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integrated filter applied when merging BETA & PROD graphs to rule our records from Datacite

This commit is contained in:
Claudio Atzori 2021-03-19 11:34:44 +01:00
parent 3256b9c836
commit a4e82a65aa
1 changed files with 60 additions and 52 deletions
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112
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java
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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import java.util.stream.Collectors;
import javax.xml.crypto.Data;
@ -52,22 +53,22 @@ public class MergeGraphTableSparkJob {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CleanGraphSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
.toString(
CleanGraphSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
String priority = Optional
.ofNullable(parser.get("priority"))
.orElse(PRIORITY_DEFAULT);
.ofNullable(parser.get("priority"))
.orElse(PRIORITY_DEFAULT);
log.info("priority: {}", priority);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String betaInputPath = parser.get("betaInputPath");
@ -89,48 +90,55 @@ public class MergeGraphTableSparkJob {
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
mergeGraphTable(spark, priority, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
});
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
mergeGraphTable(spark, priority, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
});
}
private static <P extends Oaf, B extends Oaf> void mergeGraphTable(
SparkSession spark,
String priority,
String betaInputPath,
String prodInputPath,
Class<P> p_clazz,
Class<B> b_clazz,
String outputPath) {
SparkSession spark,
String priority,
String betaInputPath,
String prodInputPath,
Class<P> p_clazz,
Class<B> b_clazz,
String outputPath) {
Dataset<Tuple2<String, B>> beta = readTableFromPath(spark, betaInputPath, b_clazz);
Dataset<Tuple2<String, P>> prod = readTableFromPath(spark, prodInputPath, p_clazz);
prod
.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
if (p.orElse((P) b.orElse((B) DATASOURCE)) instanceof Datasource) {
return mergeDatasource(p, b);
}
switch (priority) {
default:
case "BETA":
return mergeWithPriorityToBETA(p, b);
case "PROD":
return mergeWithPriorityToPROD(p, b);
}
}, Encoders.bean(p_clazz))
.filter((FilterFunction<P>) Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
if (p.orElse((P) b.orElse((B) DATASOURCE)) instanceof Datasource) {
return mergeDatasource(p, b);
}
switch (priority) {
default:
case "BETA":
return mergeWithPriorityToBETA(p, b);
case "PROD":
return mergeWithPriorityToPROD(p, b);
}
}, Encoders.bean(p_clazz))
.filter((FilterFunction<P>) Objects::nonNull)
.filter((FilterFunction<P>) o -> {
HashSet<String> collectedFromNames = Optional
.ofNullable(o.getCollectedfrom())
.map(c -> c.stream().map(KeyValue::getValue).collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<String>());
return !collectedFromNames.contains("Datacite");
})
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
/**
@ -184,19 +192,19 @@ public class MergeGraphTableSparkJob {
}
private static <T extends Oaf> Dataset<Tuple2<String, T>> readTableFromPath(
SparkSession spark, String inputEntityPath, Class<T> clazz) {
SparkSession spark, String inputEntityPath, Class<T> clazz) {
log.info("Reading Graph table from: {}", inputEntityPath);
return spark
.read()
.textFile(inputEntityPath)
.map(
(MapFunction<String, Tuple2<String, T>>) value -> {
final T t = OBJECT_MAPPER.readValue(value, clazz);
final String id = ModelSupport.idFn().apply(t);
return new Tuple2<>(id, t);
},
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
.read()
.textFile(inputEntityPath)
.map(
(MapFunction<String, Tuple2<String, T>>) value -> {
final T t = OBJECT_MAPPER.readValue(value, clazz);
final String id = ModelSupport.idFn().apply(t);
return new Tuple2<>(id, t);
},
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
}
private static void removeOutputDir(SparkSession spark, String path) {