From 79b978ec57d4bf2ee25c90b4a94ac5792251448b Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
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<ProjectResultSet> potentialUpdates, String outputPath){
-        potentialUpdates.map(u -> OBJECT_MAPPER.writeValueAsString(u))
-                .saveAsTextFile(outputPath, GzipCodec.class);
-    }
-        //JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
-
-//        JavaPairRDD<String, TypedRow> 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<String, TypedRow> 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<String, TypedRow> 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<Relation> 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<Relation> 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<ProjectResultSet> readAssocProjectResults(SparkSession spark, String potentialUpdatePath) {
         return spark
                 .read()
diff --git a/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/projecttoresult/sample/relation/relation_100.json.gz b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/projecttoresult/sample/relation/relation_100.json.gz
deleted file mode 100644
index bd4abe26f7dd34d52484ecf2319e3c251f95e1c3..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json
new file mode 100644
index 000000000..b585baf88
--- /dev/null
+++ b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json
@@ -0,0 +1,20 @@
+{"resultId":"50|acm_________::3133635707788d2180bcef09e01a903c","organizationSet":["20|dedup_wf_001::5ab59ffa94c31a140d4a56c594ea5865"]}
+{"resultId":"50|core________::0308a76f6f8bc4db75a817d53a7e76a4","organizationSet":["20|wt__________::a72760363ca885e6bef165804770e00c","20|nih_________::5c7f089c177ba49f92033f72e2aff724","20|dedup_wf_001::c88bf88e0a4dea271a3e2f832d952238"]}
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\ No newline at end of file
diff --git a/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json
new file mode 100644
index 000000000..efc3af110
--- /dev/null
+++ b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json
@@ -0,0 +1,28 @@
+{"datasourceId":"10|opendoar____::1068c6e4c8051cfd4e9ea8072e3189e2","organizationId":"20|opendoar____::4429502fa1936b0941f4647b69b844c8"}
+{"datasourceId":"10|opendoar____::211ed78fe91938b90f84a51944b08d5a","organizationId":"20|opendoar____::124266ebc4ece2934eb80edfda3f2091"}
+{"datasourceId":"10|opendoar____::21c5bba1dd6aed9ab48c2b34c1a0adde","organizationId":"20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2"}
+{"datasourceId":"10|opendoar____::376c6b9ff3bedbbea56751a84fffc10c","organizationId":"20|opendoar____::c6ac1e6c39e6f3a36e274f8d3f9f7fce"}
+{"datasourceId":"10|opendoar____::49c0fa7f96aa0a5fb95c62909d5190a6","organizationId":"20|dedup_wf_001::760a7568cbfdc750a5f92009a64bfc68"}
+{"datasourceId":"10|opendoar____::4fa177df22864518b2d7818d4db5db2d","organizationId":"20|dedup_wf_001::b6b1fdfd98370bc44a5ecb215051fc61"}
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+{"datasourceId":"10|opendoar____::a655fbe4b8d7439994aa37ddad80de56","organizationId":"20|opendoar____::bba529dfcc369815510999ccadff78d0"}
+{"datasourceId":"10|opendoar____::aebf7782a3d445f43cf30ee2c0d84dee","organizationId":"20|opendoar____::931aa8950244dea6b3fe9f7798b916ea"}
+{"datasourceId":"10|opendoar____::c4819d06b0ca810d38506453cfaae9d8","organizationId":"20|dedup_wf_001::bee19d6bbb94675a7a4aaf2b66f94ae3"}
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+{"datasourceId":"10|opendoar____::d8bf84be3800d12f74d8b05e9b89836f","organizationId":"20|dedup_wf_001::b19557d6f918479582295814b1dfb38b"}
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+{"datasourceId":"10|opendoar____::e9fb2eda3d9c55a0d89c98d6c54b5b3e","organizationId":"20|opendoar____::64cf1b2094ff19786a573980568762b4"}
+{"datasourceId":"10|opendoar____::f095cedd23b99f1696fc8caecbcf257e","organizationId":"20|dedup_wf_001::3f339760507dd23f9be59be2cff8204f"}
+{"datasourceId":"10|opendoar____::f095cedd23b99f1696fc8caecbcf257e","organizationId":"20|dedup_wf_001::76548cf94fcd27f67759cc6148ee1e7f"}
+{"datasourceId":"10|opendoar____::f35a2bc72dfdc2aae569a0c7370bd7f5","organizationId":"20|dedup_wf_001::2476836f27326ee53e586a82cbaedb1a"}
+{"datasourceId":"10|opendoar____::f91e24dfe80012e2a7984afa4480a6d6","organizationId":"20|opendoar____::5d462d78d512c1184dd384ef2dc35b7e"}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json
new file mode 100644
index 000000000..b585baf88
--- /dev/null
+++ b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json
@@ -0,0 +1,20 @@
+{"resultId":"50|acm_________::3133635707788d2180bcef09e01a903c","organizationSet":["20|dedup_wf_001::5ab59ffa94c31a140d4a56c594ea5865"]}
+{"resultId":"50|core________::0308a76f6f8bc4db75a817d53a7e76a4","organizationSet":["20|wt__________::a72760363ca885e6bef165804770e00c","20|nih_________::5c7f089c177ba49f92033f72e2aff724","20|dedup_wf_001::c88bf88e0a4dea271a3e2f832d952238"]}
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\ No newline at end of file
diff --git a/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json
new file mode 100644
index 000000000..efc3af110
--- /dev/null
+++ b/dhp-workflows/dhp-propagation/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization/datasourceOrganization_28.json
@@ -0,0 +1,28 @@
+{"datasourceId":"10|opendoar____::1068c6e4c8051cfd4e9ea8072e3189e2","organizationId":"20|opendoar____::4429502fa1936b0941f4647b69b844c8"}
+{"datasourceId":"10|opendoar____::211ed78fe91938b90f84a51944b08d5a","organizationId":"20|opendoar____::124266ebc4ece2934eb80edfda3f2091"}
+{"datasourceId":"10|opendoar____::21c5bba1dd6aed9ab48c2b34c1a0adde","organizationId":"20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2"}
+{"datasourceId":"10|opendoar____::376c6b9ff3bedbbea56751a84fffc10c","organizationId":"20|opendoar____::c6ac1e6c39e6f3a36e274f8d3f9f7fce"}
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+{"datasourceId":"10|opendoar____::4fa177df22864518b2d7818d4db5db2d","organizationId":"20|dedup_wf_001::b6b1fdfd98370bc44a5ecb215051fc61"}
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\ No newline at end of file