forked from D-Net/dnet-hadoop
95 lines
3.7 KiB
Java
95 lines
3.7 KiB
Java
package eu.dnetlib.dhp.oa.graph.raw;
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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.*;
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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.io.compress.GzipCodec;
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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.MapFunction;
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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 java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class DispatchEntitiesApplication {
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private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.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.toString(MigrateMongoMdstoresApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.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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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String sourcePath = parser.get("sourcePath");
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final String targetPath = parser.get("graphRawPath");
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SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, targetPath);
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processEntity(spark, Publication.class, sourcePath, targetPath);
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processEntity(spark, Dataset.class, sourcePath, targetPath);
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processEntity(spark, Software.class, sourcePath, targetPath);
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processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath);
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processEntity(spark, Datasource.class, sourcePath, targetPath);
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processEntity(spark, Organization.class, sourcePath, targetPath);
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processEntity(spark, Project.class, sourcePath, targetPath);
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processEntity(spark, Relation.class, sourcePath, targetPath);
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});
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}
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private static <T extends Oaf> void processEntity(final SparkSession spark, final Class<T> clazz, final String sourcePath, 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 file: %s", type, sourcePath));
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spark.read()
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.textFile(sourcePath)
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.filter((FilterFunction<String>) value -> isEntityType(value, type))
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.map((MapFunction<String, String>) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING())
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.map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(targetPath + "/" + type);
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/*
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JavaSparkContext.fromSparkContext(spark.sparkContext())
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.textFile(sourcePath)
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.filter(l -> isEntityType(l, type))
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.map(l -> StringUtils.substringAfter(l, "|"))
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.saveAsTextFile(targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ???
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*/
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}
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private static boolean isEntityType(final String line, final String type) {
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return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type);
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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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