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changed to delete the part to check if it was a test or a real execution

This commit is contained in:
Miriam Baglioni 2020-07-29 16:47:57 +02:00
parent 3ec2392904
commit a8d65b68cb
1 changed files with 12 additions and 61 deletions
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67
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java
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@ -8,8 +8,6 @@ import java.util.Optional;
import java.util.Set; import java.util.Set;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
@ -21,7 +19,9 @@ import org.slf4j.LoggerFactory;
import com.google.gson.Gson; import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -51,78 +51,29 @@ public class SparkSplitForCommunity implements Serializable {
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
// final String resultClassName = parser.get("resultTableName");
// log.info("resultTableName: {}", resultClassName);
final String isLookUpUrl = parser.get("isLookUpUrl"); final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl); log.info("isLookUpUrl: {}", isLookUpUrl);
final Optional<String> cm = Optional.ofNullable(parser.get("communityMap")); CommunitySplit split = new CommunitySplit();
SparkConf conf = new SparkConf();
CommunityMap communityMap; CommunityMap communityMap;
if (!isLookUpUrl.equals("BASEURL:8280/is/services/isLookUp")) {
QueryInformationSystem queryInformationSystem = new QueryInformationSystem(); QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(getIsLookUpService(isLookUpUrl)); queryInformationSystem.setIsLookUp(getIsLookUpService(isLookUpUrl));
communityMap = queryInformationSystem.getCommunityMap(); communityMap = queryInformationSystem.getCommunityMap();
} else {
communityMap = new Gson().fromJson(cm.get(), CommunityMap.class);
}
runWithSparkSession( split.run(isSparkSessionManaged, inputPath, outputPath, communityMap);
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
execSplit(spark, inputPath, outputPath, communityMap.keySet());// , inputClazz);
});
} }
public static ISLookUpService getIsLookUpService(String isLookUpUrl) { public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
return ISLookupClientFactory.getLookUpService(isLookUpUrl); return ISLookupClientFactory.getLookUpService(isLookUpUrl);
} }
private static void execSplit(SparkSession spark, String inputPath, String outputPath,
Set<String> communities) {// }, Class<R> inputClazz) {
Dataset<Result> result = Utils
.readPath(spark, inputPath + "/publication", Result.class)
.union(Utils.readPath(spark, inputPath + "/dataset", Result.class))
.union(Utils.readPath(spark, inputPath + "/orp", Result.class))
.union(Utils.readPath(spark, inputPath + "/software", Result.class));
communities
.stream()
.forEach(c -> printResult(c, result, outputPath));
}
private static void printResult(String c, Dataset<Result> result, String outputPath) {
Dataset<Result> community_products = result
.filter(r -> containsCommunity(r, c));
if (community_products.count() > 0) {
community_products
.repartition(1)
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath + "/" + c);
}
}
private static boolean containsCommunity(Result r, String c) {
if (Optional.ofNullable(r.getContext()).isPresent()) {
return r
.getContext()
.stream()
.filter(con -> con.getCode().equals(c))
.collect(Collectors.toList())
.size() > 0;
}
return false;
}
} }