preparation phase for the propagation of community to result from organization

2020-04-16 18:43:55 +02:00 · 2020-04-16 18:43:55 +02:00 · 3fd9d6b02f
parent a9120164aa
commit 3fd9d6b02f
1 changed files with 117 additions and 1 deletions
--- a/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java
+++ b/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java
@ -1,4 +1,120 @@
 package eu.dnetlib.dhp.resulttocommunityfromorganization;

-public class PrepareInfo {
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.TypedRow;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1;
+import eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.*;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+public class PrepareResultCommunitySet {
+
+    private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+        String jsonConfiguration = IOUtils.toString(PrepareResultCommunitySet.class
+                .getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json"));
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                jsonConfiguration);
+
+        parser.parseArgument(args);
+
+        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);
+
+        final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationtoresultcommunitymap"), OrganizationMap.class);
+        log.info("organizationMap: {}", new Gson().toJson(organizationMap));
+
+        SparkConf conf = new SparkConf();
+        conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+
+        runWithSparkHiveSession(conf, isSparkSessionManaged,
+                spark -> {
+                    if (isTest(parser)) {
+                        removeOutputDir(spark, outputPath);
+                    }
+                    prepareInfo(spark,  inputPath, outputPath, organizationMap);
+                });
+    }
+
+    private static void prepareInfo(SparkSession spark, String inputPath, String outputPath, OrganizationMap organizationMap) {
+        Dataset<Relation> relation = readRelations(spark, inputPath);
+        relation.createOrReplaceTempView("relation");
+
+        String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges " +
+                "FROM (SELECT source, target " +
+                "      FROM relation " +
+                "      WHERE datainfo.deletedbyinference = false " +
+                "      AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "') result_organization " +
+                "LEFT JOIN (SELECT source, collect_set(target) org_set " +
+                "      FROM relation " +
+                "      WHERE datainfo.deletedbyinference = false " +
+                "      AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "' " +
+                "      GROUP BY source) organization_organization " +
+                "ON result_organization.target = organization_organization.source ";
+
+        org.apache.spark.sql.Dataset<ResultOrganizations> result_organizationset = spark.sql(query)
+                .as(Encoders.bean(ResultOrganizations.class));
+
+        result_organizationset
+                .map(value -> {
+                    String rId = value.getResultId();
+                    List<String> orgs = value.getMerges();
+                    String oTarget = value.getOrgId();
+                    Set<String> communitySet = new HashSet<>();
+                    if (organizationMap.containsKey(oTarget)) {
+                        communitySet.addAll(organizationMap.get(oTarget));
+                    }
+                    try{
+                        for (String oId : orgs) {
+                            if (organizationMap.containsKey(oId)) {
+                                communitySet.addAll(organizationMap.get(oId));
+                            }
+                        }
+                    }catch(Exception e){
+
+                    }
+                    if (communitySet.size() > 0){
+                        ResultCommunityList rcl = new ResultCommunityList();
+                        rcl.setResultId(rId);
+                        ArrayList<String> communityList = new ArrayList<>();
+                        communityList.addAll(communitySet);
+                        rcl.setCommunityList(communityList);
+                        return rcl;
+                    }
+                    return null;
+                }, Encoders.bean(ResultCommunityList.class))
+        .filter(r -> r!= null)
+        .toJSON()
+        .write()
+        .mode(SaveMode.Overwrite)
+        .option("compression", "gzip")
+        .text(outputPath);
+    }
+
+
+
 }