new implementation for result to project propagation. Prepare some info to be used in propagation
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package eu.dnetlib.dhp.projecttoresult;
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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 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.SparkContext;
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import org.apache.spark.TaskResultLost;
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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 java.util.Optional;
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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 PrepareResultProjectAssociation {
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private static final Logger log = 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(PrepareDatasourceCountryAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_prepareprojecttoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String potentialUpdatePath = parser.get("potentialUpdatePath");
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log.info("potentialUpdatePath {}: ", potentialUpdatePath);
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String alreadyLinkedPath = parser.get("alreadyLinkedPath");
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log.info("alreadyLinkedPath: {} ", alreadyLinkedPath);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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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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spark -> {
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createOutputDirs(potentialUpdatePath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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prepareResultProjAssoc(spark, inputPath, potentialUpdatePath, alreadyLinkedPath, allowedsemrel);
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});
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}
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private static void prepareResultProjAssoc(SparkSession spark, String inputPath, String potentialUpdatePath,
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String alreadyLinkedPath, 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 + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), 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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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(r1target) resultSet " +
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"FROM (" +
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" SELECT r1.source as source, r1.target as r1target, r2.target as proj " +
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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 proj ";
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spark.sql(query).as(Encoders.bean(ProjectResultSet.class))
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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, collect_set(source) result_list " +
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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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.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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@ -1,69 +0,0 @@
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package eu.dnetlib.dhp.projecttoresult;
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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 org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.TaskResultLost;
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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 java.util.Optional;
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import static eu.dnetlib.dhp.PropagationConstant.TRUE;
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import static eu.dnetlib.dhp.PropagationConstant.createOutputDirs;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareResultProjectAssociation {
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private static final Logger log = 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(PrepareDatasourceCountryAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_projecttoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
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log.info("writeUpdates: {} ", writeUpdates);
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boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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log.info("saveGraph {}", saveGraph);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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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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spark -> {
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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});
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}
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}
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package eu.dnetlib.dhp.projecttoresult;
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public class ProjectResultSet {
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}
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[
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{
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"h",
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"paramLongName":"hive_metastore_uris",
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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},
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{
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"paramName":"wu",
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"paramLongName":"writeUpdate",
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"paramDescription": "true if the update must be written. No double check if information is already present",
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"paramRequired": false
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},
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{
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"paramName":"sg",
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"paramLongName":"saveGraph",
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"paramDescription": "true if the new version of the graph must be saved",
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"paramRequired": false
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},
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{
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"paramName":"tn",
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"paramLongName":"resultTableName",
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"paramDescription": "the name of the result table we are currently working on",
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"paramRequired": false
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},
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{
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"paramName": "out",
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"paramLongName": "outputPath",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": false
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},
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{
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"paramName": "p",
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"paramLongName": "preparedInfoPath",
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"paramDescription": "the path where prepared info have been stored",
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"paramRequired": false
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},
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{
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"paramName": "w",
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"paramLongName": "whitelist",
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"paramDescription": "the datasource having a type different from the allowed ones but that we want to add anyway",
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"paramRequired": true
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},
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{
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"paramName": "at",
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"paramLongName": "allowedtypes",
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"paramDescription": "the allowed datasource types for country propagation",
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"paramRequired": true
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}
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]
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[
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{
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"asr",
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"paramLongName":"allowedsemrels",
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"paramDescription": "the types of the allowed datasources. Split by ;",
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"paramRequired": true
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},
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{
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"paramName":"h",
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"paramLongName":"hive_metastore_uris",
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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},
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{
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"paramName":"wu",
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"paramLongName":"writeUpdate",
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"paramDescription": "true if the update must be writte. No double check if information is already present",
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"paramRequired": true
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},
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{
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"paramName":"sg",
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"paramLongName":"saveGraph",
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"paramDescription": "true if the new version of the graph must be saved",
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"paramRequired": true
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}
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]
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package eu.dnetlib.dhp.countrypropagation;
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public class CountryPropagationJobTest {
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}
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package eu.dnetlib.dhp.countrypropagation;
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public class PrepareDataForTest {
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}
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