
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java
View File

@ -1,4 +1,116 @@
package eu.dnetlib.dhp.oa.graph.dump;
import static org.mockito.Mockito.lenient;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.neethi.Assertion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import com.google.gson.Gson;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
public class QueryInformationSystemTest {
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>";
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 ISLookUpService isLookUpService;
private QueryInformationSystem queryInformationSystem;
private Map<String, String> map;
@BeforeEach
public void setUp() throws ISLookUpException {
lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(isLookUpService);
map = queryInformationSystem.getCommunityMap();
}
@Test
public void testSize() throws ISLookUpException {
Assertions.assertEquals(23, map.size());
}
@Test
public void testContent() {
Assertions.assertTrue(map.containsKey("egi") && map.get("egi").equals("EGI Federation"));
Assertions.assertTrue(map.containsKey("fet-fp7") && map.get("fet-fp7").equals("FET FP7"));
Assertions.assertTrue(map.containsKey("fet-h2020") && map.get("fet-h2020").equals("FET H2020"));
Assertions.assertTrue(map.containsKey("clarin") && map.get("clarin").equals("CLARIN"));
Assertions.assertTrue(map.containsKey("rda") && map.get("rda").equals("Research Data Alliance"));
Assertions.assertTrue(map.containsKey("ee") && map.get("ee").equals("SDSN - Greece"));
Assertions
.assertTrue(
map.containsKey("dh-ch") && map.get("dh-ch").equals("Digital Humanities and Cultural Heritage"));
Assertions.assertTrue(map.containsKey("fam") && map.get("fam").equals("Fisheries and Aquaculture Management"));
Assertions.assertTrue(map.containsKey("ni") && map.get("ni").equals("Neuroinformatics"));
Assertions.assertTrue(map.containsKey("mes") && map.get("mes").equals("European Marine Science"));
Assertions.assertTrue(map.containsKey("instruct") && map.get("instruct").equals("Instruct-ERIC"));
Assertions.assertTrue(map.containsKey("elixir-gr") && map.get("elixir-gr").equals("ELIXIR GR"));
Assertions
.assertTrue(map.containsKey("aginfra") && map.get("aginfra").equals("Agricultural and Food Sciences"));
Assertions.assertTrue(map.containsKey("dariah") && map.get("dariah").equals("DARIAH EU"));
Assertions.assertTrue(map.containsKey("risis") && map.get("risis").equals("RISIS"));
Assertions.assertTrue(map.containsKey("epos") && map.get("epos").equals("EPOS"));
Assertions.assertTrue(map.containsKey("beopen") && map.get("beopen").equals("Transport Research"));
Assertions.assertTrue(map.containsKey("euromarine") && map.get("euromarine").equals("EuroMarine"));
Assertions.assertTrue(map.containsKey("ifremer") && map.get("ifremer").equals("Ifremer"));
Assertions.assertTrue(map.containsKey("oa-pg") && map.get("oa-pg").equals("EC Post-Grant Open Access Pilot"));
Assertions
.assertTrue(
map.containsKey("science-innovation-policy")
&& map.get("science-innovation-policy").equals("Science and Innovation Policy Studies"));
Assertions.assertTrue(map.containsKey("covid-19") && map.get("covid-19").equals("COVID-19"));
Assertions.assertTrue(map.containsKey("enermaps") && map.get("enermaps").equals("Energy Research"));
}
}

224
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java
View File

@ -1,4 +1,228 @@
package eu.dnetlib.dhp.oa.graph.dump;
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.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.schema.dump.oaf.Software;
public class SplitForCommunityTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/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");
}
// @Mock
// private SparkDumpCommunityProducts dumpCommunityProducts;
// private QueryInformationSystem queryInformationSystem;
// @Mock
// private ISLookUpService isLookUpService;
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(SplitForCommunityTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SplitForCommunityTest.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(SplitForCommunityTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
// @BeforeEach
// public void setUp() throws ISLookUpException {
// lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
// lenient().when(dumpCommunityProducts.getIsLookUpService(MOCK_IS_LOOK_UP_URL)).thenReturn(isLookUpService);
//
// }
@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/splitForCommunity/software")
.getPath();
SparkSplitForCommunity.main(new String[] {
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/split",
"-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.dump.oaf.Software",
"-communityMap", new Gson().toJson(map)
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/split/dh-ch")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
org.apache.spark.sql.Dataset<Software> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/egi")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/ni")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/science-innovation-policy")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
Assertions.assertEquals(4, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
}
}

134
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java
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@ -1,4 +1,138 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.dump.oaf.Software;
public class UpdateProjectInfoTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class);
private static HashMap<String, String> map = new HashMap<>();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.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(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@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/addProjectInfo")
.getPath();
SparkUpdateProjectInfo.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-resultTableName", "eu.dnetlib.dhp.schema.dump.oaf.Software",
"-preparedInfoPath", sourcePath + "/preparedInfo",
"-outputPath", workingDir.toString() + "/ext/software",
"-sourcePath", sourcePath + "/software"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/ext/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
org.apache.spark.sql.Dataset<Software> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
verificationDataset.show(false);
Assertions.assertEquals(6, verificationDataset.count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, "
+
"MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream "
+ "from dataset " +
"lateral view explode(projects) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(3, resultExplodedProvenance.count());
resultExplodedProvenance.show(false);
Assertions
.assertEquals(
2,
resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'")
.count());
resultExplodedProvenance.show(false);
}
}