138 lines
4.1 KiB
Java
138 lines
4.1 KiB
Java
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package eu.dnetlib.dhp.bulktag;
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import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
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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.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.fasterxml.jackson.databind.ObjectMapper;
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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.bulktag.community.*;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class SparkBulkTagJob {
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private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.class);
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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SparkBulkTagJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bulktag/input_bulkTag_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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Boolean isTest = Optional
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.ofNullable(parser.get("isTest"))
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.map(Boolean::valueOf)
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.orElse(Boolean.FALSE);
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log.info("isTest: {} ", isTest);
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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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ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
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log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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CommunityConfiguration cc;
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String taggingConf = parser.get("taggingConf");
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if (isTest) {
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cc = CommunityConfigurationFactory.newInstance(taggingConf);
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} else {
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cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
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}
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
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});
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}
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private static <R extends Result> void execBulkTag(
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SparkSession spark,
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String inputPath,
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String outputPath,
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ProtoMap protoMappingParams,
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Class<R> resultClazz,
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CommunityConfiguration communityConfiguration) {
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ResultTagger resultTagger = new ResultTagger();
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readPath(spark, inputPath, resultClazz)
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.map(patchResult(), Encoders.bean(resultClazz))
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.map(
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(MapFunction<R, R>) value -> resultTagger
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.enrichContextCriteria(
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value, communityConfiguration, protoMappingParams),
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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);
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}
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public static <R> Dataset<R> readPath(
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SparkSession spark, String inputPath, Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
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private static <R extends Result> MapFunction<R, R> patchResult() {
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return r -> {
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if (r.getDataInfo().getDeletedbyinference() == null) {
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r.getDataInfo().setDeletedbyinference(false);
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}
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if (r.getContext() == null) {
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r.setContext(new ArrayList<>());
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}
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return r;
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};
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}
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}
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