minor
This commit is contained in:
parent
43053a286d
commit
dbf3ba051a
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@ -11,6 +11,7 @@
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<artifactId>dhp-blacklist</artifactId>
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<dependencies>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-graph-mapper</artifactId>
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@ -1,9 +1,10 @@
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package eu.dnetlib.dhp.blacklist;
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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.schema.oaf.Relation;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import java.util.Optional;
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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.api.java.function.MapFunction;
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@ -14,78 +15,78 @@ import org.apache.spark.sql.SparkSession;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class PrepareMergedRelationJob {
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private static final Logger log = LoggerFactory.getLogger(PrepareMergedRelationJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final Logger log = LoggerFactory.getLogger(PrepareMergedRelationJob.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
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.toString(
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PrepareMergedRelationJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/blacklist/input_preparerelation_parameters.json"));
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String jsonConfiguration = IOUtils
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.toString(
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PrepareMergedRelationJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/blacklist/input_preparerelation_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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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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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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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {} " , outputPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {} ", outputPath);
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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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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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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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selectMergesRelations(
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spark,
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inputPath,
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outputPath);
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});
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}
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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selectMergesRelations(
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spark,
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inputPath,
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outputPath);
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});
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}
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private static void selectMergesRelations(SparkSession spark, String inputPath, String outputPath) {
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private static void selectMergesRelations(SparkSession spark, String inputPath, String outputPath) {
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Dataset<Relation> relation = readRelations(spark, inputPath);
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relation.createOrReplaceTempView("relation");
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Dataset<Relation> relation = readRelations(spark, inputPath);
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relation.createOrReplaceTempView("relation");
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spark.sql("Select * from relation where relclass = 'merges' and datainfo.deletedbyinference = false")
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.as(Encoders.bean(Relation.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(outputPath);
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}
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spark
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.sql("Select * from relation " +
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"where relclass = 'merges' " +
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"and datainfo.deletedbyinference = false")
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.as(Encoders.bean(Relation.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(outputPath);
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}
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public static org.apache.spark.sql.Dataset<Relation> readRelations(
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SparkSession spark, String inputPath) {
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return spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
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Encoders.bean(Relation.class));
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}
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public static org.apache.spark.sql.Dataset<Relation> readRelations(
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SparkSession spark, String inputPath) {
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return spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
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Encoders.bean(Relation.class));
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}
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}
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@ -55,19 +55,20 @@ public class SparkRemoveBlacklistedRelationJob {
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log.info("mergesPath {}: ", mergesPath);
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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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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeBlacklistedRelations(
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spark,
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inputPath,
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blacklistPath,
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outputPath,
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mergesPath);
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});
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conf,
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isSparkSessionManaged,
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spark -> {
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removeBlacklistedRelations(
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spark,
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inputPath,
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blacklistPath,
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outputPath,
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mergesPath);
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});
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}
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private static void removeBlacklistedRelations(SparkSession spark, String blacklistPath, String inputPath,
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@ -78,7 +79,6 @@ public class SparkRemoveBlacklistedRelationJob {
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Dataset<Relation> dedupSource = blackListed
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.joinWith(mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")), "left_outer")
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// .joinWith(inputRelation,blackListed.col("target").equalTo(inputRelation.col("target")),"left_outer")
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.map(c -> {
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Optional<Relation> merged = Optional.ofNullable(c._2());
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Relation bl = c._1();
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@ -63,7 +63,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/relation</arg>
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<arg>--outputPath</arg><arg>${workingDir}/mergesRelation</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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</spark>
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<ok to="apply_blacklist"/>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/relation</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
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<arg>--mergesPath</arg><arg>${workingDir}/mergesRelation</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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@ -22,5 +22,12 @@
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "true if the spark session is managed",
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"paramRequired": false
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},
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{
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"paramName": "m",
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"paramLongName": "mergesPath",
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"paramDescription": "true if the spark session is managed",
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"paramRequired": true
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}
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]
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