forked from D-Net/dnet-hadoop
128 lines
4.6 KiB
Java
128 lines
4.6 KiB
Java
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import java.util.Arrays;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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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.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class PrepareResultOrcidAssociationStep1 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
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public static void main(String[] args) throws Exception {
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String jsonConf = IOUtils
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.toString(
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PrepareResultOrcidAssociationStep1.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConf);
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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 resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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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> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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String inputRelationPath = inputPath + "/relation";
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log.info("inputRelationPath: {}", inputRelationPath);
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String inputResultPath = inputPath + "/" + resultType;
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log.info("inputResultPath: {}", inputResultPath);
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String outputResultPath = outputPath + "/" + resultType;
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log.info("outputResultPath: {}", outputResultPath);
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runWithSparkHiveSession(
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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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prepareInfo(
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spark, inputRelationPath, inputResultPath, outputResultPath, resultClazz, allowedsemrel);
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});
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}
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private static <R extends Result> void prepareInfo(
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SparkSession spark,
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String inputRelationPath,
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String inputResultPath,
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String outputResultPath,
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Class<R> resultClazz,
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List<String> allowedsemrel) {
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Dataset<Relation> relation = readPath(spark, inputRelationPath, Relation.class);
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relation.createOrReplaceTempView("relation");
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log.info("Reading Graph table from: {}", inputResultPath);
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Dataset<R> result = readPath(spark, inputResultPath, resultClazz);
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result.createOrReplaceTempView("result");
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String query = "SELECT target resultId, author authorList"
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+ " FROM (SELECT id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author "
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+ " FROM ( "
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+ " SELECT DISTINCT id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid "
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+ " FROM result "
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+ " LATERAL VIEW EXPLODE (author) a AS MyT "
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+ " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP "
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+ " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or "
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+ " lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
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+ " GROUP BY id) r_t "
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+ " JOIN ("
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+ " SELECT source, target "
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+ " FROM relation "
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+ " WHERE datainfo.deletedbyinference = false "
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+ getConstraintList(" lower(relclass) = '", allowedsemrel)
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+ " ) rel_rel "
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+ " ON source = id";
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log.info("executedQuery: {}", query);
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spark
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.sql(query)
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.as(Encoders.bean(ResultOrcidList.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputResultPath);
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}
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}
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