forked from D-Net/dnet-hadoop
202 lines
6.3 KiB
Java
202 lines
6.3 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.sql.SQLException;
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import java.util.*;
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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.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.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.DbClient;
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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 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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MigrateMongoMdstoresApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/generate_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 sourcePaths = parser.get("sourcePaths");
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final String targetPath = parser.get("targetPath");
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final String dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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final String dbPassword = parser.get("postgresPassword");
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final Map<String, String> code2name = loadClassNames(dbUrl, dbUser, dbPassword);
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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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removeOutputDir(spark, targetPath);
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generateEntities(spark, code2name, 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 Map<String, String> code2name,
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final String sourcePaths,
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final String targetPath) {
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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(), code2name))
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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(Oaf o1, Oaf o2) {
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if (ModelSupport.isSubClass(o1, OafEntity.class)) {
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((OafEntity) o1).mergeFrom((OafEntity) o2);
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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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private static List<Oaf> convertToListOaf(
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final String id, final String s, final Map<String, String> code2name) {
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final String type = StringUtils.substringAfter(id, ":");
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switch (type.toLowerCase()) {
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case "native_oaf":
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return new OafToOafMapper(code2name).processMdRecord(s);
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case "native_odf":
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return new OdfToOafMapper(code2name).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 Map<String, String> loadClassNames(
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final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
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log.info("Loading vocabulary terms from db...");
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final Map<String, String> map = new HashMap<>();
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try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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dbClient
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.processResults(
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"select code, name from class",
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rs -> {
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try {
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map.put(rs.getString("code"), rs.getString("name"));
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} catch (final SQLException e) {
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e.printStackTrace();
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}
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});
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}
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log.info("Found " + map.size() + " terms.");
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return map;
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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(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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