2020-04-16 15:53:34 +02:00
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import org.apache.commons.io.IOUtils;
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2020-04-16 18:40:14 +02:00
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import org.apache.hadoop.io.compress.GzipCodec;
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2020-04-16 15:53:34 +02:00
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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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2020-04-16 15:58:42 +02:00
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import org.apache.spark.sql.SaveMode;
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2020-04-16 15:53:34 +02:00
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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 java.util.Arrays;
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import java.util.List;
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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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2020-04-16 15:58:42 +02:00
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public class PrepareResultOrcidAssociationStep1 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
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2020-04-16 15:53:34 +02:00
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private 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.toString(SparkOrcidToResultFromSemRelJob3.class
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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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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 resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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2020-04-16 18:40:14 +02:00
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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2020-04-16 15:53:34 +02:00
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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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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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2020-04-16 15:58:42 +02:00
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prepareInfo(spark, inputPath, outputPath, resultClazz, resultType, allowedsemrel);
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2020-04-16 15:53:34 +02:00
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});
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}
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private static <R extends Result> void prepareInfo(SparkSession spark, String inputPath,
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String outputPath, Class<R> resultClazz,
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2020-04-16 15:58:42 +02:00
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String resultType,
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List<String> allowedsemrel) {
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2020-04-16 15:53:34 +02:00
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//read the relation table and the table related to the result it is using
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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2020-04-16 18:40:14 +02:00
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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2020-04-16 15:53:34 +02:00
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relation.createOrReplaceTempView("relation");
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log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
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Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
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2020-04-16 15:58:42 +02:00
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result.createOrReplaceTempView("result");
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2020-04-16 15:53:34 +02:00
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2020-04-16 18:40:14 +02:00
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getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath + "/" + resultType);
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2020-04-16 15:53:34 +02:00
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2020-04-16 15:58:42 +02:00
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}
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2020-04-16 15:53:34 +02:00
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2020-04-16 15:58:42 +02:00
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private static void getPossibleResultOrcidAssociation(SparkSession spark, List<String> allowedsemrel, String outputPath){
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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 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 MyP.qualifier.classid = 'ORCID') 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(" relclass = '" ,allowedsemrel) + ") rel_rel " +
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" on source = id";
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spark.sql(query)
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.as(Encoders.bean(ResultOrcidList.class))
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2020-04-16 18:40:14 +02:00
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.toJavaRDD()
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.class);
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// .toJSON()
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// .write()
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// .mode(SaveMode.Append)
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// .option("compression","gzip")
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// .text(outputPath)
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// ;
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2020-04-16 15:53:34 +02:00
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}
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2020-04-16 15:58:42 +02:00
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2020-04-16 15:53:34 +02:00
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}
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