116 lines
3.8 KiB
Java
116 lines
3.8 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
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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.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.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.*;
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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.eosc.model.Result;
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import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
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/**
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* @author miriam.baglioni
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* @Date 27/07/22
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*/
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public class SelectEoscResultsJobStep1 implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SelectEoscResultsJobStep1.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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SelectEoscResultsJobStep1.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/eosc_select_result_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 eoscDatasourceIdsPath = parser.get("eoscDatasourceIdsPath");
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log.info("eoscDatasourceIdsPath: {}", eoscDatasourceIdsPath);
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final String communityMapPath = parser.get("communityMapPath");
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log.info("communityMapPath: {}", communityMapPath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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Class<? extends eu.dnetlib.dhp.schema.oaf.Result> inputClazz = (Class<? extends eu.dnetlib.dhp.schema.oaf.Result>) Class
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.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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selectEoscResults(spark, inputPath, outputPath, inputClazz, communityMapPath, eoscDatasourceIdsPath);
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});
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}
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private static <R extends eu.dnetlib.dhp.schema.oaf.Result> void selectEoscResults(SparkSession spark,
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String inputPath, String outputPath,
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Class<R> inputClazz, String communityMapPath, String eoscDatasourceIdsPath) {
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// final StructType structureSchema = new StructType()
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// .add("eoscId", DataTypes.StringType)
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// .add("graphId", DataTypes.StringType)
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// .add("graphName", DataTypes.StringType);
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//
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// // .fromDDL("`graphId`: STRING, `eoscId`:STRING");
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// org.apache.spark.sql.Dataset<Row> df = spark
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// .read()
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// .schema(structureSchema)
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// .json(eoscDatasourceIdsPath);
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List<MasterDuplicate> df = Utils
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.readPath(spark, eoscDatasourceIdsPath, MasterDuplicate.class)
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.collectAsList();
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log.info("number of rows ************: " + df.size());
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CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
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Utils
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.readPath(spark, inputPath, inputClazz)
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.filter(
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(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() && !r.getDataInfo().getInvisible()
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&& (r.getContext().stream().anyMatch(c -> c.getId().equals("eosc")) ||
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r
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.getCollectedfrom()
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.stream()
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.anyMatch(cf -> cf.getValue().equalsIgnoreCase("B2FIND"))))
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.map(
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(MapFunction<R, Result>) r -> (Result) ResultMapper
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.map(r, communityMap, df),
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Encoders.bean(Result.class))
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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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}
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