forked from D-Net/dnet-hadoop
seconf phase of data preparation. Groups all the possible updates by id
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548ba915ac
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0e5399bf74
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@ -1,34 +1,27 @@
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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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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.apache.spark.sql.*;
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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 scala.Tuple2;
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import java.util.HashSet;
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import java.util.Set;
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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 static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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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 class PrepareResultOrcidAssociationStep2 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.class);
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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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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult2_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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@ -44,76 +37,55 @@ public class PrepareResultOrcidAssociationStep1 {
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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("allowedsemrel").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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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkSession(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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prepareInfo(spark, inputPath, outputPath, resultClazz, resultType, allowedsemrel);
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mergeInfo(spark, inputPath, outputPath);
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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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String resultType,
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List<String> allowedsemrel) {
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private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
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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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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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relation.createOrReplaceTempView("relation");
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Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath);
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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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result.createOrReplaceTempView("result");
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getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
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resultOrcidAssoc
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.toJavaRDD()
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.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
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.reduceByKey((a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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Set<String> orcid_set = new HashSet<>();
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a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
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b.getAuthorList().stream().forEach(aa -> {
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if (!orcid_set.contains(aa.getOrcid())) {
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a.getAuthorList().add(aa);
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orcid_set.add(aa.getOrcid());
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}
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});
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return a;
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})
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.map(c -> c._2())
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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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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.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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private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
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return spark
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.read()
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.textFile(relationPath)
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.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
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}
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}
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