diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 354741690..e9a45be40 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -33,10 +33,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bulktag.community.*; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import scala.Tuple2; @@ -114,27 +111,35 @@ public class SparkBulkTagJob { extendCommunityConfigurationForEOSC(spark, inputPath, cc); execBulkTag( spark, inputPath, outputPath, protoMap, cc); + execEntityTag( + spark, inputPath + "organization", outputPath + "organization", + Utils.getCommunityOrganization(baseURL), Organization.class, TaggingConstants.CLASS_ID_ORGANIZATION, + TaggingConstants.CLASS_NAME_BULKTAG_ORGANIZATION); + execEntityTag( + spark, inputPath + "project", outputPath + "project", Utils.getCommunityProjects(baseURL), + Project.class, TaggingConstants.CLASS_ID_PROJECT, TaggingConstants.CLASS_NAME_BULKTAG_PROJECT); execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL)); - execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL)); + }); } - private static void execProjectTag(SparkSession spark, String inputPath, String outputPath, - CommunityEntityMap communityProjects) { - Dataset projects = readPath(spark, inputPath + "project", Project.class); + private static void execEntityTag(SparkSession spark, String inputPath, String outputPath, + CommunityEntityMap communityEntity, Class entityClass, + String classID, String calssName) { + Dataset entity = readPath(spark, inputPath, entityClass); Dataset pc = spark .createDataset( - communityProjects + communityEntity .keySet() .stream() - .map(k -> EntityCommunities.newInstance(k, communityProjects.get(k))) + .map(k -> EntityCommunities.newInstance(k, communityEntity.get(k))) .collect(Collectors.toList()), Encoders.bean(EntityCommunities.class)); - projects - .joinWith(pc, projects.col("id").equalTo(pc.col("entityId")), "left") - .map((MapFunction, Project>) t2 -> { - Project ds = t2._1(); + entity + .joinWith(pc, entity.col("id").equalTo(pc.col("entityId")), "left") + .map((MapFunction, E>) t2 -> { + E ds = t2._1(); if (t2._2() != null) { List context = Optional .ofNullable(ds.getContext()) @@ -156,8 +161,8 @@ public class SparkBulkTagJob { false, TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false, OafMapperUtils .qualifier( - TaggingConstants.CLASS_ID_DATASOURCE, - TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE, + classID, + calssName, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "1"))); @@ -166,17 +171,17 @@ public class SparkBulkTagJob { }); } return ds; - }, Encoders.bean(Project.class)) + }, Encoders.bean(entityClass)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath + "project"); + .json(outputPath); - readPath(spark, outputPath + "project", Project.class) + readPath(spark, outputPath, entityClass) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(inputPath + "project"); + .json(inputPath); } private static void execDatasourceTag(SparkSession spark, String inputPath, String outputPath, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java index aea21f8e5..6e6f12cfb 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java @@ -13,6 +13,9 @@ public class TaggingConstants { public static final String CLASS_ID_CZENODO = "community:zenodocommunity"; public static final String CLASS_ID_ADVANCED_CONSTRAINT = "community:advconstraint"; + public static final String CLASS_ID_PROJECT = "community:project"; + public static final String CLASS_ID_ORGANIZATION = "community:organization"; + public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/"; public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject"; @@ -20,5 +23,8 @@ public class TaggingConstants { public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo"; public static final String CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT = "Bulktagging for Community - Advanced Constraints"; + public static final String CLASS_NAME_BULKTAG_PROJECT = "Bulktagging for Community - Project"; + public static final String CLASS_NAME_BULKTAG_ORGANIZATION = "Bulktagging for Community - Organization"; + public static final String TAGGING_TRUST = "0.8"; } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index a5280a3b3..f49774574 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -465,6 +465,138 @@ public class BulkTagJobTest { } + @Test + void organizationTag() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/") + .getPath(); + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + fs + .copyFromLocalFile( + false, new org.apache.hadoop.fs.Path(getClass() + .getResource("/eu/dnetlib/dhp/bulktag/pathMap/") + .getPath()), + new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap")); + SparkBulkTagJob + .main( + new String[] { + + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + + "-outputPath", workingDir.toString() + "/", + "-baseURL", "https://services.openaire.eu/openaire/community/", + + "-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap", + "-nameNode", "local" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/organization") + .map(item -> OBJECT_MAPPER.readValue(item, Organization.class)); + + Assertions.assertEquals(4, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Organization.class)); + + verificationDataset.createOrReplaceTempView("organization"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from organization " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + idExplodeCommunity.show(false); + + Assertions.assertEquals(3, idExplodeCommunity.count()); + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:organization'").count()); + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter("name = 'Bulktagging for Community - Organization'") + .count()); + + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'netherlands'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'beopen'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); + + } + + @Test + void projectTag() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/") + .getPath(); + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + fs + .copyFromLocalFile( + false, new org.apache.hadoop.fs.Path(getClass() + .getResource("/eu/dnetlib/dhp/bulktag/pathMap/") + .getPath()), + new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap")); + SparkBulkTagJob + .main( + new String[] { + + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + + "-outputPath", workingDir.toString() + "/", + "-baseURL", "https://services.openaire.eu/openaire/community/", + + "-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap", + "-nameNode", "local" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/project") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + + Assertions.assertEquals(4, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Project.class)); + + verificationDataset.createOrReplaceTempView("project"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from project " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + idExplodeCommunity.show(false); + + Assertions.assertEquals(4, idExplodeCommunity.count()); + Assertions + .assertEquals( + 4, idExplodeCommunity.filter("provenance = 'community:project'").count()); + Assertions + .assertEquals( + 4, + idExplodeCommunity + .filter("name = 'Bulktagging for Community - Project'") + .count()); + + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'enermaps'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'clarin'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'dh-ch'").count()); + + } + @Test void bulktagByZenodoCommunityTest() throws Exception { final String sourcePath = getClass() diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization new file mode 100644 index 000000000..cf7a2f90e --- /dev/null +++ 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