From 79b978ec57d4bf2ee25c90b4a94ac5792251448b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 16 Apr 2020 10:48:41 +0200 Subject: [PATCH] refactoring --- ...SparkResultToProjectThroughSemRelJob3.java | 101 ------------------ .../sample/relation/relation_100.json.gz | Bin 3639 -> 0 bytes .../alreadyLinked/alreadyLinked_20.json | 20 ++++ .../datasourceOrganization_28.json | 28 +++++ .../alreadyLinked/alreadyLinked_20.json | 20 ++++ .../datasourceOrganization_28.json | 28 +++++ 6 files changed, 96 insertions(+), 101 deletions(-) delete mode 100644 dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/projecttoresult/sample/relation/relation_100.json.gz create mode 100644 dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json create mode 100644 dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json create mode 100644 dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json create mode 100644 dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json diff --git a/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob3.java b/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob3.java index fb726e86c..2125f351f 100644 --- a/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob3.java +++ b/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob3.java @@ -1,34 +1,16 @@ package eu.dnetlib.dhp.projecttoresult; import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.countrypropagation.DatasourceCountry; import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation; -import eu.dnetlib.dhp.countrypropagation.ResultCountrySet; import eu.dnetlib.dhp.schema.oaf.Relation; -import org.apache.arrow.flatbuf.Bool; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.FlatMapFunction2; -import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; -import org.omg.CORBA.OBJ_ADAPTER; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import scala.Tuple2; - import java.util.ArrayList; -import java.util.Arrays; import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; @@ -50,9 +32,6 @@ public class SparkResultToProjectThroughSemRelJob3 { Boolean isSparkSessionManaged = isSparkSessionManaged(parser); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath {}: ", outputPath); @@ -143,86 +122,6 @@ public class SparkResultToProjectThroughSemRelJob3 { } - private static void writeUpdates(JavaRDD potentialUpdates, String outputPath){ - potentialUpdates.map(u -> OBJECT_MAPPER.writeValueAsString(u)) - .saveAsTextFile(outputPath, GzipCodec.class); - } - //JavaPairRDD result_result = getResultResultSemRel(allowedsemrel, relations); - -// JavaPairRDD result_project = relations -// .filter(r -> !r.getDataInfo().getDeletedbyinference()) -// .filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass()) -// && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType())) -// .map(rel ->{ -// -// TypedRow tr = new TypedRow(); -// tr.setSourceId(rel.getSource()); -// tr.setTargetId(rel.getTarget()); -// return tr; -// }) -// .mapToPair(toPair()); -// -// //relationships from project to result. One pair for each relationship for results having allowed semantics relation with another result -// JavaPairRDD project_result = result_project.join(result_result) -// .map(c -> { -// String projectId = c._2()._1().getTargetId(); -// String resultId = c._2()._2().getTargetId(); -// TypedRow tr = new TypedRow(); tr.setSourceId(projectId); tr.setTargetId(resultId); -// return tr; -// }) -// .mapToPair(toPair()); -// -// //relationships from project to result. One Pair for each project => project id list of results related to the project -// JavaPairRDD project_results = relations -// .filter(r -> !r.getDataInfo().getDeletedbyinference()) -// .filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType())) -// .map(r -> { -// TypedRow tr = new TypedRow(); tr.setSourceId(r.getSource()); tr.setTargetId(r.getTarget()); -// return tr; -// }) -// .mapToPair(toPair()) -// .reduceByKey((a, b) -> { -// if (a == null) { -// return b; -// } -// if (b == null) { -// return a; -// } -// a.addAll(b.getAccumulator()); -// return a; -// }); -// -// -// -// JavaRDD newRels = project_result.join(project_results) -// .flatMap(c -> { -// String resId = c._2()._1().getTargetId(); -// -// if (c._2()._2().getAccumulator().contains(resId)) { -// return null; -// } -// String progId = c._2()._1().getSourceId(); -// List rels = new ArrayList(); -// -// rels.add(getRelation(progId, resId, RELATION_PROJECT_RESULT_REL_CLASS, -// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE, -// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME)); -// rels.add(getRelation(resId, progId, RELATION_RESULT_PROJECT_REL_CLASS, -// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE, -// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME)); -// return rels.iterator(); -// }) -// .cache(); -// -// newRels.map(p -> new ObjectMapper().writeValueAsString(p)) -// .saveAsTextFile(outputPath + "/relation_new"); -// -// newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p)) -// .saveAsTextFile(outputPath + "/relation"); - - //} - - private static Dataset readAssocProjectResults(SparkSession spark, String potentialUpdatePath) { return spark .read() diff --git 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