forked from D-Net/dnet-hadoop
137 lines
4.8 KiB
Java
137 lines
4.8 KiB
Java
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.*;
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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.JavaSparkContext;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.FlatMapFunction;
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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 com.clearspring.analytics.util.Lists;
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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.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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public class CopyHdfsOafApplication extends AbstractMigrationApplication {
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private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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
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.toString(
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CopyHdfsOafApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")));
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parser.parseArgument(args);
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final 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 mdstoreManagerUrl = parser.get("mdstoreManagerUrl");
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log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl);
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final String mdFormat = parser.get("mdFormat");
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log.info("mdFormat: {}", mdFormat);
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final String mdLayout = parser.get("mdLayout");
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log.info("mdLayout: {}", mdLayout);
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final String mdInterpretation = parser.get("mdInterpretation");
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log.info("mdInterpretation: {}", mdInterpretation);
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final String hdfsPath = parser.get("hdfsPath");
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log.info("hdfsPath: {}", hdfsPath);
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
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final Set<String> paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths));
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}
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public static void processPaths(final SparkSession spark,
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final VocabularyGroup vocs,
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final String outputPath,
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final Set<String> paths) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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log.info("Found {} mdstores", paths.size());
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paths.forEach(log::info);
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final String[] validPaths = paths
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.stream()
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
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.toArray(String[]::new);
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log.info("Non empty mdstores {}", validPaths.length);
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if (validPaths.length > 0) {
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// load the dataset
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Dataset<Oaf> oaf = spark
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.read()
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.load(validPaths)
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.as(Encoders.kryo(Oaf.class));
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// dispatch each entity type individually in the respective graph subdirectory in append mode
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for (Map.Entry<String, Class> e : ModelSupport.oafTypes.entrySet()) {
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oaf
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.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey()))
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.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue()))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.text(outputPath + "/" + e.getKey());
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}
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}
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}
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private static Relation getInverse(Relation rel, VocabularyGroup vocs) {
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final Relation inverse = new Relation();
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inverse.setProperties(rel.getProperties());
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inverse.setValidated(rel.getValidated());
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inverse.setValidationDate(rel.getValidationDate());
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inverse.setCollectedfrom(rel.getCollectedfrom());
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inverse.setDataInfo(rel.getDataInfo());
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inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp());
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inverse.setSource(rel.getTarget());
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inverse.setTarget(rel.getSource());
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inverse.setRelType(rel.getRelType());
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inverse.setSubRelType(rel.getSubRelType());
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return inverse;
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}
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}
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