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[dhp-actionmanager] promoting spark job added

This commit is contained in:
Przemysław Jacewicz 2020-04-01 18:44:35 +02:00 committed by przemek
parent e21bb89dbd
commit 5b459bcc47
47 changed files with 1546 additions and 929 deletions
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37
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/OafMergeAndGet.java
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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 <T extends Oaf> SerializableSupplier<BiFunction<T, T, T>> 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();
}
}

133
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctions.java
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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 <T extends Oaf> Dataset<T> joinOafEntityWithActionPayloadAndMerge(Dataset<T> oafDS,
Dataset<T> actionPayloadOafDS,
SerializableSupplier<Function<T, String>> oafIdFn,
SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn,
Class<T> clazz) {
Dataset<Tuple2<String, T>> oafWithIdDS = mapToTupleWithId(oafDS, oafIdFn, clazz);
Dataset<Tuple2<String, T>> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadOafDS, oafIdFn, clazz);
return oafWithIdDS
.joinWith(actionPayloadWithIdDS, oafWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "left_outer")
.map((MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, 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 <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)));
}
public static <T extends Oaf> Dataset<T> groupOafByIdAndMerge(Dataset<T> oafDS,
SerializableSupplier<Function<T, String>> oafIdFn,
SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn,
Class<T> clazz) {
return oafDS
.groupByKey((MapFunction<T, String>) x -> oafIdFn.get().apply(x), Encoders.STRING())
.reduceGroups((ReduceFunction<T>) (v1, v2) -> mergeAndGetFn.get().apply(v1, v2))
.map((MapFunction<Tuple2<String, T>, T>) Tuple2::_2, Encoders.kryo(clazz));
}
public static <T extends Oaf> Dataset<T> groupOafByIdAndMergeUsingAggregator(Dataset<T> oafDS,
SerializableSupplier<T> zeroFn,
SerializableSupplier<Function<T, String>> idFn,
Class<T> clazz) {
TypedColumn<T, T> aggregator = new OafAggregator<>(zeroFn, clazz).toColumn();
return oafDS
.groupByKey((MapFunction<T, String>) x -> idFn.get().apply(x), Encoders.STRING())
.agg(aggregator)
.map((MapFunction<Tuple2<String, T>, T>) Tuple2::_2, Encoders.kryo(clazz));
}
public static class OafAggregator<T extends Oaf> extends Aggregator<T, T, T> {
private SerializableSupplier<T> zero;
private Class<T> clazz;
public OafAggregator(SerializableSupplier<T> zero, Class<T> 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<T> bufferEncoder() {
return Encoders.kryo(clazz);
}
@Override
public Encoder<T> outputEncoder() {
return Encoders.kryo(clazz);
}
}
}

283
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJob.java
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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 <T extends Oaf> void processGraphTable(SparkSession spark,
String inputGraphTablePath,
String inputActionSetPaths,
String outputGraphTablePath,
OafMergeAndGet.Strategy strategy,
Class<T> clazz) {
Dataset<T> tableDS = readGraphTable(spark, inputGraphTablePath, clazz)
.cache();
Dataset<T> actionPayloadDS = readActionSetPayloads(spark, inputActionSetPaths, clazz)
.cache();
Dataset<T> result = promoteActionSetForGraphTable(tableDS, actionPayloadDS, strategy, clazz)
.map((MapFunction<T, T>) value -> value, Encoders.bean(clazz));
saveGraphTableAsParquet(result, outputGraphTablePath);
}
private static <T extends Oaf> Dataset<T> readGraphTable(SparkSession spark,
String inputGraphTablePath,
Class<T> clazz) {
JavaRDD<Row> 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, T>) row -> new ObjectMapper().readValue(row.<String>getAs("value"), clazz),
Encoders.bean(clazz));
}
private static <T extends Oaf> Dataset<T> readActionSetPayloads(SparkSession spark,
String inputActionSetPaths,
Class<T> 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 <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);
}
}

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dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/SerializableSupplier.java
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package eu.dnetlib.dhp.actionmanager;
import java.io.Serializable;
import java.util.function.Supplier;
@FunctionalInterface
public interface SerializableSupplier<T> extends Supplier<T>, Serializable {
}

74
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java Normal file
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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()));
}
}

271
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java Normal file
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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);
}
}

170
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java Normal file
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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);
}
}
}

38
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json
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@ -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
}
]

44
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json Normal file
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@ -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
}
]

161
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java
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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;
}
}

269
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java
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@ -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));
}
}

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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);
}
}
}

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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());
}
}

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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
dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json → dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/dataset_table/dataset.json
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