From 11a1207f9c8476db4fc926f707915c3209720106 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 22 Nov 2023 12:22:14 +0100 Subject: [PATCH] [graph cleaning] applying coar based vocabularies in bulk --- .../dhp/oa/merge/GroupEntitiesSparkJob.java | 40 +++++- .../oaf/utils/GraphCleaningFunctions.java | 95 +++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 21 ++- .../group_graph_entities_parameters.json | 6 + .../raw/AbstractMdRecordToOafMapper.java | 63 +-------- .../group/GroupEntitiesSparkJobTest.java | 131 ++++++++++++++++-- .../raw/GenerateEntitiesApplicationTest.java | 5 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 28 ++-- .../dhp/oa/graph/group/dataset/dataset.json | 6 +- .../graph/group/publication/publication.json | 6 +- pom.xml | 2 +- 11 files changed, 294 insertions(+), 109 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index f5c8eea19..0225a5063 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -21,10 +21,15 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; /** @@ -35,6 +40,12 @@ public class GroupEntitiesSparkJob { private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private ArgumentApplicationParser parser; + + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -51,6 +62,17 @@ public class GroupEntitiesSparkJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { + String graphInputPath = parser.get("graphInputPath"); log.info("graphInputPath: {}", graphInputPath); @@ -60,19 +82,21 @@ public class GroupEntitiesSparkJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible")); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); log.info("filterInvisible: {}", filterInvisible); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + runWithSparkSession( conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); }); } @@ -81,7 +105,7 @@ public class GroupEntitiesSparkJob { String inputPath, String checkpointPath, String outputPath, - boolean filterInvisible) { + boolean filterInvisible, VocabularyGroup vocs) { Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); @@ -106,10 +130,14 @@ public class GroupEntitiesSparkJob { } Dataset groupedEntities = allEntities - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> OafMapperUtils.mergeEntities(b, a)) .map( - (MapFunction, Tuple2>) t -> new Tuple2( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( t._2().getClass().getName(), t._2()), Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 324e3dd58..b23dade98 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; import java.time.LocalDate; @@ -784,4 +786,97 @@ public class GraphCleaningFunctions extends CleaningFunctions { return s; } + public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) { + + if (entity instanceof Result) { + final Result result = (Result) entity; + + Optional + .ofNullable(result.getInstance()) + .ifPresent( + instances -> instances + .forEach( + instance -> { + if (Objects.isNull(instance.getInstanceTypeMapping())) { + List mapping = Lists.newArrayList(); + mapping + .add( + OafMapperUtils + .instanceTypeMapping( + instance.getInstancetype().getClassname(), + OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + instance.setInstanceTypeMapping(mapping); + } + Optional optionalItm = instance + .getInstanceTypeMapping() + .stream() + .filter(GraphCleaningFunctions::originalResourceType) + .findFirst(); + if (optionalItm.isPresent()) { + InstanceTypeMapping coarItm = optionalItm.get(); + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType())) + .ifPresent(type -> { + coarItm.setTypeCode(type.getClassid()); + coarItm.setTypeLabel(type.getClassname()); + }); + final List mappings = Lists.newArrayList(); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode())) + .ifPresent( + type -> mappings + .add( + OafMapperUtils + .instanceTypeMapping(coarItm.getTypeCode(), type))); + } + if (!mappings.isEmpty()) { + instance.getInstanceTypeMapping().addAll(mappings); + } + } + })); + result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs)); + } + + return entity; + } + + private static boolean originalResourceType(InstanceTypeMapping itm) { + return StringUtils.isNotBlank(itm.getOriginalType()) && + OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) && + StringUtils.isBlank(itm.getTypeCode()) && + StringUtils.isBlank(itm.getTypeLabel()); + } + + private static Qualifier getMetaResourceType(final List instances, final VocabularyGroup vocs) { + + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional instanceTypeMapping = instances + .stream() + .flatMap( + i -> Optional.ofNullable(i.getInstanceTypeMapping()).map(Collection::stream).orElse(Stream.empty())) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!instanceTypeMapping.isPresent()) { + return null; + } else { + final String typeCode = instanceTypeMapping.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + } + } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 1c557c805..4cecd0895 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -140,15 +140,28 @@ public class OafMapperUtils { .collect(Collectors.toList()); } - public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label, + String vocabularyName) { final InstanceTypeMapping m = new InstanceTypeMapping(); - m.setVocabularyName(term.getSchemeid()); + m.setVocabularyName(vocabularyName); m.setOriginalType(originalType); - m.setTypeCode(term.getClassid()); - m.setTypeLabel(term.getClassname()); + m.setTypeCode(code); + m.setTypeLabel(label); return m; } + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + return instanceTypeMapping(originalType, term.getClassid(), term.getClassname(), term.getSchemeid()); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType) { + return instanceTypeMapping(originalType, null, null, null); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType, String vocabularyName) { + return instanceTypeMapping(originalType, null, null, vocabularyName); + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json index 58e3ca711..512878457 100644 --- a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "filterInvisible", "paramDescription": "if true filters out invisible entities", "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 49133cedb..a71908b02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -125,9 +125,7 @@ public abstract class AbstractMdRecordToOafMapper { final String type = getResultType(doc, instances); - final Qualifier metaResourceType = getMetaResourceType(instances); - - return createOafs(doc, type, metaResourceType, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); @@ -153,30 +151,6 @@ public abstract class AbstractMdRecordToOafMapper { return type; } - protected Qualifier getMetaResourceType(final List instances) { - - if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { - Optional instanceTypeMapping = instances - .stream() - .flatMap(i -> i.getInstanceTypeMapping().stream()) - .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) - .findFirst(); - - if (!instanceTypeMapping.isPresent()) { - return null; - } else { - final String typeCode = instanceTypeMapping.get().getTypeCode(); - return Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) - .orElseThrow( - () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + - OPENAIRE_META_RESOURCE_TYPE)); - } - } else { - throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); - } - } - private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); @@ -191,14 +165,13 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { final OafEntity entity = createEntity( - doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); + doc, type, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -231,7 +204,6 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, @@ -239,12 +211,12 @@ public abstract class AbstractMdRecordToOafMapper { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -255,7 +227,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -265,7 +237,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -402,13 +374,11 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, - final Qualifier metaResourceType, final Document doc, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - r.setMetaResourceType(metaResourceType); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); @@ -555,26 +525,7 @@ public abstract class AbstractMdRecordToOafMapper { .ofNullable(findOriginalType(doc)) .map(originalType -> { final List mappings = Lists.newArrayList(); - - if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) - .ifPresent(coarTerm -> { - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable( - vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) - .ifPresent( - type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); - } - }); - } - + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1)); return mappings; }) .orElse(new ArrayList<>()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index 0887adf45..242aed88e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -1,15 +1,23 @@ package eu.dnetlib.dhp.oa.graph.group; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; import java.io.IOException; import java.net.URISyntaxException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; @@ -17,20 +25,36 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +@ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class GroupEntitiesSparkJobTest { + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + private static SparkSession spark; private static ObjectMapper mapper = new ObjectMapper() @@ -45,10 +69,10 @@ public class GroupEntitiesSparkJobTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + workingDir = Files.createTempDirectory(GroupEntitiesSparkJobTest.class.getSimpleName()); SparkConf conf = new SparkConf(); - conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setAppName(GroupEntitiesSparkJobTest.class.getSimpleName()); conf.setMaster("local"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); @@ -56,10 +80,17 @@ public class GroupEntitiesSparkJobTest { } @BeforeEach - public void beforeEach() throws IOException, URISyntaxException { + public void beforeEach() throws IOException, URISyntaxException, ISLookUpException { dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); checkpointPath = workingDir.resolve("grouped_entity"); outputPath = workingDir.resolve("dispatched_entity"); + + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); } @AfterAll @@ -71,18 +102,17 @@ public class GroupEntitiesSparkJobTest { @Test @Order(1) void testGroupEntities() throws Exception { - GroupEntitiesSparkJob.main(new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-graphInputPath", - dataInputPath.toString(), - "-checkpointPath", - checkpointPath.toString(), - "-outputPath", - outputPath.toString(), - "-filterInvisible", - Boolean.FALSE.toString() - }); + new GroupEntitiesSparkJob( + args( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json", + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--graphInputPath", dataInputPath.toString(), + "--checkpointPath", checkpointPath.toString(), + "--outputPath", outputPath.toString(), + "--filterInvisible", Boolean.FALSE.toString(), + "--isLookupUrl", "lookupurl" + })).run(false, isLookUpService); Dataset checkpointTable = spark .read() @@ -109,6 +139,14 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); assertEquals(3, output.count()); + + List resultTypes = output + .map((MapFunction) value -> value.getResulttype().getClassid(), Encoders.STRING()) + .distinct() + .collectAsList(); + + assertEquals(2, resultTypes.size()); + assertEquals( 2, output @@ -121,5 +159,68 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) .filter((FilterFunction) s -> s.equals("dataset")) .count()); + + Result result = output + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + + result.getInstance().forEach(instance -> { + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "journal-article".equals(itm.getOriginalType())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_2df8fbb1", coarType.get().getTypeCode()); + assertEquals("research article", coarType.get().getTypeLabel()); + }); + + final Dataset filtered = output.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'"); + assertEquals(1, filtered.count()); + result = filtered.first(); + + result + .getInstance() + .stream() + .flatMap(instance -> instance.getInstanceTypeMapping().stream()) + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "Patent".equals(itm.getOriginalType())) + .forEach(itm -> { + assertEquals("http://purl.org/coar/resource_type/c_15cd", itm.getTypeCode()); + assertEquals("patent", itm.getTypeLabel()); + }); } + + private List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"))); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + GroupEntitiesSparkJobTest.class.getResourceAsStream(path))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 53b3f8432..6d6b2ffbd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -92,13 +92,14 @@ class GenerateEntitiesApplicationTest { private List vocs() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + GenerateEntitiesApplicationTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); } private List synonyms() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + GenerateEntitiesApplicationTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index e6997ac1d..1f2defa01 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,7 +122,7 @@ class MappersTest { assertTrue(instance.getPid().isEmpty()); assertNotNull(instance.getInstanceTypeMapping()); - assertEquals(2, instance.getInstanceTypeMapping().size()); + assertEquals(1, instance.getInstanceTypeMapping().size()); Optional coarType = instance .getInstanceTypeMapping() @@ -131,8 +131,8 @@ class MappersTest { .findFirst(); assertTrue(coarType.isPresent()); - assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); - assertEquals("conference paper", coarType.get().getTypeLabel()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); Optional userType = instance .getInstanceTypeMapping() @@ -140,9 +140,7 @@ class MappersTest { .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) .findFirst(); - assertTrue(userType.isPresent()); - assertEquals("Article", userType.get().getTypeCode()); - assertEquals("Article", userType.get().getTypeLabel()); + assertFalse(userType.isPresent()); assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); @@ -710,14 +708,10 @@ class MappersTest { assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); - assertNotNull(p_cleaned.getMetaResourceType()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassid()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassname()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemeid()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemename()); + assertNull(p_cleaned.getMetaResourceType()); assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); - assertEquals(2, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + assertEquals(1, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); assertTrue( p_cleaned @@ -728,8 +722,7 @@ class MappersTest { .anyMatch( t -> "journal-article".equals(t.getOriginalType()) && ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && - "http://purl.org/coar/resource_type/c_2df8fbb1".equals(t.getTypeCode()) && - "research article".equals(t.getTypeLabel()))); + Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel()))); assertTrue( p_cleaned @@ -737,11 +730,8 @@ class MappersTest { .get(0) .getInstanceTypeMapping() .stream() - .anyMatch( - t -> "journal-article".equals(t.getOriginalType()) && - ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()) && - "Article".equals(t.getTypeCode()) && - "Article".equals(t.getTypeLabel()))); + .noneMatch( + t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()))); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json index e30be47e9..efbabb3c8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json +++ 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