forked from D-Net/dnet-hadoop
95 lines
3.5 KiB
Java
95 lines
3.5 KiB
Java
package eu.dnetlib.dhp.migration;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.Text;
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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.apache.spark.sql.SparkSession;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import scala.Tuple2;
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public class ExtractEntitiesFromHDFSJob {
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private static final Log log = LogFactory.getLog(ExtractEntitiesFromHDFSJob.class);
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(MigrateMongoMdstoresApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
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parser.parseArgument(args);
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final SparkSession spark = SparkSession
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.builder()
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.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
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.master(parser.get("master"))
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.getOrCreate();
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try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
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final List<String> sourcePaths = Arrays.stream(parser.get("sourcePaths").split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList());
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final String targetPath = parser.get("graphRawPath");
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processEntity(sc, Publication.class, sourcePaths, targetPath);
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processEntity(sc, Dataset.class, sourcePaths, targetPath);
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processEntity(sc, Software.class, sourcePaths, targetPath);
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processEntity(sc, OtherResearchProduct.class, sourcePaths, targetPath);
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processEntity(sc, Datasource.class, sourcePaths, targetPath);
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processEntity(sc, Organization.class, sourcePaths, targetPath);
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processEntity(sc, Project.class, sourcePaths, targetPath);
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processEntity(sc, Relation.class, sourcePaths, targetPath);
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}
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}
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private static void processEntity(final JavaSparkContext sc, final Class<?> clazz, final List<String> sourcePaths, final String targetPath) {
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final String type = clazz.getSimpleName().toLowerCase();
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log.info(String.format("Processing entities (%s) in files:", type));
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sourcePaths.forEach(log::info);
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JavaRDD<String> inputRdd = sc.emptyRDD();
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for (final String sp : sourcePaths) {
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inputRdd = inputRdd.union(sc.sequenceFile(sp, Text.class, Text.class)
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.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
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.filter(k -> isEntityType(k._1(), type))
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.map(Tuple2::_2));
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}
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inputRdd.saveAsTextFile(targetPath + "/" + type);
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}
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private static boolean isEntityType(final String item, final String type) {
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return StringUtils.substringAfter(item, ":").equalsIgnoreCase(type);
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}
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private static boolean exists(final JavaSparkContext context, final String pathToFile) {
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try {
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final FileSystem hdfs = org.apache.hadoop.fs.FileSystem.get(context.hadoopConfiguration());
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final Path path = new Path(pathToFile);
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return hdfs.exists(path);
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} catch (final IOException e) {
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throw new RuntimeException(e);
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}
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}
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}
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