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preparation step: creates the subset of the merges relations

This commit is contained in:
Miriam Baglioni 2020-04-30 18:25:33 +02:00
parent 276b95b7b3
commit d6d6ebeae5
4 changed files with 153 additions and 0 deletions

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package eu.dnetlib.dhp.blacklist;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
public class PrepareMergedRelationJob {
private static final Logger log = LoggerFactory.getLogger(PrepareMergedRelationJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareMergedRelationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/blacklist/input_preparerelation_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {} " , outputPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
// removeOutputDir(spark, potentialUpdatePath);
// removeOutputDir(spark, alreadyLinkedPath);
selectMergesRelations(
spark,
inputPath,
outputPath);
});
}
private static void selectMergesRelations(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = readRelations(spark, inputPath);
relation.createOrReplaceTempView("relation");
spark.sql("Select * from relation where relclass = 'merges' and datainfo.deletedbyinference = false")
.as(Encoders.bean(Relation.class))
.toJSON()
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.text(outputPath);
}
public static org.apache.spark.sql.Dataset<Relation> readRelations(
SparkSession spark, String inputPath) {
return spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class));
}
}

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package eu.dnetlib.dhp.blacklist;
public class RemoveBlacklistedRelationSparkJob {
}

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[
{
"paramName": "p",
"paramLongName": "hdfsPath",
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path to the graph used to remove the relations ",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path where to store the temporary result ",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed",
"paramRequired": false
}
]

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[
{
"paramName": "p",
"paramLongName": "hdfsPath",
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the name node on hdfs",
"paramRequired": true
},
{
"paramName": "pgurl",
"paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramRequired": true
},
{
"paramName": "pguser",
"paramLongName": "postgresUser",
"paramDescription": "postgres user",
"paramRequired": false
},
{
"paramName": "pgpasswd",
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false
}
]