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