forked from antonis.lempesis/dnet-hadoop
preparation step: creates the subset of the merges relations
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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 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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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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 static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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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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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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final ArgumentApplicationParser parser = new ArgumentApplicationParser(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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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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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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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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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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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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@ -0,0 +1,4 @@
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package eu.dnetlib.dhp.blacklist;
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public class RemoveBlacklistedRelationSparkJob {
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}
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@ -0,0 +1,26 @@
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[
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{
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"paramName": "p",
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"paramLongName": "hdfsPath",
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"paramDescription": "the path where storing the sequential file",
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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 to the graph used to remove the relations ",
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"paramRequired": true
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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 where to store the temporary result ",
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"paramRequired": true
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},
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{
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"paramName": "issm",
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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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@ -0,0 +1,32 @@
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[
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{
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"paramName": "p",
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"paramLongName": "hdfsPath",
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"paramDescription": "the path where storing the sequential file",
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"paramRequired": true
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},
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{
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"paramName": "nn",
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"paramLongName": "hdfsNameNode",
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"paramDescription": "the name node on hdfs",
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"paramRequired": true
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},
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{
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"paramName": "pgurl",
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"paramLongName": "postgresUrl",
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"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
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"paramRequired": true
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},
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{
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"paramName": "pguser",
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"paramLongName": "postgresUser",
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"paramDescription": "postgres user",
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"paramRequired": false
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},
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{
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"paramName": "pgpasswd",
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"paramLongName": "postgresPassword",
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"paramDescription": "postgres password",
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"paramRequired": false
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}
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]
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