From b98f904d48a2923b13225a656510da850c07d533 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 17:52:27 +0200 Subject: [PATCH 1/4] [Funder Products Dump] new way to avoid using hive --- .../community/SparkPrepareResultProject.java | 6 +- .../funderresults/SparkDumpFunderResults.java | 171 ++++----- .../SparkResultLinkedToProject.java | 102 ++--- .../graph/dump/funder_result_parameters.json | 12 +- .../dump/input_parameter_select_relation.json | 20 + .../graph/dump/input_parameters_link_prj.json | 6 + .../oozie_app/config-default.xml | 30 -- .../oozie_app/workflow.xml | 347 ------------------ .../community/oozie_app/import.txt | 2 - .../community/oozie_app/workflow.xml | 273 ++++++++++++-- .../complete/oozie_app/workflow.xml | 1 + .../subworkflows/funder/oozie_app/import.txt | 2 - .../funder/oozie_app/workflow.xml | 71 ++-- .../dump/PrepareResultProjectJobTest.java | 281 +++++++------- .../ResultLinkedToProjectTest.java | 85 +++-- .../dump/funderresult/SplitPerFunderTest.java | 74 ++-- .../communityMapPath/communityMap | 1 + .../{extendeddump/orp => ext/dataset} | 0 .../funderresource/ext/otherresearchproduct | 0 .../oa/graph/dump/funderresource/ext/project | 12 + .../graph/dump/funderresource/ext/publication | 13 + .../oa/graph/dump/funderresource/ext/software | 0 .../extendeddump/otherresearchproduct | 32 ++ .../dump/funderresource/fundersList/list | 8 + .../funderresource/preparedInfo/resultProject | 1 + 25 files changed, 744 insertions(+), 806 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/{extendeddump/orp => ext/dataset} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/fundersList/list create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 87ac20948..410feea02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; 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.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -81,8 +82,9 @@ public class SparkPrepareResultProject implements Serializable { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); + Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 6aed9d7a8..cfe47f29f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,140 +1,119 @@ - package eu.dnetlib.dhp.oa.graph.dump.funderresults; - import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - import java.io.Serializable; import java.util.List; import java.util.Objects; 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.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_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); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - - final String graphPath = parser.get("graphPath"); - log.info("relationPath: {}", graphPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { - - Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); - + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + log.info("Number of result {}", result.count()); + Dataset tmp = result + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); + List funderList = tmp.collectAsList(); funderList.forEach(funder -> { - String fundernsp = funder.substring(3); - String funderdump; - if (fundernsp.startsWith("corda")) { - funderdump = "EC_"; - if (fundernsp.endsWith("h2020")) { - funderdump += "H2020"; - } else { - funderdump += "FP7"; - } - } else { - funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); - } - writeFunderResult(funder, result, outputPath, funderdump); + dumpResults(funder, result, outputPath); }); - } - - private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { - - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; + @NotNull + private static String getFunderName(Project p) { + Optional ofunder = Optional.ofNullable(p.getFunder()); + if (ofunder.isPresent()) { + String fName = ofunder.get().getShortName(); + if (fName.equalsIgnoreCase("ec")) { + fName += "_" + ofunder.get().getFundingStream(); } - for (Project p : r.getProjects()) { - if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { - if (p.getFunder().getShortName().equals(funderName)) - return r; - else - return null; - } - return r; + return fName; + } else { + String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); + if (fName.equalsIgnoreCase("ec")) { + if (p.getId().contains("h2020")) { + fName += "_H2020"; + } else { + fName += "_FP7"; } + } else if (fName.equalsIgnoreCase("conicytf")) { + fName = "CONICYT"; + } else if (fName.equalsIgnoreCase("dfgf")) { + fName = "DFG"; + } else if (fName.equalsIgnoreCase("tubitakf")) { + fName = "TUBITAK"; + } else if (fName.equalsIgnoreCase("euenvagency")) { + fName = "EEA"; } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + return fName; + } } - - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { - - if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); - } else - dumpResults(funder, results, outputPath, funderDump); - + private static void dumpResults(String funder, Dataset results, String outputPath) { + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } - -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index d89b9e86d..5eed64e89 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -5,9 +5,12 @@ 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.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; @@ -18,11 +21,18 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. @@ -35,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.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); final String inputPath = parser.get("sourcePath"); @@ -58,59 +68,51 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); + final String resultProjectsPath = parser.get("graphPath"); + log.info("graphPath: {}", resultProjectsPath); + + String communityMapPath = parser.get("communityMapPath"); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } - private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String graphPath) { + private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); - Dataset relations = Utils - .readPath(spark, graphPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - - results.createOrReplaceTempView("result"); - relations.createOrReplaceTempView("relation"); - project.createOrReplaceTempView("project"); - - Dataset tmp = spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)); - tmp - .groupByKey( - (MapFunction) value -> value - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); + Dataset resultProjectDataset = Utils + .readPath(spark, resultProjectsPath, ResultProject.class); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + results + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 5dc8e8910..5669dca37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,10 +17,10 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, -{ - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": true -} + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the relationPath", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json new file mode 100644 index 000000000..1a67134a6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index f5641bc45..6c45538cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -28,6 +28,12 @@ "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the relations", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml deleted file mode 100644 index 5f954ff38..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml +++ /dev/null @@ -1,347 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - communityMapPath - the path to the community map - - - selectedResults - the path the the possible subset ot results to be dumped - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --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.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --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.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --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.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --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.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index 319517026..b559a25dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -77,42 +77,259 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + - + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index 8eab56992..7cc133323 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -298,6 +298,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath} --outputPath${workingDir}/validrelation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml index b990f4e49..2c05256cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -77,12 +77,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --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.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + @@ -111,7 +135,8 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/result/publication - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -137,7 +162,8 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -163,7 +189,8 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -189,41 +216,14 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} - - - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${workingDir}/result - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - - + @@ -242,9 +242,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${workingDir}/ext + --sourcePath${workingDir}/result --outputPath${outputPath} - --graphPath${sourcePath} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 86d2f93c9..c6798ac58 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,121 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } + + @Test + void testMatchx() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 4967ae5a5..579958a62 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; @@ -34,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -56,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,32 +73,34 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, tmp.count()); } @@ -105,32 +108,34 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", relationPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 477481c08..5bb5a1178 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -5,10 +5,14 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; 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.ForeachFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -52,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -68,86 +72,80 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-graphPath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - // FP7 3 + // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); - // CONICYT 0 - tmp = sc - .textFile(workingDir.toString() + "/split/CONICYTF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(0, tmp.count()); - } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap new file mode 100644 index 000000000..905cdabe9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap @@ -0,0 +1 @@ +{"ee":"SDSN - Greece","epos":"EPOS","enrmaps":"Energy Research","fet-h2020":"FET H2020","instruct":"Instruct-Eric","egi":"EGI Federation","euromarine":"Euromarine","covid-19":"COVID-19","dariah":"DARIAH EU","rda":"Research Data 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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project new file mode 100644 index 000000000..f68cead77 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project @@ -0,0 +1,12 @@ 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} +{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 5T32HG004947-04)"],"format":["application/pdf"],"id":"50|dedup_wf_001::025dff86cc73c1c865ed35e5b7646e73","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"hostedby":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","publicationdate":"2014-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/11858/00-001M-0000-0024-1F46-B","http://hdl.handle.net/11858/00-001M-0000-0024-1F8F-7","http://hdl.handle.net/11858/00-001M-0000-0024-1F90-1"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"hostedby":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"publicationdate":"2014-05-27","refereed":"nonPeerReviewed","type":"Preprint","url":["http://dx.doi.org/10.1101/005603"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} +{"author":[{"fullname":"K.P. 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This study focuses on estimating the evapotranspiration and crop coefficients of table grapes vineyards trained on overhead “tendone” systems in the Apulia region (Italy). Maximum vineyard transpiration was estimated by adopting the “direct” methodology for ETp proposed by the Food and Agriculture Organization in Irrigation and Drainage Paper No. 56, with crop parameters estimated from Landsat 8 and RapidEye satellite data in combination with ground-based meteorological data. The modeling results of two growing seasons (2013 and 2014) indicated that canopy growth, seasonal and 10-day sums evapotranspiration values were strictly related to thermal requirements and rainfall events. The estimated values of mean seasonal daily evapotranspiration ranged between 4.2 and 4.1 mm·d−1, while midseason estimated values of crop coefficients ranged from 0.88 to 0.93 in 2013, and 1.02 to 1.04 in 2014, respectively. The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. Using the bi-functional protein, cellulose nanofibrils could be assembled into tightly packed thin films at the air/water interface and at the oil/water interface. It was shown that the combination of protein and cellulose nanofibrils resulted in a synergistic improvement in the formation and stability of oil-in-water emulsions resulting in emulsions that were stable for several months. The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:02:51 +0200 Subject: [PATCH 2/4] [DUMP NEW FUNDED PRODUCTS] change in resources --- .../dhp/oa/graph/dump/funderresource/nomatch/papers.json | 2 +- .../dhp/oa/graph/dump/funderresource/preparedInfo/resultProject | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json index fda631c2f..dd6026980 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json @@ -12,7 +12,7 @@ {"author":[{"fullname":"Sharp, 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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject index 515d1c9a6..5749f731d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject @@ -1 +1 @@ -{"resultId":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585","projectsList":[{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","funder":{"shortName":"AKA","name":"Academy of 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Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null},{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null}]} \ No newline at end of file From f561f13dd9d9796613198c1cdb54f8f74b166d5a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:18:17 +0200 Subject: [PATCH 3/4] [Funder Products Dump] fixed names of parameters in workflow --- .../community/oozie_app/workflow.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index b559a25dc..dfbe93b67 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -107,7 +107,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/publication + --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${communityMapPath} @@ -134,7 +134,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/dataset + --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${communityMapPath} @@ -160,7 +160,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/otherresearchproduct + --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${communityMapPath} @@ -186,7 +186,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/software + --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${communityMapPath} @@ -246,7 +246,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication + --outputPath${workingDir}/ext/publication --preparedInfoPath${workingDir}/preparedInfo @@ -271,7 +271,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset + --outputPath${workingDir}/ext/dataset --preparedInfoPath${workingDir}/preparedInfo @@ -296,7 +296,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp + --outputPath${workingDir}/ext/orp --preparedInfoPath${workingDir}/preparedInfo @@ -321,7 +321,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software + --outputPath${workingDir}/ext/software --preparedInfoPath${workingDir}/preparedInfo From 0cb1c7078826ceca91a652ab8e23931728621a97 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 10:44:08 +0200 Subject: [PATCH 4/4] code formatting --- .../dhp/common/api/ZenodoAPIClient.java | 19 +- .../transformation/TransformationJobTest.java | 10 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 2 +- .../funderresults/SparkDumpFunderResults.java | 86 +++--- .../SparkResultLinkedToProject.java | 68 ++--- .../ProjectsSubsetSparkJob.java | 3 + .../dump/PrepareResultProjectJobTest.java | 272 +++++++++--------- .../ResultLinkedToProjectTest.java | 70 ++--- .../dump/funderresult/SplitPerFunderTest.java | 60 ++-- .../projectssubset/ProjectSubsetTest.java | 1 - 10 files changed, 304 insertions(+), 287 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 56366bc72..63f890a10 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -255,7 +255,8 @@ public class ZenodoAPIClient implements Serializable { private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson() + .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,8 +264,9 @@ public class ZenodoAPIClient implements Serializable { return; } } - if(zenodoModelList.size() == 0) - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if (zenodoModelList.size() == 0) + throw new MissingConceptDoiException( + "The concept record id specified was missing in the list of depositions"); setDepositionId(concept_rec_id, page + 1); } @@ -278,11 +280,11 @@ public class ZenodoAPIClient implements Serializable { String url = urlBuilder.build().toString(); Request request = new Request.Builder() - .url(url) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -295,7 +297,6 @@ public class ZenodoAPIClient implements Serializable { } - private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index fea7b53ac..7fc80d168 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -142,7 +142,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -152,7 +153,9 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule( + "simpleTRule", + "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +206,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir final Path testDir) throws Exception { + void transformTest(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { 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 ad1e8721a..982e8ea75 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 @@ -103,7 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index cfe47f29f..34ca6697c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresults; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.List; import java.util.Objects; 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.FlatMapFunction; @@ -14,29 +18,32 @@ import org.apache.spark.sql.*; import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_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); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); @@ -44,30 +51,32 @@ public class SparkDumpFunderResults implements Serializable { log.info("outputPath: {}", outputPath); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); log.info("Number of result {}", result.count()); Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); List funderList = tmp.collectAsList(); funderList.forEach(funder -> { dumpResults(funder, result, outputPath); }); } + @NotNull private static String getFunderName(Project p) { Optional ofunder = Optional.ofNullable(p.getFunder()); @@ -97,23 +106,24 @@ public class SparkDumpFunderResults implements Serializable { return fName; } } + private static void dumpResults(String funder, Dataset results, String outputPath) { results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 5eed64e89..4b0072944 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -45,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.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); final String inputPath = parser.get("sourcePath"); @@ -78,41 +78,41 @@ public class SparkResultLinkedToProject implements Serializable { SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); + .readPath(spark, resultProjectsPath, ResultProject.class); CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 83a9f3464..38eb3cb37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -2,9 +2,11 @@ package eu.dnetlib.dhp.oa.graph.dump.projectssubset; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.Objects; import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,6 +16,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index c6798ac58..f3b7246b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,98 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -326,20 +326,20 @@ public class PrepareResultProjectJobTest { void testMatchx() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 579958a62..7046b02c2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -35,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -73,32 +73,32 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(0, tmp.count()); @@ -108,32 +108,32 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 5bb5a1178..e9d739db2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -56,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,13 +72,13 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); @@ -86,64 +86,64 @@ public class SplitPerFunderTest { // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index 4ff1e1b96..8cdb285e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -30,7 +30,6 @@ public class ProjectSubsetTest { private static final Logger log = LoggerFactory .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files