forked from D-Net/dnet-hadoop
128 lines
4.2 KiB
Java
128 lines
4.2 KiB
Java
|
|
package eu.dnetlib.dhp.oa.graph.dump.pid;
|
|
|
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|
|
|
import java.io.Serializable;
|
|
import java.util.ArrayList;
|
|
import java.util.List;
|
|
import java.util.Objects;
|
|
import java.util.Optional;
|
|
|
|
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.SaveMode;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.slf4j.Logger;
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
import com.google.gson.Gson;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
|
import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
|
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
|
|
public class SparkPrepareResultPids implements Serializable {
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultPids.class);
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
String jsonConfiguration = IOUtils
|
|
.toString(
|
|
SparkPrepareResultPids.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/oa/graph/dump_pid/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);
|
|
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);
|
|
|
|
final List<String> allowedResultPid = new Gson().fromJson(parser.get("allowedResultPids"), List.class);
|
|
final List<String> allowedAuthorPid = new Gson().fromJson(parser.get("allowedAuthorPids"), List.class);
|
|
|
|
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
|
|
log.info("resultType: {}", resultType);
|
|
|
|
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
|
|
|
SparkConf conf = new SparkConf();
|
|
runWithSparkSession(
|
|
conf,
|
|
isSparkSessionManaged,
|
|
spark -> {
|
|
Utils.removeOutputDir(spark, outputPath);
|
|
preparePidEntities(
|
|
spark, inputPath, outputPath + "/" + resultType, inputClazz, allowedResultPid, allowedAuthorPid);
|
|
|
|
});
|
|
|
|
}
|
|
|
|
private static <R extends Result> void preparePidEntities(SparkSession spark, String inputPath, String outputPath,
|
|
Class<R> inputClazz, List<String> allowedResultPid,
|
|
List<String> allowedAuthorPid) {
|
|
|
|
Dataset<R> result = Utils.readPath(spark, inputPath, inputClazz);
|
|
|
|
result.map((MapFunction<R, ResultPidsList>) res -> {
|
|
ResultPidsList ret = new ResultPidsList();
|
|
ret.setResultId(res.getId());
|
|
List<KeyValue> pidList = new ArrayList<>();
|
|
Optional
|
|
.ofNullable(res.getPid())
|
|
.ifPresent(pids -> pids.forEach(pid -> {
|
|
if (allowedResultPid.contains(pid.getQualifier().getClassid().toLowerCase())) {
|
|
pidList.add(KeyValue.newInstance(pid.getQualifier().getClassid(), pid.getValue()));
|
|
}
|
|
}));
|
|
ret.setResultAllowedPids(pidList);
|
|
List<List<KeyValue>> authorPidList = new ArrayList<>();
|
|
Optional
|
|
.ofNullable(res.getAuthor())
|
|
.ifPresent(authors -> authors.forEach(a -> {
|
|
Optional
|
|
.ofNullable(a.getPid())
|
|
.ifPresent(pids -> pids.forEach(p -> {
|
|
List<KeyValue> authorPids = new ArrayList<>();
|
|
if (allowedAuthorPid.contains(p.getQualifier().getClassid().toLowerCase())) {
|
|
authorPids.add(KeyValue.newInstance(p.getQualifier().getClassid(), p.getValue()));
|
|
}
|
|
if (authorPids.size() > 0) {
|
|
authorPidList.add(authorPids);
|
|
}
|
|
}));
|
|
}));
|
|
ret.setAuthorAllowedPids(authorPidList);
|
|
|
|
if (authorPidList.size() == 0 && pidList.size() == 0) {
|
|
return null;
|
|
}
|
|
return ret;
|
|
}, Encoders.bean(ResultPidsList.class))
|
|
.filter(Objects::nonNull)
|
|
.write()
|
|
.mode(SaveMode.Append)
|
|
.option("compression", "gzip")
|
|
.json(outputPath);
|
|
}
|
|
|
|
}
|