forked from D-Net/dnet-hadoop
refactoring
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parent
d8dc31d4af
commit
769aa8178a
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@ -1,37 +1,36 @@
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package eu.dnetlib.dhp.projecttoresult;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.getConstraintList;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.util.Arrays;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.Arrays;
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import java.util.List;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.getConstraintList;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareProjectResultsAssociation {
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private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final Logger log =
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LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception{
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(PrepareProjectResultsAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_prepareprojecttoresult_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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PrepareProjectResultsAssociation.class.getResourceAsStream(
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"/eu/dnetlib/dhp/projecttoresult/input_prepareprojecttoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -53,69 +52,88 @@ public class PrepareProjectResultsAssociation {
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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// removeOutputDir(spark, potentialUpdatePath);
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// removeOutputDir(spark, alreadyLinkedPath);
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prepareResultProjProjectResults(spark, inputPath, potentialUpdatePath, alreadyLinkedPath, allowedsemrel);
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// removeOutputDir(spark, potentialUpdatePath);
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// removeOutputDir(spark, alreadyLinkedPath);
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prepareResultProjProjectResults(
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spark,
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inputPath,
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potentialUpdatePath,
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alreadyLinkedPath,
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allowedsemrel);
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});
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}
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private static void prepareResultProjProjectResults(SparkSession spark, String inputPath, String potentialUpdatePath,
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String alreadyLinkedPath, List<String> allowedsemrel) {
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private static void prepareResultProjProjectResults(
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SparkSession spark,
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String inputPath,
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String potentialUpdatePath,
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String alreadyLinkedPath,
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List<String> allowedsemrel) {
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JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath )
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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Dataset<Relation> relation =
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spark.createDataset(
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sc.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
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.rdd(),
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Encoders.bean(Relation.class));
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relation.createOrReplaceTempView("relation");
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String query = "SELECT source, target " +
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" FROM relation " +
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" WHERE datainfo.deletedbyinference = false " +
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" AND relClass = '" + RELATION_RESULT_PROJECT_REL_CLASS + "'";
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String query =
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"SELECT source, target "
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+ " FROM relation "
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+ " WHERE datainfo.deletedbyinference = false "
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+ " AND relClass = '"
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+ RELATION_RESULT_PROJECT_REL_CLASS
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+ "'";
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Dataset<Row> resproj_relation = spark.sql(query);
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resproj_relation.createOrReplaceTempView("resproj_relation");
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query ="SELECT projectId, collect_set(resId) resultSet " +
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"FROM (" +
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" SELECT r1.target resId, r2.target projectId " +
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" FROM (SELECT source, target " +
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" FROM relation " +
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" WHERE datainfo.deletedbyinference = false " +
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getConstraintList(" relClass = '", allowedsemrel ) + ") r1" +
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" JOIN resproj_relation r2 " +
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" ON r1.source = r2.source " +
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" ) tmp " +
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"GROUP BY projectId ";
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spark.sql(query).as(Encoders.bean(ProjectResultSet.class))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(potentialUpdatePath);
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// .toJavaRDD()
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// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
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// .saveAsTextFile(potentialUpdatePath, GzipCodec.class);
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query = "SELECT target projectId, collect_set(source) resultSet " +
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"FROM resproj_relation " +
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"GROUP BY target";
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query =
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"SELECT projectId, collect_set(resId) resultSet "
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+ "FROM ("
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+ " SELECT r1.target resId, r2.target projectId "
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+ " FROM (SELECT source, target "
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+ " FROM relation "
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+ " WHERE datainfo.deletedbyinference = false "
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+ getConstraintList(" relClass = '", allowedsemrel)
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+ ") r1"
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+ " JOIN resproj_relation r2 "
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+ " ON r1.source = r2.source "
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+ " ) tmp "
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+ "GROUP BY projectId ";
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spark.sql(query)
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.as(Encoders.bean(ProjectResultSet.class))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(alreadyLinkedPath);
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// .toJavaRDD()
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// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
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// .saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
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.option("compression", "gzip")
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.text(potentialUpdatePath);
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// .toJavaRDD()
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// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
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// .saveAsTextFile(potentialUpdatePath, GzipCodec.class);
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query =
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"SELECT target projectId, collect_set(source) resultSet "
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+ "FROM resproj_relation "
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+ "GROUP BY target";
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spark.sql(query)
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.as(Encoders.bean(ProjectResultSet.class))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(alreadyLinkedPath);
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// .toJavaRDD()
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// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
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// .saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
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}
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}
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@ -1,31 +1,34 @@
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package eu.dnetlib.dhp.projecttoresult;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.ArrayList;
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import java.util.List;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class SparkResultToProjectThroughSemRelJob3 {
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private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final Logger log =
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LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(SparkResultToProjectThroughSemRelJob3.class
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.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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SparkResultToProjectThroughSemRelJob3.class.getResourceAsStream(
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"/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -49,84 +52,104 @@ public class SparkResultToProjectThroughSemRelJob3 {
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SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged,
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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if(isTest(parser)) {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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execPropagation(spark, outputPath, alreadyLinkedPath, potentialUpdatePath, writeUpdates, saveGraph);
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execPropagation(
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spark,
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outputPath,
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alreadyLinkedPath,
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potentialUpdatePath,
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writeUpdates,
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saveGraph);
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});
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}
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private static void execPropagation(
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SparkSession spark,
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String outputPath,
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String alreadyLinkedPath,
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String potentialUpdatePath,
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Boolean writeUpdate,
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Boolean saveGraph) {
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private static void execPropagation(SparkSession spark, String outputPath, String alreadyLinkedPath, String potentialUpdatePath,
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Boolean writeUpdate, Boolean saveGraph){
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Dataset<ProjectResultSet> toaddrelations = readAssocProjectResults(spark, potentialUpdatePath);
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Dataset<ProjectResultSet> toaddrelations =
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readAssocProjectResults(spark, potentialUpdatePath);
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Dataset<ProjectResultSet> alreadyLinked = readAssocProjectResults(spark, alreadyLinkedPath);
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if(writeUpdate){
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if (writeUpdate) {
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toaddrelations
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(outputPath +"/potential_updates");
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.option("compression", "gzip")
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.text(outputPath + "/potential_updates");
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}
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if (saveGraph){
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if (saveGraph) {
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getNewRelations(alreadyLinked, toaddrelations)
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.toJSON()
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.text(outputPath);
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}
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}
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}
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private static Dataset<Relation> getNewRelations(Dataset<ProjectResultSet> alreadyLinked,
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Dataset<ProjectResultSet> toaddrelations){
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private static Dataset<Relation> getNewRelations(
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Dataset<ProjectResultSet> alreadyLinked, Dataset<ProjectResultSet> toaddrelations) {
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return toaddrelations
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.joinWith(alreadyLinked, toaddrelations.col("projectId").equalTo(alreadyLinked.col("projectId")), "left")
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.flatMap(value -> {
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.joinWith(
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alreadyLinked,
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toaddrelations.col("projectId").equalTo(alreadyLinked.col("projectId")),
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"left")
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.flatMap(
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value -> {
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List<Relation> new_relations = new ArrayList<>();
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ProjectResultSet potential_update = value._1();
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ProjectResultSet already_linked = value._2();
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String projId = already_linked.getProjectId();
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potential_update
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.getResultSet()
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.stream()
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.forEach(rId -> {
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if (!already_linked.getResultSet().contains(rId)){
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new_relations.add(getRelation(rId, projId, RELATION_RESULT_PROJECT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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potential_update.getResultSet().stream()
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.forEach(
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rId -> {
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if (!already_linked.getResultSet().contains(rId)) {
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new_relations.add(
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getRelation(
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rId,
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projId,
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RELATION_RESULT_PROJECT_REL_CLASS,
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RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE,
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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new_relations.add(getRelation(projId, rId, RELATION_PROJECT_RESULT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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new_relations.add(
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getRelation(
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projId,
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rId,
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RELATION_PROJECT_RESULT_REL_CLASS,
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RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE,
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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}
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});
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return new_relations.iterator();
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}
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,Encoders.bean(Relation.class));
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},
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Encoders.bean(Relation.class));
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}
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private static Dataset<ProjectResultSet> readAssocProjectResults(SparkSession spark, String potentialUpdatePath) {
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return spark
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.read()
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private static Dataset<ProjectResultSet> readAssocProjectResults(
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SparkSession spark, String potentialUpdatePath) {
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return spark.read()
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.textFile(potentialUpdatePath)
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.map(value -> OBJECT_MAPPER.readValue(value, ProjectResultSet.class), Encoders.bean(ProjectResultSet.class));
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.map(
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value -> OBJECT_MAPPER.readValue(value, ProjectResultSet.class),
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Encoders.bean(ProjectResultSet.class));
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}
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}
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