159 lines
4.7 KiB
Java
159 lines
4.7 KiB
Java
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Context;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import scala.Tuple2;
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public class SparkResultToCommunityFromOrganizationJob {
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private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityFromOrganizationJob.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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SparkResultToCommunityFromOrganizationJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromorganization/input_communitytoresult_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 = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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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 possibleupdatespath = parser.get("preparedInfoPath");
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log.info("preparedInfoPath: {}", possibleupdatespath);
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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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execPropagation(spark, inputPath, outputPath, possibleupdatespath);
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});
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}
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private static <R extends Result> void execPropagation(
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SparkSession spark,
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String inputPath,
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String outputPath,
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String possibleUpdatesPath) {
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Dataset<ResultCommunityList> possibleUpdates = readPath(spark, possibleUpdatesPath, ResultCommunityList.class);
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ModelSupport.entityTypes
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.keySet()
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.parallelStream()
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.filter(e -> ModelSupport.isResult(e))
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// .parallelStream()
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.forEach(e -> {
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// if () {
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Class<R> resultClazz = ModelSupport.entityTypes.get(e);
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removeOutputDir(spark, outputPath + e.name());
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Dataset<R> result = readPath(spark, inputPath + e.name(), resultClazz);
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log.info("executing left join");
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result
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.joinWith(
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possibleUpdates,
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result.col("id").equalTo(possibleUpdates.col("resultId")),
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"left_outer")
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.map(resultCommunityFn(), Encoders.bean(resultClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + e.name());
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// log
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// .info(
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// "reading results from " + outputPath + e.name() + " and copying them to " + inputPath
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// + e.name());
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// Dataset<R> tmp = readPath(spark, outputPath + e.name(), resultClazz);
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// if (tmp.count() > 0){
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//
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// tmp
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// .write()
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// .mode(SaveMode.Overwrite)
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// .option("compression", "gzip")
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// .json(inputPath + e.name());
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// }
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// }
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});
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}
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private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> resultCommunityFn() {
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return value -> {
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R ret = value._1();
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Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
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if (rcl.isPresent()) {
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ArrayList<String> communitySet = rcl.get().getCommunityList();
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List<String> contextList = ret
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.getContext()
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.stream()
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.map(Context::getId)
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.collect(Collectors.toList());
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// @SuppressWarnings("unchecked")
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// R res = (R) ret.getClass().newInstance();
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// res.setId(ret.getId());
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// List<Context> propagatedContexts = new ArrayList<>();
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for (String cId : communitySet) {
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if (!contextList.contains(cId)) {
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Context newContext = new Context();
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newContext.setId(cId);
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newContext
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.setDataInfo(
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Arrays
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.asList(
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getDataInfo(
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS)));
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ret.getContext().add(newContext);
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}
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}
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// res.setContext(propagatedContexts);
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// return MergeUtils.mergeResult(ret, res);
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}
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return ret;
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};
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}
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}
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