From a653e1b3eac653c758cb10d089f6d8eb37101261 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 4 Oct 2022 15:01:28 +0200 Subject: [PATCH 01/10] [Enrichment - result to community through organization] reimplementation of the data preparation step using spark --- .../PrepareResultCommunitySet.java | 47 +++++++++++-------- 1 file changed, 27 insertions(+), 20 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 1a008797d..19b985964 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -9,7 +9,9 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -70,28 +72,33 @@ public class PrepareResultCommunitySet { String outputPath, OrganizationMap organizationMap) { - Dataset relation = readPath(spark, inputPath, Relation.class); - relation.createOrReplaceTempView("relation"); + Dataset relationAffiliation = readPath(spark, inputPath, Relation.class) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.HAS_AUTHOR_INSTITUTION)); - String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges " - + "FROM (SELECT source, target " - + " FROM relation " - + " WHERE datainfo.deletedbyinference = false " - + " AND lower(relClass) = '" - + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase() - + "') result_organization " - + "LEFT JOIN (SELECT source, collect_set(target) org_set " - + " FROM relation " - + " WHERE datainfo.deletedbyinference = false " - + " AND lower(relClass) = '" - + ModelConstants.MERGES.toLowerCase() - + "' " - + " GROUP BY source) organization_organization " - + "ON result_organization.target = organization_organization.source "; + Dataset relationOrganization = readPath(spark, inputPath, Relation.class) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.MERGES)); - Dataset result_organizationset = spark - .sql(query) - .as(Encoders.bean(ResultOrganizations.class)); + Dataset result_organizationset = relationAffiliation + .joinWith( + relationOrganization, + relationAffiliation.col("target").equalTo(relationOrganization.col("source")), + "left") + .groupByKey((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING()) + .mapGroups((MapGroupsFunction, ResultOrganizations>) (k, it) -> { + ResultOrganizations rOrgs = new ResultOrganizations(); + rOrgs.setOrgId(k); + Tuple2 first = it.next(); + rOrgs.setResultId(first._1().getSource()); + ArrayList merges = new ArrayList<>(); + merges.add(first._2().getTarget()); + it.forEachRemaining(t -> merges.add(t._2().getTarget())); + rOrgs.setMerges(merges); + return rOrgs; + }, Encoders.bean(ResultOrganizations.class)); result_organizationset .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class)) From 6d3d18d8b58fd207d50b170925a855229bf35012 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Mar 2023 17:23:36 +0100 Subject: [PATCH 02/10] [graph cleaning] WIP: refactoring of the cleaning stages --- .../oaf/utils/GraphCleaningFunctions.java | 118 ++++++ .../oa/graph/clean/CleanGraphSparkJob.java | 46 ++- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 351 ++++-------------- .../graph/input_clean_graph_parameters.json | 30 ++ .../oa/provision/XmlRecordFactoryTest.java | 2 +- 5 files changed, 268 insertions(+), 279 deletions(-) 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 fc515b5b1..e40de935e 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 @@ -38,6 +38,124 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; + public static T cleanContext(T value, String contextId, String verifyParam) { + if (ModelSupport.isSubClass(value, Result.class)) { + final Result res = (Result) value; + if (res + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .noneMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return (T) res; + } + res + .setContext( + res + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return (T) res; + } else { + return value; + } + } + + public static T cleanCountry(T value, String[] verifyParam, Set hostedBy, + String collectedfrom, String country) { + if (ModelSupport.isSubClass(value, Result.class)) { + final Result res = (Result) value; + if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { + return (T) res; + } + + List ids = getPidsAndAltIds(res).collect(Collectors.toList()); + if (ids + .stream() + .anyMatch( + p -> p + .getQualifier() + .getClassid() + .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { + res + .setCountry( + res + .getCountry() + .stream() + .filter( + c -> toTakeCountry(c, country)) + .collect(Collectors.toList())); + } + + return (T) res; + } else { + return value; + } + } + + private static Stream getPidsAndAltIds(T r) { + final Stream resultPids = Optional + .ofNullable(r.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()); + + final Stream instancePids = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + final Stream instanceAltIds = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getAlternateIdentifier()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + return Stream + .concat( + Stream.concat(resultPids, instancePids), + instanceAltIds); + } + + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam) + if (value.startsWith(s)) + return true; + return false; + } + + private static boolean toTakeCountry(Country c, String country) { + // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be + // inserted via propagation + if (!Optional.ofNullable(c.getDataInfo()).isPresent()) + return true; + if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) + return true; + return !(c + .getClassid() + .equalsIgnoreCase(country) && + c.getDataInfo().getInferenceprovenance().equals("propagation")); + } + public static T fixVocabularyNames(T value) { if (value instanceof Datasource) { // nothing to clean here diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 2e2ea567a..0099798f6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -3,7 +3,10 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.List; import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -17,12 +20,16 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; 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.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -61,6 +68,24 @@ public class CleanGraphSparkJob { String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + String datasourcePath = parser.get("hostedBy"); + log.info("datasourcePath: {}", datasourcePath); + + String country = parser.get("country"); + log.info("country: {}", country); + + String[] verifyCountryParam = parser.get("verifyCountryParam").split(";"); + log.info("verifyCountryParam: {}", verifyCountryParam); + + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); + Class entityClazz = (Class) Class.forName(graphTableClassName); final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); @@ -72,7 +97,9 @@ public class CleanGraphSparkJob { isSparkSessionManaged, spark -> { HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath); + cleanGraphTable( + spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, + verifyCountryParam, collectedfrom); }); } @@ -81,7 +108,15 @@ public class CleanGraphSparkJob { VocabularyGroup vocs, String inputPath, Class clazz, - String outputPath) { + String outputPath, String contextId, String verifyParam, String datasourcePath, String country, + String[] verifyCountryParam, String collectedfrom) { + + Set hostedBy = Sets + .newHashSet( + spark + .read() + .textFile(datasourcePath) + .collectAsList()); final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); @@ -90,6 +125,13 @@ public class CleanGraphSparkJob { .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) .filter((FilterFunction) GraphCleaningFunctions::filter) + .map( + (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), + Encoders.bean(clazz)) + .map( + (MapFunction) value -> GraphCleaningFunctions + .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), + Encoders.bean(clazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 683c2417b..2d6371a9b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -83,12 +83,37 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Select datasource ID from country + eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath} + --workingDir${workingDir}/working/hostedby + --country${country} + + + + + @@ -121,6 +146,12 @@ --outputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -147,6 +178,12 @@ --outputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -173,6 +210,12 @@ --outputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -199,6 +242,12 @@ --outputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -225,6 +274,12 @@ --outputPath${graphOutputPath}/datasource --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -251,6 +306,12 @@ --outputPath${graphOutputPath}/organization --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -277,6 +338,12 @@ --outputPath${graphOutputPath}/project --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} @@ -303,286 +370,18 @@ --outputPath${graphOutputPath}/relation --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} - - - - - ${wf:conf('shouldClean') eq true} - - - - - - - - - - - - - - yarn - cluster - Clean publications context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingDir${workingDir}/working/publication - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean datasets Context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingDir${workingDir}/working/dataset - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean otherresearchproducts context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingDir${workingDir}/working/otherresearchproduct - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean softwares context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingDir${workingDir}/working/software - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - - - yarn - cluster - Select datasource ID from country - eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath} - --workingDir${workingDir}/working/hostedby - --country${country} - - - - - - - - - - - - - - - yarn - cluster - Clean publication country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingDir${workingDir}/working/publication - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean dataset country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingDir${workingDir}/working/dataset - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean otherresearchproduct country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingDir${workingDir}/working/otherresearchproduct - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean software country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingDir${workingDir}/working/software - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json index 9cfed1e91..928215316 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json @@ -28,5 +28,35 @@ "paramLongName": "graphTableClassName", "paramDescription": "class name moelling the graph table", "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + }, + { + "paramName": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + }, + { + "paramName": "vfc", + "paramLongName": "verifyCountryParam", + "paramDescription": "the parameter to be verified to remove the country", + "paramRequired": true + }, + { + "paramName": "cf", + "paramLongName": "collectedfrom", + "paramDescription": "the collectedfrom value for which we should apply the cleaning", + "paramRequired": true + }, + { + "paramName": "hb", + "paramLongName": "hostedBy", + "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 4d93138f4..8802b546d 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -56,7 +56,7 @@ public class XmlRecordFactoryTest { assertNotNull(doc); - //System.out.println(doc.asXML()); + // System.out.println(doc.asXML()); assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid")); assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending")); From 4f5ba0ed5232028f41691313ca6c5da76262a1a0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Mar 2023 14:41:20 +0100 Subject: [PATCH 03/10] [graph cleaning] WIP: refactoring of the cleaning stages, unit tests --- .../oa/graph/clean/CleanGraphSparkJob.java | 258 +++++++++-- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 236 ++-------- .../graph/input_clean_graph_parameters.json | 26 +- .../graph/clean/CleanGraphSparkJobTest.java | 435 ++++++++++++++++++ .../clean/GraphCleaningFunctionsTest.java | 3 +- .../entities => graph}/dataset/dataset.json | 0 .../clean/graph/publication/publication.json | 1 + .../clean/{ => graph/relation}/relation.json | 0 .../src/test/resources/logback.xml | 11 + 9 files changed, 718 insertions(+), 252 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/{cfhb/entities => graph}/dataset/dataset.json (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/{ => graph/relation}/relation.json (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/logback.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 0099798f6..ca77be3c6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -3,15 +3,18 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.util.List; -import java.util.Optional; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -24,15 +27,19 @@ import com.google.common.collect.Sets; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.action.model.MasterDuplicate; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.cfhb.IdCfHbMapping; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Tuple2; public class CleanGraphSparkJob { @@ -40,31 +47,43 @@ public class CleanGraphSparkJob { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + private ArgumentApplicationParser parser; + public CleanGraphSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - CleanGraphSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); + .toString( + CleanGraphSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) throws ISLookUpException, ClassNotFoundException { + String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); - String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); @@ -80,27 +99,38 @@ public class CleanGraphSparkJob { String country = parser.get("country"); log.info("country: {}", country); - String[] verifyCountryParam = parser.get("verifyCountryParam").split(";"); + String[] verifyCountryParam = Optional.ofNullable(parser.get("verifyCountryParam")) + .map(s -> s.split(";")) + .orElse(new String[]{}); log.info("verifyCountryParam: {}", verifyCountryParam); String collectedfrom = parser.get("collectedfrom"); log.info("collectedfrom: {}", collectedfrom); + String dsMasterDuplicatePath = parser.get("masterDuplicatePath"); + log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); + + Boolean deepClean = Optional + .ofNullable(parser.get("deepClean")) + .map(Boolean::valueOf) + .orElse(Boolean.FALSE); + log.info("deepClean: {}", deepClean); + Class entityClazz = (Class) Class.forName(graphTableClassName); - final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); SparkConf conf = new SparkConf(); + conf.setAppName(CleanGraphSparkJob.class.getSimpleName() + "#" + entityClazz.getSimpleName()); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - cleanGraphTable( - spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, - verifyCountryParam, collectedfrom); - }); + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); + cleanGraphTable( + spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, + verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean); + }); } private static void cleanGraphTable( @@ -109,33 +139,74 @@ public class CleanGraphSparkJob { String inputPath, Class clazz, String outputPath, String contextId, String verifyParam, String datasourcePath, String country, - String[] verifyCountryParam, String collectedfrom) { - - Set hostedBy = Sets - .newHashSet( - spark - .read() - .textFile(datasourcePath) - .collectAsList()); + String[] verifyCountryParam, String collectedfrom, String dsMasterDuplicatePath, + Boolean deepClean) { final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); - readTableFromPath(spark, inputPath, clazz) + final Dataset cleaned_basic = readTableFromPath(spark, inputPath, clazz) .map((MapFunction) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz)) .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) - .filter((FilterFunction) GraphCleaningFunctions::filter) - .map( - (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), - Encoders.bean(clazz)) - .map( - (MapFunction) value -> GraphCleaningFunctions - .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), - Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .filter((FilterFunction) GraphCleaningFunctions::filter); + + if (Boolean.FALSE.equals(deepClean)) { + cleaned_basic + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + + } else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { + + // read the master-duplicate tuples + Dataset md = spark + .read() + .textFile(dsMasterDuplicatePath) + .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); + + // prepare the resolved CF|HB references with the corresponding EMPTY master ID + Dataset resolved = spark + .read() + .textFile(inputPath) + .map(as(clazz), Encoders.bean(clazz)) + .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); + + // set the EMPTY master ID/NAME and save it + resolved + .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) + .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) + .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())); + + // load the hostedby mapping + Set hostedBy = Sets + .newHashSet( + spark + .read() + .textFile(datasourcePath) + .collectAsList()); + + // perform the deep cleaning steps + final Dataset cleaned_deep = cleaned_basic + .map( + (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), + Encoders.bean(clazz)) + .map( + (MapFunction) value -> GraphCleaningFunctions + .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), + Encoders.bean(clazz)); + + // Join the results with the resolved CF|HB mapping, apply the mapping and save it + cleaned_deep + .joinWith(resolved, cleaned_deep.col("id").equalTo(resolved.col("resultId")), "left") + .groupByKey( + (MapFunction, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) + .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } } private static Dataset readTableFromPath( @@ -145,9 +216,98 @@ public class CleanGraphSparkJob { return spark .read() .textFile(inputEntityPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), - Encoders.bean(clazz)); + .map(as(clazz), Encoders.bean(clazz)); + } + + private static MapFunction as(Class clazz) { + return s -> OBJECT_MAPPER.readValue(s, clazz); + } + + private static FlatMapFunction flattenCfHbFn() { + return r -> Stream + .concat( + Optional + .ofNullable(r.getCollectedfrom()) + .map(cf -> cf.stream().map(KeyValue::getKey)) + .orElse(Stream.empty()), + Stream + .concat( + Optional + .ofNullable(((Result) r).getInstance()) + .map( + instances -> instances + .stream() + .map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank), + Optional + .ofNullable(((Result) r).getInstance()) + .map( + instances -> instances + .stream() + .map( + i -> Optional + .ofNullable(i.getCollectedfrom()) + .map(KeyValue::getKey) + .orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank))) + .distinct() + .filter(StringUtils::isNotBlank) + .map(cfHb -> asIdCfHbMapping(((Result) r).getId(), cfHb)) + .iterator(); + } + + private static MapFunction, IdCfHbMapping> asIdCfHbMapping() { + return t -> { + final IdCfHbMapping mapping = t._1(); + Optional + .ofNullable(t._2()) + .ifPresent(t2 -> { + mapping.setMasterId(t2.getMasterId()); + mapping.setMasterName(t2.getMasterName()); + + }); + return mapping; + }; + } + + private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) { + IdCfHbMapping m = new IdCfHbMapping(resultId); + m.setCfhb(cfHb); + return m; + } + + private static MapGroupsFunction, T> getMapGroupsFunction() { + return new MapGroupsFunction, T>() { + @Override + public T call(String key, Iterator> values) { + final Tuple2 first = values.next(); + final T res = first._1(); + + updateResult(res, first._2()); + values.forEachRemaining(t -> updateResult(res, t._2())); + return res; + } + + private void updateResult(T res, IdCfHbMapping m) { + if (Objects.nonNull(m)) { + res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m)); + ((Result) res).getInstance().forEach(i -> { + updateKeyValue(i.getHostedby(), m); + updateKeyValue(i.getCollectedfrom(), m); + }); + } + } + + private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { + if (kv.getKey().equals(a.getCfhb())) { + kv.setKey(a.getMasterId()); + kv.setValue(a.getMasterName()); + } + } + + }; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 2d6371a9b..b5179b1fc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -83,12 +83,17 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn @@ -110,10 +115,25 @@ --workingDir${workingDir}/working/hostedby --country${country} - + + + + eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + --hdfsPath${workingDir}/masterduplicate + --hdfsNameNode${nameNode} + + + + + + + @@ -152,6 +172,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -184,6 +206,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -216,6 +240,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -248,6 +274,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -280,6 +308,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -312,6 +342,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -344,6 +376,8 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -376,206 +410,14 @@ --verifyCountryParam${verifyCountryParam} --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} - - - - - ${wf:conf('shouldClean') eq true} - - - - - - - eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction - --postgresUrl${postgresURL} - --postgresUser${postgresUser} - --postgresPassword${postgresPassword} - --hdfsPath${workingDir}/masterduplicate - --hdfsNameNode${nameNode} - - - - - - - - - - - - - - - yarn - cluster - patch publication cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --resolvedPath${workingDir}/cfHbResolved/publication - --outputPath${workingDir}/cfHbPatched/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch dataset cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --resolvedPath${workingDir}/cfHbResolved/dataset - --outputPath${workingDir}/cfHbPatched/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch otherresearchproduct cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --resolvedPath${workingDir}/cfHbResolved/otherresearchproduct - --outputPath${workingDir}/cfHbPatched/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch software cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --resolvedPath${workingDir}/cfHbResolved/software - --outputPath${workingDir}/cfHbPatched/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - - - - - - - - - - - - - ${workingDir}/cfHbPatched/publication - ${graphOutputPath}/publication - - - - - - - - - - - ${workingDir}/cfHbPatched/dataset - ${graphOutputPath}/dataset - - - - - - - - - - - ${workingDir}/cfHbPatched/otherresearchproduct - ${graphOutputPath}/otherresearchproduct - - - - - - - - - - - ${workingDir}/cfHbPatched/software - ${graphOutputPath}/software - - - - - - + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json index 928215316..0a703763b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json @@ -33,30 +33,48 @@ "paramName": "ci", "paramLongName": "contextId", "paramDescription": "the id of the context to be removed", - "paramRequired": true + "paramRequired": false + }, + { + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "the parameter to be verified to remove the context", + "paramRequired": false }, { "paramName": "c", "paramLongName": "country", "paramDescription": "the id of the context to be removed", - "paramRequired": true + "paramRequired": false }, { "paramName": "vfc", "paramLongName": "verifyCountryParam", "paramDescription": "the parameter to be verified to remove the country", - "paramRequired": true + "paramRequired": false }, { "paramName": "cf", "paramLongName": "collectedfrom", "paramDescription": "the collectedfrom value for which we should apply the cleaning", - "paramRequired": true + "paramRequired": false }, { "paramName": "hb", "paramLongName": "hostedBy", "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results", + "paramRequired": false + }, + { + "paramName": "md", + "paramLongName": "masterDuplicatePath", + "paramDescription": "path to the file on HDFS holding the datasource id tuples [master, duplicate]", + "paramRequired": false + }, + { + "paramName": "dc", + "paramLongName": "deepClean", + "paramDescription": "flag to activate further cleaning steps", "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java new file mode 100644 index 000000000..f01c53d5f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -0,0 +1,435 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.io.filefilter.*; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +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 org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +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.Collection; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; + +@ExtendWith(MockitoExtension.class) +public class CleanGraphSparkJobTest { + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + public static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + + private CleaningRuleMap mapping; + + private static SparkSession spark; + + private static Path workingDir; + + private static Path testBaseTmpPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static String dsMasterDuplicatePath; + + @BeforeAll + public static void beforeAll() throws IOException, URISyntaxException { + testBaseTmpPath = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); + log.info("using test base path {}", testBaseTmpPath); + + File basePath = Paths + .get(CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph").toURI()) + .toFile(); + + + List paths = FileUtils + .listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE) + .stream() + .filter(f -> !f.getAbsolutePath().endsWith("/graph")) + .collect(Collectors.toList()); + + for(File path : paths) { + String type = StringUtils.substringAfterLast(path.getAbsolutePath(), "/"); + FileUtils + .copyDirectory( + path, + testBaseTmpPath.resolve("input").resolve("graph").resolve(type).toFile()); + } + + FileUtils + .copyFileToDirectory( + Paths + .get( + CleanGraphSparkJobTest.class + .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); + + graphInputPath = testBaseTmpPath.resolve("input").resolve("graph").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString(); + dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); + + + + workingDir = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CleanGraphSparkJobTest.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() + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + mapping = CleaningRuleMap.create(vocabularies); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testCleanRelations() throws Exception { + + spark.read() + .textFile(graphInputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach(r -> assertFalse(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()))); + + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/relation", + "--outputPath", graphOutputPath.toString() + "/relation", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Relation.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); + + spark.read() + .textFile(graphOutputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach(r -> { + + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())); + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r.getSubRelType())); + + assertEquals("iis", r.getDataInfo().getProvenanceaction().getClassid()); + assertEquals("Inferred by OpenAIRE", r.getDataInfo().getProvenanceaction().getClassname()); + }); + } + + @Test + void testFilter_invisible_true() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_true_nothing_to_filter() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_missing_invisible() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testCleaning_publication() throws Exception { + + spark.read() + .textFile(graphInputPath.toString() + "/publication") + .map(as(Publication.class), Encoders.bean(Publication.class)) + .collectAsList() + .forEach(p -> { + assertNull(p.getBestaccessright()); + assertTrue(p instanceof Result); + assertTrue(p instanceof Publication); + }); + + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/publication", + "--outputPath", graphOutputPath.toString() + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); + + Publication p = spark.read() + .textFile(graphOutputPath.toString() + "/publication") + .map(as(Publication.class), Encoders.bean(Publication.class)) + .first(); + + assertNull(p.getPublisher()); + + assertEquals("und", p.getLanguage().getClassid()); + assertEquals("Undetermined", p.getLanguage().getClassname()); + + assertEquals("DE", p.getCountry().get(0).getClassid()); + assertEquals("Germany", p.getCountry().get(0).getClassname()); + + assertEquals("0018", p.getInstance().get(0).getInstancetype().getClassid()); + assertEquals("Annotation", p.getInstance().get(0).getInstancetype().getClassname()); + + assertEquals("0027", p.getInstance().get(1).getInstancetype().getClassid()); + assertEquals("Model", p.getInstance().get(1).getInstancetype().getClassname()); + + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + assertEquals("CLOSED", p.getInstance().get(0).getAccessright().getClassid()); + assertEquals("Closed Access", p.getInstance().get(0).getAccessright().getClassname()); + + Set pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES); + assertTrue( + p + .getPid() + .stream() + .map(StructuredProperty::getQualifier) + .allMatch(q -> pidTerms.contains(q.getClassid()))); + + List poi = p.getInstance(); + assertNotNull(poi); + assertEquals(3, poi.size()); + + final Instance poii = poi.get(0); + assertNotNull(poii); + assertNotNull(poii.getPid()); + + assertEquals(2, poii.getPid().size()); + + assertTrue( + poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(poii.getAlternateIdentifier()); + assertEquals(1, poii.getAlternateIdentifier().size()); + + assertTrue( + poii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertEquals(3, p.getTitle().size()); + + + List titles = p + .getTitle() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList()); + assertTrue(titles.contains("omic")); + assertTrue( + titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test")); + assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳")); + + assertEquals("CLOSED", p.getBestaccessright().getClassid()); + assertNull(p.getPublisher()); + + assertEquals("1970-10-07", p.getDateofacceptance().getValue()); + + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + final List pci = p.getInstance(); + assertNotNull(pci); + assertEquals(3, pci.size()); + + final Instance pcii = pci.get(0); + assertNotNull(pcii); + assertNotNull(pcii.getPid()); + + assertEquals(2, pcii.getPid().size()); + + assertTrue( + pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(pcii.getAlternateIdentifier()); + assertEquals(1, pcii.getAlternateIdentifier().size()); + assertTrue( + pcii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertNotNull(p.getSubject()); + + List fos_subjects = p + .getSubject() + .stream() + .filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())) + .collect(Collectors.toList()); + + assertNotNull(fos_subjects); + assertEquals(2, fos_subjects.size()); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0101 mathematics".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & + "sysimport:crosswalk:datasetarchive" + .equals(s.getDataInfo().getProvenanceaction().getClassid()))); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0102 computer and information sciences".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + + verify_keyword(p, "In Situ Hybridization"); + verify_keyword(p, "Avicennia"); + } + + private List vocs() throws IOException { + return IOUtils + .readLines( + GraphCleaningFunctionsTest.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")); + } + + private static MapFunction as(Class clazz) { + return s -> MAPPER.readValue(s, clazz); + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + CleanGraphSparkJobTest.class + .getResourceAsStream(path)); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static void verify_keyword(Publication p_cleaned, String subject) { + Optional s1 = p_cleaned + .getSubject() + .stream() + .filter(s -> s.getValue().equals(subject)) + .findFirst(); + + assertTrue(s1.isPresent()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); + } + + private Stream getAuthorPids(Result pub) { + return pub + .getAuthor() + .stream() + .map(Author::getPid) + .flatMap(Collection::stream); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index fc7c6e5f1..24b942f4d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -13,7 +13,6 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.hdfs.server.datanode.fsdataset.impl.MappableBlock; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -59,7 +58,7 @@ public class GraphCleaningFunctionsTest { void testCleanRelations() throws Exception { List lines = IOUtils - .readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/relation.json")); + .readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/graph/relation/relation.json")); for (String json : lines) { Relation r_in = MAPPER.readValue(json, Relation.class); assertNotNull(r_in); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json new file mode 100644 index 000000000..5bac26fdc --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json @@ -0,0 +1 @@ +{"author":[{"affiliation":[],"fullname":"Brien, Tom","name":"Tom","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"https://orcid.org/0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"orcid","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"}],"rank":1,"surname":"Brien"},{"affiliation":[],"fullname":"Ade, Peter","name":"Peter","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"xyz","classname":"XYZ","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"qwerty"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"","schemename":""},"value":"asdasd"}],"rank":2,"surname":"Ade"},{"affiliation":[],"fullname":"Barry, Peter S.","name":"Peter S.","pid":null,"rank":3,"surname":"Barry"},{"affiliation":[],"fullname":"Dunscombe, Chris J.","name":"Chris J.","pid":[],"rank":4,"surname":"Dunscombe"},{"affiliation":[],"fullname":"Leadley, David R.","name":"David R.","pid":[],"rank":5,"surname":"Leadley"},{"affiliation":[],"fullname":"Morozov, Dmitry V.","name":"Dmitry V.","pid":[],"rank":6,"surname":"Morozov"},{"affiliation":[],"fullname":"Myronov, Maksym","name":"Maksym","pid":[],"rank":7,"surname":"Myronov"},{"affiliation":[],"fullname":"Parker, Evan","name":"Evan","pid":[],"rank":8,"surname":"Parker"},{"affiliation":[],"fullname":"Prest, Martin J.","name":"Martin J.","pid":[],"rank":9,"surname":"Prest"},{"affiliation":[],"fullname":"Prunnila, Mika","name":"Mika","pid":[],"rank":10,"surname":"Prunnila"},{"affiliation":[],"fullname":"Sudiwala, Rashmi V.","name":"Rashmi V.","pid":[],"rank":11,"surname":"Sudiwala"},{"affiliation":[],"fullname":"Whall, Terry E.","name":"Terry E.","pid":[],"rank":12,"surname":"Whall"},{"affiliation":[],"fullname":"Mauskopf","name":"","pid":[],"rank":13,"surname":""},{"affiliation":[],"fullname":" P. 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dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/relation/relation.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/logback.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/logback.xml new file mode 100644 index 000000000..77a7627b5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/logback.xml @@ -0,0 +1,11 @@ + + + + %d{HH:mm:ss.SSS} %-5level %logger{36} - %msg%n + + + + + + + \ No newline at end of file From 488d9a5eaa5eccecaac7549d918858adabc72799 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 23 Mar 2023 10:41:13 +0100 Subject: [PATCH 04/10] [graph cleaning] WIP: refactoring of the cleaning stages, unit tests --- .../oa/graph/clean/CleanGraphSparkJob.java | 10 +- .../graph/clean/CleanGraphSparkJobTest.java | 429 +++++++++++++++++- .../oa/graph/clean/graph/dataset/dataset.json | 3 - .../clean/graph/publication/publication.json | 21 +- .../clean/publication_clean_context.json | 7 - .../clean/publication_clean_country.json | 16 +- 6 files changed, 448 insertions(+), 38 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index ca77be3c6..23a56a445 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -292,7 +292,7 @@ public class CleanGraphSparkJob { private void updateResult(T res, IdCfHbMapping m) { if (Objects.nonNull(m)) { - res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m)); + filter(res.getCollectedfrom()).forEach(kv -> updateKeyValue(kv, m)); ((Result) res).getInstance().forEach(i -> { updateKeyValue(i.getHostedby(), m); updateKeyValue(i.getCollectedfrom(), m); @@ -300,8 +300,14 @@ public class CleanGraphSparkJob { } } + private Stream filter(List kvs) { + return kvs + .stream() + .filter(kv -> StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue())); + } + private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { - if (kv.getKey().equals(a.getCfhb())) { + if (Objects.nonNull(kv) && Objects.nonNull(kv.getKey()) && kv.getKey().equals(a.getCfhb())) { kv.setKey(a.getMasterId()); kv.setValue(a.getMasterName()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index f01c53d5f..68fdf699f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -4,6 +4,8 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; @@ -15,15 +17,15 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.io.filefilter.*; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; @@ -233,16 +235,16 @@ public class CleanGraphSparkJobTest { @Test void testCleaning_publication() throws Exception { - spark.read() - .textFile(graphInputPath.toString() + "/publication") - .map(as(Publication.class), Encoders.bean(Publication.class)) - .collectAsList() - .forEach(p -> { - assertNull(p.getBestaccessright()); - assertTrue(p instanceof Result); - assertTrue(p instanceof Publication); - }); - + final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; + + Publication p_in = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) + .first(); + + assertNull(p_in.getBestaccessright()); + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + new CleanGraphSparkJob( args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", new String[] { @@ -253,9 +255,8 @@ public class CleanGraphSparkJobTest { "--deepClean", "false" })).run(false, isLookUpService); - Publication p = spark.read() - .textFile(graphOutputPath.toString() + "/publication") - .map(as(Publication.class), Encoders.bean(Publication.class)) + Publication p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) .first(); assertNull(p.getPublisher()); @@ -383,6 +384,393 @@ public class CleanGraphSparkJobTest { verify_keyword(p, "Avicennia"); } + @Test + public void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2"); + } + + @Test + public void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656"); + } + + private void verifyFiltering(int expectedCount, String id) throws ISLookUpException, ClassNotFoundException, IOException, ParseException { + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/publication", + "--outputPath", graphOutputPath.toString() + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); + + Dataset p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)); + + assertEquals(expectedCount, p.count()); + } + + @Test + public void testCleanContext() throws Exception { + final String prefix = "gcube "; + + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/publication", + "--outputPath", graphOutputPath.toString() + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + })).run(false, isLookUpService); + + Dataset pubs = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter((FilterFunction) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); + + Assertions.assertEquals(7, pubs.count()); + + // original result with sobigdata context and gcube as starting string in the main title for the publication + assertEquals( + 0, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx")) + .first() + .getContext() + .size()); + + // original result with sobigdata context without gcube as starting string in the main title for the publication + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + // original result with sobigdata context with gcube as starting string in the subtitle + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + List titles = pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata context with gcube not as starting string in the main title + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::1", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + // original result without sobigdata in context with gcube as starting string for the main title + assertEquals( + 1, + pubs + .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + } + + @Test + void testCleanCfHbSparkJob() throws Exception { + + final Dataset pubs_in = read(spark, graphInputPath.toString() + "/publication", Publication.class); + final Publication p1_in = pubs_in + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_in = pubs_in + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar - DUP", p2_in.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_in = pubs_in + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue()); + + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/publication", + "--outputPath", graphOutputPath.toString() + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + })).run(false, isLookUpService); + + assertTrue(Files.exists(Paths.get(graphOutputPath, "publication"))); + + final Dataset pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_cfhb")); + + assertEquals(3, pubs_out.count()); + + final Publication p1_out = pubs_out + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_out = pubs_out + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey()); + assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar", p2_out.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_out = pubs_out + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue()); + } + + @Test + public void testCleanCountry() throws Exception { + + new CleanGraphSparkJob( + args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath.toString() + "/publication", + "--outputPath", graphOutputPath.toString() + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + })).run(false, isLookUpService); + + + final Dataset pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_country")); + + Assertions.assertEquals(7, pubs_out.count()); + + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + assertEquals( + 1, + pubs_out + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and pid not starting with Mendely prefix + assertEquals( + 1, + pubs_out + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not + // inserted with propagation + assertEquals( + 1, + pubs_out + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with + // propagation + assertEquals( + 0, + pubs_out + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) + .first() + .getCountry() + .size()); + } + private List vocs() throws IOException { return IOUtils .readLines( @@ -395,6 +783,13 @@ public class CleanGraphSparkJobTest { GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } + private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { + return spark + .read() + .textFile(path) + .map(as(clazz), Encoders.bean(clazz)); + } + private static MapFunction as(Class clazz) { return s -> MAPPER.readValue(s, clazz); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json index bf2f2d963..e69de29bb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/dataset/dataset.json @@ -1,3 +0,0 @@ -{"author":[{"affiliation":[],"fullname":"Greenough, B","name":"B","pid":[],"rank":1,"surname":"Greenough"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc","value":"Bacterial Protein Interaction Database - DUP"}],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofcollection":"2021-09-25T10:55:00.639Z","dateoftransformation":"2021-09-25T11:00:04.201Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Heritage Education"}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"geolocation":[],"id":"50|doi_________::09821844208a5cd6300b2bfb13bca1b9","instance":[{"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"urn","classname":"urn","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"urn:nbn:nl:ui:13-59-cjhf"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.17632/96bpgw5j9d.1"}],"collectedfrom":{"key":"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc","value":"Bacterial Protein Interaction Database - DUP"},"hostedby":{"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"},"instancetype":{"classid":"0021","classname":"Dataset","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"alternateIdentifier":[],"refereed":{"classid":"0000","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["","http://dx.doi.org/10.17632/96bpgw5j9d.1"]}],"language":{"classid":"und","classname":"Undetermined","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1635434801681,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"http%3A%2F%2Fservices.nod.dans.knaw.nl%2Foa-cerif","datestamp":"2021-08-16T15:29:45Z","harvestDate":"2021-09-25T10:55:00.639Z","identifier":"oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:211323","metadataNamespace":""}},"originalId":["50|DansKnawCris::09821844208a5cd6300b2bfb13bca1b9","oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:211323"],"pid":[],"relevantdate":[],"resourcetype":{"classid":"0021","classname":"0021","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[],"subject":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Interdisciplinary sciences"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Interdisciplinary sciences"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Heritage Education"}]} -{"author":[{"affiliation":[],"fullname":"Keijers, D.M.G.","name":"D.M.G.","pid":[],"rank":1,"surname":"Keijers"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35","value":"FILUR DATA - 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Claudio Atzori Date: Thu, 23 Mar 2023 15:03:26 +0100 Subject: [PATCH 05/10] [graph cleaning] WIP: refactoring of the cleaning stages, unit tests --- .../dhp/oa/graph/clean/CleanGraphSparkJobTest.java | 8 ++++---- .../dhp/oa/graph/clean/graph/publication/publication.json | 3 ++- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 68fdf699f..f27169082 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -237,7 +237,7 @@ public class CleanGraphSparkJobTest { final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; - Publication p_in = read(spark, graphOutputPath.toString() + "/publication", Publication.class) + Publication p_in = read(spark, graphInputPath.toString() + "/publication", Publication.class) .filter(String.format("id = '%s'", id)) .first(); @@ -437,7 +437,7 @@ public class CleanGraphSparkJobTest { Dataset pubs = read(spark, graphOutputPath.toString() + "/publication", Publication.class) .filter((FilterFunction) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); - Assertions.assertEquals(7, pubs.count()); + assertEquals(7, pubs.count()); // original result with sobigdata context and gcube as starting string in the main title for the publication assertEquals( @@ -730,7 +730,7 @@ public class CleanGraphSparkJobTest { final Dataset pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_country")); - Assertions.assertEquals(7, pubs_out.count()); + assertEquals(8, pubs_out.count()); // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS assertEquals( @@ -765,7 +765,7 @@ public class CleanGraphSparkJobTest { assertEquals( 0, pubs_out - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) + .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country")) .first() .getCountry() .size()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json index f0476e13c..e5d7c88db 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json @@ -17,4 +17,5 @@ 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17 00:00:00 2001 From: Claudio Atzori Date: Thu, 23 Mar 2023 15:57:47 +0100 Subject: [PATCH 06/10] [graph cleaning] unit tests & cleanup --- .../oa/graph/clean/CleanContextSparkJob.java | 122 -- .../oa/graph/clean/CleanGraphSparkJob.java | 85 +- .../GetDatasourceFromCountry.java | 4 +- .../graph/clean/{cfhb => }/IdCfHbMapping.java | 2 +- .../graph/clean/cfhb/CleanCfHbSparkJob.java | 227 --- .../clean/country/CleanCountrySparkJob.java | 211 -- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 2 +- .../dhp/oa/graph/clean/CleanContextTest.java | 289 --- .../dhp/oa/graph/clean/CleanCountryTest.java | 190 -- .../graph/clean/CleanGraphSparkJobTest.java | 1707 +++++++++-------- .../clean/cfhb/CleanCfHbSparkJobTest.java | 213 -- 11 files changed, 944 insertions(+), 2108 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/{country => }/GetDatasourceFromCountry.java (96%) rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/{cfhb => }/IdCfHbMapping.java (94%) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java deleted file mode 100644 index 10a3d4465..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ /dev/null @@ -1,122 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); - - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); - - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir); - }); - } - - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, - String inputPath, Class entityClazz, String workingDir) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if (!r - .getTitle() - .stream() - .filter( - t -> t - .getQualifier() - .getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { - return r; - } - r - .setContext( - r - .getContext() - .stream() - .filter( - c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)) - .collect(Collectors.toList())); - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir); - - spark - .read() - .textFile(workingDir) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 23a56a445..e97ff3cb2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -4,10 +4,8 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import java.util.stream.Collectors; import java.util.stream.Stream; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -29,8 +27,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.action.model.MasterDuplicate; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.cfhb.IdCfHbMapping; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; @@ -38,6 +34,7 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; 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; @@ -55,17 +52,17 @@ public class CleanGraphSparkJob { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - CleanGraphSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); + .toString( + CleanGraphSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String isLookupUrl = parser.get("isLookupUrl"); @@ -76,7 +73,8 @@ public class CleanGraphSparkJob { new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup); } - public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) throws ISLookUpException, ClassNotFoundException { + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException, ClassNotFoundException { String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); @@ -99,9 +97,10 @@ public class CleanGraphSparkJob { String country = parser.get("country"); log.info("country: {}", country); - String[] verifyCountryParam = Optional.ofNullable(parser.get("verifyCountryParam")) - .map(s -> s.split(";")) - .orElse(new String[]{}); + String[] verifyCountryParam = Optional + .ofNullable(parser.get("verifyCountryParam")) + .map(s -> s.split(";")) + .orElse(new String[] {}); log.info("verifyCountryParam: {}", verifyCountryParam); String collectedfrom = parser.get("collectedfrom"); @@ -111,9 +110,9 @@ public class CleanGraphSparkJob { log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); Boolean deepClean = Optional - .ofNullable(parser.get("deepClean")) - .map(Boolean::valueOf) - .orElse(Boolean.FALSE); + .ofNullable(parser.get("deepClean")) + .map(Boolean::valueOf) + .orElse(Boolean.FALSE); log.info("deepClean: {}", deepClean); Class entityClazz = (Class) Class.forName(graphTableClassName); @@ -123,14 +122,14 @@ public class CleanGraphSparkJob { SparkConf conf = new SparkConf(); conf.setAppName(CleanGraphSparkJob.class.getSimpleName() + "#" + entityClazz.getSimpleName()); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - cleanGraphTable( - spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, - verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean); - }); + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); + cleanGraphTable( + spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, + verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean); + }); } private static void cleanGraphTable( @@ -172,33 +171,33 @@ public class CleanGraphSparkJob { .map(as(clazz), Encoders.bean(clazz)) .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); - // set the EMPTY master ID/NAME and save it - resolved + // set the EMPTY master ID/NAME + Dataset resolvedDs = resolved .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())); // load the hostedby mapping Set hostedBy = Sets - .newHashSet( - spark - .read() - .textFile(datasourcePath) - .collectAsList()); + .newHashSet( + spark + .read() + .textFile(datasourcePath) + .collectAsList()); // perform the deep cleaning steps final Dataset cleaned_deep = cleaned_basic - .map( - (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), - Encoders.bean(clazz)) - .map( - (MapFunction) value -> GraphCleaningFunctions - .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), - Encoders.bean(clazz)); + .map( + (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), + Encoders.bean(clazz)) + .map( + (MapFunction) value -> GraphCleaningFunctions + .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), + Encoders.bean(clazz)); // Join the results with the resolved CF|HB mapping, apply the mapping and save it cleaned_deep - .joinWith(resolved, cleaned_deep.col("id").equalTo(resolved.col("resultId")), "left") + .joinWith(resolvedDs, cleaned_deep.col("id").equalTo(resolvedDs.col("resultId")), "left") .groupByKey( (MapFunction, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)) @@ -302,8 +301,8 @@ public class CleanGraphSparkJob { private Stream filter(List kvs) { return kvs - .stream() - .filter(kv -> StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue())); + .stream() + .filter(kv -> StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue())); } private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java similarity index 96% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java index 598fccdd7..a69b1a8bf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java @@ -1,10 +1,9 @@ -package eu.dnetlib.dhp.oa.graph.clean.country; +package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -21,7 +20,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java similarity index 94% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java index fad1129c5..a560360ba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.oa.graph.clean.cfhb; +package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java deleted file mode 100644 index 531b415ed..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java +++ /dev/null @@ -1,227 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.cfhb; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Iterator; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; -import org.apache.spark.sql.expressions.Aggregator; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.action.model.MasterDuplicate; -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -public class CleanCfHbSparkJob { - - private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanCountrySparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String resolvedPath = parser.get("resolvedPath"); - log.info("resolvedPath: {}", resolvedPath); - - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - String dsMasterDuplicatePath = parser.get("masterDuplicatePath"); - log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration()); - cleanCfHb( - spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath); - }); - } - - private static void cleanCfHb(SparkSession spark, String inputPath, Class entityClazz, - String resolvedPath, String masterDuplicatePath, String outputPath) { - - // read the master-duplicate tuples - Dataset md = spark - .read() - .textFile(masterDuplicatePath) - .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); - - // prepare the resolved CF|HB references with the corresponding EMPTY master ID - Dataset resolved = spark - .read() - .textFile(inputPath) - .map(as(entityClazz), Encoders.bean(entityClazz)) - .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); - - // set the EMPTY master ID/NAME and save it - resolved - .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) - .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) - .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())) - .write() - .mode(SaveMode.Overwrite) - .json(resolvedPath); - - // read again the resolved CF|HB mapping - Dataset resolvedDS = spark - .read() - .textFile(resolvedPath) - .map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class)); - - // read the result table - Dataset res = spark - .read() - .textFile(inputPath) - .map(as(entityClazz), Encoders.bean(entityClazz)); - - // Join the results with the resolved CF|HB mapping, apply the mapping and save it - res - .joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left") - .groupByKey((MapFunction, String>) t -> t._1().getId(), Encoders.STRING()) - .mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static MapFunction, IdCfHbMapping> asIdCfHbMapping() { - return t -> { - final IdCfHbMapping mapping = t._1(); - Optional - .ofNullable(t._2()) - .ifPresent(t2 -> { - mapping.setMasterId(t2.getMasterId()); - mapping.setMasterName(t2.getMasterName()); - - }); - return mapping; - }; - } - - private static FlatMapFunction flattenCfHbFn() { - return r -> Stream - .concat( - Optional - .ofNullable(r.getCollectedfrom()) - .map(cf -> cf.stream().map(KeyValue::getKey)) - .orElse(Stream.empty()), - Stream - .concat( - Optional - .ofNullable(r.getInstance()) - .map( - instances -> instances - .stream() - .map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse(""))) - .orElse(Stream.empty()) - .filter(StringUtils::isNotBlank), - Optional - .ofNullable(r.getInstance()) - .map( - instances -> instances - .stream() - .map( - i -> Optional - .ofNullable(i.getCollectedfrom()) - .map(KeyValue::getKey) - .orElse(""))) - .orElse(Stream.empty()) - .filter(StringUtils::isNotBlank))) - .distinct() - .filter(StringUtils::isNotBlank) - .map(cfHb -> asIdCfHbMapping(r.getId(), cfHb)) - .iterator(); - } - - private static MapGroupsFunction, T> getMapGroupsFunction() { - return new MapGroupsFunction, T>() { - @Override - public T call(String key, Iterator> values) { - final Tuple2 first = values.next(); - final T res = first._1(); - - updateResult(res, first._2()); - values.forEachRemaining(t -> updateResult(res, t._2())); - return res; - } - - private void updateResult(T res, IdCfHbMapping m) { - if (Objects.nonNull(m)) { - res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m)); - res.getInstance().forEach(i -> { - updateKeyValue(i.getHostedby(), m); - updateKeyValue(i.getCollectedfrom(), m); - }); - } - } - - private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { - if (kv.getKey().equals(a.getCfhb())) { - kv.setKey(a.getMasterId()); - kv.setValue(a.getMasterName()); - } - } - - }; - } - - private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) { - IdCfHbMapping m = new IdCfHbMapping(resultId); - m.setCfhb(cfHb); - return m; - } - - private static MapFunction as(Class clazz) { - return s -> OBJECT_MAPPER.readValue(s, clazz); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java deleted file mode 100644 index 37e693de9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ /dev/null @@ -1,211 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.country; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Collection; -import java.util.List; -import java.util.Optional; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import javax.swing.text.html.Option; - -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; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; - -public class CleanCountrySparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanCountrySparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); - - String datasourcePath = parser.get("hostedBy"); - log.info("datasourcePath: {}", datasourcePath); - - String country = parser.get("country"); - log.info("country: {}", country); - - String[] verifyParam = parser.get("verifyParam").split(";"); - log.info("verifyParam: {}", verifyParam); - - String collectedfrom = parser.get("collectedfrom"); - log.info("collectedfrom: {}", collectedfrom); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - - cleanCountry( - spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath); - }); - } - - private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, - String inputPath, Class entityClazz, String workingDir, String collectedfrom, String datasourcePath) { - - List hostedBy = spark - .read() - .textFile(datasourcePath) - .collectAsList(); - - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || - !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { - return r; - } - - List ids = getPidsAndAltIds(r).collect(Collectors.toList()); - if (ids - .stream() - .anyMatch( - p -> p - .getQualifier() - .getClassid() - .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { - r - .setCountry( - r - .getCountry() - .stream() - .filter( - c -> toTakeCountry(c, country)) - .collect(Collectors.toList())); - - } - - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir); - - spark - .read() - .textFile(workingDir) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath); - } - - private static Stream getPidsAndAltIds(T r) { - final Stream resultPids = Optional - .ofNullable(r.getPid()) - .map(Collection::stream) - .orElse(Stream.empty()); - - final Stream instancePids = Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .flatMap( - i -> Optional - .ofNullable(i.getPid()) - .map(Collection::stream) - .orElse(Stream.empty()))) - .orElse(Stream.empty()); - - final Stream instanceAltIds = Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .flatMap( - i -> Optional - .ofNullable(i.getAlternateIdentifier()) - .map(Collection::stream) - .orElse(Stream.empty()))) - .orElse(Stream.empty()); - - return Stream - .concat( - Stream.concat(resultPids, instancePids), - instanceAltIds); - } - - private static boolean pidInParam(String value, String[] verifyParam) { - for (String s : verifyParam) - if (value.startsWith(s)) - return true; - return false; - } - - private static boolean toTakeCountry(Country c, String country) { - // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be - // inserted via propagation - if (!Optional.ofNullable(c.getDataInfo()).isPresent()) - return true; - if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) - return true; - return !(c - .getClassid() - .equalsIgnoreCase(country) && - c.getDataInfo().getInferenceprovenance().equals("propagation")); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index b5179b1fc..505c78c34 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -99,7 +99,7 @@ yarn cluster Select datasource ID from country - eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry + eu.dnetlib.dhp.oa.graph.clean.GetDatasourceFromCountry dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCores} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java deleted file mode 100644 index 91094f534..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ /dev/null @@ -1,289 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -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.api.java.function.MapFunction; -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 eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; - -public class CleanContextTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanContextTest.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(CleanContextTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), - Encoders.bean(Publication.class)) - .write() - .json(workingDir.toString() + "/publication"); - - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--workingDir", workingDir.toString() + "/working", - "--contextId", "sobigdata", - "--verifyParam", "gCube " - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(7, tmp.count()); - - // original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getContext() - .size()); - - // original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::2", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - - // original result with sobigdata context with gcube as starting string in the subtitle - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::2", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - List titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata context with gcube not as starting string in the main title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::1", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata in context and also other contexts with gcube as starting string for the main - // title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions - .assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - // original result without sobigdata in context with gcube as starting string for the main title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions - .assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java deleted file mode 100644 index 3bc69cfd1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ /dev/null @@ -1,190 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -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.api.java.function.MapFunction; -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; - -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Publication; - -public class CleanCountryTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanCountryTest.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(CleanCountryTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") - .getPath(); - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), - Encoders.bean(Publication.class)) - .write() - .json(workingDir.toString() + "/publication"); - - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--workingDir", workingDir.toString() + "/working", - "--country", "NL", - "--verifyParam", "10.17632", - "--collectedfrom", "NARCIS", - "--hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(8, tmp.count()); - - // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and pid not starting with Mendely prefix - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not - // inserted with propagation - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with - // propagation - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag")) - .collect() - .get(0) - .getCountry() - .size()); - } - - @Test - public void testDatasetClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") - .getPath(); - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .json(workingDir.toString() + "/dataset"); - - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/dataset", - "-graphTableClassName", Dataset.class.getCanonicalName(), - "-workingDir", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS", - "-hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(1, tmp.count()); - - Assertions.assertEquals(0, tmp.first().getCountry().size()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index f27169082..5b021af01 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -1,36 +1,8 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob; -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import org.apache.commons.cli.ParseException; -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.apache.commons.io.filefilter.*; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.api.java.function.MapFunction; -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 org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; import java.io.File; import java.io.IOException; @@ -38,793 +10,912 @@ import java.net.URISyntaxException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; -import java.util.Collection; -import java.util.List; -import java.util.Optional; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; -import java.util.stream.Stream; -import static org.junit.jupiter.api.Assertions.*; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.io.filefilter.FalseFileFilter; +import org.apache.commons.io.filefilter.TrueFileFilter; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +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 org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class CleanGraphSparkJobTest { - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJobTest.class); + + public static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + + private CleaningRuleMap mapping; + + private static SparkSession spark; + + private static Path testBaseTmpPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static String dsMasterDuplicatePath; + + @BeforeAll + public static void beforeAll() throws IOException, URISyntaxException { + testBaseTmpPath = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); + log.info("using test base path {}", testBaseTmpPath); + + File basePath = Paths + .get( + Objects + .requireNonNull( + CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph")) + .toURI()) + .toFile(); + + List paths = FileUtils + .listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE) + .stream() + .filter(f -> !f.getAbsolutePath().endsWith("/graph")) + .collect(Collectors.toList()); + + for (File path : paths) { + String type = StringUtils.substringAfterLast(path.getAbsolutePath(), "/"); + FileUtils + .copyDirectory( + path, + testBaseTmpPath.resolve("input").resolve("graph").resolve(type).toFile()); + } + + FileUtils + .copyFileToDirectory( + Paths + .get( + CleanGraphSparkJobTest.class + .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); + + graphInputPath = testBaseTmpPath.resolve("input").resolve("graph").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString(); + dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); + + SparkConf conf = new SparkConf(); + conf.setAppName(CleanGraphSparkJobTest.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", testBaseTmpPath.toString()); + conf.set("hive.metastore.warehouse.dir", testBaseTmpPath.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + mapping = CleaningRuleMap.create(vocabularies); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + spark.stop(); + } + + @Test + void testCleanRelations() throws Exception { + + spark + .read() + .textFile(graphInputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach( + r -> assertFalse( + vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()))); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/relation", + "--outputPath", graphOutputPath + "/relation", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Relation.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); + + spark + .read() + .textFile(graphOutputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach(r -> { + + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())); + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r.getSubRelType())); + + assertEquals("iis", r.getDataInfo().getProvenanceaction().getClassid()); + assertEquals("Inferred by OpenAIRE", r.getDataInfo().getProvenanceaction().getClassname()); + }); + } + + @Test + void testFilter_invisible_true() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_true_nothing_to_filter() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_missing_invisible() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testCleaning_publication() throws Exception { + + final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; + + Publication p_in = read(spark, graphInputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) + .first(); + + assertNull(p_in.getBestaccessright()); + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); - public static final ObjectMapper MAPPER = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + Publication p = read(spark, graphOutputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) + .first(); + + assertNull(p.getPublisher()); - @Mock - private ISLookUpService isLookUpService; + assertEquals("und", p.getLanguage().getClassid()); + assertEquals("Undetermined", p.getLanguage().getClassname()); - private VocabularyGroup vocabularies; + assertEquals("DE", p.getCountry().get(0).getClassid()); + assertEquals("Germany", p.getCountry().get(0).getClassname()); - private CleaningRuleMap mapping; + assertEquals("0018", p.getInstance().get(0).getInstancetype().getClassid()); + assertEquals("Annotation", p.getInstance().get(0).getInstancetype().getClassname()); + + assertEquals("0027", p.getInstance().get(1).getInstancetype().getClassid()); + assertEquals("Model", p.getInstance().get(1).getInstancetype().getClassname()); - private static SparkSession spark; - - private static Path workingDir; - - private static Path testBaseTmpPath; - - private static String graphInputPath; - - private static String graphOutputPath; - - private static String dsMasterDuplicatePath; - - @BeforeAll - public static void beforeAll() throws IOException, URISyntaxException { - testBaseTmpPath = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); - log.info("using test base path {}", testBaseTmpPath); - - File basePath = Paths - .get(CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph").toURI()) - .toFile(); - - - List paths = FileUtils - .listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE) - .stream() - .filter(f -> !f.getAbsolutePath().endsWith("/graph")) - .collect(Collectors.toList()); - - for(File path : paths) { - String type = StringUtils.substringAfterLast(path.getAbsolutePath(), "/"); - FileUtils - .copyDirectory( - path, - testBaseTmpPath.resolve("input").resolve("graph").resolve(type).toFile()); - } - - FileUtils - .copyFileToDirectory( - Paths - .get( - CleanGraphSparkJobTest.class - .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") - .toURI()) - .toFile(), - testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); - - graphInputPath = testBaseTmpPath.resolve("input").resolve("graph").toString(); - graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString(); - dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); - - - - workingDir = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanGraphSparkJobTest.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() - .config(conf) - .getOrCreate(); - } - - @BeforeEach - public void setUp() throws ISLookUpException, IOException { - lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); - lenient() - .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) - .thenReturn(synonyms()); - - vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); - mapping = CleaningRuleMap.create(vocabularies); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testCleanRelations() throws Exception { - - spark.read() - .textFile(graphInputPath.toString() + "/relation") - .map(as(Relation.class), Encoders.bean(Relation.class)) - .collectAsList() - .forEach(r -> assertFalse(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()))); - - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/relation", - "--outputPath", graphOutputPath.toString() + "/relation", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Relation.class.getCanonicalName(), - "--deepClean", "false" - })).run(false, isLookUpService); - - spark.read() - .textFile(graphOutputPath.toString() + "/relation") - .map(as(Relation.class), Encoders.bean(Relation.class)) - .collectAsList() - .forEach(r -> { - - assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())); - assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r.getSubRelType())); - - assertEquals("iis", r.getDataInfo().getProvenanceaction().getClassid()); - assertEquals("Inferred by OpenAIRE", r.getDataInfo().getProvenanceaction().getClassname()); - }); - } - - @Test - void testFilter_invisible_true() throws Exception { - - assertNotNull(vocabularies); - assertNotNull(mapping); - - String json = IOUtils - .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")); - Publication p_in = MAPPER.readValue(json, Publication.class); - - assertTrue(p_in instanceof Result); - assertTrue(p_in instanceof Publication); - - assertEquals(true, GraphCleaningFunctions.filter(p_in)); - } - - @Test - void testFilter_true_nothing_to_filter() throws Exception { - - assertNotNull(vocabularies); - assertNotNull(mapping); - - String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); - Publication p_in = MAPPER.readValue(json, Publication.class); - - assertTrue(p_in instanceof Result); - assertTrue(p_in instanceof Publication); - - assertEquals(true, GraphCleaningFunctions.filter(p_in)); - } - - @Test - void testFilter_missing_invisible() throws Exception { - - assertNotNull(vocabularies); - assertNotNull(mapping); - - String json = IOUtils - .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")); - Publication p_in = MAPPER.readValue(json, Publication.class); - - assertTrue(p_in instanceof Result); - assertTrue(p_in instanceof Publication); - - assertEquals(true, GraphCleaningFunctions.filter(p_in)); - } - - @Test - void testCleaning_publication() throws Exception { - - final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; - - Publication p_in = read(spark, graphInputPath.toString() + "/publication", Publication.class) - .filter(String.format("id = '%s'", id)) - .first(); - - assertNull(p_in.getBestaccessright()); - assertTrue(p_in instanceof Result); - assertTrue(p_in instanceof Publication); - - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/publication", - "--outputPath", graphOutputPath.toString() + "/publication", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "false" - })).run(false, isLookUpService); - - Publication p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) - .filter(String.format("id = '%s'", id)) - .first(); - - assertNull(p.getPublisher()); - - assertEquals("und", p.getLanguage().getClassid()); - assertEquals("Undetermined", p.getLanguage().getClassname()); - - assertEquals("DE", p.getCountry().get(0).getClassid()); - assertEquals("Germany", p.getCountry().get(0).getClassname()); - - assertEquals("0018", p.getInstance().get(0).getInstancetype().getClassid()); - assertEquals("Annotation", p.getInstance().get(0).getInstancetype().getClassname()); - - assertEquals("0027", p.getInstance().get(1).getInstancetype().getClassid()); - assertEquals("Model", p.getInstance().get(1).getInstancetype().getClassname()); - - assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); - assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); - - assertEquals("CLOSED", p.getInstance().get(0).getAccessright().getClassid()); - assertEquals("Closed Access", p.getInstance().get(0).getAccessright().getClassname()); - - Set pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES); - assertTrue( - p - .getPid() - .stream() - .map(StructuredProperty::getQualifier) - .allMatch(q -> pidTerms.contains(q.getClassid()))); - - List poi = p.getInstance(); - assertNotNull(poi); - assertEquals(3, poi.size()); - - final Instance poii = poi.get(0); - assertNotNull(poii); - assertNotNull(poii.getPid()); - - assertEquals(2, poii.getPid().size()); - - assertTrue( - poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); - assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); - - assertNotNull(poii.getAlternateIdentifier()); - assertEquals(1, poii.getAlternateIdentifier().size()); - - assertTrue( - poii - .getAlternateIdentifier() - .stream() - .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); - - assertEquals(3, p.getTitle().size()); - - - List titles = p - .getTitle() - .stream() - .map(StructuredProperty::getValue) - .collect(Collectors.toList()); - assertTrue(titles.contains("omic")); - assertTrue( - titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test")); - assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳")); - - assertEquals("CLOSED", p.getBestaccessright().getClassid()); - assertNull(p.getPublisher()); - - assertEquals("1970-10-07", p.getDateofacceptance().getValue()); - - assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); - assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); - - final List pci = p.getInstance(); - assertNotNull(pci); - assertEquals(3, pci.size()); - - final Instance pcii = pci.get(0); - assertNotNull(pcii); - assertNotNull(pcii.getPid()); - - assertEquals(2, pcii.getPid().size()); - - assertTrue( - pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); - assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); - - assertNotNull(pcii.getAlternateIdentifier()); - assertEquals(1, pcii.getAlternateIdentifier().size()); - assertTrue( - pcii - .getAlternateIdentifier() - .stream() - .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); - - assertNotNull(p.getSubject()); - - List fos_subjects = p - .getSubject() - .stream() - .filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())) - .collect(Collectors.toList()); - - assertNotNull(fos_subjects); - assertEquals(2, fos_subjects.size()); - - assertTrue( - fos_subjects - .stream() - .anyMatch( - s -> "0101 mathematics".equals(s.getValue()) & - ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & - "sysimport:crosswalk:datasetarchive" - .equals(s.getDataInfo().getProvenanceaction().getClassid()))); - - assertTrue( - fos_subjects - .stream() - .anyMatch( - s -> "0102 computer and information sciences".equals(s.getValue()) & - ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); - - verify_keyword(p, "In Situ Hybridization"); - verify_keyword(p, "Avicennia"); - } - - @Test - public void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { - verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2"); - } - - @Test - public void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { - verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656"); - } - - private void verifyFiltering(int expectedCount, String id) throws ISLookUpException, ClassNotFoundException, IOException, ParseException { - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/publication", - "--outputPath", graphOutputPath.toString() + "/publication", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "false" - })).run(false, isLookUpService); - - Dataset p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) - .filter(String.format("id = '%s'", id)); - - assertEquals(expectedCount, p.count()); - } - - @Test - public void testCleanContext() throws Exception { - final String prefix = "gcube "; - - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/publication", - "--outputPath", graphOutputPath.toString() + "/publication", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "true", - "--contextId", "sobigdata", - "--verifyParam", "gCube ", - "--masterDuplicatePath", dsMasterDuplicatePath, - "--country", "NL", - "--verifyCountryParam", "10.17632", - "--collectedfrom", "NARCIS", - "--hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - })).run(false, isLookUpService); - - Dataset pubs = read(spark, graphOutputPath.toString() + "/publication", Publication.class) - .filter((FilterFunction) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); - - assertEquals(7, pubs.count()); - - // original result with sobigdata context and gcube as starting string in the main title for the publication - assertEquals( - 0, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx")) - .first() - .getContext() - .size()); - - // original result with sobigdata context without gcube as starting string in the main title for the publication - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "sobigdata::projects::2", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) - .first() - .getContext() - .get(0) - .getId()); - - // original result with sobigdata context with gcube as starting string in the subtitle - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "sobigdata::projects::2", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) - .first() - .getContext() - .get(0) - .getId()); - - List titles = pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) - .first() - .getTitle(); - - assertEquals(1, titles.size()); - assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata context with gcube not as starting string in the main title - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "sobigdata::projects::1", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) - .first() - .getContext() - .get(0) - .getId()); - titles = pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) - .first() - .getTitle(); - - assertEquals(1, titles.size()); - assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); - assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata in context and also other contexts with gcube as starting string for the main - // title - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "dh-ch", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) - .first() - .getContext() - .get(0) - .getId()); - titles = pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) - .first() - .getTitle(); - - assertEquals(1, titles.size()); - assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with multiple main title one of which whith gcube as starting string and with 2 contextes - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "dh-ch", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) - .first() - .getContext() - .get(0) - .getId()); - titles = pubs - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) - .first() - .getTitle(); - - assertEquals(2, titles.size()); - assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - // original result without sobigdata in context with gcube as starting string for the main title - assertEquals( - 1, - pubs - .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) - .first() - .getContext() - .size()); - assertEquals( - "dh-ch", - pubs - .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) - .first() - .getContext() - .get(0) - .getId()); - titles = pubs - .filter((FilterFunction) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) - .first() - .getTitle(); - - assertEquals(2, titles.size()); - - assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - } - - @Test - void testCleanCfHbSparkJob() throws Exception { - - final Dataset pubs_in = read(spark, graphInputPath.toString() + "/publication", Publication.class); - final Publication p1_in = pubs_in - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") - .first(); - assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue()); - - final Publication p2_in = pubs_in - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") - .first(); - assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey()); - assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar - DUP", p2_in.getInstance().get(0).getHostedby().getValue()); - - final Publication p3_in = pubs_in - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue()); - - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/publication", - "--outputPath", graphOutputPath.toString() + "/publication", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "true", - "--contextId", "sobigdata", - "--verifyParam", "gCube ", - "--masterDuplicatePath", dsMasterDuplicatePath, - "--country", "NL", - "--verifyCountryParam", "10.17632", - "--collectedfrom", "NARCIS", - "--hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - })).run(false, isLookUpService); - - assertTrue(Files.exists(Paths.get(graphOutputPath, "publication"))); - - final Dataset pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) - .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_cfhb")); - - assertEquals(3, pubs_out.count()); - - final Publication p1_out = pubs_out - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") - .first(); - assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue()); - - final Publication p2_out = pubs_out - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") - .first(); - assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey()); - assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar", p2_out.getInstance().get(0).getHostedby().getValue()); - - final Publication p3_out = pubs_out - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue()); - } - - @Test - public void testCleanCountry() throws Exception { - - new CleanGraphSparkJob( - args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", - new String[] { - "--inputPath", graphInputPath.toString() + "/publication", - "--outputPath", graphOutputPath.toString() + "/publication", - "--isLookupUrl", "lookupurl", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "true", - "--contextId", "sobigdata", - "--verifyParam", "gCube ", - "--masterDuplicatePath", dsMasterDuplicatePath, - "--country", "NL", - "--verifyCountryParam", "10.17632", - "--collectedfrom", "NARCIS", - "--hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - })).run(false, isLookUpService); - - - final Dataset pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) - .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_country")); - - assertEquals(8, pubs_out.count()); - - // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS - assertEquals( - 1, - pubs_out - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6_country")) - .first() - .getCountry() - .size()); - - // original result with NL country and pid not starting with Mendely prefix - assertEquals( - 1, - pubs_out - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country")) - .first() - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not - // inserted with propagation - assertEquals( - 1, - pubs_out - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) - .first() - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with - // propagation - assertEquals( - 0, - pubs_out - .filter((FilterFunction) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country")) - .first() - .getCountry() - .size()); - } - - private List vocs() throws IOException { - return IOUtils - .readLines( - GraphCleaningFunctionsTest.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")); - } - - private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { - return spark - .read() - .textFile(path) - .map(as(clazz), Encoders.bean(clazz)); - } - - private static MapFunction as(Class clazz) { - return s -> MAPPER.readValue(s, clazz); - } - - private static String classPathResourceAsString(String path) throws IOException { - return IOUtils - .toString( - CleanGraphSparkJobTest.class - .getResourceAsStream(path)); - } - - private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { - ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); - parser.parseArgument(args); - return parser; - } - - private static void verify_keyword(Publication p_cleaned, String subject) { - Optional s1 = p_cleaned - .getSubject() - .stream() - .filter(s -> s.getValue().equals(subject)) - .findFirst(); - - assertTrue(s1.isPresent()); - assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid()); - assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); - } - - private Stream getAuthorPids(Result pub) { - return pub - .getAuthor() - .stream() - .map(Author::getPid) - .flatMap(Collection::stream); - } + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + assertEquals("CLOSED", p.getInstance().get(0).getAccessright().getClassid()); + assertEquals("Closed Access", p.getInstance().get(0).getAccessright().getClassname()); + + Set pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES); + assertTrue( + p + .getPid() + .stream() + .map(StructuredProperty::getQualifier) + .allMatch(q -> pidTerms.contains(q.getClassid()))); + + List poi = p.getInstance(); + assertNotNull(poi); + assertEquals(3, poi.size()); + + final Instance poii = poi.get(0); + assertNotNull(poii); + assertNotNull(poii.getPid()); + + assertEquals(2, poii.getPid().size()); + + assertTrue( + poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(poii.getAlternateIdentifier()); + assertEquals(1, poii.getAlternateIdentifier().size()); + + assertTrue( + poii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertEquals(3, p.getTitle().size()); + + List titles = p + .getTitle() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList()); + assertTrue(titles.contains("omic")); + assertTrue( + titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test")); + assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳")); + + assertEquals("CLOSED", p.getBestaccessright().getClassid()); + assertNull(p.getPublisher()); + + assertEquals("1970-10-07", p.getDateofacceptance().getValue()); + + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + final List pci = p.getInstance(); + assertNotNull(pci); + assertEquals(3, pci.size()); + + final Instance pcii = pci.get(0); + assertNotNull(pcii); + assertNotNull(pcii.getPid()); + + assertEquals(2, pcii.getPid().size()); + + assertTrue( + pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(pcii.getAlternateIdentifier()); + assertEquals(1, pcii.getAlternateIdentifier().size()); + assertTrue( + pcii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertNotNull(p.getSubject()); + + List fos_subjects = p + .getSubject() + .stream() + .filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())) + .collect(Collectors.toList()); + + assertNotNull(fos_subjects); + assertEquals(2, fos_subjects.size()); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0101 mathematics".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & + "sysimport:crosswalk:datasetarchive" + .equals(s.getDataInfo().getProvenanceaction().getClassid()))); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0102 computer and information sciences".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + + verify_keyword(p, "In Situ Hybridization"); + verify_keyword(p, "Avicennia"); + } + + @Test + void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2"); + } + + @Test + void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656"); + } + + private void verifyFiltering(int expectedCount, String id) + throws ISLookUpException, ClassNotFoundException, IOException, ParseException { + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false" + })).run(false, isLookUpService); + + Dataset p = read(spark, graphOutputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)); + + assertEquals(expectedCount, p.count()); + } + + @Test + void testCleanContext() throws Exception { + final String prefix = "gcube "; + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + Dataset pubs = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); + + assertEquals(7, pubs.count()); + + // original result with sobigdata context and gcube as starting string in the main title for the publication + assertEquals( + 0, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx")) + .first() + .getContext() + .size()); + + // original result with sobigdata context without gcube as starting string in the main title for the publication + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + // original result with sobigdata context with gcube as starting string in the subtitle + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + List titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata context with gcube not as starting string in the main title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::1", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + // original result without sobigdata in context with gcube as starting string for the main title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + } + + @Test + void testCleanCfHbSparkJob() throws Exception { + + final Dataset pubs_in = read(spark, graphInputPath + "/publication", Publication.class); + final Publication p1_in = pubs_in + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", + p1_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_in = pubs_in + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", + p2_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar - DUP", p2_in.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_in = pubs_in + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", + p3_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue()); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + assertTrue(Files.exists(Paths.get(graphOutputPath, "publication"))); + + final Dataset pubs_out = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_cfhb")); + + assertEquals(3, pubs_out.count()); + + final Publication p1_out = pubs_out + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", + p1_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_out = pubs_out + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey()); + assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::fc1db64b3964826913b1e9eafe830490", + p2_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar", p2_out.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_out = pubs_out + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", + p3_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue()); + } + + @Test + void testCleanCountry() throws Exception { + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + final Dataset pubs_out = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_country")); + + assertEquals(8, pubs_out.count()); + + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::0224aae28af558f21768dbc6_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and pid not starting with Mendely prefix + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not + // inserted with propagation + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with + // propagation + assertEquals( + 0, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country")) + .first() + .getCountry() + .size()); + } + + 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 org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { + return spark + .read() + .textFile(path) + .map(as(clazz), Encoders.bean(clazz)); + } + + private static MapFunction as(Class clazz) { + return s -> MAPPER.readValue(s, clazz); + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + CleanGraphSparkJobTest.class.getResourceAsStream(path))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static void verify_keyword(Publication p_cleaned, String subject) { + Optional s1 = p_cleaned + .getSubject() + .stream() + .filter(s -> s.getValue().equals(subject)) + .findFirst(); + + assertTrue(s1.isPresent()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java deleted file mode 100644 index 9096180ef..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java +++ /dev/null @@ -1,213 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.cfhb; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; - -import java.io.File; -import java.io.IOException; -import java.net.URISyntaxException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -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 com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Publication; - -public class CleanCfHbSparkJobTest { - - private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path testBaseTmpPath; - - private static String resolvedPath; - - private static String graphInputPath; - - private static String graphOutputPath; - - private static String dsMasterDuplicatePath; - - @BeforeAll - public static void beforeAll() throws IOException, URISyntaxException { - - testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName()); - log.info("using test base path {}", testBaseTmpPath); - - final File entitiesSources = Paths - .get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI()) - .toFile(); - - FileUtils - .copyDirectory( - entitiesSources, - testBaseTmpPath.resolve("input").resolve("entities").toFile()); - - FileUtils - .copyFileToDirectory( - Paths - .get( - CleanCfHbSparkJobTest.class - .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") - .toURI()) - .toFile(), - testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); - - graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); - resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString(); - graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString(); - dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("spark.ui.enabled", "false"); - - spark = SparkSession - .builder() - .appName(CleanCfHbSparkJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(testBaseTmpPath.toFile()); - spark.stop(); - } - - @Test - void testCleanCfHbSparkJob() throws Exception { - final String outputPath = graphOutputPath + "/dataset"; - final String inputPath = graphInputPath + "/dataset"; - - org.apache.spark.sql.Dataset records = read(spark, inputPath, Dataset.class); - Dataset d = records - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") - .first(); - assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); - - d = records - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") - .first(); - assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey()); - assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - - CleanCfHbSparkJob - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", inputPath, - "--outputPath", outputPath, - "--resolvedPath", resolvedPath + "/dataset", - "--graphTableClassName", Dataset.class.getCanonicalName(), - "--masterDuplicatePath", dsMasterDuplicatePath - }); - - assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset"))); - - records = read(spark, outputPath, Dataset.class); - - assertEquals(3, records.count()); - - d = records - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") - .first(); - assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue()); - - d = records - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") - .first(); - assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey()); - assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - } - - private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { - return spark - .read() - .textFile(path) - .map(as(clazz), Encoders.bean(clazz)); - } - - private static MapFunction as(Class clazz) { - return s -> OBJECT_MAPPER.readValue(s, clazz); - } -} From b502f865235bb9408410d83b4c87755a706d3a9e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 24 Mar 2023 13:09:12 +0100 Subject: [PATCH 07/10] fixed input path supplemented to GetDatasourceFromCountry; adjusted the various spark.sql.shuffle.partitions --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 505c78c34..f6bf053cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -109,9 +109,9 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=10000 - --inputPath${graphOutputPath} + --inputPath${graphInputPath} --workingDir${workingDir}/working/hostedby --country${country} @@ -160,7 +160,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=15000 --inputPath${graphInputPath}/publication --outputPath${graphOutputPath}/publication @@ -194,7 +194,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=8000 --inputPath${graphInputPath}/dataset --outputPath${graphOutputPath}/dataset @@ -228,7 +228,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=5000 --inputPath${graphInputPath}/otherresearchproduct --outputPath${graphOutputPath}/otherresearchproduct @@ -262,7 +262,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/software --outputPath${graphOutputPath}/software @@ -296,7 +296,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/datasource --outputPath${graphOutputPath}/datasource @@ -330,7 +330,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/organization --outputPath${graphOutputPath}/organization @@ -364,7 +364,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/project --outputPath${graphOutputPath}/project @@ -398,7 +398,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=20000 --inputPath${graphInputPath}/relation --outputPath${graphOutputPath}/relation From 2a6ba29b64cbbf68f8e6fb5c8ae0af1b65ba9dc1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Apr 2023 12:34:51 +0200 Subject: [PATCH 08/10] [graph cleaning] unit tests & cleanup --- .../oaf/utils/GraphCleaningFunctions.java | 43 +++++----- .../oa/graph/clean/CleanGraphSparkJob.java | 80 +++++++++++-------- .../graph/clean/CleanGraphSparkJobTest.java | 9 ++- 3 files changed, 75 insertions(+), 57 deletions(-) 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 e40de935e..1aee72f09 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 @@ -16,6 +16,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; import com.google.common.collect.Sets; @@ -41,32 +43,35 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static T cleanContext(T value, String contextId, String verifyParam) { if (ModelSupport.isSubClass(value, Result.class)) { final Result res = (Result) value; - if (res - .getTitle() - .stream() - .filter( - t -> t - .getQualifier() - .getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .noneMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { - return (T) res; + if (shouldCleanContext(res, verifyParam)) { + res + .setContext( + res + .getContext() + .stream() + .filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId)) + .collect(Collectors.toList())); } - res - .setContext( - res - .getContext() - .stream() - .filter( - c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)) - .collect(Collectors.toList())); return (T) res; } else { return value; } } + private static boolean shouldCleanContext(Result res, String verifyParam) { + boolean titleMatch = res + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase())); + + return titleMatch && Objects.nonNull(res.getContext()); + } + public static T cleanCountry(T value, String[] verifyParam, Set hostedBy, String collectedfrom, String country) { if (ModelSupport.isSubClass(value, Result.class)) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index e97ff3cb2..01baca226 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -149,34 +149,29 @@ public class CleanGraphSparkJob { .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) .filter((FilterFunction) GraphCleaningFunctions::filter); + // read the master-duplicate tuples + Dataset md = spark + .read() + .textFile(dsMasterDuplicatePath) + .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); + + // prepare the resolved CF|HB references with the corresponding EMPTY master ID + Dataset resolved = spark + .read() + .textFile(inputPath) + .map(as(clazz), Encoders.bean(clazz)) + .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); + if (Boolean.FALSE.equals(deepClean)) { - cleaned_basic - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + + if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { + save(fixCFHB(clazz, cleaned_basic, md, resolved), outputPath); + } else { + save(cleaned_basic, outputPath); + } } else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { - // read the master-duplicate tuples - Dataset md = spark - .read() - .textFile(dsMasterDuplicatePath) - .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); - - // prepare the resolved CF|HB references with the corresponding EMPTY master ID - Dataset resolved = spark - .read() - .textFile(inputPath) - .map(as(clazz), Encoders.bean(clazz)) - .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); - - // set the EMPTY master ID/NAME - Dataset resolvedDs = resolved - .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) - .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) - .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())); - // load the hostedby mapping Set hostedBy = Sets .newHashSet( @@ -186,7 +181,7 @@ public class CleanGraphSparkJob { .collectAsList()); // perform the deep cleaning steps - final Dataset cleaned_deep = cleaned_basic + final Dataset cleaned_deep = fixCFHB(clazz, cleaned_basic, md, resolved) .map( (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), Encoders.bean(clazz)) @@ -195,19 +190,34 @@ public class CleanGraphSparkJob { .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), Encoders.bean(clazz)); - // Join the results with the resolved CF|HB mapping, apply the mapping and save it - cleaned_deep - .joinWith(resolvedDs, cleaned_deep.col("id").equalTo(resolvedDs.col("resultId")), "left") - .groupByKey( - (MapFunction, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) - .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + save(cleaned_deep, outputPath); } } + private static void save(final Dataset dataset, final String outputPath) { + dataset + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Dataset fixCFHB(Class clazz, Dataset results, Dataset md, + Dataset resolved) { + + // set the EMPTY master ID/NAME + Dataset resolvedDs = resolved + .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) + .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) + .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())); + + return results + .joinWith(resolvedDs, results.col("id").equalTo(resolvedDs.col("resultId")), "left") + .groupByKey( + (MapFunction, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) + .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)); + } + private static Dataset readTableFromPath( SparkSession spark, String inputEntityPath, Class clazz) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 5b021af01..65182108e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -165,7 +165,8 @@ public class CleanGraphSparkJobTest { "--outputPath", graphOutputPath + "/relation", "--isLookupUrl", "lookupurl", "--graphTableClassName", Relation.class.getCanonicalName(), - "--deepClean", "false" + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, })).run(false, isLookUpService); spark @@ -262,7 +263,8 @@ public class CleanGraphSparkJobTest { "--outputPath", graphOutputPath + "/publication", "--isLookupUrl", "lookupurl", "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "false" + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, })).run(false, isLookUpService); Publication p = read(spark, graphOutputPath + "/publication", Publication.class) @@ -413,7 +415,8 @@ public class CleanGraphSparkJobTest { "--outputPath", graphOutputPath + "/publication", "--isLookupUrl", "lookupurl", "--graphTableClassName", Publication.class.getCanonicalName(), - "--deepClean", "false" + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, })).run(false, isLookUpService); Dataset p = read(spark, graphOutputPath + "/publication", Publication.class) From dead87917f9c875a3a640c6da07889c17b6fa4a3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Apr 2023 13:13:43 +0200 Subject: [PATCH 09/10] [graph cleaning] cleanup --- .../dnetlib/dhp/oa/graph/clean/dataset_clean_country.json | 1 - .../dhp/oa/graph/clean/publication_clean_country.json | 8 -------- 2 files changed, 9 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json deleted file mode 100644 index f5c1fc334..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json +++ /dev/null @@ -1 +0,0 @@ -{"geolocation": [], "dataInfo": {"provenanceaction": {"classid": "sysimport:dedup", "classname": "sysimport:dedup", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-result-decisiontree-v3", "invisible": false, "trust": "0.8"}, "resourcetype": {"classid": "dataset", "classname": "dataset", "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource"}, "pid": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17632/v6cgs4jpbk.2"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17632/v6cgs4jpbk.3"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17632/v6cgs4jpbk"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17632/v6cgs4jpbk.1"}], "contributor": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "somok bhowmik"}], "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "issued", "classname": "issued", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2022-08-16"}, {"qualifier": {"classid": "available", "classname": "available", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2023-08-23"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2022-08-16"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "available", "classname": "available", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2022-08-16"}], "collectedfrom": [{"key": "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254", "value": "Datacite"}, {"key": "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", "value": "DANS (Data Archiving and Networked Services)"}, {"key": "10|eurocrisdris::fe4903425d9040f680d8610d9079ea14", "value": "NARCIS"}, {"key": "10|re3data_____::84e123776089ce3c7a33db98d9cd15a8", "value": "EASY"}], "id": "50|doi_dedup___::e04c8cbefb6f0b8378a04c57e6edbd82", "subject": [{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Interdisciplinary sciences"}], "lastupdatetimestamp": 1670362508719, "author": [{"surname": "Bhowmik", "name": "S.", "pid": [], "rank": 1, "affiliation": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "via Mendeley Data"}], "fullname": "bhowmik, S"}], "instance": [{"refereed": {"classid": "0000", "classname": "Unknown", "schemeid": "dnet:review_levels", "schemename": "dnet:review_levels"}, "hostedby": {"key": "10|re3data_____::db814dc656a911b556dba42a331cebe9", "value": "Mendeley Data"}, "license": {"value": "https://creativecommons.org/licenses/by/4.0/legalcode"}, "url": ["https://dx.doi.org/10.17632/v6cgs4jpbk.2"], "pid": [{"dataInfo": 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Claudio Atzori Date: Wed, 5 Apr 2023 11:35:47 +0200 Subject: [PATCH 10/10] [graph cleaning] added missing case --- .../java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 01baca226..5542215b3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -169,7 +169,6 @@ public class CleanGraphSparkJob { } else { save(cleaned_basic, outputPath); } - } else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { // load the hostedby mapping @@ -191,6 +190,8 @@ public class CleanGraphSparkJob { Encoders.bean(clazz)); save(cleaned_deep, outputPath); + } else { + save(cleaned_basic, outputPath); } }