forked from D-Net/dnet-hadoop
[dhp-actionmanager] promoting spark job added
This commit is contained in:
przemek
parent
e21bb89dbd
commit
5b459bcc47
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package eu.dnetlib.dhp.actionmanager;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.util.function.BiFunction;
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public class OafMergeAndGet {
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public enum Strategy {
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MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET
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}
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public static <T extends Oaf> SerializableSupplier<BiFunction<T, T, T>> functionFor(Strategy strategy) {
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switch (strategy) {
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case MERGE_FROM_AND_GET:
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return () -> (x, y) -> {
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if (x instanceof Relation) {
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((Relation) x).mergeFrom((Relation) y);
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return x;
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}
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((OafEntity) x).mergeFrom((OafEntity) y);
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return x;
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};
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case SELECT_NEWER_AND_GET:
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return () -> (x, y) -> {
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if (x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
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return x;
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}
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return y;
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};
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}
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throw new RuntimeException();
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}
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}
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package eu.dnetlib.dhp.actionmanager;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.TypedColumn;
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import org.apache.spark.sql.expressions.Aggregator;
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import scala.Tuple2;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.function.BiFunction;
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import java.util.function.Function;
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public class PromoteActionSetFromHDFSFunctions {
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public static <T extends Oaf> Dataset<T> joinOafEntityWithActionPayloadAndMerge(Dataset<T> oafDS,
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Dataset<T> actionPayloadOafDS,
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SerializableSupplier<Function<T, String>> oafIdFn,
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SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn,
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Class<T> clazz) {
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Dataset<Tuple2<String, T>> oafWithIdDS = mapToTupleWithId(oafDS, oafIdFn, clazz);
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Dataset<Tuple2<String, T>> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadOafDS, oafIdFn, clazz);
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return oafWithIdDS
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.joinWith(actionPayloadWithIdDS, oafWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "left_outer")
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.map((MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, T>) value -> {
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T left = value._1()._2();
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return Optional
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.ofNullable(value._2())
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.map(Tuple2::_2)
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.map(x -> mergeAndGetFn.get().apply(left, x))
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.orElse(left);
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}, Encoders.kryo(clazz));
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}
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private static <T extends Oaf> Dataset<Tuple2<String, T>> mapToTupleWithId(Dataset<T> ds,
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SerializableSupplier<Function<T, String>> idFn,
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Class<T> clazz) {
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return ds
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.map((MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(idFn.get().apply(value), value),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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}
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public static <T extends Oaf> Dataset<T> groupOafByIdAndMerge(Dataset<T> oafDS,
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SerializableSupplier<Function<T, String>> oafIdFn,
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SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn,
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Class<T> clazz) {
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return oafDS
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.groupByKey((MapFunction<T, String>) x -> oafIdFn.get().apply(x), Encoders.STRING())
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.reduceGroups((ReduceFunction<T>) (v1, v2) -> mergeAndGetFn.get().apply(v1, v2))
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.map((MapFunction<Tuple2<String, T>, T>) Tuple2::_2, Encoders.kryo(clazz));
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}
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public static <T extends Oaf> Dataset<T> groupOafByIdAndMergeUsingAggregator(Dataset<T> oafDS,
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SerializableSupplier<T> zeroFn,
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SerializableSupplier<Function<T, String>> idFn,
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Class<T> clazz) {
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TypedColumn<T, T> aggregator = new OafAggregator<>(zeroFn, clazz).toColumn();
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return oafDS
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.groupByKey((MapFunction<T, String>) x -> idFn.get().apply(x), Encoders.STRING())
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.agg(aggregator)
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.map((MapFunction<Tuple2<String, T>, T>) Tuple2::_2, Encoders.kryo(clazz));
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}
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public static class OafAggregator<T extends Oaf> extends Aggregator<T, T, T> {
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private SerializableSupplier<T> zero;
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private Class<T> clazz;
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public OafAggregator(SerializableSupplier<T> zero, Class<T> clazz) {
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this.zero = zero;
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this.clazz = clazz;
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}
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@Override
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public T zero() {
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return zero.get();
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}
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@Override
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public T reduce(T b, T a) {
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return mergeFrom(b, a);
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}
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@Override
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public T merge(T b1, T b2) {
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return mergeFrom(b1, b2);
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}
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private T mergeFrom(T left, T right) {
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if (isNonNull(left)) {
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if (left instanceof Relation) {
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((Relation) left).mergeFrom((Relation) right);
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return left;
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}
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((OafEntity) left).mergeFrom((OafEntity) right);
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return left;
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}
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if (right instanceof Relation) {
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((Relation) right).mergeFrom((Relation) left);
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return right;
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}
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((OafEntity) right).mergeFrom((OafEntity) left);
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return right;
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}
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private Boolean isNonNull(T a) {
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return Objects.nonNull(a.getLastupdatetimestamp());
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}
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@Override
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public T finish(T reduction) {
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return reduction;
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}
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@Override
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public Encoder<T> bufferEncoder() {
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return Encoders.kryo(clazz);
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}
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@Override
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public Encoder<T> outputEncoder() {
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return Encoders.kryo(clazz);
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}
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}
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}
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@ -1,283 +0,0 @@
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package eu.dnetlib.dhp.actionmanager;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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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.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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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.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.*;
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import org.apache.spark.sql.types.*;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.function.BiFunction;
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import java.util.function.Function;
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import static org.apache.spark.sql.functions.*;
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public class PromoteActionSetFromHDFSJob {
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// TODO replace with project's common implementation
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public enum GraphTableName {
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DATASET, DATASOURCE, ORGANIZATION, OTHERRESEARCHPRODUCT, PROJECT, PUBLICATION, RELATION, SOFTWARE
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}
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private static final StructType KV_SCHEMA = StructType$.MODULE$.apply(
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Arrays.asList(
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StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
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StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())
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));
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(
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PromoteActionSetFromHDFSJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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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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String inputGraphPath = parser.get("inputGraphPath");
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String inputActionSetPaths = parser.get("inputActionSetPaths");
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GraphTableName graphTableName = GraphTableName.valueOf(parser.get("graphTableName").toUpperCase());
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String outputGraphPath = parser.get("outputGraphPath");
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OafMergeAndGet.Strategy strategy = OafMergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
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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(new Class[]{
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Author.class,
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Context.class,
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Country.class,
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DataInfo.class,
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eu.dnetlib.dhp.schema.oaf.Dataset.class,
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Datasource.class,
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ExternalReference.class,
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ExtraInfo.class,
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Field.class,
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GeoLocation.class,
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Instance.class,
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Journal.class,
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KeyValue.class,
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Oaf.class,
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OafEntity.class,
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OAIProvenance.class,
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Organization.class,
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OriginDescription.class,
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OtherResearchProduct.class,
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Project.class,
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Publication.class,
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Qualifier.class,
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Relation.class,
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Result.class,
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Software.class,
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StructuredProperty.class
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});
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SparkSession spark = null;
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try {
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spark = SparkSession.builder().config(conf).getOrCreate();
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String inputGraphTablePath = String.format("%s/%s", inputGraphPath, graphTableName.name().toLowerCase());
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String outputGraphTablePath = String.format("%s/%s", outputGraphPath, graphTableName.name().toLowerCase());
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switch (graphTableName) {
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case DATASET:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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eu.dnetlib.dhp.schema.oaf.Dataset.class);
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break;
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case DATASOURCE:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Datasource.class);
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break;
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case ORGANIZATION:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Organization.class);
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break;
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case OTHERRESEARCHPRODUCT:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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OtherResearchProduct.class);
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break;
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case PROJECT:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Project.class);
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break;
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case PUBLICATION:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Publication.class);
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break;
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case RELATION:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Relation.class);
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break;
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case SOFTWARE:
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processGraphTable(spark,
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inputGraphTablePath,
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inputActionSetPaths,
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outputGraphTablePath,
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strategy,
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Software.class);
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break;
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default:
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throw new RuntimeException("error processing table: " + graphTableName);
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}
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} finally {
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if (Objects.nonNull(spark) && isSparkSessionManaged) {
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spark.stop();
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}
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}
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}
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private static <T extends Oaf> void processGraphTable(SparkSession spark,
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String inputGraphTablePath,
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String inputActionSetPaths,
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String outputGraphTablePath,
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OafMergeAndGet.Strategy strategy,
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Class<T> clazz) {
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Dataset<T> tableDS = readGraphTable(spark, inputGraphTablePath, clazz)
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.cache();
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Dataset<T> actionPayloadDS = readActionSetPayloads(spark, inputActionSetPaths, clazz)
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.cache();
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Dataset<T> result = promoteActionSetForGraphTable(tableDS, actionPayloadDS, strategy, clazz)
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.map((MapFunction<T, T>) value -> value, Encoders.bean(clazz));
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saveGraphTableAsParquet(result, outputGraphTablePath);
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}
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private static <T extends Oaf> Dataset<T> readGraphTable(SparkSession spark,
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String inputGraphTablePath,
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Class<T> clazz) {
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JavaRDD<Row> rows = JavaSparkContext
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.fromSparkContext(spark.sparkContext())
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.sequenceFile(inputGraphTablePath, Text.class, Text.class)
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.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
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return spark.createDataFrame(rows, KV_SCHEMA)
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.map((MapFunction<Row, T>) row -> new ObjectMapper().readValue(row.<String>getAs("value"), clazz),
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Encoders.bean(clazz));
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}
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private static <T extends Oaf> Dataset<T> readActionSetPayloads(SparkSession spark,
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String inputActionSetPaths,
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Class<T> clazz) {
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return Arrays
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.stream(inputActionSetPaths.split(","))
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.map(inputActionSetPath -> readActionSetPayload(spark, inputActionSetPath, clazz))
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.reduce(Dataset::union)
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.orElseThrow(() -> new RuntimeException("error reading action sets: " + inputActionSetPaths));
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|
||||||
}
|
|
||||||
|
|
||||||
private static <T extends Oaf> Dataset<T> readActionSetPayload(SparkSession spark,
|
|
||||||
String inputActionSetPath,
|
|
||||||
Class<T> clazz) {
|
|
||||||
JavaRDD<Row> actionsRDD = JavaSparkContext
|
|
||||||
.fromSparkContext(spark.sparkContext())
|
|
||||||
.sequenceFile(inputActionSetPath, Text.class, Text.class)
|
|
||||||
.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
|
|
||||||
|
|
||||||
SerializableSupplier<BiFunction<String, Class<T>, T>> actionPayloadToOafFn = () -> (json, c) -> {
|
|
||||||
try {
|
|
||||||
return new ObjectMapper().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES).readValue(json, c);
|
|
||||||
} catch (IOException e) {
|
|
||||||
return null;
|
|
||||||
}
|
|
||||||
};
|
|
||||||
|
|
||||||
return spark.createDataFrame(actionsRDD, KV_SCHEMA)
|
|
||||||
.select(unbase64(get_json_object(col("value"), "$.TargetValue"))
|
|
||||||
.cast(DataTypes.StringType).as("target_value_json"))
|
|
||||||
.as(Encoders.STRING())
|
|
||||||
.map((MapFunction<String, T>) value -> actionPayloadToOafFn.get().apply(value, clazz), Encoders.bean(clazz))
|
|
||||||
.filter((FilterFunction<T>) Objects::nonNull);
|
|
||||||
}
|
|
||||||
|
|
||||||
private static <T extends Oaf> Dataset<T> promoteActionSetForGraphTable(Dataset<T> tableDS,
|
|
||||||
Dataset<T> actionPayloadDS,
|
|
||||||
OafMergeAndGet.Strategy strategy,
|
|
||||||
Class<T> clazz) {
|
|
||||||
SerializableSupplier<Function<T, String>> oafIdFn = () -> x -> {
|
|
||||||
if (x instanceof Relation) {
|
|
||||||
Relation r = (Relation) x;
|
|
||||||
return Optional.ofNullable(r.getSource())
|
|
||||||
.map(source -> Optional.ofNullable(r.getTarget())
|
|
||||||
.map(target -> Optional.ofNullable(r.getRelType())
|
|
||||||
.map(relType -> Optional.ofNullable(r.getSubRelType())
|
|
||||||
.map(subRelType -> Optional.ofNullable(r.getRelClass())
|
|
||||||
.map(relClass -> String.join(source, target, relType, subRelType, relClass))
|
|
||||||
.orElse(String.join(source, target, relType, subRelType))
|
|
||||||
)
|
|
||||||
.orElse(String.join(source, target, relType))
|
|
||||||
)
|
|
||||||
.orElse(String.join(source, target))
|
|
||||||
)
|
|
||||||
.orElse(source)
|
|
||||||
)
|
|
||||||
.orElse(null);
|
|
||||||
}
|
|
||||||
return ((OafEntity) x).getId();
|
|
||||||
};
|
|
||||||
|
|
||||||
SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn = OafMergeAndGet.functionFor(strategy);
|
|
||||||
|
|
||||||
Dataset<T> joinedAndMerged = PromoteActionSetFromHDFSFunctions
|
|
||||||
.joinOafEntityWithActionPayloadAndMerge(
|
|
||||||
tableDS,
|
|
||||||
actionPayloadDS,
|
|
||||||
oafIdFn,
|
|
||||||
mergeAndGetFn,
|
|
||||||
clazz);
|
|
||||||
|
|
||||||
return PromoteActionSetFromHDFSFunctions
|
|
||||||
.groupOafByIdAndMerge(
|
|
||||||
joinedAndMerged,
|
|
||||||
oafIdFn,
|
|
||||||
mergeAndGetFn,
|
|
||||||
clazz
|
|
||||||
);
|
|
||||||
}
|
|
||||||
|
|
||||||
private static <T extends Oaf> void saveGraphTableAsParquet(Dataset<T> result, String outputGraphTablePath) {
|
|
||||||
result.write()
|
|
||||||
.format("parquet")
|
|
||||||
.save(outputGraphTablePath);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
package eu.dnetlib.dhp.actionmanager;
|
|
||||||
|
|
||||||
import java.io.Serializable;
|
|
||||||
import java.util.function.Supplier;
|
|
||||||
|
|
||||||
@FunctionalInterface
|
|
||||||
public interface SerializableSupplier<T> extends Supplier<T>, Serializable {
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,74 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.common.ModelSupport.isSubClass;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* OAF model merging support.
|
||||||
|
*/
|
||||||
|
public class MergeAndGet {
|
||||||
|
|
||||||
|
private MergeAndGet() {
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Strategy for merging OAF model objects.
|
||||||
|
* <p>
|
||||||
|
* MERGE_FROM_AND_GET: use OAF 'mergeFrom' method
|
||||||
|
* SELECT_NEWER_AND_GET: use last update timestamp to return newer instance
|
||||||
|
*/
|
||||||
|
public enum Strategy {
|
||||||
|
MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns a function for merging OAF model objects.
|
||||||
|
*
|
||||||
|
* @param strategy Strategy to be used to merge objects
|
||||||
|
* @param <G> Graph table type
|
||||||
|
* @param <A> Action payload type
|
||||||
|
* @return BiFunction to be used to merge OAF objects
|
||||||
|
*/
|
||||||
|
public static <G extends Oaf, A extends Oaf> SerializableSupplier<BiFunction<G, A, G>> functionFor(Strategy strategy) {
|
||||||
|
switch (strategy) {
|
||||||
|
case MERGE_FROM_AND_GET:
|
||||||
|
return () -> MergeAndGet::mergeFromAndGet;
|
||||||
|
case SELECT_NEWER_AND_GET:
|
||||||
|
return () -> MergeAndGet::selectNewerAndGet;
|
||||||
|
}
|
||||||
|
throw new RuntimeException();
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
|
||||||
|
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
|
||||||
|
((Relation) x).mergeFrom((Relation) y);
|
||||||
|
return x;
|
||||||
|
} else if (isSubClass(x, OafEntity.class) && isSubClass(y, OafEntity.class) && isSubClass(x, y)) {
|
||||||
|
((OafEntity) x).mergeFrom((OafEntity) y);
|
||||||
|
return x;
|
||||||
|
}
|
||||||
|
throw new RuntimeException(String.format("MERGE_FROM_AND_GET incompatible types: %s, %s",
|
||||||
|
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
|
||||||
|
if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
|
||||||
|
return x;
|
||||||
|
} else if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
|
||||||
|
return (G) y;
|
||||||
|
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
|
||||||
|
return x;
|
||||||
|
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
|
||||||
|
throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s",
|
||||||
|
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
|
||||||
|
}
|
||||||
|
throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s",
|
||||||
|
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,271 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.HdfsSupport;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.Row;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import java.util.Objects;
|
||||||
|
import java.util.Optional;
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
import java.util.function.Function;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.common.ModelSupport.isSubClass;
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Applies a given action payload file to graph table of compatible type.
|
||||||
|
*/
|
||||||
|
public class PromoteActionPayloadForGraphTableJob {
|
||||||
|
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
|
||||||
|
|
||||||
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
String jsonConfiguration = IOUtils.toString(
|
||||||
|
PromoteActionPayloadForGraphTableJob.class
|
||||||
|
.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json"));
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
Boolean isSparkSessionManaged = Optional
|
||||||
|
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||||
|
.map(Boolean::valueOf)
|
||||||
|
.orElse(Boolean.TRUE);
|
||||||
|
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||||
|
|
||||||
|
String inputGraphTablePath = parser.get("inputGraphTablePath");
|
||||||
|
logger.info("inputGraphTablePath: {}", inputGraphTablePath);
|
||||||
|
|
||||||
|
String graphTableClassName = parser.get("graphTableClassName");
|
||||||
|
logger.info("graphTableClassName: {}", graphTableClassName);
|
||||||
|
|
||||||
|
String inputActionPayloadPath = parser.get("inputActionPayloadPath");
|
||||||
|
logger.info("inputActionPayloadPath: {}", inputActionPayloadPath);
|
||||||
|
|
||||||
|
String actionPayloadClassName = parser.get("actionPayloadClassName");
|
||||||
|
logger.info("actionPayloadClassName: {}", actionPayloadClassName);
|
||||||
|
|
||||||
|
String outputGraphTablePath = parser.get("outputGraphTablePath");
|
||||||
|
logger.info("outputGraphTablePath: {}", outputGraphTablePath);
|
||||||
|
|
||||||
|
MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
|
||||||
|
logger.info("strategy: {}", strategy);
|
||||||
|
|
||||||
|
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
|
||||||
|
Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
|
||||||
|
|
||||||
|
throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||||
|
conf.registerKryoClasses(new Class[]{
|
||||||
|
Author.class,
|
||||||
|
Context.class,
|
||||||
|
Country.class,
|
||||||
|
DataInfo.class,
|
||||||
|
eu.dnetlib.dhp.schema.oaf.Dataset.class,
|
||||||
|
Datasource.class,
|
||||||
|
ExternalReference.class,
|
||||||
|
ExtraInfo.class,
|
||||||
|
Field.class,
|
||||||
|
GeoLocation.class,
|
||||||
|
Instance.class,
|
||||||
|
Journal.class,
|
||||||
|
KeyValue.class,
|
||||||
|
Oaf.class,
|
||||||
|
OafEntity.class,
|
||||||
|
OAIProvenance.class,
|
||||||
|
Organization.class,
|
||||||
|
OriginDescription.class,
|
||||||
|
OtherResearchProduct.class,
|
||||||
|
Project.class,
|
||||||
|
Publication.class,
|
||||||
|
Qualifier.class,
|
||||||
|
Relation.class,
|
||||||
|
Result.class,
|
||||||
|
Software.class,
|
||||||
|
StructuredProperty.class
|
||||||
|
});
|
||||||
|
|
||||||
|
runWithSparkSession(conf, isSparkSessionManaged,
|
||||||
|
spark -> {
|
||||||
|
removeOutputDir(spark, outputGraphTablePath);
|
||||||
|
promoteActionPayloadForGraphTable(spark,
|
||||||
|
inputGraphTablePath,
|
||||||
|
inputActionPayloadPath,
|
||||||
|
outputGraphTablePath,
|
||||||
|
strategy,
|
||||||
|
rowClazz,
|
||||||
|
actionPayloadClazz);
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(Class<? extends Oaf> rowClazz,
|
||||||
|
Class<? extends Oaf> actionPayloadClazz) {
|
||||||
|
if (!isSubClass(rowClazz, actionPayloadClazz)) {
|
||||||
|
String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s",
|
||||||
|
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
|
||||||
|
throw new RuntimeException(msg);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void removeOutputDir(SparkSession spark, String path) {
|
||||||
|
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(SparkSession spark,
|
||||||
|
String inputGraphTablePath,
|
||||||
|
String inputActionPayloadPath,
|
||||||
|
String outputGraphTablePath,
|
||||||
|
MergeAndGet.Strategy strategy,
|
||||||
|
Class<G> rowClazz,
|
||||||
|
Class<A> actionPayloadClazz) {
|
||||||
|
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
|
||||||
|
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
|
||||||
|
|
||||||
|
Dataset<G> result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
|
||||||
|
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
|
||||||
|
|
||||||
|
saveGraphTable(result, outputGraphTablePath);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> Dataset<G> readGraphTable(SparkSession spark,
|
||||||
|
String path,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
logger.info("Reading graph table from path: {}", path);
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.textFile(path)
|
||||||
|
.map((MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <A extends Oaf> Dataset<A> readActionPayload(SparkSession spark,
|
||||||
|
String path,
|
||||||
|
Class<A> actionPayloadClazz) {
|
||||||
|
logger.info("Reading action payload from path: {}", path);
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.parquet(path)
|
||||||
|
.map((MapFunction<Row, A>) value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"),
|
||||||
|
actionPayloadClazz), Encoders.bean(actionPayloadClazz));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(Dataset<G> rowDS,
|
||||||
|
Dataset<A> actionPayloadDS,
|
||||||
|
MergeAndGet.Strategy strategy,
|
||||||
|
Class<G> rowClazz,
|
||||||
|
Class<A> actionPayloadClazz) {
|
||||||
|
logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName());
|
||||||
|
|
||||||
|
SerializableSupplier<Function<G, String>> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn;
|
||||||
|
SerializableSupplier<Function<A, String>> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn;
|
||||||
|
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
|
||||||
|
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
|
||||||
|
SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
|
||||||
|
SerializableSupplier<Function<G, Boolean>> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource;
|
||||||
|
|
||||||
|
Dataset<G> joinedAndMerged = PromoteActionPayloadFunctions
|
||||||
|
.joinGraphTableWithActionPayloadAndMerge(
|
||||||
|
rowDS,
|
||||||
|
actionPayloadDS,
|
||||||
|
rowIdFn,
|
||||||
|
actionPayloadIdFn,
|
||||||
|
mergeRowWithActionPayloadAndGetFn,
|
||||||
|
rowClazz,
|
||||||
|
actionPayloadClazz);
|
||||||
|
|
||||||
|
return PromoteActionPayloadFunctions
|
||||||
|
.groupGraphTableByIdAndMerge(
|
||||||
|
joinedAndMerged,
|
||||||
|
rowIdFn,
|
||||||
|
mergeRowsAndGetFn,
|
||||||
|
zeroFn,
|
||||||
|
isNotZeroFn,
|
||||||
|
rowClazz);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> Function<T, String> idFn() {
|
||||||
|
return x -> {
|
||||||
|
if (isSubClass(x, Relation.class)) {
|
||||||
|
return idFnForRelation(x);
|
||||||
|
}
|
||||||
|
return idFnForOafEntity(x);
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> String idFnForRelation(T t) {
|
||||||
|
Relation r = (Relation) t;
|
||||||
|
return Optional.ofNullable(r.getSource())
|
||||||
|
.map(source -> Optional.ofNullable(r.getTarget())
|
||||||
|
.map(target -> Optional.ofNullable(r.getRelType())
|
||||||
|
.map(relType -> Optional.ofNullable(r.getSubRelType())
|
||||||
|
.map(subRelType -> Optional.ofNullable(r.getRelClass())
|
||||||
|
.map(relClass -> String.join(source, target, relType, subRelType, relClass))
|
||||||
|
.orElse(String.join(source, target, relType, subRelType))
|
||||||
|
)
|
||||||
|
.orElse(String.join(source, target, relType))
|
||||||
|
)
|
||||||
|
.orElse(String.join(source, target))
|
||||||
|
)
|
||||||
|
.orElse(source)
|
||||||
|
)
|
||||||
|
.orElse(null);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> String idFnForOafEntity(T t) {
|
||||||
|
return ((OafEntity) t).getId();
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {
|
||||||
|
switch (clazz.getCanonicalName()) {
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Dataset":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Dataset());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Datasource":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Datasource());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Organization":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Organization());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.OtherResearchProduct());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Project":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Project());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Publication":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Relation":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Relation());
|
||||||
|
case "eu.dnetlib.dhp.schema.oaf.Software":
|
||||||
|
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Software());
|
||||||
|
default:
|
||||||
|
throw new RuntimeException("unknown class: " + clazz.getCanonicalName());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSource() {
|
||||||
|
return t -> {
|
||||||
|
if (isSubClass(t, Relation.class)) {
|
||||||
|
return Objects.nonNull(((Relation) t).getSource());
|
||||||
|
}
|
||||||
|
return Objects.nonNull(((OafEntity) t).getId());
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> void saveGraphTable(Dataset<G> result,
|
||||||
|
String path) {
|
||||||
|
logger.info("Saving graph table to path: {}", path);
|
||||||
|
result
|
||||||
|
.toJSON()
|
||||||
|
.write()
|
||||||
|
.option("compression", "gzip")
|
||||||
|
.text(path);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,170 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoder;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.TypedColumn;
|
||||||
|
import org.apache.spark.sql.expressions.Aggregator;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
import java.util.Objects;
|
||||||
|
import java.util.Optional;
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
import java.util.function.Function;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.common.ModelSupport.isSubClass;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Promote action payload functions.
|
||||||
|
*/
|
||||||
|
public class PromoteActionPayloadFunctions {
|
||||||
|
|
||||||
|
private PromoteActionPayloadFunctions() {
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Joins dataset representing graph table with dataset representing action payload using supplied functions.
|
||||||
|
*
|
||||||
|
* @param rowDS Dataset representing graph table
|
||||||
|
* @param actionPayloadDS Dataset representing action payload
|
||||||
|
* @param rowIdFn Function used to get the id of graph table row
|
||||||
|
* @param actionPayloadIdFn Function used to get id of action payload instance
|
||||||
|
* @param mergeAndGetFn Function used to merge graph table row and action payload instance
|
||||||
|
* @param rowClazz Class of graph table
|
||||||
|
* @param actionPayloadClazz Class of action payload
|
||||||
|
* @param <G> Type of graph table row
|
||||||
|
* @param <A> Type of action payload
|
||||||
|
* @return Dataset of merged graph table rows and action payload
|
||||||
|
*/
|
||||||
|
public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge(Dataset<G> rowDS,
|
||||||
|
Dataset<A> actionPayloadDS,
|
||||||
|
SerializableSupplier<Function<G, String>> rowIdFn,
|
||||||
|
SerializableSupplier<Function<A, String>> actionPayloadIdFn,
|
||||||
|
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
|
||||||
|
Class<G> rowClazz,
|
||||||
|
Class<A> actionPayloadClazz) {
|
||||||
|
if (!isSubClass(rowClazz, actionPayloadClazz)) {
|
||||||
|
throw new RuntimeException("action payload type must be the same or be a super type of table row type");
|
||||||
|
}
|
||||||
|
|
||||||
|
Dataset<Tuple2<String, G>> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz);
|
||||||
|
Dataset<Tuple2<String, A>> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz);
|
||||||
|
|
||||||
|
return rowWithIdDS
|
||||||
|
.joinWith(actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "full_outer")
|
||||||
|
.map((MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>) value -> {
|
||||||
|
Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);
|
||||||
|
Optional<A> actionPayloadOpt = Optional.ofNullable(value._2()).map(Tuple2::_2);
|
||||||
|
return rowOpt
|
||||||
|
.map(row -> actionPayloadOpt
|
||||||
|
.map(actionPayload -> mergeAndGetFn.get().apply(row, actionPayload))
|
||||||
|
.orElse(row))
|
||||||
|
.orElseGet(() -> actionPayloadOpt
|
||||||
|
.filter(actionPayload -> actionPayload.getClass().equals(rowClazz))
|
||||||
|
.map(rowClazz::cast)
|
||||||
|
.orElse(null));
|
||||||
|
}, Encoders.kryo(rowClazz))
|
||||||
|
.filter((FilterFunction<G>) Objects::nonNull);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends Oaf> Dataset<Tuple2<String, T>> mapToTupleWithId(Dataset<T> ds,
|
||||||
|
SerializableSupplier<Function<T, String>> idFn,
|
||||||
|
Class<T> clazz) {
|
||||||
|
return ds
|
||||||
|
.map((MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(idFn.get().apply(value), value),
|
||||||
|
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Groups graph table by id and aggregates using supplied functions.
|
||||||
|
*
|
||||||
|
* @param rowDS Dataset representing graph table
|
||||||
|
* @param rowIdFn Function used to get the id of graph table row
|
||||||
|
* @param mergeAndGetFn Function used to merge graph table row and action payload instance
|
||||||
|
* @param zeroFn Function to create a zero/empty instance of graph table row
|
||||||
|
* @param isNotZeroFn Function to check if graph table row is not zero/empty
|
||||||
|
* @param rowClazz Class of graph table
|
||||||
|
* @param <G> Type of graph table row
|
||||||
|
* @return Dataset of aggregated graph table rows
|
||||||
|
*/
|
||||||
|
public static <G extends Oaf> Dataset<G> groupGraphTableByIdAndMerge(Dataset<G> rowDS,
|
||||||
|
SerializableSupplier<Function<G, String>> rowIdFn,
|
||||||
|
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
|
||||||
|
SerializableSupplier<G> zeroFn,
|
||||||
|
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
TypedColumn<G, G> aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn();
|
||||||
|
return rowDS
|
||||||
|
.groupByKey((MapFunction<G, String>) x -> rowIdFn.get().apply(x), Encoders.STRING())
|
||||||
|
.agg(aggregator)
|
||||||
|
.map((MapFunction<Tuple2<String, G>, G>) Tuple2::_2, Encoders.kryo(rowClazz));
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Aggregator to be used for aggregating graph table rows during grouping.
|
||||||
|
*
|
||||||
|
* @param <G> Type of graph table row
|
||||||
|
*/
|
||||||
|
public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
|
||||||
|
private SerializableSupplier<G> zeroFn;
|
||||||
|
private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
|
||||||
|
private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
|
||||||
|
private Class<G> rowClazz;
|
||||||
|
|
||||||
|
public TableAggregator(SerializableSupplier<G> zeroFn,
|
||||||
|
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
|
||||||
|
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
this.zeroFn = zeroFn;
|
||||||
|
this.mergeAndGetFn = mergeAndGetFn;
|
||||||
|
this.isNotZeroFn = isNotZeroFn;
|
||||||
|
this.rowClazz = rowClazz;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public G zero() {
|
||||||
|
return zeroFn.get();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public G reduce(G b, G a) {
|
||||||
|
return zeroSafeMergeAndGet(b, a);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public G merge(G b1, G b2) {
|
||||||
|
return zeroSafeMergeAndGet(b1, b2);
|
||||||
|
}
|
||||||
|
|
||||||
|
private G zeroSafeMergeAndGet(G left, G right) {
|
||||||
|
Function<G, Boolean> isNotZero = isNotZeroFn.get();
|
||||||
|
if (isNotZero.apply(left) && isNotZero.apply(right)) {
|
||||||
|
return mergeAndGetFn.get().apply(left, right);
|
||||||
|
} else if (isNotZero.apply(left) && !isNotZero.apply(right)) {
|
||||||
|
return left;
|
||||||
|
} else if (!isNotZero.apply(left) && isNotZero.apply(right)) {
|
||||||
|
return right;
|
||||||
|
}
|
||||||
|
throw new RuntimeException("internal aggregation error: left and right objects are zero");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public G finish(G reduction) {
|
||||||
|
return reduction;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Encoder<G> bufferEncoder() {
|
||||||
|
return Encoders.kryo(rowClazz);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Encoder<G> outputEncoder() {
|
||||||
|
return Encoders.kryo(rowClazz);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -1,38 +0,0 @@
|
||||||
[
|
|
||||||
{
|
|
||||||
"paramName": "issm",
|
|
||||||
"paramLongName": "isSparkSessionManaged",
|
|
||||||
"paramDescription": "TODO",
|
|
||||||
"paramRequired": false
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName": "igp",
|
|
||||||
"paramLongName": "inputGraphPath",
|
|
||||||
"paramDescription": "TODO: input graph path",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName": "iasp",
|
|
||||||
"paramLongName": "inputActionSetPaths",
|
|
||||||
"paramDescription": "TODO: comma separated list of paths to input action sets",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName": "gtn",
|
|
||||||
"paramLongName": "graphTableName",
|
|
||||||
"paramDescription": "TODO",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName": "ogp",
|
|
||||||
"paramLongName": "outputGraphPath",
|
|
||||||
"paramDescription": "TODO: the path of the result DataFrame on HDFS",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName": "mags",
|
|
||||||
"paramLongName": "mergeAndGetStrategy",
|
|
||||||
"paramDescription": "TODO",
|
|
||||||
"paramRequired": true
|
|
||||||
}
|
|
||||||
]
|
|
||||||
|
|
@ -0,0 +1,44 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "issm",
|
||||||
|
"paramLongName": "isSparkSessionManaged",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "igtp",
|
||||||
|
"paramLongName": "inputGraphTablePath",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "gtcn",
|
||||||
|
"paramLongName": "graphTableClassName",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "iapp",
|
||||||
|
"paramLongName": "inputActionPayloadPath",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "apcn",
|
||||||
|
"paramLongName": "actionPayloadClassName",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "ogtp",
|
||||||
|
"paramLongName": "outputGraphTablePath",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "mags",
|
||||||
|
"paramLongName": "mergeAndGetStrategy",
|
||||||
|
"paramDescription": "TODO",
|
||||||
|
"paramRequired": true
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -1,161 +0,0 @@
|
||||||
package eu.dnetlib.dhp.actionmanager;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.sql.Dataset;
|
|
||||||
import org.apache.spark.sql.Encoders;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
import org.junit.AfterClass;
|
|
||||||
import org.junit.BeforeClass;
|
|
||||||
import org.junit.Test;
|
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.function.BiFunction;
|
|
||||||
import java.util.function.Function;
|
|
||||||
|
|
||||||
import static org.junit.Assert.assertEquals;
|
|
||||||
|
|
||||||
public class PromoteActionSetFromHDFSFunctionsTest {
|
|
||||||
|
|
||||||
private static SparkSession spark;
|
|
||||||
|
|
||||||
@BeforeClass
|
|
||||||
public static void beforeClass() {
|
|
||||||
SparkConf conf = new SparkConf();
|
|
||||||
conf.setMaster("local");
|
|
||||||
conf.setAppName(PromoteActionSetFromHDFSFunctionsTest.class.getSimpleName());
|
|
||||||
conf.set("spark.driver.host", "localhost");
|
|
||||||
|
|
||||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
|
||||||
}
|
|
||||||
|
|
||||||
@AfterClass
|
|
||||||
public static void afterClass() {
|
|
||||||
spark.stop();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldJoinWithActionPayloadUsingIdAndMerge() {
|
|
||||||
// given
|
|
||||||
String id1 = "id1";
|
|
||||||
String id2 = "id2";
|
|
||||||
String id3 = "id3";
|
|
||||||
String id4 = "id4";
|
|
||||||
List<OafImpl> oafData = Arrays.asList(
|
|
||||||
createOafImpl(id1), createOafImpl(id2), createOafImpl(id3), createOafImpl(id4)
|
|
||||||
);
|
|
||||||
Dataset<OafImpl> oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class));
|
|
||||||
|
|
||||||
List<OafImpl> actionPayloadData = Arrays.asList(
|
|
||||||
createOafImpl(id1),
|
|
||||||
createOafImpl(id2), createOafImpl(id2),
|
|
||||||
createOafImpl(id3), createOafImpl(id3), createOafImpl(id3)
|
|
||||||
);
|
|
||||||
Dataset<OafImpl> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImpl.class));
|
|
||||||
|
|
||||||
SerializableSupplier<Function<OafImpl, String>> oafIdFn = () -> OafImpl::getId;
|
|
||||||
SerializableSupplier<BiFunction<OafImpl, OafImpl, OafImpl>> mergeAndGetFn = () -> OafImpl::mergeAngGet;
|
|
||||||
|
|
||||||
// when
|
|
||||||
List<OafImpl> results = PromoteActionSetFromHDFSFunctions
|
|
||||||
.joinOafEntityWithActionPayloadAndMerge(oafDS,
|
|
||||||
actionPayloadDS,
|
|
||||||
oafIdFn,
|
|
||||||
mergeAndGetFn,
|
|
||||||
OafImpl.class)
|
|
||||||
.collectAsList();
|
|
||||||
|
|
||||||
// then
|
|
||||||
assertEquals(7, results.size());
|
|
||||||
results.forEach(result -> {
|
|
||||||
switch (result.getId()) {
|
|
||||||
case "id1":
|
|
||||||
case "id2":
|
|
||||||
case "id3":
|
|
||||||
assertEquals(2, result.merged);
|
|
||||||
break;
|
|
||||||
case "id4":
|
|
||||||
assertEquals(1, result.merged);
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
throw new RuntimeException();
|
|
||||||
}
|
|
||||||
});
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldGroupOafEntitiesByIdAndMergeWithinGroup() {
|
|
||||||
// given
|
|
||||||
String id1 = "id1";
|
|
||||||
String id2 = "id2";
|
|
||||||
String id3 = "id3";
|
|
||||||
List<OafImpl> oafData = Arrays.asList(
|
|
||||||
createOafImpl(id1),
|
|
||||||
createOafImpl(id2), createOafImpl(id2),
|
|
||||||
createOafImpl(id3), createOafImpl(id3), createOafImpl(id3)
|
|
||||||
);
|
|
||||||
Dataset<OafImpl> oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class));
|
|
||||||
SerializableSupplier<Function<OafImpl, String>> idFn = () -> OafImpl::getId;
|
|
||||||
SerializableSupplier<BiFunction<OafImpl, OafImpl, OafImpl>> mergeAndGetFn = () -> OafImpl::mergeAngGet;
|
|
||||||
|
|
||||||
// when
|
|
||||||
List<OafImpl> results = PromoteActionSetFromHDFSFunctions
|
|
||||||
.groupOafByIdAndMerge(oafDS,
|
|
||||||
idFn,
|
|
||||||
mergeAndGetFn,
|
|
||||||
OafImpl.class)
|
|
||||||
.collectAsList();
|
|
||||||
|
|
||||||
// then
|
|
||||||
assertEquals(3, results.size());
|
|
||||||
results.forEach(result -> {
|
|
||||||
switch (result.getId()) {
|
|
||||||
case "id1":
|
|
||||||
assertEquals(1, result.merged);
|
|
||||||
break;
|
|
||||||
case "id2":
|
|
||||||
assertEquals(2, result.merged);
|
|
||||||
break;
|
|
||||||
case "id3":
|
|
||||||
assertEquals(3, result.merged);
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
throw new RuntimeException();
|
|
||||||
}
|
|
||||||
});
|
|
||||||
}
|
|
||||||
|
|
||||||
public static class OafImpl extends Oaf {
|
|
||||||
private String id;
|
|
||||||
private int merged = 1;
|
|
||||||
|
|
||||||
public OafImpl mergeAngGet(OafImpl e) {
|
|
||||||
merged += e.merged;
|
|
||||||
return this;
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getId() {
|
|
||||||
return id;
|
|
||||||
}
|
|
||||||
|
|
||||||
public void setId(String id) {
|
|
||||||
this.id = id;
|
|
||||||
}
|
|
||||||
|
|
||||||
public int getMerged() {
|
|
||||||
return merged;
|
|
||||||
}
|
|
||||||
|
|
||||||
public void setMerged(int merged) {
|
|
||||||
this.merged = merged;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private static OafImpl createOafImpl(String id) {
|
|
||||||
OafImpl x = new OafImpl();
|
|
||||||
x.setId(id);
|
|
||||||
return x;
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,269 +0,0 @@
|
||||||
package eu.dnetlib.dhp.actionmanager;
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import org.apache.commons.io.FileUtils;
|
|
||||||
import org.apache.hadoop.conf.Configuration;
|
|
||||||
import org.apache.hadoop.io.Text;
|
|
||||||
import org.apache.hadoop.mapreduce.Job;
|
|
||||||
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
|
||||||
import org.apache.spark.sql.Dataset;
|
|
||||||
import org.apache.spark.sql.Encoders;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
import org.junit.*;
|
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
import java.io.IOException;
|
|
||||||
import java.nio.file.Files;
|
|
||||||
import java.nio.file.Path;
|
|
||||||
import java.nio.file.Paths;
|
|
||||||
import java.util.Comparator;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.Objects;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
|
|
||||||
import static org.apache.spark.sql.functions.base64;
|
|
||||||
import static org.apache.spark.sql.functions.col;
|
|
||||||
import static org.junit.Assert.*;
|
|
||||||
|
|
||||||
public class PromoteActionSetFromHDFSJobTest {
|
|
||||||
private static SparkSession spark;
|
|
||||||
private static Configuration configuration;
|
|
||||||
|
|
||||||
private Path workingDir;
|
|
||||||
private Path inputDir;
|
|
||||||
private Path inputGraphDir;
|
|
||||||
private Path inputActionSetsDir;
|
|
||||||
private Path outputDir;
|
|
||||||
|
|
||||||
private ClassLoader cl = getClass().getClassLoader();
|
|
||||||
|
|
||||||
@BeforeClass
|
|
||||||
public static void beforeClass() throws IOException {
|
|
||||||
SparkConf conf = new SparkConf();
|
|
||||||
conf.setAppName(PromoteActionSetFromHDFSJobTest.class.getSimpleName());
|
|
||||||
conf.setMaster("local");
|
|
||||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
|
||||||
conf.registerKryoClasses(new Class[]{
|
|
||||||
Author.class,
|
|
||||||
Context.class,
|
|
||||||
Country.class,
|
|
||||||
DataInfo.class,
|
|
||||||
eu.dnetlib.dhp.schema.oaf.Dataset.class,
|
|
||||||
Datasource.class,
|
|
||||||
ExternalReference.class,
|
|
||||||
ExtraInfo.class,
|
|
||||||
Field.class,
|
|
||||||
GeoLocation.class,
|
|
||||||
Instance.class,
|
|
||||||
Journal.class,
|
|
||||||
KeyValue.class,
|
|
||||||
Oaf.class,
|
|
||||||
OafEntity.class,
|
|
||||||
OAIProvenance.class,
|
|
||||||
Organization.class,
|
|
||||||
OriginDescription.class,
|
|
||||||
OtherResearchProduct.class,
|
|
||||||
Project.class,
|
|
||||||
Publication.class,
|
|
||||||
Qualifier.class,
|
|
||||||
Relation.class,
|
|
||||||
Result.class,
|
|
||||||
Software.class,
|
|
||||||
StructuredProperty.class
|
|
||||||
});
|
|
||||||
|
|
||||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
|
||||||
|
|
||||||
configuration = Job.getInstance().getConfiguration();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Before
|
|
||||||
public void before() throws IOException {
|
|
||||||
workingDir = Files.createTempDirectory("promote_action_set");
|
|
||||||
inputDir = workingDir.resolve("input");
|
|
||||||
inputGraphDir = inputDir.resolve("graph");
|
|
||||||
|
|
||||||
inputActionSetsDir = inputDir.resolve("action_sets");
|
|
||||||
|
|
||||||
outputDir = workingDir.resolve("output");
|
|
||||||
}
|
|
||||||
|
|
||||||
@After
|
|
||||||
public void after() throws IOException {
|
|
||||||
FileUtils.deleteDirectory(workingDir.toFile());
|
|
||||||
}
|
|
||||||
|
|
||||||
@AfterClass
|
|
||||||
public static void afterAll() {
|
|
||||||
spark.stop();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldThrowWhenGraphTableIsInvalid() {
|
|
||||||
fail("not yet implemented");
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForDatasetsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.DATASET,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
eu.dnetlib.dhp.schema.oaf.Dataset.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForDatasourcesUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.DATASOURCE,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Datasource.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForOrganizationsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.ORGANIZATION,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Organization.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForOtherResearchProductsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.OTHERRESEARCHPRODUCT,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
OtherResearchProduct.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForProjectsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.PROJECT,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Project.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForPublicationsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.PUBLICATION,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Publication.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForRelationsUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.RELATION,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Relation.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void shouldReadActionsFromHDFSAndPromoteThemForSoftwaresUsingMergeFromStrategy() throws Exception {
|
|
||||||
readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName.SOFTWARE,
|
|
||||||
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
|
|
||||||
Software.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
private <T extends Oaf> void readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName graphTableName,
|
|
||||||
OafMergeAndGet.Strategy strategy,
|
|
||||||
Class<T> clazz) throws Exception {
|
|
||||||
// given
|
|
||||||
String inputGraphTableJsonDumpPath =
|
|
||||||
String.format("%s/%s.json", "eu/dnetlib/dhp/actionmanager/input/graph", graphTableName.name().toLowerCase());
|
|
||||||
createGraphTableFor(inputGraphTableJsonDumpPath, graphTableName.name().toLowerCase(), clazz);
|
|
||||||
String inputActionSetPaths = createActionSets();
|
|
||||||
Path outputGraphDir = outputDir.resolve("graph");
|
|
||||||
|
|
||||||
// when
|
|
||||||
PromoteActionSetFromHDFSJob.main(new String[]{
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
||||||
"-inputGraphPath", inputGraphDir.toString(),
|
|
||||||
"-inputActionSetPaths", inputActionSetPaths,
|
|
||||||
"-graphTableName", graphTableName.name(),
|
|
||||||
"-outputGraphPath", outputGraphDir.toString(),
|
|
||||||
"-mergeAndGetStrategy", strategy.name()
|
|
||||||
});
|
|
||||||
|
|
||||||
// then
|
|
||||||
Path outputGraphTableDir = outputGraphDir.resolve(graphTableName.name().toLowerCase());
|
|
||||||
assertTrue(Files.exists(outputGraphDir));
|
|
||||||
|
|
||||||
List<T> outputGraphTableRows = readGraphTableFromParquet(outputGraphTableDir.toString(), clazz).collectAsList();
|
|
||||||
outputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode));
|
|
||||||
|
|
||||||
assertEquals(10, outputGraphTableRows.size());
|
|
||||||
|
|
||||||
String expectedOutputGraphTableJsonDumpPath =
|
|
||||||
String.format("%s/%s/%s.json", "eu/dnetlib/dhp/actionmanager/output/graph", strategy.name().toLowerCase(), graphTableName.name().toLowerCase());
|
|
||||||
Path expectedOutputGraphTableJsonDumpFile = Paths
|
|
||||||
.get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile());
|
|
||||||
List<T> expectedOutputGraphTableRows = readGraphTableFromJSON(
|
|
||||||
expectedOutputGraphTableJsonDumpFile, clazz)
|
|
||||||
.collectAsList();
|
|
||||||
expectedOutputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode));
|
|
||||||
|
|
||||||
assertArrayEquals(expectedOutputGraphTableRows.toArray(), outputGraphTableRows.toArray());
|
|
||||||
}
|
|
||||||
|
|
||||||
private <T extends Oaf> void createGraphTableFor(String inputGraphTableJsonDumpPath,
|
|
||||||
String inputGraphTableDirRelativePath,
|
|
||||||
Class<T> clazz) {
|
|
||||||
Path inputGraphTableJsonDumpFile = Paths
|
|
||||||
.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
|
|
||||||
Dataset<T> inputGraphTableDS = readGraphTableFromJSON(inputGraphTableJsonDumpFile, clazz);
|
|
||||||
Path inputGraphTableDir = inputGraphDir.resolve(inputGraphTableDirRelativePath);
|
|
||||||
inputGraphTableDS
|
|
||||||
.toJSON()
|
|
||||||
.javaRDD()
|
|
||||||
.mapToPair(json -> new Tuple2<>(new Text(clazz.getCanonicalName()), new Text(json)))
|
|
||||||
.saveAsNewAPIHadoopFile(inputGraphTableDir.toString(),
|
|
||||||
Text.class,
|
|
||||||
Text.class,
|
|
||||||
SequenceFileOutputFormat.class,
|
|
||||||
configuration);
|
|
||||||
}
|
|
||||||
|
|
||||||
private String createActionSets() throws IOException {
|
|
||||||
Path inputActionPayloadJsonDumpsDir = Paths
|
|
||||||
.get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/input/action_sets/"))
|
|
||||||
.getFile());
|
|
||||||
Files
|
|
||||||
.list(inputActionPayloadJsonDumpsDir)
|
|
||||||
.forEach(inputActionPayloadJsonDump -> {
|
|
||||||
String inputActionSetId = inputActionPayloadJsonDump.getFileName().toString();
|
|
||||||
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionPayloadJsonDump.getFileName());
|
|
||||||
spark.read()
|
|
||||||
.textFile(inputActionPayloadJsonDump.toString())
|
|
||||||
.withColumn("TargetValue", base64(col("value")))
|
|
||||||
.select("TargetValue")
|
|
||||||
.toJSON()
|
|
||||||
.javaRDD()
|
|
||||||
.mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
|
|
||||||
.saveAsNewAPIHadoopFile(inputActionSetDir.toString(),
|
|
||||||
Text.class,
|
|
||||||
Text.class,
|
|
||||||
SequenceFileOutputFormat.class,
|
|
||||||
configuration);
|
|
||||||
});
|
|
||||||
return Files.list(inputActionSetsDir).map(Path::toString).collect(Collectors.joining(","));
|
|
||||||
}
|
|
||||||
|
|
||||||
private static <T extends Oaf> Dataset<T> readGraphTableFromJSON(Path path, Class<T> clazz) {
|
|
||||||
return spark.read()
|
|
||||||
.format("json")
|
|
||||||
.load(path.toString())
|
|
||||||
.toJSON()
|
|
||||||
.map((MapFunction<String, T>) json -> newObjectMapper().readValue(json, clazz), Encoders.bean(clazz));
|
|
||||||
}
|
|
||||||
|
|
||||||
//TODO: enable strict deserialization later
|
|
||||||
private static ObjectMapper newObjectMapper() {
|
|
||||||
return new ObjectMapper().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
|
|
||||||
}
|
|
||||||
|
|
||||||
private static <T extends Oaf> Dataset<T> readGraphTableFromParquet(String outputGraphTablePath, Class<T> clazz) {
|
|
||||||
return spark.read()
|
|
||||||
.format("parquet")
|
|
||||||
.load(outputGraphTablePath)
|
|
||||||
.as(Encoders.bean(clazz));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,268 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import org.junit.jupiter.api.Nested;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.Strategy;
|
||||||
|
import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor;
|
||||||
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
|
import static org.mockito.Mockito.*;
|
||||||
|
|
||||||
|
public class MergeAndGetTest {
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
class MergeFromAndGetStrategy {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafAndOaf() {
|
||||||
|
// given
|
||||||
|
Oaf a = mock(Oaf.class);
|
||||||
|
Oaf b = mock(Oaf.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafAndRelation() {
|
||||||
|
// given
|
||||||
|
Oaf a = mock(Oaf.class);
|
||||||
|
Relation b = mock(Relation.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafAndOafEntity() {
|
||||||
|
// given
|
||||||
|
Oaf a = mock(Oaf.class);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForRelationAndOaf() {
|
||||||
|
// given
|
||||||
|
Relation a = mock(Relation.class);
|
||||||
|
Oaf b = mock(Oaf.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForRelationAndOafEntity() {
|
||||||
|
// given
|
||||||
|
Relation a = mock(Relation.class);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldBehaveProperlyForRelationAndRelation() {
|
||||||
|
// given
|
||||||
|
Relation a = mock(Relation.class);
|
||||||
|
Relation b = mock(Relation.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
Oaf x = fn.get().apply(a, b);
|
||||||
|
assertTrue(Relation.class.isAssignableFrom(x.getClass()));
|
||||||
|
verify(a).mergeFrom(b);
|
||||||
|
assertEquals(a, x);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafEntityAndOaf() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
Oaf b = mock(Oaf.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafEntityAndRelation() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
Relation b = mock(Relation.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
|
||||||
|
// given
|
||||||
|
class OafEntitySub1 extends OafEntity {
|
||||||
|
}
|
||||||
|
class OafEntitySub2 extends OafEntity {
|
||||||
|
}
|
||||||
|
|
||||||
|
OafEntitySub1 a = mock(OafEntitySub1.class);
|
||||||
|
OafEntitySub2 b = mock(OafEntitySub2.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldBehaveProperlyForOafEntityAndOafEntity() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
Oaf x = fn.get().apply(a, b);
|
||||||
|
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
|
||||||
|
verify(a).mergeFrom(b);
|
||||||
|
assertEquals(a, x);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
class SelectNewerAndGetStrategy {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafEntityAndRelation() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
Relation b = mock(Relation.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForRelationAndOafEntity() {
|
||||||
|
// given
|
||||||
|
Relation a = mock(Relation.class);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowForOafEntityAndResult() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
Result b = mock(Result.class);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
|
||||||
|
// given
|
||||||
|
// real types must be used because subclass-superclass resolution does not work for mocks
|
||||||
|
Dataset a = new Dataset();
|
||||||
|
a.setLastupdatetimestamp(1L);
|
||||||
|
Result b = new Result();
|
||||||
|
b.setLastupdatetimestamp(2L);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
fn.get().apply(a, b));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
when(a.getLastupdatetimestamp()).thenReturn(1L);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
when(b.getLastupdatetimestamp()).thenReturn(2L);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
|
||||||
|
functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
Oaf x = fn.get().apply(a, b);
|
||||||
|
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
|
||||||
|
assertEquals(b, x);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldShouldReturnRightForOafEntityAndOafEntity() {
|
||||||
|
// given
|
||||||
|
OafEntity a = mock(OafEntity.class);
|
||||||
|
when(a.getLastupdatetimestamp()).thenReturn(2L);
|
||||||
|
OafEntity b = mock(OafEntity.class);
|
||||||
|
when(b.getLastupdatetimestamp()).thenReturn(1L);
|
||||||
|
|
||||||
|
// when
|
||||||
|
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
|
||||||
|
functionFor(Strategy.SELECT_NEWER_AND_GET);
|
||||||
|
|
||||||
|
// then
|
||||||
|
Oaf x = fn.get().apply(a, b);
|
||||||
|
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
|
||||||
|
assertEquals(a, x);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,265 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import org.apache.commons.io.FileUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.junit.jupiter.api.*;
|
||||||
|
import org.junit.jupiter.params.ParameterizedTest;
|
||||||
|
import org.junit.jupiter.params.provider.Arguments;
|
||||||
|
import org.junit.jupiter.params.provider.MethodSource;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.nio.file.Files;
|
||||||
|
import java.nio.file.Path;
|
||||||
|
import java.nio.file.Paths;
|
||||||
|
import java.util.Comparator;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Objects;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
|
import static org.junit.jupiter.params.provider.Arguments.arguments;
|
||||||
|
|
||||||
|
public class PromoteActionPayloadForGraphTableJobTest {
|
||||||
|
private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
|
||||||
|
|
||||||
|
private static SparkSession spark;
|
||||||
|
|
||||||
|
private Path workingDir;
|
||||||
|
private Path inputDir;
|
||||||
|
private Path inputGraphRootDir;
|
||||||
|
private Path inputActionPayloadRootDir;
|
||||||
|
private Path outputDir;
|
||||||
|
|
||||||
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeAll() {
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
|
||||||
|
conf.setMaster("local");
|
||||||
|
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||||
|
conf.registerKryoClasses(new Class[]{
|
||||||
|
Author.class,
|
||||||
|
Context.class,
|
||||||
|
Country.class,
|
||||||
|
DataInfo.class,
|
||||||
|
eu.dnetlib.dhp.schema.oaf.Dataset.class,
|
||||||
|
Datasource.class,
|
||||||
|
ExternalReference.class,
|
||||||
|
ExtraInfo.class,
|
||||||
|
Field.class,
|
||||||
|
GeoLocation.class,
|
||||||
|
Instance.class,
|
||||||
|
Journal.class,
|
||||||
|
KeyValue.class,
|
||||||
|
Oaf.class,
|
||||||
|
OafEntity.class,
|
||||||
|
OAIProvenance.class,
|
||||||
|
Organization.class,
|
||||||
|
OriginDescription.class,
|
||||||
|
OtherResearchProduct.class,
|
||||||
|
Project.class,
|
||||||
|
Publication.class,
|
||||||
|
Qualifier.class,
|
||||||
|
Relation.class,
|
||||||
|
Result.class,
|
||||||
|
Software.class,
|
||||||
|
StructuredProperty.class
|
||||||
|
});
|
||||||
|
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
public void beforeEach() throws IOException {
|
||||||
|
workingDir = Files.createTempDirectory(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
|
||||||
|
inputDir = workingDir.resolve("input");
|
||||||
|
inputGraphRootDir = inputDir.resolve("graph");
|
||||||
|
inputActionPayloadRootDir = inputDir.resolve("action_payload");
|
||||||
|
outputDir = workingDir.resolve("output");
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterEach
|
||||||
|
public void afterEach() throws IOException {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() {
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@DisplayName("Job")
|
||||||
|
@Nested
|
||||||
|
class Main {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
|
||||||
|
// given
|
||||||
|
Class<Relation> rowClazz = Relation.class;
|
||||||
|
Class<OafEntity> actionPayloadClazz = OafEntity.class;
|
||||||
|
|
||||||
|
// when
|
||||||
|
RuntimeException exception = assertThrows(RuntimeException.class, () ->
|
||||||
|
PromoteActionPayloadForGraphTableJob.main(new String[]{
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-inputGraphTablePath", "",
|
||||||
|
"-graphTableClassName", rowClazz.getCanonicalName(),
|
||||||
|
"-inputActionPayloadPath", "",
|
||||||
|
"-actionPayloadClassName", actionPayloadClazz.getCanonicalName(),
|
||||||
|
"-outputGraphTablePath", "",
|
||||||
|
"-mergeAndGetStrategy", MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name()
|
||||||
|
}));
|
||||||
|
|
||||||
|
// then
|
||||||
|
String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s",
|
||||||
|
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
|
||||||
|
assertTrue(exception.getMessage().contains(msg));
|
||||||
|
}
|
||||||
|
|
||||||
|
@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
|
||||||
|
@MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
|
||||||
|
public void shouldPromoteActionPayloadForGraphTable(MergeAndGet.Strategy strategy,
|
||||||
|
Class<? extends Oaf> rowClazz,
|
||||||
|
Class<? extends Oaf> actionPayloadClazz) throws Exception {
|
||||||
|
// given
|
||||||
|
Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz);
|
||||||
|
Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz);
|
||||||
|
Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase());
|
||||||
|
|
||||||
|
// when
|
||||||
|
PromoteActionPayloadForGraphTableJob.main(new String[]{
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-inputGraphTablePath", inputGraphTableDir.toString(),
|
||||||
|
"-graphTableClassName", rowClazz.getCanonicalName(),
|
||||||
|
"-inputActionPayloadPath", inputActionPayloadDir.toString(),
|
||||||
|
"-actionPayloadClassName", actionPayloadClazz.getCanonicalName(),
|
||||||
|
"-outputGraphTablePath", outputGraphTableDir.toString(),
|
||||||
|
"-mergeAndGetStrategy", strategy.name()
|
||||||
|
});
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertTrue(Files.exists(outputGraphTableDir));
|
||||||
|
|
||||||
|
List<? extends Oaf> actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz)
|
||||||
|
.collectAsList()
|
||||||
|
.stream()
|
||||||
|
.sorted(Comparator.comparingInt(Object::hashCode))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
String expectedOutputGraphTableJsonDumpPath = resultFileLocation(strategy, rowClazz, actionPayloadClazz);
|
||||||
|
Path expectedOutputGraphTableJsonDumpFile = Paths
|
||||||
|
.get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile());
|
||||||
|
List<? extends Oaf> expectedOutputRows = readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz)
|
||||||
|
.collectAsList()
|
||||||
|
.stream()
|
||||||
|
.sorted(Comparator.comparingInt(Object::hashCode))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
assertIterableEquals(expectedOutputRows, actualOutputRows);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Stream<Arguments> promoteJobTestParams() {
|
||||||
|
return Stream.of(
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Dataset.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Result.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Datasource.class, Datasource.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Organization.class, Organization.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, OtherResearchProduct.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, Result.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Project.class, Project.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Publication.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Result.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Relation.class, Relation.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Software.class),
|
||||||
|
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class)
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> Path createGraphTable(Path inputGraphRootDir,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz);
|
||||||
|
Path inputGraphTableJsonDumpFile = Paths
|
||||||
|
.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
|
||||||
|
Dataset<G> rowDS = readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz);
|
||||||
|
String inputGraphTableName = rowClazz.getSimpleName().toLowerCase();
|
||||||
|
Path inputGraphTableDir = inputGraphRootDir.resolve(inputGraphTableName);
|
||||||
|
writeGraphTableAaJobInput(rowDS, inputGraphTableDir.toString());
|
||||||
|
return inputGraphTableDir;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String inputGraphTableJsonDumpLocation(Class<? extends Oaf> rowClazz) {
|
||||||
|
return String.format(
|
||||||
|
"%s/%s.json", "eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase());
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> Dataset<G> readGraphTableFromJsonDump(String path,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.textFile(path)
|
||||||
|
.map((MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> void writeGraphTableAaJobInput(Dataset<G> rowDS,
|
||||||
|
String path) {
|
||||||
|
rowDS
|
||||||
|
.write()
|
||||||
|
.option("compression", "gzip")
|
||||||
|
.json(path);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf, A extends Oaf> Path createActionPayload(Path inputActionPayloadRootDir,
|
||||||
|
Class<G> rowClazz,
|
||||||
|
Class<A> actionPayloadClazz) {
|
||||||
|
String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz);
|
||||||
|
Path inputActionPayloadJsonDumpFile = Paths
|
||||||
|
.get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile());
|
||||||
|
Dataset<String> actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString());
|
||||||
|
Path inputActionPayloadDir = inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase());
|
||||||
|
writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString());
|
||||||
|
return inputActionPayloadDir;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String inputActionPayloadJsonDumpLocation(Class<? extends Oaf> rowClazz,
|
||||||
|
Class<? extends Oaf> actionPayloadClazz) {
|
||||||
|
|
||||||
|
return String.format("eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json",
|
||||||
|
rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase());
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Dataset<String> readActionPayloadFromJsonDump(String path) {
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.textFile(path);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void writeActionPayloadAsJobInput(Dataset<String> actionPayloadDS,
|
||||||
|
String path) {
|
||||||
|
actionPayloadDS
|
||||||
|
.withColumnRenamed("value", "payload")
|
||||||
|
.write()
|
||||||
|
.parquet(path);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <G extends Oaf> Dataset<G> readGraphTableFromJobOutput(String path,
|
||||||
|
Class<G> rowClazz) {
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.textFile(path)
|
||||||
|
.map((MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String resultFileLocation(MergeAndGet.Strategy strategy,
|
||||||
|
Class<? extends Oaf> rowClazz,
|
||||||
|
Class<? extends Oaf> actionPayloadClazz) {
|
||||||
|
return String
|
||||||
|
.format("eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json",
|
||||||
|
strategy.name().toLowerCase(), rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,314 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.junit.jupiter.api.AfterAll;
|
||||||
|
import org.junit.jupiter.api.BeforeAll;
|
||||||
|
import org.junit.jupiter.api.Nested;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Objects;
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
import java.util.function.Function;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||||
|
|
||||||
|
public class PromoteActionPayloadFunctionsTest {
|
||||||
|
|
||||||
|
private static SparkSession spark;
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeAll() {
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.setMaster("local");
|
||||||
|
conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName());
|
||||||
|
conf.set("spark.driver.host", "localhost");
|
||||||
|
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() {
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
class JoinTableWithActionPayloadAndMerge {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
|
||||||
|
// given
|
||||||
|
class OafImpl extends Oaf {
|
||||||
|
}
|
||||||
|
|
||||||
|
// when
|
||||||
|
assertThrows(RuntimeException.class, () ->
|
||||||
|
PromoteActionPayloadFunctions
|
||||||
|
.joinGraphTableWithActionPayloadAndMerge(null,
|
||||||
|
null,
|
||||||
|
null,
|
||||||
|
null,
|
||||||
|
null,
|
||||||
|
OafImplSubSub.class,
|
||||||
|
OafImpl.class
|
||||||
|
));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
|
||||||
|
// given
|
||||||
|
String id0 = "id0";
|
||||||
|
String id1 = "id1";
|
||||||
|
String id2 = "id2";
|
||||||
|
String id3 = "id3";
|
||||||
|
String id4 = "id4";
|
||||||
|
List<OafImplSubSub> rowData = Arrays.asList(
|
||||||
|
createOafImplSubSub(id0),
|
||||||
|
createOafImplSubSub(id1),
|
||||||
|
createOafImplSubSub(id2),
|
||||||
|
createOafImplSubSub(id3)
|
||||||
|
);
|
||||||
|
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
|
||||||
|
|
||||||
|
List<OafImplSubSub> actionPayloadData = Arrays.asList(
|
||||||
|
createOafImplSubSub(id1),
|
||||||
|
createOafImplSubSub(id2), createOafImplSubSub(id2),
|
||||||
|
createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3),
|
||||||
|
createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4)
|
||||||
|
);
|
||||||
|
Dataset<OafImplSubSub> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class));
|
||||||
|
|
||||||
|
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
|
||||||
|
SerializableSupplier<Function<OafImplSubSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
|
||||||
|
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
|
||||||
|
x.merge(y);
|
||||||
|
return x;
|
||||||
|
};
|
||||||
|
|
||||||
|
// when
|
||||||
|
List<OafImplSubSub> results = PromoteActionPayloadFunctions
|
||||||
|
.joinGraphTableWithActionPayloadAndMerge(rowDS,
|
||||||
|
actionPayloadDS,
|
||||||
|
rowIdFn,
|
||||||
|
actionPayloadIdFn,
|
||||||
|
mergeAndGetFn,
|
||||||
|
OafImplSubSub.class,
|
||||||
|
OafImplSubSub.class
|
||||||
|
)
|
||||||
|
.collectAsList();
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertEquals(11, results.size());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
|
||||||
|
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
|
||||||
|
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
|
||||||
|
assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count());
|
||||||
|
|
||||||
|
results.forEach(result -> {
|
||||||
|
switch (result.getId()) {
|
||||||
|
case "id0":
|
||||||
|
assertEquals(1, result.getMerged());
|
||||||
|
break;
|
||||||
|
case "id1":
|
||||||
|
case "id2":
|
||||||
|
case "id3":
|
||||||
|
assertEquals(2, result.getMerged());
|
||||||
|
break;
|
||||||
|
case "id4":
|
||||||
|
assertEquals(1, result.getMerged());
|
||||||
|
break;
|
||||||
|
default:
|
||||||
|
throw new RuntimeException();
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
|
||||||
|
// given
|
||||||
|
String id0 = "id0";
|
||||||
|
String id1 = "id1";
|
||||||
|
String id2 = "id2";
|
||||||
|
String id3 = "id3";
|
||||||
|
String id4 = "id4";
|
||||||
|
List<OafImplSubSub> rowData = Arrays.asList(
|
||||||
|
createOafImplSubSub(id0),
|
||||||
|
createOafImplSubSub(id1),
|
||||||
|
createOafImplSubSub(id2),
|
||||||
|
createOafImplSubSub(id3)
|
||||||
|
);
|
||||||
|
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
|
||||||
|
|
||||||
|
List<OafImplSub> actionPayloadData = Arrays.asList(
|
||||||
|
createOafImplSub(id1),
|
||||||
|
createOafImplSub(id2), createOafImplSub(id2),
|
||||||
|
createOafImplSub(id3), createOafImplSub(id3), createOafImplSub(id3),
|
||||||
|
createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4)
|
||||||
|
);
|
||||||
|
Dataset<OafImplSub> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class));
|
||||||
|
|
||||||
|
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
|
||||||
|
SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
|
||||||
|
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
|
||||||
|
x.merge(y);
|
||||||
|
return x;
|
||||||
|
};
|
||||||
|
|
||||||
|
// when
|
||||||
|
List<OafImplSubSub> results = PromoteActionPayloadFunctions
|
||||||
|
.joinGraphTableWithActionPayloadAndMerge(rowDS,
|
||||||
|
actionPayloadDS,
|
||||||
|
rowIdFn,
|
||||||
|
actionPayloadIdFn,
|
||||||
|
mergeAndGetFn,
|
||||||
|
OafImplSubSub.class,
|
||||||
|
OafImplSub.class
|
||||||
|
)
|
||||||
|
.collectAsList();
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertEquals(7, results.size());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
|
||||||
|
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
|
||||||
|
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
|
||||||
|
assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count());
|
||||||
|
|
||||||
|
results.forEach(result -> {
|
||||||
|
switch (result.getId()) {
|
||||||
|
case "id0":
|
||||||
|
assertEquals(1, result.getMerged());
|
||||||
|
break;
|
||||||
|
case "id1":
|
||||||
|
case "id2":
|
||||||
|
case "id3":
|
||||||
|
assertEquals(2, result.getMerged());
|
||||||
|
break;
|
||||||
|
default:
|
||||||
|
throw new RuntimeException();
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
class GroupTableByIdAndMerge {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void shouldRunProperly() {
|
||||||
|
// given
|
||||||
|
String id1 = "id1";
|
||||||
|
String id2 = "id2";
|
||||||
|
String id3 = "id3";
|
||||||
|
List<OafImplSubSub> rowData = Arrays.asList(
|
||||||
|
createOafImplSubSub(id1),
|
||||||
|
createOafImplSubSub(id2), createOafImplSubSub(id2),
|
||||||
|
createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3)
|
||||||
|
);
|
||||||
|
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
|
||||||
|
|
||||||
|
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
|
||||||
|
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
|
||||||
|
x.merge(y);
|
||||||
|
return x;
|
||||||
|
};
|
||||||
|
SerializableSupplier<OafImplSubSub> zeroFn = OafImplSubSub::new;
|
||||||
|
SerializableSupplier<Function<OafImplSubSub, Boolean>> isNotZeroFn = () -> x -> Objects.nonNull(x.getId());
|
||||||
|
|
||||||
|
// when
|
||||||
|
List<OafImplSubSub> results = PromoteActionPayloadFunctions
|
||||||
|
.groupGraphTableByIdAndMerge(rowDS,
|
||||||
|
rowIdFn,
|
||||||
|
mergeAndGetFn,
|
||||||
|
zeroFn,
|
||||||
|
isNotZeroFn,
|
||||||
|
OafImplSubSub.class)
|
||||||
|
.collectAsList();
|
||||||
|
|
||||||
|
// then
|
||||||
|
assertEquals(3, results.size());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count());
|
||||||
|
assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count());
|
||||||
|
|
||||||
|
results.forEach(result -> {
|
||||||
|
switch (result.getId()) {
|
||||||
|
case "id1":
|
||||||
|
assertEquals(1, result.getMerged());
|
||||||
|
break;
|
||||||
|
case "id2":
|
||||||
|
assertEquals(2, result.getMerged());
|
||||||
|
break;
|
||||||
|
case "id3":
|
||||||
|
assertEquals(3, result.getMerged());
|
||||||
|
break;
|
||||||
|
default:
|
||||||
|
throw new RuntimeException();
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public static class OafImplRoot extends Oaf {
|
||||||
|
private String id;
|
||||||
|
private int merged = 1;
|
||||||
|
|
||||||
|
public void merge(OafImplRoot e) {
|
||||||
|
merged += e.merged;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getId() {
|
||||||
|
return id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setId(String id) {
|
||||||
|
this.id = id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getMerged() {
|
||||||
|
return merged;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setMerged(int merged) {
|
||||||
|
this.merged = merged;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static class OafImplSub extends OafImplRoot {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void merge(OafImplRoot e) {
|
||||||
|
super.merge(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static OafImplSub createOafImplSub(String id) {
|
||||||
|
OafImplSub x = new OafImplSub();
|
||||||
|
x.setId(id);
|
||||||
|
return x;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static class OafImplSubSub extends OafImplSub {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void merge(OafImplRoot e) {
|
||||||
|
super.merge(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static OafImplSubSub createOafImplSubSub(String id) {
|
||||||
|
OafImplSubSub x = new OafImplSubSub();
|
||||||
|
x.setId(id);
|
||||||
|
return x;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,20 @@
|
||||||
|
{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018225380,"id":"50|CrisUnsNoviS::8b1b8c70de97b1e074b50b816becae0f","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"ComputingMilieux_PERSONALCOMPUTING","qualifier":{"classid":"acm","classname":"acm","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.891","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]}
|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018287185,"id":"50|DansKnawCris::0000c0e2fad89b37efeb343fbdc87894","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Quantitative Biology::Biomolecules","qualifier":{"classid":"arxiv","classname":"arxiv","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.891","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Physics::Biological Physics","qualifier":{"classid":"arxiv","classname":"arxiv","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.8136","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]}
|
||||||
|
{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018287185,"id":"50|DansKnawCris::0000c0e2fad89b37efeb343fbdc87894","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Quantitative Biology::Biomolecules","qualifier":{"classid":"arxiv","classname":"arxiv","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.891","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Physics::Biological Physics","qualifier":{"classid":"arxiv","classname":"arxiv","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.8136","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]}
|
||||||
|
{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018261654,"id":"50|DansKnawCris::0000dbc0cc4d3dd44d77866686a7ebcf","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"human activities","qualifier":{"classid":"mesheuropmc","classname":"mesheuropmc","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.7371","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]}
|
||||||
|
{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018261654,"id":"50|DansKnawCris::0000dbc0cc4d3dd44d77866686a7ebcf","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"human activities","qualifier":{"classid":"mesheuropmc","classname":"mesheuropmc","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.7371","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]}
|
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