206 lines
6.5 KiB
Java
206 lines
6.5 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.ArrayList;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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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.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.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.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.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 MergeClaimsApplication {
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private static final Logger log = LoggerFactory.getLogger(MergeClaimsApplication.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/merge_claims_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 rawGraphPath = parser.get("rawGraphPath");
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log.info("rawGraphPath: {}", rawGraphPath);
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final String claimsGraphPath = parser.get("claimsGraphPath");
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log.info("claimsGraphPath: {}", claimsGraphPath);
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final String outputRawGaphPath = parser.get("outputRawGaphPath");
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log.info("outputRawGaphPath: {}", outputRawGaphPath);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends Oaf> clazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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String type = clazz.getSimpleName().toLowerCase();
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String rawPath = rawGraphPath + "/" + type;
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String claimPath = claimsGraphPath + "/" + type;
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String outPath = outputRawGaphPath + "/" + type;
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removeOutputDir(spark, outPath);
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mergeByType(spark, rawPath, claimPath, outPath, clazz);
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});
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}
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private static <T extends Oaf> void mergeByType(
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SparkSession spark, String rawPath, String claimPath, String outPath, Class<T> clazz) {
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Dataset<Tuple2<String, T>> raw = readFromPath(spark, rawPath, clazz)
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.map(
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(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(ModelSupport.idFn().apply(value), value),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Tuple2<String, T>> claim = jsc
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.broadcast(readFromPath(spark, claimPath, clazz))
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.getValue()
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.map(
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(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(ModelSupport.idFn().apply(value), value),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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raw
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.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer")
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.map(
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(MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, T>) value -> processClaims(
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Optional.ofNullable(value._1()),
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Optional.ofNullable(value._2())),
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Encoders.bean(clazz))
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.filter(Objects::nonNull)
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.map(
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(MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
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Encoders.STRING())
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(outPath);
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}
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private static <T extends Oaf> T processClaims(Optional<Tuple2<String, T>> opRaw,
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Optional<Tuple2<String, T>> opClaim) {
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// when both are present
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if (opClaim.isPresent() && opRaw.isPresent()) {
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T oafClaim = opClaim.get()._2();
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if (oafClaim instanceof Result) {
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T oafRaw = opRaw.get()._2();
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// merge the context lists from both oaf objects ...
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final List<Context> context = mergeContexts((Result) oafClaim, (Result) oafRaw);
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// ... and set it on the result from the aggregator
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((Result) oafRaw).setContext(context);
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return oafRaw;
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}
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}
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// otherwise prefer the result from the aggregator
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return opRaw.isPresent()
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? opRaw.get()._2()
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: opClaim.map(Tuple2::_2).orElse(null);
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}
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private static List<Context> mergeContexts(Result oafClaim, Result oafRaw) {
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return new ArrayList<>(
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Stream
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.concat(
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Optional
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.ofNullable(oafClaim.getContext())
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.map(List::stream)
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.orElse(Stream.empty()),
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Optional
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.ofNullable(oafRaw.getContext())
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.map(List::stream)
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.orElse(Stream.empty()))
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.collect(
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Collectors
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.toMap(
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Context::getId,
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c -> c,
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(c1, c2) -> {
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Context c = new Context();
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c.setId(c1.getId());
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c
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.setDataInfo(
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new ArrayList<>(
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Stream
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.concat(
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Optional
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.ofNullable(c1.getDataInfo())
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.map(List::stream)
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.orElse(Stream.empty()),
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Optional
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.ofNullable(c2.getDataInfo())
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.map(List::stream)
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.orElse(Stream.empty()))
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.collect(
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Collectors
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.toMap(
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d -> Optional
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.ofNullable(d.getProvenanceaction())
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.map(Qualifier::getClassid)
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.orElse(""),
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d -> d,
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(d1, d2) -> d1))
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.values()));
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return c;
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}))
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.values());
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}
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private static <T extends Oaf> Dataset<T> readFromPath(
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SparkSession spark, String path, Class<T> clazz) {
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return spark
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.read()
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.textFile(path)
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
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Encoders.bean(clazz))
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.filter((FilterFunction<T>) value -> Objects.nonNull(ModelSupport.idFn().apply(value)));
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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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