forked from D-Net/dnet-hadoop
83 lines
2.8 KiB
Java
83 lines
2.8 KiB
Java
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package eu.dnetlib.dhp.rdfconverter.bioschema;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Objects;
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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.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.rdfconverter.utils.CompressorUtil;
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import eu.dnetlib.dhp.rdfconverter.utils.RDFConverter;
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import ucar.nc2.stream.NcStreamProto;
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public class SparkRdfToDatacite {
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static Logger logger = LoggerFactory.getLogger(SparkRdfToDatacite.class);
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkRdfToDatacite.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/rdfconverter/bioschema/generate_dataset.json")));
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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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final String workingPath = parser.get("workingPath");
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final String rdfNquadsRecords = parser.get("rdfInput");
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final String output = parser.get("output");
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final String profile = parser.get("profile");
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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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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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String base64GzippedNquadsPath = workingPath.concat(rdfNquadsRecords);
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JavaRDD<String> base64GzippedNquadsRDD = sc
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.textFile(base64GzippedNquadsPath);
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logger.info("Rdf nquads records retrieved: {}", base64GzippedNquadsRDD.count());
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JavaRDD<String> proteins2 = base64GzippedNquadsRDD
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.flatMap(nquads -> {
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RDFConverter converter = new RDFConverter();
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ArrayList<String> jsonlds = null;
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try {
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jsonlds = converter
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.nQuadsFile2DataciteJson(CompressorUtil.decompressValue(nquads), profile);
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} catch (Exception e) {
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logger.error("converting: " + nquads, e);
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return Arrays.asList(new String()).iterator();
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}
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return jsonlds.iterator();
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});
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logger.info("json datacite non filtered: {}", proteins2.count());
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JavaRDD<Text> proteins = proteins2
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.filter(Objects::nonNull)
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.filter(jsonld -> !jsonld.isEmpty())
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.distinct()
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.map(jsonld -> new Text(jsonld));
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logger.info("json datacite generated: {}", proteins.count());
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proteins.saveAsTextFile(workingPath.concat(output), GzipCodec.class);
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});
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}
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}
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