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[EOSC Dump] dump of only products related to the eosc. No other entities so far

This commit is contained in:
Miriam Baglioni 2022-07-28 17:52:37 +02:00
parent 5d730ab08b
commit 065ffcf815
2 changed files with 178 additions and 0 deletions
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90
src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/SelectEoscRelationsStep2.java Normal file
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import javax.rmi.CORBA.Util;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
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.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
/**
* @author miriam.baglioni
* @Date 27/07/22
*/
public class SelectEoscRelationsStep2 implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SelectEoscRelationsStep2.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SelectEoscRelationsStep2.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/reletion_selection_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String resultPath = parser.get("resultPath");
log.info("resultPath: {}", resultPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, resultPath + "/relation");
selectRelations(spark, inputPath, resultPath + "/relation", resultPath);
});
}
private static void selectRelations(SparkSession spark, String inputPath, String outputPath, String resultPath) {
Dataset<GraphResult> results = Utils
.readPath(spark, resultPath + "/publication", GraphResult.class)
.union(
Utils
.readPath(spark, resultPath + "/dataset", GraphResult.class))
.union(
Utils
.readPath(spark, resultPath + "/software", GraphResult.class))
.union(
Utils
.readPath(spark, resultPath + "/otherresearchproduct", GraphResult.class));
Dataset<Relation> relations = Utils
.readPath(spark, inputPath + "/relation", Relation.class)
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
!r.getDataInfo().getInvisible());
// relations.joinWith(results, relations.col("source").equalTo(results.col("id")), "left")
// .map((MapFunction<Tuple2<Relation, GraphResult>, eu.dnetlib.dhp.schema.dump.oaf.Relation) );
}
}

88
src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/SelectEoscResultsJobStep1.java Normal file
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* @author miriam.baglioni
* @Date 27/07/22
*/
public class SelectEoscResultsJobStep1 implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SelectEoscResultsJobStep1.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SelectEoscResultsJobStep1.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/eosc_select_result_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
selectEoscResults(spark, inputPath, outputPath, inputClazz);
});
}
private static <R extends Result> void selectEoscResults(SparkSession spark, String inputPath, String outputPath,
Class<R> inputClazz) {
Utils
.readPath(spark, inputPath, inputClazz)
.filter(
(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() && !r.getDataInfo().getInvisible()
&& r.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.map(
(MapFunction<R, GraphResult>) r -> (GraphResult) ResultMapper
.map(r, null, Constants.DUMPTYPE.COMPLETE.getType()),
Encoders.bean(GraphResult.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
}