forked from D-Net/dnet-hadoop
85 lines
2.7 KiB
Java
85 lines
2.7 KiB
Java
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package eu.dnetlib.dhp.actionmanager.bipfinder;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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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.hadoop.io.Text;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.Result;
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/**
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* Just collects all the atomic actions produced for the different results and saves them in
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* outputpath for the ActionSet
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*/
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public class CollectAndSave implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CollectAndSave.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.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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final String inputPath = parser.get("inputPath");
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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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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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collectAndSave(spark, inputPath, outputPath);
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});
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}
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private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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sc
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.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
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.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
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.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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