212 lines
7.0 KiB
Java
212 lines
7.0 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.io.IOException;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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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.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.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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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 org.jetbrains.annotations.NotNull;
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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.oa.graph.raw.common.VocabularyGroup;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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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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import scala.Tuple2;
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public class GenerateEntitiesApplication {
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private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.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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GenerateEntitiesApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_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 sourcePaths = parser.get("sourcePaths");
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log.info("sourcePaths: {}", sourcePaths);
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final String targetPath = parser.get("targetPath");
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log.info("targetPath: {}", targetPath);
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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 SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, targetPath);
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generateEntities(spark, vocs, sourcePaths, targetPath);
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});
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}
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private static void generateEntities(
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final SparkSession spark,
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final VocabularyGroup vocs,
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final String sourcePaths,
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final String targetPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final List<String> existingSourcePaths = Arrays
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.stream(sourcePaths.split(","))
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.filter(p -> exists(sc, p))
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.collect(Collectors.toList());
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log.info("Generate entities from files:");
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existingSourcePaths.forEach(log::info);
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JavaRDD<Oaf> inputRdd = sc.emptyRDD();
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for (final String sp : existingSourcePaths) {
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inputRdd = inputRdd
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.union(
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sc
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.sequenceFile(sp, Text.class, Text.class)
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.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
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.map(k -> convertToListOaf(k._1(), k._2(), vocs))
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.filter(Objects::nonNull)
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.flatMap(list -> list.iterator()));
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}
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inputRdd
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.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
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.reduceByKey((o1, o2) -> merge(o1, o2))
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.map(Tuple2::_2)
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.map(
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oaf -> oaf.getClass().getSimpleName().toLowerCase()
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+ "|"
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+ OBJECT_MAPPER.writeValueAsString(oaf))
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.saveAsTextFile(targetPath, GzipCodec.class);
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}
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private static Oaf merge(final Oaf o1, final Oaf o2) {
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if (ModelSupport.isSubClass(o1, OafEntity.class)) {
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if (ModelSupport.isSubClass(o1, Result.class)) {
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return mergeResults((Result) o1, (Result) o2);
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} else if (ModelSupport.isSubClass(o1, Datasource.class)) {
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((Datasource) o1).mergeFrom((Datasource) o2);
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} else if (ModelSupport.isSubClass(o1, Organization.class)) {
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((Organization) o1).mergeFrom((Organization) o2);
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} else if (ModelSupport.isSubClass(o1, Project.class)) {
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((Project) o1).mergeFrom((Project) o2);
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} else {
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throw new RuntimeException("invalid OafEntity subtype:" + o1.getClass().getCanonicalName());
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}
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} else if (ModelSupport.isSubClass(o1, Relation.class)) {
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((Relation) o1).mergeFrom((Relation) o2);
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} else {
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throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
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}
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return o1;
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}
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protected static Result mergeResults(Result o1, Result o2) {
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Result r1 = o1;
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Result r2 = o2;
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if (new ResultTypeComparator().compare(r1, r2) < 0) {
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r1.mergeFrom(r2);
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return r1;
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} else {
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r2.mergeFrom(r1);
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return r2;
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}
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}
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private static List<Oaf> convertToListOaf(
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final String id,
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final String s,
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final VocabularyGroup vocs) {
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final String type = StringUtils.substringAfter(id, ":");
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switch (type.toLowerCase()) {
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case "oaf-store-cleaned":
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case "oaf-store-claim":
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return new OafToOafMapper(vocs, false).processMdRecord(s);
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case "odf-store-cleaned":
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case "odf-store-claim":
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return new OdfToOafMapper(vocs, false).processMdRecord(s);
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case "oaf-store-intersection":
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return new OafToOafMapper(vocs, true).processMdRecord(s);
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case "odf-store-intersection":
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return new OdfToOafMapper(vocs, true).processMdRecord(s);
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case "datasource":
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return Arrays.asList(convertFromJson(s, Datasource.class));
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case "organization":
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return Arrays.asList(convertFromJson(s, Organization.class));
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case "project":
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return Arrays.asList(convertFromJson(s, Project.class));
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case "relation":
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return Arrays.asList(convertFromJson(s, Relation.class));
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case "publication":
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return Arrays.asList(convertFromJson(s, Publication.class));
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case "dataset":
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return Arrays.asList(convertFromJson(s, Dataset.class));
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case "software":
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return Arrays.asList(convertFromJson(s, Software.class));
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case "otherresearchproduct":
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return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
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default:
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throw new RuntimeException("type not managed: " + type.toLowerCase());
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}
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}
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private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
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try {
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return OBJECT_MAPPER.readValue(s, clazz);
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} catch (final Exception e) {
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log.error("Error parsing object of class: " + clazz);
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log.error(s);
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throw new RuntimeException(e);
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}
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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 = 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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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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