From 57cac3689801929d651404fbe47c6a1cb7998f14 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 13:38:03 +0100 Subject: [PATCH 01/54] changed the workflow name --- .../dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml index 4c286e4a24..b809b58fb4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + From 46ba3793f61084d59ed251a48b74aef1c157026c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:47:31 +0100 Subject: [PATCH 02/54] code, workflow and parameters for the dump of the results associated to funders --- .../dump/funderresults/FunderResults.java | 19 ++ .../SparkPrepareResultProject.java | 165 ++++++++++++++++ .../graph/dump/funder_result_parameters.json | 26 +++ .../oozie_app/config-default.xml | 30 +++ .../dump/funderresults/oozie_app/workflow.xml | 179 ++++++++++++++++++ 5 files changed, 419 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java new file mode 100644 index 0000000000..18884a327a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -0,0 +1,19 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.Result; + +public class FunderResults implements Serializable { + private List results; + + public List getResults() { + return results; + } + + public void setResults(List results) { + this.results = results; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java new file mode 100644 index 0000000000..179c449f68 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +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.ResultMapper; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +/** + * Preparation of the Project information to be added to the dumped results. For each result associated to at least one + * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to + */ +public class SparkPrepareResultProject implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkPrepareResultProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String communityMapPath = parser.get("communityMapPath"); + log.info("communityMapPath: {}", communityMapPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath); + }); + } + + private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { + + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + + Dataset relation = Utils + .readPath(spark, inputPath + "/relation", Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) + .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + + result + .joinWith(relation, result.col("id").equalTo(relation.col("target"))) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getSource() + .substring(3, 15), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, Tuple2>) ( + s, it) -> { + Tuple2 first = it.next(); + FunderResults fr = new FunderResults(); + List resultList = new ArrayList<>(); + resultList.add(ResultMapper.map(first._1(), communityMap, true)); + it.forEachRemaining(c -> { + resultList.add(ResultMapper.map(c._1(), communityMap, true)); + + }); + fr.setResults(resultList); + return new Tuple2<>(s, fr); + }, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class))) + .foreach(t -> { + String funder = t._1(); + spark + .createDataFrame(t._2.getResults(), Result.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); + }); + + } + + private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { + + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + + Dataset relation = Utils + .readPath(spark, inputPath + "/relation", Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) + .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + + result + .joinWith(relation, result.col("id").equalTo(relation.col("target"))) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getSource() + .substring(3, 15), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, String>) (s, it) -> { + Tuple2 first = it.next(); + List resultList = new ArrayList<>(); + resultList.add(ResultMapper.map(first._1(), communityMap, true)); + it.forEachRemaining(c -> { + resultList.add(ResultMapper.map(c._1(), communityMap, true)); + + }); + spark + .createDataFrame(resultList, Result.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + s); + + return new String(); + }, Encoders.STRING()); + + } + +} 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 new file mode 100644 index 0000000000..f5eb819838 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -0,0 +1,26 @@ +[ + { + "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 + }, + { + "paramName": "cmp", + "paramLongName": "communityMapPath", + "paramDescription": "the community map path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + 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/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml new file mode 100644 index 0000000000..5ddab3398e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -0,0 +1,179 @@ + + + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + 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())}] + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkPrepareResultProject + dhp-graph-mapper-${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${workingDir}/result + --communityMapPath${workingDir}/communityMap + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --communityMapPath${workingDir}/communityMap + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + + + \ No newline at end of file From a172a37ad1c8259d95c1fb7acb83701ea057763a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:55:07 +0100 Subject: [PATCH 03/54] fixed typo --- .../dhp/oa/graph/dump/community/SparkPrepareResultProject.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 39850b5b8e..612af6d169 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 @@ -34,7 +34,7 @@ import scala.Tuple2; /** * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to */ public class SparkPrepareResultProject implements Serializable { From 5402062ff52df8183016d248f70e4aa95f737dc3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:58:20 +0100 Subject: [PATCH 04/54] changed parameter file with the ono associated to the job --- .../oa/graph/dump/funderresults/SparkPrepareResultProject.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java index 179c449f68..9b254088a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -38,7 +38,7 @@ public class SparkPrepareResultProject implements Serializable { .toString( SparkPrepareResultProject.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); From 906db690d2c4c1cfd69a05c5d5f5dc75db2229e9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 17:43:08 +0100 Subject: [PATCH 05/54] - --- .../SparkPrepareResultProject.java | 47 +------------------ 1 file changed, 1 insertion(+), 46 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java index 9b254088a7..21b4f4dc77 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -65,7 +65,7 @@ public class SparkPrepareResultProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath); + prepareResultProjectList(spark, inputPath, outputPath, communityMapPath); }); } @@ -115,51 +115,6 @@ public class SparkPrepareResultProject implements Serializable { .option("compression", "gzip") .json(outputPath + "/" + funder); }); - - } - - private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); - - Dataset result = Utils - .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) - .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); - - result - .joinWith(relation, result.col("id").equalTo(relation.col("target"))) - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource() - .substring(3, 15), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, String>) (s, it) -> { - Tuple2 first = it.next(); - List resultList = new ArrayList<>(); - resultList.add(ResultMapper.map(first._1(), communityMap, true)); - it.forEachRemaining(c -> { - resultList.add(ResultMapper.map(c._1(), communityMap, true)); - - }); - spark - .createDataFrame(resultList, Result.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + s); - - return new String(); - }, Encoders.STRING()); - } } From fafb6888871367a18bebf3b9f1b1dff3dd369174 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 18:56:48 +0100 Subject: [PATCH 06/54] - --- .../dump/funderresults/FunderResults.java | 13 +++-- ...oject.java => SparkDumpFunderResults.java} | 53 ++++++------------- .../dump/funderresults/oozie_app/workflow.xml | 2 +- 3 files changed, 23 insertions(+), 45 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/{SparkPrepareResultProject.java => SparkDumpFunderResults.java} (66%) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java index 18884a327a..c3d2d4c2c2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -2,18 +2,17 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults; import java.io.Serializable; -import java.util.List; import eu.dnetlib.dhp.schema.dump.oaf.Result; -public class FunderResults implements Serializable { - private List results; +public class FunderResults extends Result implements Serializable { + private String funder_id; - public List getResults() { - return results; + public String getFunder_id() { + return funder_id; } - public void setResults(List results) { - this.results = results; + public void setFunder_id(String funder_id) { + this.funder_id = funder_id; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java similarity index 66% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 21b4f4dc77..f84a5fd118 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -9,7 +9,6 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -21,7 +20,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; 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.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -30,13 +28,13 @@ import scala.Tuple2; * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to */ -public class SparkPrepareResultProject implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); +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( - SparkPrepareResultProject.class + SparkDumpFunderResults.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); @@ -65,12 +63,12 @@ public class SparkPrepareResultProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList(spark, inputPath, outputPath, communityMapPath); + writeResultProjectList(spark, inputPath, outputPath, communityMapPath); }); } - private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); @@ -85,36 +83,17 @@ public class SparkPrepareResultProject implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); result - .joinWith(relation, result.col("id").equalTo(relation.col("target"))) - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource() - .substring(3, 15), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, Tuple2>) ( - s, it) -> { - Tuple2 first = it.next(); - FunderResults fr = new FunderResults(); - List resultList = new ArrayList<>(); - resultList.add(ResultMapper.map(first._1(), communityMap, true)); - it.forEachRemaining(c -> { - resultList.add(ResultMapper.map(c._1(), communityMap, true)); + .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") + .map((MapFunction, FunderResults>) value ->{ + FunderResults res = (FunderResults) ResultMapper.map(value._1(), communityMap, false); + res.setFunder_id(value._2().getSource().substring(3,15)); + return res; + }, Encoders.bean(FunderResults.class)) + .write() + .partitionBy("funder_id") + .mode(SaveMode.Overwrite) + .json(outputPath); - }); - fr.setResults(resultList); - return new Tuple2<>(s, fr); - }, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class))) - .foreach(t -> { - String funder = t._1(); - spark - .createDataFrame(t._2.getResults(), Result.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); - }); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index 5ddab3398e..aca8f97142 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -137,7 +137,7 @@ yarn cluster Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkPrepareResultProject + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} From 24c56fa7a3584c4a258e9674e089ce36f23b7125 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 19 Nov 2020 19:15:39 +0100 Subject: [PATCH 07/54] new logic and workflow for dump of results with link to projects. In this implementation the result match the model of the communityresult. --- .../dump/funderresults/FunderResults.java | 4 +- .../funderresults/SparkDumpFunderResults.java | 41 +- .../SparkResultLinkedToProject.java | 82 ++++ .../dump/funderresults/oozie_app/workflow.xml | 365 +++++++++++++++++- .../graph/dump/input_parameters_link_prj.json | 36 ++ 5 files changed, 501 insertions(+), 27 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java index c3d2d4c2c2..138e262e46 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -3,9 +3,9 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults; import java.io.Serializable; -import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -public class FunderResults extends Result implements Serializable { +public class FunderResults extends CommunityResult implements Serializable { private String funder_id; public String getFunder_id() { 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 f84a5fd118..d4e294735b 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 @@ -17,9 +17,11 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.api.zenodo.Community; 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.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -53,8 +55,8 @@ public class SparkDumpFunderResults implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); SparkConf conf = new SparkConf(); @@ -63,36 +65,33 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, communityMapPath); + writeResultProjectList(spark, inputPath, outputPath); }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); - Dataset result = Utils - .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) - .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + 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)); result .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") - .map((MapFunction, FunderResults>) value ->{ - FunderResults res = (FunderResults) ResultMapper.map(value._1(), communityMap, false); - res.setFunder_id(value._2().getSource().substring(3,15)); - return res; - }, Encoders.bean(FunderResults.class)) - .write() - .partitionBy("funder_id") - .mode(SaveMode.Overwrite) - .json(outputPath); + .map((MapFunction, FunderResults>) value -> { + FunderResults res = (FunderResults) value._1(); + res.setFunder_id(value._2().getSource().substring(3, 15)); + return res; + }, Encoders.bean(FunderResults.class)) + .write() + .partitionBy("funder_id") + .mode(SaveMode.Overwrite) + .json(outputPath); } 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 new file mode 100644 index 0000000000..456e444478 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -0,0 +1,82 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +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.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkResultLinkedToProject implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); + + 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")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); + + Class inputClazz = (Class) Class.forName(resultClassName); + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLikedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + }); + } + + private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, + String inputPath, String outputPath, String relationPath) { + + Dataset results = Utils.readPath(spark, inputPath, inputClazz); + Dataset relations = Utils + .readPath(spark, relationPath, Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + relations + .joinWith( + results, relations.col("target").equalTo(results.col("id")), + "inner") + .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/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index aca8f97142..d0acdf0518 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -127,10 +127,367 @@ --nameNode${nameNode} --isLookUpUrl${isLookUpUrl} - + + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${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}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + 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${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/dataset + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${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}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/otherresearchproduct + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + 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${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/software + --relationPath${sourcePath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table dataset 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${workingDir}/result/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${workingDir}/communityMap + + + + + + + + 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${workingDir}/result/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${workingDir}/communityMap + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${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${workingDir}/ext/publication + --preparedInfoPath${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${workingDir}/dump/dataset + --outputPath${workingDir}/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${workingDir}/ext/orp + --preparedInfoPath${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${workingDir}/dump/software + --outputPath${workingDir}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + @@ -149,9 +506,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${sourcePath} - --outputPath${workingDir}/result - --communityMapPath${workingDir}/communityMap + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --relationPath${sourcePath}/relation 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 new file mode 100644 index 0000000000..b1f4c026ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -0,0 +1,36 @@ +[ + + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": true + }, + { + "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 + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + } +] + + + From cf3f47563fbca758ba69e6a50a9096fc252c00f4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 19 Nov 2020 19:16:05 +0100 Subject: [PATCH 08/54] new parameter files --- .../dhp/oa/graph/dump/funder_result_parameters.json | 7 ++++++- .../dhp/oa/graph/dump/input_parameters_link_prj.json | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) 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 f5eb819838..2128c91e4b 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 @@ -22,5 +22,10 @@ "paramLongName": "communityMapPath", "paramDescription": "the community map path", "paramRequired": true - } + },{ + "paramName": "rp", + "paramLongName": "relationPath", + "paramDescription": "the relationPath", + "paramRequired": true +} ] \ 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 b1f4c026ae..aab929e43a 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 @@ -29,7 +29,12 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - } + }, { + "paramName":"rp", + "paramLongName":"relationPath", + "paramDescription": "the path to the relations", + "paramRequired": true +} ] From 0a9db67eecb01753a9b144bf3dd98ff4ce17f06e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 Nov 2020 12:21:33 +0100 Subject: [PATCH 09/54] - --- .../dump/funderresults/SparkResultLinkedToProject.java | 5 +++++ .../dhp/oa/graph/dump/funder_result_parameters.json | 7 +------ .../dhp/oa/graph/dump/input_parameters_link_prj.json | 7 ------- 3 files changed, 6 insertions(+), 13 deletions(-) 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 456e444478..6d059567c5 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 @@ -8,7 +8,10 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; @@ -18,6 +21,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; public class SparkResultLinkedToProject implements Serializable { @@ -74,6 +78,7 @@ public class SparkResultLinkedToProject implements Serializable { .joinWith( results, relations.col("target").equalTo(results.col("id")), "inner") + .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") 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 2128c91e4b..9a5a553b1f 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 @@ -17,12 +17,7 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { - "paramName": "cmp", - "paramLongName": "communityMapPath", - "paramDescription": "the community map path", - "paramRequired": true - },{ +{ "paramName": "rp", "paramLongName": "relationPath", "paramDescription": "the relationPath", 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 aab929e43a..5c48867413 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 @@ -1,11 +1,4 @@ [ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, { "paramName":"s", "paramLongName":"sourcePath", From 259c67ce365b58aa052ae2df85a20a4e526ccb2c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 Nov 2020 12:32:23 +0100 Subject: [PATCH 10/54] fixed issue in path name --- .../oa/graph/dump/funderresults/SparkDumpFunderResults.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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 d4e294735b..acafa968a9 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 @@ -65,14 +65,14 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); + writeResultProjectList(spark, inputPath, outputPath, relationPath); }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, String relationPath) { Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) + .readPath(spark, relationPath + "/relation", Relation.class) .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); Dataset result = Utils From 73dbb79602aa2665b8238bf08feae98d09028545 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:36:15 +0100 Subject: [PATCH 11/54] removed the checl for the community name in the common version on MakeTar --- .../src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 4047fdca4f..89fa09f3cb 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,9 +90,9 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); - if (name.trim().equalsIgnoreCase("communities_infrastructures")) { - name = "communities_infrastructures.json"; - } +// if (name.trim().equalsIgnoreCase("communities_infrastructures")) { +// name = "communities_infrastructures.json"; +// } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); From 1832708c42bfddf065ac19db28cf39ce6a328c87 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:37:36 +0100 Subject: [PATCH 12/54] modified boolean variable with string one whcih specify the type of dump we are performing: complete, community or funder --- .../dhp/oa/graph/dump/DumpProducts.java | 22 ++++++++----------- .../dhp/oa/graph/dump/ResultMapper.java | 8 +++---- .../community/SparkDumpCommunityProducts.java | 10 ++++++++- 3 files changed, 22 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index 1279ede533..d20a3036e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,17 +11,12 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import 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.schema.dump.oaf.graph.ResearchInitiative; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -33,7 +28,7 @@ public class DumpProducts implements Serializable { public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { SparkConf conf = new SparkConf(); @@ -42,7 +37,7 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph); + execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } @@ -53,13 +48,13 @@ public class DumpProducts implements Serializable { String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); Utils .readPath(spark, inputPath, inputClazz) - .map((MapFunction) value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz)) + .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) @@ -70,18 +65,18 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - boolean graph) { + String dumpType) { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { - if (odInfo.get().getDeletedbyinference()) { + if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) { return null; } } else { return null; } - if (!graph) { + if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) { Set communities = communityMap.keySet(); Optional> inputContext = Optional @@ -102,7 +97,8 @@ public class DumpProducts implements Serializable { return null; } } - return (O) ResultMapper.map(value, communityMap, graph); + + return (O) ResultMapper.map(value, communityMap, dumpType); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 4c3bc0dd52..cb052ebaa8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -21,10 +21,10 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, boolean graph) { + E in, Map communityMap, String dumpType) { Result out; - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { out = new GraphResult(); } else { out = new CommunityResult(); @@ -217,7 +217,7 @@ public class ResultMapper implements Serializable { .ofNullable(input.getInstance()); if (oInst.isPresent()) { - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((GraphResult) out) .setInstance(oInst.get().stream().map(i -> getGraphInstance(i)).collect(Collectors.toList())); } else { @@ -296,7 +296,7 @@ public class ResultMapper implements Serializable { out.setType(input.getResulttype().getClassid()); } - if (!graph) { + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((CommunityResult) out) .setCollectedfrom( input diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java index c4b89936ff..63970d14bc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java @@ -4,12 +4,15 @@ package eu.dnetlib.dhp.oa.graph.dump.community; import java.io.Serializable; import java.util.*; +import javax.swing.text.html.Option; + import org.apache.commons.io.IOUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Result; @@ -48,6 +51,11 @@ public class SparkDumpCommunityProducts implements Serializable { String communityMapPath = parser.get("communityMapPath"); + final String dumpType = Optional + .ofNullable(parser.get("dumpType")) + .map(String::valueOf) + .orElse("community"); + Class inputClazz = (Class) Class.forName(resultClassName); DumpProducts dump = new DumpProducts(); @@ -55,7 +63,7 @@ public class SparkDumpCommunityProducts implements Serializable { dump .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, - false); + dumpType); } From 44db258dc4324d03be64091e114a885c75a9a752 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:38:06 +0100 Subject: [PATCH 13/54] added enumerated for the dump type --- .../eu/dnetlib/dhp/oa/graph/dump/Constants.java | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index a466cf0742..86a275ae22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -40,4 +40,18 @@ public class Constants { coarCodeLabelMap.put("c_14cb", "CLOSED"); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } + + public enum DUMPTYPE { + COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder"); + + private String type; + + DUMPTYPE(String type) { + this.type = type; + } + + public String getType() { + return type; + } + } } From 00c377dac2b53380b24fe75fd908aed5676c15cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:40:22 +0100 Subject: [PATCH 14/54] added specification of MapFunction types in map --- .../dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java index 1276d8495e..2b80b1d861 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java @@ -8,6 +8,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -20,6 +21,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import scala.Tuple2; public class SparkUpdateProjectInfo implements Serializable { @@ -73,7 +75,7 @@ public class SparkUpdateProjectInfo implements Serializable { .joinWith( resultProject, result.col("id").equalTo(resultProject.col("resultId")), "left") - .map(value -> { + .map((MapFunction, CommunityResult>) value -> { CommunityResult r = value._1(); Optional.ofNullable(value._2()).ifPresent(rp -> { r.setProjects(rp.getProjectsList()); From 3319440c5348ec03399f7b4e77c7e165ee3de882 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:41:09 +0100 Subject: [PATCH 15/54] changed the direction of the relation between projects and result considered to select the results linked to projects --- .../graph/dump/community/SparkPrepareResultProject.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 612af6d169..2d43888b46 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 @@ -76,16 +76,16 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); projects - .joinWith(relation, projects.col("id").equalTo(relation.col("source"))) + .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") .groupByKey( (MapFunction, String>) value -> value ._2() - .getTarget(), + .getSource(), Encoders.STRING()) .mapGroups( (MapGroupsFunction, ResultProject>) (s, @@ -93,7 +93,7 @@ public class SparkPrepareResultProject implements Serializable { Set projectSet = new HashSet<>(); Tuple2 first = it.next(); ResultProject rp = new ResultProject(); - rp.setResultId(first._2().getTarget()); + rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); Project ps = getProject(p); From 62928ef7a5a68c8c45fb9f7662b4bb25153b908d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:42:41 +0100 Subject: [PATCH 16/54] changed to save the communities_infrastructures information as the other entity dumps: in a json.gz file --- .../dump/complete/CreateContextEntities.java | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java index 23224f8dba..ccb84c7138 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java @@ -1,22 +1,25 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; +import java.io.*; import java.nio.charset.StandardCharsets; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.crypto.utils.IoUtils; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.CompressionOutputStream; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; @@ -76,8 +79,11 @@ public class CreateContextEntities implements Serializable { } else { fsDataOutputStream = fileSystem.create(hdfsWritePath); } + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); } From 7e940f1991c1755d2ec51b11e85675dee212b5f7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:43:34 +0100 Subject: [PATCH 17/54] changed to consider the modification for the specification of the type of dump --- .../dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 773068dfb2..36ced3a4ab 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -49,7 +49,7 @@ public class DumpGraphEntities implements Serializable { d .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class, - true); + eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType()); break; case "40": runWithSparkSession( From b9b6bdb2e67f99d14abeaca83783d3450b015fb4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:44:53 +0100 Subject: [PATCH 18/54] fixing issue on previous implementation --- .../funderresults/SparkDumpFunderResults.java | 55 +++++++++++++------ .../SparkResultLinkedToProject.java | 19 +++++-- 2 files changed, 53 insertions(+), 21 deletions(-) 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 acafa968a9..740a4245de 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 @@ -9,10 +9,7 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -22,6 +19,7 @@ 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.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -69,11 +67,12 @@ public class SparkDumpFunderResults implements Serializable { }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, String relationPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, + String relationPath) { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and relClass = 'isProducedBy'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -81,18 +80,40 @@ public class SparkDumpFunderResults implements Serializable { .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - result - .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") - .map((MapFunction, FunderResults>) value -> { - FunderResults res = (FunderResults) value._1(); - res.setFunder_id(value._2().getSource().substring(3, 15)); - return res; - }, Encoders.bean(FunderResults.class)) - .write() - .partitionBy("funder_id") - .mode(SaveMode.Overwrite) - .json(outputPath); + List funderList = relation + .select("target") + .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) + .distinct() + .collectAsList(); + +// Dataset results = result +// .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") +// .map((MapFunction, CommunityResult>) value -> { +// return value._1(); +// }, Encoders.bean(CommunityResult.class)); + + funderList.forEach(funder -> writeFunderResult(funder, result, outputPath)); } + private static void writeFunderResult(String funder, Dataset results, String outputPath) { + + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + if (p.getId().startsWith(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); + } + } 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 6d059567c5..e5d7e2254f 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 @@ -10,6 +10,7 @@ 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; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -70,15 +71,25 @@ public class SparkResultLinkedToProject implements Serializable { private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, String inputPath, String outputPath, String relationPath) { - Dataset results = Utils.readPath(spark, inputPath, inputClazz); + Dataset results = Utils + .readPath(spark, inputPath, inputClazz) + .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + relations .joinWith( - results, relations.col("target").equalTo(results.col("id")), + results, relations.col("source").equalTo(results.col("id")), "inner") - .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(inputClazz)) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getId(), + Encoders.STRING()) + .mapGroups((MapGroupsFunction, R>) (k, it) -> { + return it.next()._2(); + }, Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") From 35ecea8842886c9952a4b3abfdffdf4514e01b2f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:15 +0100 Subject: [PATCH 19/54] changed to consider the modification for the specification of the type of dump --- .../dnetlib/dhp/oa/graph/dump/DumpJobTest.java | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 54a610b9c4..271ae8fc1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -8,7 +8,6 @@ import java.util.Arrays; import java.util.List; import org.apache.commons.io.FileUtils; -import org.apache.hadoop.yarn.webapp.hamlet.Hamlet; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -23,7 +22,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -155,7 +153,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -220,7 +218,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, true); + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -253,7 +251,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -285,7 +283,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -321,7 +319,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -357,7 +355,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -392,7 +390,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); From 54a309bb6bec5a7b7629c2257485579637e18b96 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:30 +0100 Subject: [PATCH 20/54] refactoring --- .../graph/dump/complete/CreateEntityTest.java | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 411e6f4b01..7028115496 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -3,13 +3,25 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; import static org.mockito.Mockito.lenient; +import java.io.BufferedWriter; import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.function.Consumer; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -60,6 +72,8 @@ public class CreateEntityTest { private QueryInformationSystem queryInformationSystem; + private static String workingDir; + @BeforeEach public void setUp() throws ISLookUpException { lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); @@ -67,6 +81,13 @@ public class CreateEntityTest { queryInformationSystem.setIsLookUp(isLookUpService); } + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName()) + .toString(); + } + @Test public void test1() throws ISLookUpException, IOException { List cInfoList = new ArrayList<>(); @@ -123,4 +144,30 @@ public class CreateEntityTest { riList.forEach(c -> System.out.println(new Gson().toJson(c))); } + + @Test + public void test2() throws IOException, ISLookUpException { + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + Path hdfsWritePath = new Path(workingDir + "/prova"); + FSDataOutputStream fsDataOutputStream = null; + if (fs.exists(hdfsWritePath)) { + fsDataOutputStream = fs.append(hdfsWritePath); + } else { + fsDataOutputStream = fs.create(hdfsWritePath); + } + CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); + + BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + List riList = new ArrayList<>(); + cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); + + } } From c167a18057f3b5326c76f73ae144cb64c5347762 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:50 +0100 Subject: [PATCH 21/54] added new parameter for the dumpType --- .../eu/dnetlib/dhp/oa/graph/dump/input_parameters.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index b1f4c026ae..ca12ae3ec6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -29,7 +29,12 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - } + },{ + "paramName":"dt", + "paramLongName":"dumpType", + "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", + "paramRequired": false +} ] From 7e14452a87ba88657abda8f41ea6731ee5751502 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:46:34 +0100 Subject: [PATCH 22/54] final versione of the wf to get the dump of results associated to at least one funder per funder --- .../dump/funderresults/oozie_app/workflow.xml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d0acdf0518..d258d4dd47 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -182,7 +182,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset --relationPath${sourcePath}/relation @@ -208,7 +208,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct --relationPath${sourcePath}/relation @@ -234,7 +234,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software --relationPath${sourcePath}/relation @@ -269,9 +269,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -295,9 +297,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -321,9 +325,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -347,9 +353,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -508,7 +516,7 @@ --sourcePath${workingDir}/ext --outputPath${outputPath} - --relationPath${sourcePath}/relation + --relationPath${sourcePath} From 39f4a2087300f90bc64cbe928655c13bb0dcc2ff Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:47:32 +0100 Subject: [PATCH 23/54] chenged the path and the name for saving the communities_infrastructures dump file --- .../dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml index b809b58fb4..8189e25945 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml @@ -368,7 +368,7 @@ eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${workingDir}/collect/communities_infrastructures + --hdfsPath${workingDir}/collect/communities_infrastructures/communities_infrastructure.json.gz --nameNode${nameNode} --isLookUpUrl${isLookUpUrl} From 72bb0fe360747bed534890b72f4142f165a6e8e4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 16:47:07 +0100 Subject: [PATCH 24/54] changed directory name --- .../dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 740a4245de..232459c19a 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 @@ -77,7 +77,7 @@ public class SparkDumpFunderResults implements Serializable { 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 + "/orp", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); List funderList = relation From b37b9352d7cd96febbe2c9aab4a5f22aef43d675 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:41:08 +0100 Subject: [PATCH 25/54] added constant value for semantic relationship between projects and results --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 2 ++ .../dump/funderresults/FunderResults.java | 18 ----------- .../ResultLinkedToProjectTest.java | 4 +++ .../dump/funderresult/SplitPerFunderTest.java | 4 +++ .../dump/funderresource/extendeddump/dataset | 0 .../dump/funderresource/extendeddump/orp | 0 .../funderresource/extendeddump/publication | 12 +++++++ .../dump/funderresource/extendeddump/relation | 8 +++++ .../dump/funderresource/extendeddump/software | 0 .../dump/funderresource/match/papers.json | 32 +++++++++++++++++++ .../dump/funderresource/match/relations.json | 30 +++++++++++++++++ .../dump/funderresource/nomatch/papers.json | 32 +++++++++++++++++++ .../funderresource/nomatch/relations.json | 30 +++++++++++++++++ 13 files changed, 154 insertions(+), 18 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 86a275ae22..c64554555d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,6 +26,8 @@ public class Constants { public static String ORCID = "orcid"; + public static String RESULT_PROJECT_IS_PRODUCED_BY = "isProducedBy"; + static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java deleted file mode 100644 index 138e262e46..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ /dev/null @@ -1,18 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import java.io.Serializable; - -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class FunderResults extends CommunityResult implements Serializable { - private String funder_id; - - public String getFunder_id() { - return funder_id; - } - - public void setFunder_id(String funder_id) { - this.funder_id = funder_id; - } -} 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 new file mode 100644 index 0000000000..3696db7f87 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +public class ResultLinkedToProjectTest { +} 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 new file mode 100644 index 0000000000..8e49b9fc6b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +public class DumpResultPerFunderTest { +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication new file mode 100644 index 0000000000..901b34abc0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication @@ -0,0 +1,12 @@ +{"author":[{"fullname":"Eric A. Wright","name":"Eric A.","pid":{"id":{"scheme":"orcid","value":"0000-0001-8604-7026"}},"rank":1,"surname":"Wright"},{"fullname":"Christopher D. d’Esterre","name":"Christopher D.","rank":2,"surname":"d’Esterre"},{"fullname":"Laura B. Morrison","name":"Laura B.","rank":3,"surname":"Morrison"},{"fullname":"Neil Cockburn","name":"Neil","rank":4,"surname":"Cockburn"},{"fullname":"Michael Kovacs","name":"Michael","rank":5,"surname":"Kovacs"},{"fullname":"Ting-Yim Lee","name":"Ting-Yim","rank":6,"surname":"Lee"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"}],"context":[{"code":"ni","label":"Neuroinformatics","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Jiang, Quan"],"country":[],"coverage":[],"dateofcollection":"","description":["CT Perfusion (CTP) derived cerebral blood flow (CBF) thresholds have been proposed as the optimal parameter for distinguishing the infarct core prior to reperfusion. Previous threshold-derivation studies have been limited by uncertainties introduced by infarct expansion between the acute phase of stroke and follow-up imaging, or DWI lesion reversibility. In this study a model is proposed for determining infarction CBF thresholds at 3hr ischemia time by comparing contemporaneously acquired CTP derived CBF maps to 18F-FFMZ-PET imaging, with the objective of deriving a CBF threshold for infarction after 3 hours of ischemia. Endothelin-1 (ET-1) was injected into the brain of Duroc-Cross pigs (n = 11) through a burr hole in the skull. CTP images were acquired 10 and 30 minutes post ET-1 injection and then every 30 minutes for 150 minutes. 370 MBq of 18F-FFMZ was injected ~120 minutes post ET-1 injection and PET images were acquired for 25 minutes starting ~155-180 minutes post ET-1 injection. CBF maps from each CTP acquisition were co-registered and converted into a median CBF map. The median CBF map was co-registered to blood volume maps for vessel exclusion, an average CT image for grey/white matter segmentation, and 18F-FFMZ-PET images for infarct delineation. Logistic regression and ROC analysis were performed on infarcted and non-infarcted pixel CBF values for each animal that developed infarct. Six of the eleven animals developed infarction. The mean CBF value corresponding to the optimal operating point of the ROC curves for the 6 animals was 12.6 ± 2.8 mL·min-1·100g-1 for infarction after 3 hours of ischemia. The porcine ET-1 model of cerebral ischemia is easier to implement then other large animal models of stroke, and performs similarly as long as CBF is monitored using CTP to prevent reperfusion."],"format":[],"id":"50|dedup_wf_001::0017bb7bb6a0e2f5624db2721a1bc1a5","instance":[{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"http://creativecommons.org/licenses/by/4.0","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1371/journal.pone.0158157"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},"hostedby":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"publicationdate":"2016-06-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566"]},{"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::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Article","url":["http://dx.plos.org/10.1371/journal.pone.0158157","http://dx.doi.org/10.1371/journal.pone.0158157"]},{"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::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0158157&type=printable"]},{"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::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"refereed":"UNKNOWN","type":"Article","url":["https://www.ncbi.nlm.nih.gov/pubmed/27347877","http://ui.adsabs.harvard.edu/abs/2016PLoSO..1158157W/abstract","https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158157","https://paperity.org/p/80470187/absolute-cerebral-blood-flow-infarction-threshold-for-3-hour-ischemia-time-determined","https://dx.plos.org/10.1371/journal.pone.0158157","https://academic.microsoft.com/#/detail/2460634846"]},{"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::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566?pdf=render","https://doaj.org/toc/1932-6203"]},{"collectedfrom":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2016-06-27T17:32:46Z","refereed":"UNKNOWN","type":"UNKNOWN","url":["https://dx.doi.org/10.1371/journal.pone.0158157"]}],"language":{"code":"UNKNOWN","label":"UNKNOWN"},"lastupdatetimestamp":1603727328518,"maintitle":"Absolute Cerebral Blood Flow Infarction Threshold for 3-Hour Ischemia Time Determined with CT Perfusion and 18F-FFMZ-PET Imaging in a Porcine Model of Cerebral Ischemia","originalId":["10.1371/journal.pone.0158157","oai:pubmedcentral.nih.gov:4922566","2460634846","oai:doaj.org/article:a0a0f971217e4277aae02c2ddb0243ed","27347877"],"pid":[{"scheme":"doi","value":"10.1371/journal.pone.0158157"},{"scheme":"pmc","value":"PMC4922566"},{"scheme":"pmid","value":"27347877"}],"projects":[{"code":"unidentified","funder":{"jurisdiction":"CA","name":"Canadian Institutes of Health Research","shortName":"CIHR"},"id":"40|cihr________::1e5e62235d094afd01cd56e65112fc63","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"unidentified"}],"publicationdate":"2016-06-27","publisher":"Public Library of Science (PLoS)","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research Article"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine and Health Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Signs and Symptoms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Infarction"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pathology and Laboratory Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Critical Care and Emergency Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Reperfusion"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research and Analysis Methods"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Imaging Techniques"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroimaging"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Positron Emission Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Biology and Life Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroscience"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Radiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Radiology and 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Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Model Organisms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Animal Models"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pig Models"}},{"subject":{"scheme":"keywords","value":"General Biochemistry, Genetics and Molecular Biology"}},{"subject":{"scheme":"keywords","value":"General Agricultural and Biological Sciences"}},{"subject":{"scheme":"keywords","value":"General Medicine"}},{"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":"Inferred by OpenAIRE","trust":"0.8487"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular system"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.7884"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular diseases"}}],"type":"publication"} +{"author":[{"fullname":"NIOO-KNAW KNAW","name":"NIOO-KNAW","pid":{"id":{"scheme":"orcid","value":"0000-0002-3835-159X"}},"rank":1,"surname":"KNAW"}],"bestaccessright":{"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"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de","value":"NARCIS"},{"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|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Universidad de Alicante. 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 California"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|opendoar____::8f19793b2671094e63a15ab883d50137","value":"Digital Access to Scholarship at Harvard"},{"key":"10|opendoar____::2a38a4a9316c49e5a833517c45d31070","value":"DSpace@MIT"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Massachusetts Institute of Technology. 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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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. 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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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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. 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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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Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::b733217d1cd609001dd3c75af419d872"} +{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::c33dee8231ad0374caf93e52c5a473e5"} \ No newline at end of file From bde6d337dd9178c51a9fdd5028b3d42683bfef52 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:42:01 +0100 Subject: [PATCH 26/54] test classes for dump of results related to funders --- .../ResultLinkedToProjectTest.java | 129 ++++++++++++++++ .../dump/funderresult/SplitPerFunderTest.java | 140 +++++++++++++++++- 2 files changed, 268 insertions(+), 1 deletion(-) 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 3696db7f87..b7ee5b122b 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 @@ -1,4 +1,133 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresult; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + public class ResultLinkedToProjectTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testNoMatch() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); + + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Result.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + } + + @Test + public void testMatchOne() throws Exception { + + final String sourcePath = getClass() + .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/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + + Assertions.assertEquals(1, verificationDataset.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 8e49b9fc6b..3381dabe11 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 @@ -1,4 +1,142 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresult; -public class DumpResultPerFunderTest { +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class SplitPerFunderTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SplitPerFunderTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getPath(); + + + SparkDumpFunderResults.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath, + "-relationPath", sourcePath + + }); + + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + // FP7 3 + JavaRDD tmp = sc + .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)); + + Assertions.assertEquals(3, verificationDataset.count()); + + Assertions + .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)); + Assertions.assertEquals(2, tmp.count()); + + //NWO 1 + tmp = sc + .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)); + Assertions.assertEquals(2, tmp.count()); + + //NSF 1 + tmp = sc + .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)); + Assertions.assertEquals(1, tmp.count()); + + //NHMRC 1 + tmp = sc + .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)); + Assertions.assertEquals(3, tmp.count()); + + } } From 21ce175d176f76283cf4f0754842bd967e8f5d68 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:42:31 +0100 Subject: [PATCH 27/54] added FilterFunction specification if filter operation --- .../eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 6be1befce1..55f075e954 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -9,6 +9,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -54,7 +55,7 @@ public class CommunitySplit implements Serializable { private static void printResult(String c, Dataset result, String outputPath) { Dataset community_products = result - .filter(r -> containsCommunity(r, c)); + .filter((FilterFunction) r -> containsCommunity(r, c)); try { community_products.first(); From 305e3d0c9c13b74d99f4dfcc547dae5df68af826 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:43:41 +0100 Subject: [PATCH 28/54] added resource file for relation with relClass = isProducedBy --- .../dhp/oa/graph/dump/funderresource/extendeddump/relation | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation index 3cb855c1ab..3ed91f4513 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation @@ -1,7 +1,7 @@ {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|cihr________::1e5e62235d094afd01cd56e65112fc63"} {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::5ac587eb28411c351c2e357eb097fd3d","subRelType":"provision","target":"40|nwo_________::dc69ada721bf21ed51055b6421850d73"} 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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::b566fa319c3923454e1e8eb886ab62d2","subRelType":"provision","target":"40|nhmrc_______::4e6c928fef9851b37ec73f4f6daca35b"} From e7e418e444cab97084faa167c0fe3057b09a9de0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:44:10 +0100 Subject: [PATCH 29/54] added decision node to verify if to upload in Zenodo --- .../dump/funderresults/oozie_app/workflow.xml | 30 +++++++++++++++++-- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d258d4dd47..d310390b70 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -1,6 +1,11 @@ + + upload + false + true to upload the dump for the funders in Zenodo + sourcePath the source path @@ -116,7 +121,7 @@ - + @@ -515,12 +520,31 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/ext - --outputPath${outputPath} + --outputPath${workingDir}/resultperfunder --relationPath${sourcePath} - + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + + --sourcePath/user/miriam.baglioni/graph_dump_whole_production_funder_results + + + + + + + + ${wf:conf('upload') eq true} + + + From 87a9f616ae3d38062c136d1533c258dbbb68ac4f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:45:41 +0100 Subject: [PATCH 30/54] refactoring and addition of the funder nsp first part as nome for the dump insteasd of the whole nsp --- .../funderresults/SparkDumpFunderResults.java | 26 +++++++++++++------ 1 file changed, 18 insertions(+), 8 deletions(-) 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 232459c19a..e2d8d7cb19 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 @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; +import eu.dnetlib.dhp.oa.graph.dump.Constants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -72,7 +73,7 @@ public class SparkDumpFunderResults implements Serializable { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'isProducedBy'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase()+ "'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -86,13 +87,22 @@ public class SparkDumpFunderResults implements Serializable { .distinct() .collectAsList(); -// Dataset results = result -// .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") -// .map((MapFunction, CommunityResult>) value -> { -// return value._1(); -// }, Encoders.bean(CommunityResult.class)); - funderList.forEach(funder -> writeFunderResult(funder, result, outputPath)); + 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); + }); } @@ -113,7 +123,7 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath + "/" + funder); + .json(outputPath); } } From e758d5d9b4f6253a1b5deb65a35689705ffff2ce Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:46:39 +0100 Subject: [PATCH 31/54] refactoring --- .../dump/funderresults/SparkResultLinkedToProject.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 e5d7e2254f..8c91fbf1fa 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 @@ -6,9 +6,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import eu.dnetlib.dhp.oa.graph.dump.Constants; 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; @@ -64,19 +64,19 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLikedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); }); } - private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, + String inputPath, String outputPath, String relationPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase() + "'"); relations .joinWith( From 1f130cdf92ea2335824d77d81888e00aedbdd24e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:04:26 +0100 Subject: [PATCH 32/54] changed the relation (produces -> isProducedBy) due to the change in the code --- .../graph/dump/resultProject/match/relation | 16 +-- .../dump/resultProject/match_one/relation | 16 +-- .../dump/resultProject/no_match/relation | 119 +++--------------- 3 files changed, 35 insertions(+), 116 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation index e23eebcc6d..b1c793e2ab 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation @@ -1,8 +1,8 @@ -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::03376222b28a3aebf2730ac514818d04","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} 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b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one/relation @@ -1,8 +1,8 @@ -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} 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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395830521,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::01703d216eb2d01f73e9f476302cd341","subRelType":"outcome","source":"50|dedup_wf_001::d4b9ca4bf332403c15abb47d21963ddc"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395830521,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::01703d216eb2d01f73e9f476302cd341","subRelType":"outcome","source":"50|dedup_wf_001::d4b9ca4bf332403c15abb47d21963ddc"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395828850,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::0229a330cb3e72e8f976a93bef7e0982","subRelType":"outcome","source":"50|od________18::0fa23557cd83522c7db8ccfefad1f12e"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:project:semrel","classname":"Propagation of result to project through semantic relation","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"trust":"0.85"},"lastupdatetimestamp":null,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::7f0f296b5e4ec1a1d61cfe4da63406c7","subRelType":"outcome","source":"50|dedup_wf_001::595ab3bf9261fbd616fb0240fb78add2"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395837446,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::a7322657c4ea4c9a3dc7cb77deb51620","subRelType":"outcome","source":"50|od_______166::953fd0631804ebda31b415fea855d570"} \ No newline at end of file From b2c455f8837ef82e39cf2af8444b02ed61bccc0f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:08:09 +0100 Subject: [PATCH 33/54] added java doc --- .../oa/graph/dump/funderresults/SparkDumpFunderResults.java | 5 ++--- .../graph/dump/funderresults/SparkResultLinkedToProject.java | 5 +++++ 2 files changed, 7 insertions(+), 3 deletions(-) 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 e2d8d7cb19..7049bdacf6 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 @@ -25,9 +25,8 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; /** - * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the - * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to + * 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); 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 8c91fbf1fa..4c72cd526d 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 @@ -24,6 +24,11 @@ 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. + * The code to perform the dump and to expend the dumped results with the informaiton related to projects + * is the one used for the dump of the community products + */ public class SparkResultLinkedToProject implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); From 90d4369fd207663e6baadeb2e0b3a4858910387e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:34:58 +0100 Subject: [PATCH 34/54] added test to verify the compression in writing community info on hdfs --- .../graph/dump/complete/CreateEntityTest.java | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 7028115496..4a3c6ed209 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -20,10 +20,7 @@ import org.apache.hadoop.fs.LocalFileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; @@ -146,6 +143,7 @@ public class CreateEntityTest { } @Test + @Disabled public void test2() throws IOException, ISLookUpException { LocalFileSystem fs = FileSystem.getLocal(new Configuration()); @@ -166,8 +164,16 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - List riList = new ArrayList<>(); - cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); + //List riList = new ArrayList<>(); + cInfoList.forEach(cInfo -> { + try { + writer.write(new Gson().toJson(Process.getEntity(cInfo))); + } catch (IOException e) { + e.printStackTrace(); + } + }); + + writer.close(); } } From 66c0e3e574d79da701b9cdf45f9d2c0616113675 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:52:17 +0100 Subject: [PATCH 35/54] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2489 --- .../src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 89fa09f3cb..76017d5b70 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,9 +90,6 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); -// if (name.trim().equalsIgnoreCase("communities_infrastructures")) { -// name = "communities_infrastructures.json"; -// } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); From 1df94b85b4f037b400498f1b0e462c2ccc9f03d5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:57:43 +0100 Subject: [PATCH 36/54] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2491 --- .../eu/dnetlib/dhp/oa/graph/dump/Constants.java | 1 - .../funderresults/SparkDumpFunderResults.java | 16 +++++++++------- .../SparkResultLinkedToProject.java | 9 ++++++--- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index c64554555d..eb01ebf328 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,7 +26,6 @@ public class Constants { public static String ORCID = "orcid"; - public static String RESULT_PROJECT_IS_PRODUCED_BY = "isProducedBy"; static { accessRightsCoarMap.put("OPEN", "c_abf2"); 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 7049bdacf6..826b4be8c0 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 @@ -6,7 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -16,6 +16,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.zenodo.Community; +import eu.dnetlib.dhp.oa.graph.dump.Constants; 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; @@ -72,7 +73,9 @@ public class SparkDumpFunderResults implements Serializable { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase()+ "'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -86,18 +89,17 @@ public class SparkDumpFunderResults implements Serializable { .distinct() .collectAsList(); - funderList.forEach(funder -> { String fundernsp = funder.substring(3); String funderdump; - if (fundernsp.startsWith("corda")){ + if (fundernsp.startsWith("corda")) { funderdump = "EC_"; - if(fundernsp.endsWith("h2020")){ + if (fundernsp.endsWith("h2020")) { funderdump += "H2020"; - }else{ + } else { funderdump += "FP7"; } - }else{ + } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } writeFunderResult(funder, result, outputPath + "/" + funderdump); 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 4c72cd526d..07e289cbd5 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 @@ -6,7 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -19,6 +19,7 @@ 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.Utils; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; @@ -74,14 +75,16 @@ public class SparkResultLinkedToProject implements Serializable { } private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + String inputPath, String outputPath, String relationPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase() + "'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); relations .joinWith( From f5e5e92a101feca613bc5a1232e43eb17d3edca2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:58:53 +0100 Subject: [PATCH 37/54] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2493 --- .../oa/graph/dump/funderresults/oozie_app/workflow.xml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d310390b70..650b972fa3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -121,7 +121,7 @@ - + @@ -274,7 +274,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${workingDir}/communityMap @@ -302,7 +301,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${workingDir}/communityMap @@ -330,7 +328,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${workingDir}/communityMap @@ -358,7 +355,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${workingDir}/communityMap @@ -532,8 +528,7 @@ eu.dnetlib.dhp.oa.graph.dump.MakeTar --hdfsPath${outputPath} --nameNode${nameNode} - - --sourcePath/user/miriam.baglioni/graph_dump_whole_production_funder_results + --sourcePath${workingDir}/resultperfunder From d4ddde2ef2d5b6d8d2d50b36882a8e6e0b005cae Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:01:01 +0100 Subject: [PATCH 38/54] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2503 --- .../eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 4a3c6ed209..f179e9de56 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,7 +164,6 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - //List riList = new ArrayList<>(); cInfoList.forEach(cInfo -> { try { writer.write(new Gson().toJson(Process.getEntity(cInfo))); From ed01e5a5e1feef7ba37ee7568290b75c31e74ede Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:09:34 +0100 Subject: [PATCH 39/54] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2507 --- .../dnetlib/dhp/oa/graph/dump/input_parameters.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index ca12ae3ec6..1d986fc261 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -29,12 +29,13 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - },{ - "paramName":"dt", - "paramLongName":"dumpType", - "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", - "paramRequired": false -} + }, + { + "paramName":"dt", + "paramLongName":"dumpType", + "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", + "paramRequired": false + } ] From 5fbe54ef54b68e4ec972666ea112a6c81494a1c6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:10:28 +0100 Subject: [PATCH 40/54] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2509 --- .../oa/graph/dump/input_parameters_link_prj.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) 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 5c48867413..fdd9492fe7 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 @@ -22,12 +22,13 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - }, { - "paramName":"rp", - "paramLongName":"relationPath", - "paramDescription": "the path to the relations", - "paramRequired": true -} + }, + { + "paramName":"rp", + "paramLongName":"relationPath", + "paramDescription": "the path to the relations", + "paramRequired": true + } ] From 1a89f8211c6ec589305a77188a84b54268ff30d6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:12:40 +0100 Subject: [PATCH 41/54] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2505 --- .../dhp/oa/graph/dump/complete/CreateEntityTest.java | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index f179e9de56..20c578738d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,14 +164,9 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - cInfoList.forEach(cInfo -> { - try { - writer.write(new Gson().toJson(Process.getEntity(cInfo))); - } catch (IOException e) { - e.printStackTrace(); - } - }); - + for(ContextInfo cInfo: cInfoList){ + writer.write(new Gson().toJson(Process.getEntity(cInfo))); + } writer.close(); } From 124591a7f32d58b70166b22a6d1ad297c67d6c36 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:23:28 +0100 Subject: [PATCH 42/54] refactoring --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 1 - .../funderresults/SparkDumpFunderResults.java | 2 +- .../SparkResultLinkedToProject.java | 2 +- .../graph/dump/complete/CreateEntityTest.java | 2 +- .../ResultLinkedToProjectTest.java | 172 +++++++-------- .../dump/funderresult/SplitPerFunderTest.java | 195 +++++++++--------- 6 files changed, 188 insertions(+), 186 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index eb01ebf328..86a275ae22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,7 +26,6 @@ public class Constants { public static String ORCID = "orcid"; - static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); 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 826b4be8c0..00f604b14b 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 @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -20,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.Constants; 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.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import eu.dnetlib.dhp.schema.oaf.Relation; 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 07e289cbd5..1a28a21f43 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 @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,6 +20,7 @@ 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.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 20c578738d..3ecbd18943 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,7 +164,7 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - for(ContextInfo cInfo: cInfoList){ + for (ContextInfo cInfo : cInfoList) { writer.write(new Gson().toJson(Process.getEntity(cInfo))); } writer.close(); 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 b7ee5b122b..dbe3db6fe2 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 @@ -1,9 +1,11 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresult; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -17,117 +19,119 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; public class ResultLinkedToProjectTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); - private static HashMap map = new HashMap<>(); + private static HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testNoMatch() throws Exception { + @Test + public void testNoMatch() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") - .getPath(); + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + .getPath(); - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath - }); + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + 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, Result.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, verificationDataset.count()); - } + } - @Test - public void testMatchOne() throws Exception { + @Test + public void testMatchOne() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + final String sourcePath = getClass() + .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/relations.json") - .getPath(); + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getPath(); - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath - }); + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + 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, Publication.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, verificationDataset.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 3381dabe11..71bf5d9421 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 @@ -1,11 +1,10 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresult; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -19,124 +18,124 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; public class SplitPerFunderTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); + private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(SplitPerFunderTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(SplitPerFunderTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void test1() throws Exception { + @Test + public void test1() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + SparkDumpFunderResults.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath, + "-relationPath", sourcePath + }); - SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-relationPath", sourcePath + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - }); + // FP7 3 + JavaRDD tmp = sc + .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)); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + Assertions.assertEquals(3, verificationDataset.count()); - // FP7 3 - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + // CIHR 2 + tmp = sc + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); - Assertions.assertEquals(3, verificationDataset.count()); + // NWO 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + // NIH 3 + tmp = sc + .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)); + Assertions.assertEquals(1, tmp.count()); - // CIHR 2 - tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); + // SNSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - //NWO 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .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)); + Assertions.assertEquals(1, tmp.count()); - //NIH 3 - tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); + // H2020 3 + tmp = sc + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(3, tmp.count()); - //NSF 1 - tmp = sc - .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)); - Assertions.assertEquals(1, tmp.count()); - - //NHMRC 1 - tmp = sc - .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)); - Assertions.assertEquals(3, tmp.count()); - - } + } } From d5efa6963a1fd8af983fe5fa71ffc4cd7d18d8ac Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 2 Dec 2020 11:20:26 +0100 Subject: [PATCH 43/54] using constants in ModelCOnstants --- .../dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index aeaa8a3c11..4989e09d14 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -7,6 +7,7 @@ import java.nio.file.Path; import com.cloudera.org.codehaus.jackson.map.jsontype.impl.ClassNameIdResolver; import eu.dnetlib.dhp.PropagationConstant; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -169,7 +170,7 @@ public class OrcidPropagationJobTest { .filter( "id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' " + "and name = 'Vajinder' and surname = 'Kumar' and pidType = '" + - PropagationConstant.PROPAGATION_AUTHOR_PID_CLASSID +"'") + ModelConstants.ORCID_PENDING + "'") .count()); Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count()); From 4c58bd1c93297bfc0e99b6e82268fa86f3d83067 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 3 Dec 2020 11:24:00 +0100 Subject: [PATCH 44/54] merge with upstream --- .../dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index 1bfb79dcab..238375197f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; - import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; From ea88dc3401e656682c8c13343684fa05a5e5e692 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 3 Dec 2020 11:24:23 +0100 Subject: [PATCH 45/54] fixed issue in property name --- .../dhp/oa/graph/dump/community/oozie_app/workflow.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml index 161fd2dec1..fcef2547ac 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml @@ -26,8 +26,8 @@ the metadata associated to the deposition - newDeposition - true if it is a brand new depositon. false for new version of an old deposition + depositionType + one among {new, update, version} conceptRecordId @@ -419,6 +419,7 @@ --metadata${metadata} --communityMapPath${workingDir}/communityMap --conceptRecordId${conceptRecordId} + --depositionId${depositionId} --depositionType${depositionType} From 620e1307a39e54e3ee5d3da50a5675355f36d08e Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 10:30:47 +0100 Subject: [PATCH 46/54] indentation --- .../broker/oa/PartitionEventsByDsIdJob.java | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 65d5e6f946..efb7a035c8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -40,8 +40,9 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString( + PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -63,11 +64,14 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { - validOpendoarIds.addAll(Arrays.stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + validOpendoarIds + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } runWithSparkSession(conf, isSparkSessionManaged, spark -> { From 370a5e650b0c9bdfac969f4d952e8491cd805694 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 11:18:26 +0100 Subject: [PATCH 47/54] validation attributes in resultProject relations --- .../raw/AbstractMdRecordToOafMapper.java | 168 ++++++++---------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 9 +- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 2 +- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 2 +- 4 files changed, 88 insertions(+), 93 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 95dd1e1cad..4e60e9fdd4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -70,10 +70,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( - "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier( - "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -87,8 +85,7 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( - "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible) { this.vocs = vocs; @@ -100,26 +97,20 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText( - xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + .parseText(xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { - return null; - } + if (collectedFrom == null) { return null; } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { - return null; - } + if (hostedBy == null) { return null; } final DataInfo info = prepareDataInfo(doc, invisible); final long lastUpdateTimestamp = new Date().getTime(); @@ -161,9 +152,7 @@ public abstract class AbstractMdRecordToOafMapper { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { - return null; - } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } return keyValue(createOpenaireId(10, dsId, true), dsName); } @@ -179,47 +168,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -244,25 +233,37 @@ public abstract class AbstractMdRecordToOafMapper { final String originalId = ((Node) o).getText(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + if (StringUtils.isNotBlank(originalId)) { final String projectId = createOpenaireId(40, originalId, true); res - .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelationWithValidationDate(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp, validationdDate)); res - .add( - getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelationWithValidationDate(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp, validationdDate)); } } return res; } + protected Relation getRelationWithValidationDate(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp, + final String validationDate) { + + final Relation r = getRelation(source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); + r.setValidated(StringUtils.isNotBlank(validationDate)); + r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + return r; + } + protected Relation getRelation(final String source, final String target, final String relType, @@ -455,9 +456,7 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); - } + if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } } return null; } @@ -466,9 +465,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); if (n != null) { final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { - return id; - } + if (StringUtils.isNotBlank(id)) { return id; } } return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']"); @@ -537,10 +534,7 @@ public abstract class AbstractMdRecordToOafMapper { for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add( - structuredProperty( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); + .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); } return res; } @@ -548,9 +542,7 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { - return null; - } + if (n == null) { return null; } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -565,9 +557,7 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { - return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); - } + if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -579,9 +569,7 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo( - deletedbyinference, inferenceprovenance, inferred, invisible, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 46cb1a5359..a0348f8ec1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -141,7 +141,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); - + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); // System.out.println(new ObjectMapper().writeValueAsString(p)); // System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r2)); @@ -246,6 +249,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 2c6c98ebb3..f4b0c477fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -51,7 +51,7 @@ 0001 2017-01-01 - corda_______::226852 + corda_______::226852 OPEN und - corda_______::226852 + corda_______::226852 0001s From 5f21a356fd61432713af2431ff36987d8d0b2e40 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 11:24:30 +0100 Subject: [PATCH 48/54] reindent --- .../raw/AbstractMdRecordToOafMapper.java | 153 +++++++++++------- 1 file changed, 92 insertions(+), 61 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 4e60e9fdd4..267c6026d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -70,8 +70,10 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier ORCID_PID_TYPE = qualifier( + "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier( + "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -85,7 +87,8 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( + "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible) { this.vocs = vocs; @@ -97,20 +100,26 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText(xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { return null; } + if (collectedFrom == null) { + return null; + } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { return null; } + if (hostedBy == null) { + return null; + } final DataInfo info = prepareDataInfo(doc, invisible); final long lastUpdateTimestamp = new Date().getTime(); @@ -152,7 +161,9 @@ public abstract class AbstractMdRecordToOafMapper { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { + return null; + } return keyValue(createOpenaireId(10, dsId, true), dsName); } @@ -168,47 +179,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -239,9 +250,15 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add(getRelationWithValidationDate(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp, validationdDate)); + .add( + getRelationWithValidationDate( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp, validationdDate)); res - .add(getRelationWithValidationDate(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp, validationdDate)); + .add( + getRelationWithValidationDate( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp, validationdDate)); } } @@ -258,7 +275,8 @@ public abstract class AbstractMdRecordToOafMapper { final long lastUpdateTimestamp, final String validationDate) { - final Relation r = getRelation(source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); + final Relation r = getRelation( + source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); r.setValidated(StringUtils.isNotBlank(validationDate)); r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); return r; @@ -456,7 +474,9 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } + if (StringUtils.isNotBlank(name)) { + return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); + } } return null; } @@ -465,7 +485,9 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); if (n != null) { final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { return id; } + if (StringUtils.isNotBlank(id)) { + return id; + } } return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']"); @@ -534,7 +556,10 @@ public abstract class AbstractMdRecordToOafMapper { for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); + .add( + structuredProperty( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); } return res; } @@ -542,7 +567,9 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { return null; } + if (n == null) { + return null; + } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -557,7 +584,9 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } + if (n == null) { + return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -569,7 +598,9 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + return dataInfo( + deletedbyinference, inferenceprovenance, inferred, invisible, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { From 1bc9adc10d79455cd910249fcc431ef23b7a214f Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 16:18:37 +0100 Subject: [PATCH 49/54] default trust for validated rels --- .../oa/graph/raw/AbstractMdRecordToOafMapper.java | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 267c6026d3..cccf15398f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -75,6 +75,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final Qualifier MAG_PID_TYPE = qualifier( "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; + protected static final Map nsContext = new HashMap<>(); static { @@ -279,6 +281,16 @@ public abstract class AbstractMdRecordToOafMapper { source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); r.setValidated(StringUtils.isNotBlank(validationDate)); r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + + if (StringUtils.isNotBlank(validationDate)) { + r.setValidated(true); + r.setValidationDate(validationDate); + r.getDataInfo().setTrust(DEFAULT_TRUST_FOR_VALIDATED_RELS); + } else { + r.setValidated(false); + r.setValidationDate(null); + } + return r; } From 212b52614fefa9a08dc3fc08c8325a0c5a0dc5b5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 9 Dec 2020 16:59:02 +0100 Subject: [PATCH 50/54] added graph mapper versus community result without context and project in common to be used for the doiboost mapping --- .../java/eu/dnetlib/dhp/common/Constants.java | 44 ++ .../dnetlib/dhp/common/GraphResultMapper.java | 415 ++++++++++++++++++ 2 files changed, 459 insertions(+) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java new file mode 100644 index 0000000000..c9d15ff763 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.common; + +import com.google.common.collect.Maps; + +import java.util.Map; + +public class Constants { + + public static final Map accessRightsCoarMap = Maps.newHashMap(); + public static final Map coarCodeLabelMap = Maps.newHashMap(); + + public static final String INFERRED = "Inferred by OpenAIRE"; + + public static final String HARVESTED = "Harvested"; + public static final String DEFAULT_TRUST = "0.9"; + public static final String USER_CLAIM = "Linked by user";; + + public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + + public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + + public static String RESEARCH_COMMUNITY = "Research Community"; + + public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + + public static String ORCID = "orcid"; + + static { + accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put("RESTRICTED", "c_16ec"); + accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); + accessRightsCoarMap.put("CLOSED", "c_14cb"); + accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + } + + static { + coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put("c_16ec", "RESTRICTED"); + coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_f1cf", "EMBARGO"); + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java new file mode 100644 index 0000000000..5e37f15db6 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -0,0 +1,415 @@ + +package eu.dnetlib.dhp.common; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +public class GraphResultMapper implements Serializable { + + public static Result map( + E in) { + + CommunityResult out = new CommunityResult(); + + eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; + Optional ort = Optional.ofNullable(input.getResulttype()); + if (ort.isPresent()) { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + } + + Optional + .ofNullable(input.getAuthor()) + .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + + // I do not map Access Right UNKNOWN or OTHER + + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); + + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance + .newInstance( + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); + + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); + + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + Optional> oInst = Optional + .ofNullable(input.getInstance()); + + if (oInst.isPresent()) { + out + .setInstance( + oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); + + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + } + + out + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + + return out; + + } + + + private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { + CommunityInstance instance = new CommunityInstance(); + + setCommonValue(i, instance); + + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + + return instance; + + } + + private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { + Optional opAr = Optional + .ofNullable(i.getAccessright()); + if (opAr.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + Optional + .ofNullable(i.getLicense()) + .ifPresent(value -> instance.setLicense(value.getValue())); + Optional + .ofNullable(i.getDateofacceptance()) + .ifPresent(value -> instance.setPublicationdate(value.getValue())); + Optional + .ofNullable(i.getRefereed()) + .ifPresent(value -> instance.setRefereed(value.getClassname())); + Optional + .ofNullable(i.getInstancetype()) + .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + + } + + + private static Subject getSubject(StructuredProperty s) { + Subject subject = new Subject(); + subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + Optional di = Optional.ofNullable(s.getDataInfo()); + if (di.isPresent()) { + Provenance p = new Provenance(); + p.setProvenance(di.get().getProvenanceaction().getClassname()); + p.setTrust(di.get().getTrust()); + subject.setProvenance(p); + } + + return subject; + } + + private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { + Author a = new Author(); + a.setFullname(oa.getFullname()); + a.setName(oa.getName()); + a.setSurname(oa.getSurname()); + a.setRank(oa.getRank()); + + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } + + return a; + } + + private static Pid getOrcid(List p) { + for (StructuredProperty pid : p) { + if (pid.getQualifier().getClassid().equals(Constants.ORCID)) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) + + ); + } + + } + } + return null; + } + +} From 6fbc67a9595564c5df9976e0751016c4843317c7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 9 Dec 2020 17:10:20 +0100 Subject: [PATCH 51/54] using ModelConstant.ORCID and removing not used constants --- .../main/java/eu/dnetlib/dhp/common/Constants.java | 14 -------------- .../eu/dnetlib/dhp/common/GraphResultMapper.java | 2 +- 2 files changed, 1 insertion(+), 15 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index c9d15ff763..6a986e145d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -10,22 +10,8 @@ public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); public static final Map coarCodeLabelMap = Maps.newHashMap(); - public static final String INFERRED = "Inferred by OpenAIRE"; - - public static final String HARVESTED = "Harvested"; - public static final String DEFAULT_TRUST = "0.9"; - public static final String USER_CLAIM = "Linked by user";; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - - public static String RESEARCH_COMMUNITY = "Research Community"; - - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; - - public static String ORCID = "orcid"; - static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java index 5e37f15db6..3956410d57 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -383,7 +383,7 @@ public class GraphResultMapper implements Serializable { private static Pid getOrcid(List p) { for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(Constants.ORCID)) { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { Optional di = Optional.ofNullable(pid.getDataInfo()); if (di.isPresent()) { return Pid From db4e400a0b77e29f3ccc9e48286024263465925b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 9 Dec 2020 18:01:45 +0100 Subject: [PATCH 52/54] introduced Oaf.mergeFrom method to allow merging of dataInfo(s), with prevalence based on datainfo.trust --- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 38 +++++++++++++++++-- .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 6 +-- .../eu/dnetlib/dhp/schema/oaf/Relation.java | 14 +------ 3 files changed, 36 insertions(+), 22 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 3496492e8e..fef32c0c6b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -2,8 +2,12 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Collection; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; public abstract class Oaf implements Serializable { @@ -40,9 +44,35 @@ public abstract class Oaf implements Serializable { this.lastupdatetimestamp = lastupdatetimestamp; } - public void mergeOAFDataInfo(Oaf e) { - if (e.getDataInfo() != null && compareTrust(this, e) < 0) - dataInfo = e.getDataInfo(); + public void mergeFrom(Oaf o) { + if (Objects.isNull(o)) { + return; + } + setCollectedfrom( + Stream + .concat( + Optional + .ofNullable(getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(o.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + + mergeOAFDataInfo(o); + + setLastupdatetimestamp( + Math.max( + Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), + Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); + } + + public void mergeOAFDataInfo(Oaf o) { + if (o.getDataInfo() != null && compareTrust(this, o) < 0) + dataInfo = o.getDataInfo(); } protected String extractTrust(Oaf e) { @@ -62,7 +92,7 @@ public abstract class Oaf implements Serializable { if (o == null || getClass() != o.getClass()) return false; Oaf oaf = (Oaf) o; - return Objects.equals(dataInfo, oaf.dataInfo) + return Objects.equals(getDataInfo(), oaf.getDataInfo()) && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 2823ee49dd..17c3e6bddc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -78,14 +78,10 @@ public abstract class OafEntity extends Oaf implements Serializable { } public void mergeFrom(OafEntity e) { - - if (e == null) - return; + super.mergeFrom(e); originalId = mergeLists(originalId, e.getOriginalId()); - collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom()); - pid = mergeLists(pid, e.getPid()); if (e.getDateofcollection() != null && compareTrust(this, e) < 0) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 17a50d7aca..0de34dbecc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -130,19 +130,7 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedfrom( - Stream - .concat( - Optional - .ofNullable(getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty()), - Optional - .ofNullable(r.getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + super.mergeFrom(r); } @Override From 426b76ee8eb70265dd3103d7da48d6b774606b61 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 9 Dec 2020 19:46:11 +0100 Subject: [PATCH 53/54] more asserts for TextGrid record --- .../eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 46cb1a5359..737a255e87 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -355,7 +355,20 @@ public class MappersTest { assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - System.out.println(p.getTitle().get(0).getValue()); + assertEquals(1, p.getAuthor().size()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue())); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid())); + assertEquals("dataset", p.getResulttype().getClassname()); + assertEquals(1, p.getInstance().size()); + assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); + assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); + assertValidId(p.getInstance().get(0).getHostedby().getKey()); + assertEquals("http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); + assertEquals(1, p.getInstance().get(0).getUrl().size()); +// System.out.println(p.getInstance().get(0).getUrl().get(0)); +// System.out.println(p.getInstance().get(0).getHostedby().getValue()); + System.out.println(p.getPid().get(0).getValue()); } @Test From 112da6d76a8c53777944d475f5115186b3b0e31c Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 9 Dec 2020 20:00:27 +0100 Subject: [PATCH 54/54] in theory, just auto-formatting after mvn compile --- .../java/eu/dnetlib/dhp/common/Constants.java | 4 +- .../dnetlib/dhp/common/GraphResultMapper.java | 695 +++++++++--------- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 27 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 3 +- 4 files changed, 364 insertions(+), 365 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index 6a986e145d..2b8ef4e300 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.common; -import com.google.common.collect.Maps; - import java.util.Map; +import com.google.common.collect.Maps; + public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java index 3956410d57..44599eb83f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -1,6 +1,10 @@ package eu.dnetlib.dhp.common; +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; @@ -10,406 +14,399 @@ import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Journal; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - public class GraphResultMapper implements Serializable { - public static Result map( - E in) { + public static Result map( + E in) { - CommunityResult out = new CommunityResult(); + CommunityResult out = new CommunityResult(); - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; + Optional ort = Optional.ofNullable(input.getResulttype()); + if (ort.isPresent()) { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": - eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); + eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) - .orElse(null)); + eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) - .orElse(null)); + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) + .orElse(null)); - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - break; - } + break; + } - Optional - .ofNullable(input.getAuthor()) - .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + Optional + .ofNullable(input.getAuthor()) + .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); - // I do not map Access Right UNKNOWN or OTHER + // I do not map Access Right UNKNOWN or OTHER - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - Country country = new Country(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance + .newInstance( + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); - out.setDateofcollection(input.getDateofcollection()); + out.setDateofcollection(input.getDateofcollection()); - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); - Optional> oInst = Optional - .ofNullable(input.getInstance()); + Optional> oInst = Optional + .ofNullable(input.getInstance()); - if (oInst.isPresent()) { - out - .setInstance( - oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); + if (oInst.isPresent()) { + out + .setInstance( + oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); - } + } - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setMaintitle(iTitle.get(0).getValue()); - } + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setSubtitle(iTitle.get(0).getValue()); - } + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } - } + } - List pids = new ArrayList<>(); - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> value - .stream() - .forEach( - p -> pids - .add( - ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())))); - out.setPid(pids); - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } - List sourceList = new ArrayList<>(); - Optional - .ofNullable(input.getSource()) - .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); - out.setSubjects(subjectList); + out.setSubjects(subjectList); - out.setType(input.getResulttype().getClassid()); - } + out.setType(input.getResulttype().getClassid()); + } - out - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); + out + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + return out; - return out; + } - } + private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { + CommunityInstance instance = new CommunityInstance(); + setCommonValue(i, instance); - private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - setCommonValue(i, instance); + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - instance - .setCollectedfrom( - KeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + return instance; - instance - .setHostedby( - KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + } - return instance; + private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { + Optional opAr = Optional + .ofNullable(i.getAccessright()); + if (opAr.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } - } + Optional + .ofNullable(i.getLicense()) + .ifPresent(value -> instance.setLicense(value.getValue())); + Optional + .ofNullable(i.getDateofacceptance()) + .ifPresent(value -> instance.setPublicationdate(value.getValue())); + Optional + .ofNullable(i.getRefereed()) + .ifPresent(value -> instance.setRefereed(value.getClassname())); + Optional + .ofNullable(i.getInstancetype()) + .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional - .ofNullable(i.getAccessright()); - if (opAr.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } + } - Optional - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + private static Subject getSubject(StructuredProperty s) { + Subject subject = new Subject(); + subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + Optional di = Optional.ofNullable(s.getDataInfo()); + if (di.isPresent()) { + Provenance p = new Provenance(); + p.setProvenance(di.get().getProvenanceaction().getClassname()); + p.setTrust(di.get().getTrust()); + subject.setProvenance(p); + } - } + return subject; + } + private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { + Author a = new Author(); + a.setFullname(oa.getFullname()); + a.setName(oa.getName()); + a.setSurname(oa.getSurname()); + a.setRank(oa.getRank()); - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } - return subject; - } + return a; + } - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); + private static Pid getOrcid(List p) { + for (StructuredProperty pid : p) { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - Pid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } + ); + } - return a; - } - - private static Pid getOrcid(List p) { - for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - - } - } - return null; - } + } + } + return null; + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index fef32c0c6b..f4f5baa7bb 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -49,23 +49,24 @@ public abstract class Oaf implements Serializable { return; } setCollectedfrom( - Stream - .concat( - Optional - .ofNullable(getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty()), - Optional - .ofNullable(o.getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + Stream + .concat( + Optional + .ofNullable(getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(o.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); mergeOAFDataInfo(o); setLastupdatetimestamp( - Math.max( + Math + .max( Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 3f80127f88..2a62e25b2a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -371,7 +371,8 @@ public class MappersTest { assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); assertValidId(p.getInstance().get(0).getHostedby().getKey()); - assertEquals("http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); + assertEquals( + "http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); assertEquals(1, p.getInstance().get(0).getUrl().size()); // System.out.println(p.getInstance().get(0).getUrl().get(0)); // System.out.println(p.getInstance().get(0).getHostedby().getValue());