From 5b459bcc4750fb9a1569a6475821607ed26c3f75 Mon Sep 17 00:00:00 2001 From: pjacewicz Date: Wed, 1 Apr 2020 18:44:35 +0200 Subject: [PATCH] [dhp-actionmanager] promoting spark job added --- .../dhp/actionmanager/OafMergeAndGet.java | 37 --- .../PromoteActionSetFromHDFSFunctions.java | 133 -------- .../PromoteActionSetFromHDFSJob.java | 283 ---------------- .../actionmanager/SerializableSupplier.java | 8 - .../actionmanager/promote/MergeAndGet.java | 74 +++++ .../PromoteActionPayloadForGraphTableJob.java | 271 +++++++++++++++ .../PromoteActionPayloadFunctions.java | 170 ++++++++++ .../actionmanager_input_parameters.json | 38 --- ...load_for_graph_table_input_parameters.json | 44 +++ ...PromoteActionSetFromHDFSFunctionsTest.java | 161 --------- .../PromoteActionSetFromHDFSJobTest.java | 269 --------------- .../promote/MergeAndGetTest.java | 268 +++++++++++++++ ...moteActionPayloadForGraphTableJobTest.java | 265 +++++++++++++++ .../PromoteActionPayloadFunctionsTest.java | 314 ++++++++++++++++++ .../dataset_table/dataset.json} | 0 .../action_payload/dataset_table/result.json | 20 ++ .../datasource_table/datasource.json} | 0 .../organization_table/organization.json} | 0 .../otherresearchproduct.json} | 0 .../otherresearchproduct_table/result.json | 20 ++ .../project_table/project.json} | 0 .../publication_table/publication.json} | 0 .../publication_table/result.json | 20 ++ .../relation_table/relation.json} | 0 .../promote/input/action_payload/result.json | 20 ++ .../action_payload/software_table/result.json | 20 ++ .../software_table/software.json} | 0 .../{ => promote}/input/graph/dataset.json | 0 .../{ => promote}/input/graph/datasource.json | 0 .../input/graph/organization.json | 0 .../input/graph/otherresearchproduct.json | 0 .../{ => promote}/input/graph/project.json | 0 .../input/graph/publication.json | 0 .../{ => promote}/input/graph/relation.json | 0 .../{ => promote}/input/graph/software.json | 0 .../dataset_action_payload/result.json} | 0 .../dataset/result_action_payload/result.json | 10 + .../datasource_action_payload/result.json} | 0 .../organization_action_payload/result.json} | 0 .../result.json} | 0 .../result_action_payload/result.json | 10 + .../project_action_payload/result.json} | 0 .../publication_action_payload/result.json} | 0 .../result_action_payload/result.json | 10 + .../relation_action_payload/result.json} | 0 .../result_action_payload/result.json | 10 + .../software_action_payload/result.json} | 0 47 files changed, 1546 insertions(+), 929 deletions(-) delete mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/OafMergeAndGet.java delete mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctions.java delete mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJob.java delete mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/SerializableSupplier.java create mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java create mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java create mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java delete mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json create mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json delete mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java delete mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_dataset.json => promote/input/action_payload/dataset_table/dataset.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_datasource.json => promote/input/action_payload/datasource_table/datasource.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_organization.json => promote/input/action_payload/organization_table/organization.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_otherresearchproduct.json => promote/input/action_payload/otherresearchproduct_table/otherresearchproduct.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/otherresearchproduct_table/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_project.json => promote/input/action_payload/project_table/project.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_publication.json => promote/input/action_payload/publication_table/publication.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_relation.json => promote/input/action_payload/relation_table/relation.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/result.json create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/software_table/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{input/action_sets/payload_software.json => promote/input/action_payload/software_table/software.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/dataset.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/datasource.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/organization.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/otherresearchproduct.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/project.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/publication.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/relation.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => promote}/input/graph/software.json (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/dataset.json => promote/output/graph/merge_from_and_get/dataset/dataset_action_payload/result.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/dataset/result_action_payload/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/datasource.json => promote/output/graph/merge_from_and_get/datasource/datasource_action_payload/result.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/organization.json => promote/output/graph/merge_from_and_get/organization/organization_action_payload/result.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/otherresearchproduct.json => promote/output/graph/merge_from_and_get/otherresearchproduct/otherresearchproduct_action_payload/result.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/otherresearchproduct/result_action_payload/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/project.json => promote/output/graph/merge_from_and_get/project/project_action_payload/result.json} (100%) rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/publication.json => promote/output/graph/merge_from_and_get/publication/publication_action_payload/result.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/publication/result_action_payload/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/relation.json => promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json} (100%) create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/software/result_action_payload/result.json rename dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/{output/graph/merge_from_and_get/software.json => promote/output/graph/merge_from_and_get/software/software_action_payload/result.json} (100%) diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/OafMergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/OafMergeAndGet.java deleted file mode 100644 index dff82c0a5..000000000 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/OafMergeAndGet.java +++ /dev/null @@ -1,37 +0,0 @@ -package eu.dnetlib.dhp.actionmanager; - -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; - -public class OafMergeAndGet { - - public enum Strategy { - MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET - } - - public static SerializableSupplier> functionFor(Strategy strategy) { - switch (strategy) { - case MERGE_FROM_AND_GET: - return () -> (x, y) -> { - if (x instanceof Relation) { - ((Relation) x).mergeFrom((Relation) y); - return x; - } - ((OafEntity) x).mergeFrom((OafEntity) y); - return x; - }; - case SELECT_NEWER_AND_GET: - return () -> (x, y) -> { - if (x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { - return x; - } - return y; - }; - } - throw new RuntimeException(); - } - -} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctions.java deleted file mode 100644 index 994989e45..000000000 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctions.java +++ /dev/null @@ -1,133 +0,0 @@ -package eu.dnetlib.dhp.actionmanager; - -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Relation; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.ReduceFunction; -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; - -public class PromoteActionSetFromHDFSFunctions { - - public static Dataset joinOafEntityWithActionPayloadAndMerge(Dataset oafDS, - Dataset actionPayloadOafDS, - SerializableSupplier> oafIdFn, - SerializableSupplier> mergeAndGetFn, - Class clazz) { - Dataset> oafWithIdDS = mapToTupleWithId(oafDS, oafIdFn, clazz); - Dataset> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadOafDS, oafIdFn, clazz); - - return oafWithIdDS - .joinWith(actionPayloadWithIdDS, oafWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "left_outer") - .map((MapFunction, Tuple2>, T>) value -> { - T left = value._1()._2(); - return Optional - .ofNullable(value._2()) - .map(Tuple2::_2) - .map(x -> mergeAndGetFn.get().apply(left, x)) - .orElse(left); - }, Encoders.kryo(clazz)); - } - - private static Dataset> mapToTupleWithId(Dataset ds, - SerializableSupplier> idFn, - Class clazz) { - return ds - .map((MapFunction>) value -> new Tuple2<>(idFn.get().apply(value), value), - Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); - } - - public static Dataset groupOafByIdAndMerge(Dataset oafDS, - SerializableSupplier> oafIdFn, - SerializableSupplier> mergeAndGetFn, - Class clazz) { - return oafDS - .groupByKey((MapFunction) x -> oafIdFn.get().apply(x), Encoders.STRING()) - .reduceGroups((ReduceFunction) (v1, v2) -> mergeAndGetFn.get().apply(v1, v2)) - .map((MapFunction, T>) Tuple2::_2, Encoders.kryo(clazz)); - } - - public static Dataset groupOafByIdAndMergeUsingAggregator(Dataset oafDS, - SerializableSupplier zeroFn, - SerializableSupplier> idFn, - Class clazz) { - TypedColumn aggregator = new OafAggregator<>(zeroFn, clazz).toColumn(); - return oafDS - .groupByKey((MapFunction) x -> idFn.get().apply(x), Encoders.STRING()) - .agg(aggregator) - .map((MapFunction, T>) Tuple2::_2, Encoders.kryo(clazz)); - } - - public static class OafAggregator extends Aggregator { - private SerializableSupplier zero; - private Class clazz; - - public OafAggregator(SerializableSupplier zero, Class clazz) { - this.zero = zero; - this.clazz = clazz; - } - - @Override - public T zero() { - return zero.get(); - } - - @Override - public T reduce(T b, T a) { - return mergeFrom(b, a); - } - - @Override - public T merge(T b1, T b2) { - return mergeFrom(b1, b2); - } - - private T mergeFrom(T left, T right) { - if (isNonNull(left)) { - if (left instanceof Relation) { - ((Relation) left).mergeFrom((Relation) right); - return left; - } - ((OafEntity) left).mergeFrom((OafEntity) right); - return left; - } - - if (right instanceof Relation) { - ((Relation) right).mergeFrom((Relation) left); - return right; - } - ((OafEntity) right).mergeFrom((OafEntity) left); - return right; - } - - private Boolean isNonNull(T a) { - return Objects.nonNull(a.getLastupdatetimestamp()); - } - - @Override - public T finish(T reduction) { - return reduction; - } - - @Override - public Encoder bufferEncoder() { - return Encoders.kryo(clazz); - } - - @Override - public Encoder outputEncoder() { - return Encoders.kryo(clazz); - } - - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJob.java deleted file mode 100644 index b0239a39c..000000000 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJob.java +++ /dev/null @@ -1,283 +0,0 @@ -package eu.dnetlib.dhp.actionmanager; - -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -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.*; -import org.apache.spark.sql.types.*; - -import java.io.IOException; -import java.util.Arrays; -import java.util.Objects; -import java.util.Optional; -import java.util.function.BiFunction; -import java.util.function.Function; - -import static org.apache.spark.sql.functions.*; - -public class PromoteActionSetFromHDFSJob { - - // TODO replace with project's common implementation - public enum GraphTableName { - DATASET, DATASOURCE, ORGANIZATION, OTHERRESEARCHPRODUCT, PROJECT, PUBLICATION, RELATION, SOFTWARE - } - - private static final StructType KV_SCHEMA = StructType$.MODULE$.apply( - Arrays.asList( - StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()), - StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty()) - )); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PromoteActionSetFromHDFSJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/actionmanager_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); - String inputGraphPath = parser.get("inputGraphPath"); - String inputActionSetPaths = parser.get("inputActionSetPaths"); - GraphTableName graphTableName = GraphTableName.valueOf(parser.get("graphTableName").toUpperCase()); - String outputGraphPath = parser.get("outputGraphPath"); - OafMergeAndGet.Strategy strategy = OafMergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); - - 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 - }); - - SparkSession spark = null; - try { - spark = SparkSession.builder().config(conf).getOrCreate(); - String inputGraphTablePath = String.format("%s/%s", inputGraphPath, graphTableName.name().toLowerCase()); - String outputGraphTablePath = String.format("%s/%s", outputGraphPath, graphTableName.name().toLowerCase()); - - switch (graphTableName) { - case DATASET: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - eu.dnetlib.dhp.schema.oaf.Dataset.class); - break; - case DATASOURCE: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Datasource.class); - break; - case ORGANIZATION: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Organization.class); - break; - case OTHERRESEARCHPRODUCT: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - OtherResearchProduct.class); - break; - case PROJECT: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Project.class); - break; - case PUBLICATION: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Publication.class); - break; - case RELATION: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Relation.class); - break; - case SOFTWARE: - processGraphTable(spark, - inputGraphTablePath, - inputActionSetPaths, - outputGraphTablePath, - strategy, - Software.class); - break; - default: - throw new RuntimeException("error processing table: " + graphTableName); - } - } finally { - if (Objects.nonNull(spark) && isSparkSessionManaged) { - spark.stop(); - } - } - } - - private static void processGraphTable(SparkSession spark, - String inputGraphTablePath, - String inputActionSetPaths, - String outputGraphTablePath, - OafMergeAndGet.Strategy strategy, - Class clazz) { - Dataset tableDS = readGraphTable(spark, inputGraphTablePath, clazz) - .cache(); - Dataset actionPayloadDS = readActionSetPayloads(spark, inputActionSetPaths, clazz) - .cache(); - - Dataset result = promoteActionSetForGraphTable(tableDS, actionPayloadDS, strategy, clazz) - .map((MapFunction) value -> value, Encoders.bean(clazz)); - - saveGraphTableAsParquet(result, outputGraphTablePath); - } - - private static Dataset readGraphTable(SparkSession spark, - String inputGraphTablePath, - Class clazz) { - JavaRDD rows = JavaSparkContext - .fromSparkContext(spark.sparkContext()) - .sequenceFile(inputGraphTablePath, Text.class, Text.class) - .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); - - return spark.createDataFrame(rows, KV_SCHEMA) - .map((MapFunction) row -> new ObjectMapper().readValue(row.getAs("value"), clazz), - Encoders.bean(clazz)); - } - - private static Dataset readActionSetPayloads(SparkSession spark, - String inputActionSetPaths, - Class clazz) { - return Arrays - .stream(inputActionSetPaths.split(",")) - .map(inputActionSetPath -> readActionSetPayload(spark, inputActionSetPath, clazz)) - .reduce(Dataset::union) - .orElseThrow(() -> new RuntimeException("error reading action sets: " + inputActionSetPaths)); - } - - private static Dataset readActionSetPayload(SparkSession spark, - String inputActionSetPath, - Class clazz) { - JavaRDD actionsRDD = JavaSparkContext - .fromSparkContext(spark.sparkContext()) - .sequenceFile(inputActionSetPath, Text.class, Text.class) - .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); - - SerializableSupplier, 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) value -> actionPayloadToOafFn.get().apply(value, clazz), Encoders.bean(clazz)) - .filter((FilterFunction) Objects::nonNull); - } - - private static Dataset promoteActionSetForGraphTable(Dataset tableDS, - Dataset actionPayloadDS, - OafMergeAndGet.Strategy strategy, - Class clazz) { - SerializableSupplier> 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> mergeAndGetFn = OafMergeAndGet.functionFor(strategy); - - Dataset joinedAndMerged = PromoteActionSetFromHDFSFunctions - .joinOafEntityWithActionPayloadAndMerge( - tableDS, - actionPayloadDS, - oafIdFn, - mergeAndGetFn, - clazz); - - return PromoteActionSetFromHDFSFunctions - .groupOafByIdAndMerge( - joinedAndMerged, - oafIdFn, - mergeAndGetFn, - clazz - ); - } - - private static void saveGraphTableAsParquet(Dataset result, String outputGraphTablePath) { - result.write() - .format("parquet") - .save(outputGraphTablePath); - } -} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/SerializableSupplier.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/SerializableSupplier.java deleted file mode 100644 index 8df25bbe1..000000000 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/SerializableSupplier.java +++ /dev/null @@ -1,8 +0,0 @@ -package eu.dnetlib.dhp.actionmanager; - -import java.io.Serializable; -import java.util.function.Supplier; - -@FunctionalInterface -public interface SerializableSupplier extends Supplier, Serializable { -} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java new file mode 100644 index 000000000..55346f612 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java @@ -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. + *

+ * 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 Graph table type + * @param Action payload type + * @return BiFunction to be used to merge OAF objects + */ + public static SerializableSupplier> 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 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 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())); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java new file mode 100644 index 000000000..21607a7dc --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java @@ -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 rowClazz = (Class) Class.forName(graphTableClassName); + Class actionPayloadClazz = (Class) 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 rowClazz, + Class 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 void promoteActionPayloadForGraphTable(SparkSession spark, + String inputGraphTablePath, + String inputActionPayloadPath, + String outputGraphTablePath, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + Dataset rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz); + Dataset actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); + + Dataset result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz) + .map((MapFunction) value -> value, Encoders.bean(rowClazz)); + + saveGraphTable(result, outputGraphTablePath); + } + + private static Dataset readGraphTable(SparkSession spark, + String path, + Class rowClazz) { + logger.info("Reading graph table from path: {}", path); + return spark + .read() + .textFile(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz)); + } + + private static Dataset readActionPayload(SparkSession spark, + String path, + Class actionPayloadClazz) { + logger.info("Reading action payload from path: {}", path); + return spark + .read() + .parquet(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), + actionPayloadClazz), Encoders.bean(actionPayloadClazz)); + } + + private static Dataset promoteActionPayloadForGraphTable(Dataset rowDS, + Dataset actionPayloadDS, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName()); + + SerializableSupplier> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier zeroFn = zeroFn(rowClazz); + SerializableSupplier> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource; + + Dataset joinedAndMerged = PromoteActionPayloadFunctions + .joinGraphTableWithActionPayloadAndMerge( + rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeRowWithActionPayloadAndGetFn, + rowClazz, + actionPayloadClazz); + + return PromoteActionPayloadFunctions + .groupGraphTableByIdAndMerge( + joinedAndMerged, + rowIdFn, + mergeRowsAndGetFn, + zeroFn, + isNotZeroFn, + rowClazz); + } + + private static Function idFn() { + return x -> { + if (isSubClass(x, Relation.class)) { + return idFnForRelation(x); + } + return idFnForOafEntity(x); + }; + } + + private static 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 String idFnForOafEntity(T t) { + return ((OafEntity) t).getId(); + } + + private static SerializableSupplier zeroFn(Class 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 Function isNotZeroFnUsingIdOrSource() { + return t -> { + if (isSubClass(t, Relation.class)) { + return Objects.nonNull(((Relation) t).getSource()); + } + return Objects.nonNull(((OafEntity) t).getId()); + }; + } + + private static void saveGraphTable(Dataset result, + String path) { + logger.info("Saving graph table to path: {}", path); + result + .toJSON() + .write() + .option("compression", "gzip") + .text(path); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java new file mode 100644 index 000000000..dce1c72a5 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java @@ -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 Type of graph table row + * @param Type of action payload + * @return Dataset of merged graph table rows and action payload + */ + public static Dataset joinGraphTableWithActionPayloadAndMerge(Dataset rowDS, + Dataset actionPayloadDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> actionPayloadIdFn, + SerializableSupplier> mergeAndGetFn, + Class rowClazz, + Class 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> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz); + Dataset> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz); + + return rowWithIdDS + .joinWith(actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "full_outer") + .map((MapFunction, Tuple2>, G>) value -> { + Optional rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2); + Optional 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) Objects::nonNull); + } + + private static Dataset> mapToTupleWithId(Dataset ds, + SerializableSupplier> idFn, + Class clazz) { + return ds + .map((MapFunction>) 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 Type of graph table row + * @return Dataset of aggregated graph table rows + */ + public static Dataset groupGraphTableByIdAndMerge(Dataset rowDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier zeroFn, + SerializableSupplier> isNotZeroFn, + Class rowClazz) { + TypedColumn aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn(); + return rowDS + .groupByKey((MapFunction) x -> rowIdFn.get().apply(x), Encoders.STRING()) + .agg(aggregator) + .map((MapFunction, G>) Tuple2::_2, Encoders.kryo(rowClazz)); + } + + /** + * Aggregator to be used for aggregating graph table rows during grouping. + * + * @param Type of graph table row + */ + public static class TableAggregator extends Aggregator { + private SerializableSupplier zeroFn; + private SerializableSupplier> mergeAndGetFn; + private SerializableSupplier> isNotZeroFn; + private Class rowClazz; + + public TableAggregator(SerializableSupplier zeroFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier> isNotZeroFn, + Class 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 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 bufferEncoder() { + return Encoders.kryo(rowClazz); + } + + @Override + public Encoder outputEncoder() { + return Encoders.kryo(rowClazz); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json deleted file mode 100644 index 8face9e85..000000000 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json +++ /dev/null @@ -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 - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json new file mode 100644 index 000000000..8da862573 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json @@ -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 + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java deleted file mode 100644 index a05dac910..000000000 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java +++ /dev/null @@ -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 oafData = Arrays.asList( - createOafImpl(id1), createOafImpl(id2), createOafImpl(id3), createOafImpl(id4) - ); - Dataset oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class)); - - List actionPayloadData = Arrays.asList( - createOafImpl(id1), - createOafImpl(id2), createOafImpl(id2), - createOafImpl(id3), createOafImpl(id3), createOafImpl(id3) - ); - Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImpl.class)); - - SerializableSupplier> oafIdFn = () -> OafImpl::getId; - SerializableSupplier> mergeAndGetFn = () -> OafImpl::mergeAngGet; - - // when - List 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 oafData = Arrays.asList( - createOafImpl(id1), - createOafImpl(id2), createOafImpl(id2), - createOafImpl(id3), createOafImpl(id3), createOafImpl(id3) - ); - Dataset oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class)); - SerializableSupplier> idFn = () -> OafImpl::getId; - SerializableSupplier> mergeAndGetFn = () -> OafImpl::mergeAngGet; - - // when - List 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; - } - -} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java deleted file mode 100644 index 61c954af3..000000000 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java +++ /dev/null @@ -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 void readActionsFromHDFSAndPromoteThemFor(PromoteActionSetFromHDFSJob.GraphTableName graphTableName, - OafMergeAndGet.Strategy strategy, - Class 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 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 expectedOutputGraphTableRows = readGraphTableFromJSON( - expectedOutputGraphTableJsonDumpFile, clazz) - .collectAsList(); - expectedOutputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode)); - - assertArrayEquals(expectedOutputGraphTableRows.toArray(), outputGraphTableRows.toArray()); - } - - private void createGraphTableFor(String inputGraphTableJsonDumpPath, - String inputGraphTableDirRelativePath, - Class clazz) { - Path inputGraphTableJsonDumpFile = Paths - .get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile()); - Dataset 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 Dataset readGraphTableFromJSON(Path path, Class clazz) { - return spark.read() - .format("json") - .load(path.toString()) - .toJSON() - .map((MapFunction) 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 Dataset readGraphTableFromParquet(String outputGraphTablePath, Class clazz) { - return spark.read() - .format("parquet") - .load(outputGraphTablePath) - .as(Encoders.bean(clazz)); - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java new file mode 100644 index 000000000..caacada49 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java @@ -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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + Oaf x = fn.get().apply(a, b); + assertTrue(OafEntity.class.isAssignableFrom(x.getClass())); + assertEquals(a, x); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java new file mode 100644 index 000000000..755679903 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -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 rowClazz = Relation.class; + Class 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 rowClazz, + Class 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 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 expectedOutputRows = readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + assertIterableEquals(expectedOutputRows, actualOutputRows); + } + } + + public static Stream 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 Path createGraphTable(Path inputGraphRootDir, + Class rowClazz) { + String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz); + Path inputGraphTableJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile()); + Dataset 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 rowClazz) { + return String.format( + "%s/%s.json", "eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase()); + } + + private static Dataset readGraphTableFromJsonDump(String path, + Class rowClazz) { + return spark + .read() + .textFile(path) + .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + } + + private static void writeGraphTableAaJobInput(Dataset rowDS, + String path) { + rowDS + .write() + .option("compression", "gzip") + .json(path); + } + + private static Path createActionPayload(Path inputActionPayloadRootDir, + Class rowClazz, + Class actionPayloadClazz) { + String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz); + Path inputActionPayloadJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile()); + Dataset actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString()); + Path inputActionPayloadDir = inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase()); + writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString()); + return inputActionPayloadDir; + } + + private static String inputActionPayloadJsonDumpLocation(Class rowClazz, + Class 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 readActionPayloadFromJsonDump(String path) { + return spark + .read() + .textFile(path); + } + + private static void writeActionPayloadAsJobInput(Dataset actionPayloadDS, + String path) { + actionPayloadDS + .withColumnRenamed("value", "payload") + .write() + .parquet(path); + } + + private static Dataset readGraphTableFromJobOutput(String path, + Class rowClazz) { + return spark + .read() + .textFile(path) + .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + } + + private static String resultFileLocation(MergeAndGet.Strategy strategy, + Class rowClazz, + Class 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()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java new file mode 100644 index 000000000..39574e274 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java @@ -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 rowData = Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + List actionPayloadData = Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), createOafImplSubSub(id2), + createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3), + createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4) + ); + Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + + // when + List 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 rowData = Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + List actionPayloadData = Arrays.asList( + createOafImplSub(id1), + createOafImplSub(id2), createOafImplSub(id2), + createOafImplSub(id3), createOafImplSub(id3), createOafImplSub(id3), + createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4) + ); + Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + + // when + List 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 rowData = Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), createOafImplSubSub(id2), + createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + SerializableSupplier zeroFn = OafImplSubSub::new; + SerializableSupplier> isNotZeroFn = () -> x -> Objects.nonNull(x.getId()); + + // when + List 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; + } + +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/dataset.json similarity index 100% rename from dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json rename to dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/dataset.json diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/result.json new file mode 100644 index 000000000..50284fdfb --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/result.json @@ -0,0 +1,20 @@ 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