seconf phase of data preparation. Groups all the possible updates by id
This commit is contained in:
parent
548ba915ac
commit
0e5399bf74
|
|
@ -1,34 +1,27 @@
|
|||
package eu.dnetlib.dhp.orcidtoresultfromsemrel;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.gson.Gson;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.compress.GzipCodec;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import scala.Tuple2;
|
||||
import java.util.HashSet;
|
||||
import java.util.Set;
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class PrepareResultOrcidAssociationStep1 {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
|
||||
public class PrepareResultOrcidAssociationStep2 {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult2_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
jsonConfiguration);
|
||||
|
|
@ -44,76 +37,55 @@ public class PrepareResultOrcidAssociationStep1 {
|
|||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
|
||||
log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
|
||||
|
||||
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
|
||||
log.info("resultType: {}", resultType);
|
||||
|
||||
|
||||
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
|
||||
runWithSparkHiveSession(conf, isSparkSessionManaged,
|
||||
runWithSparkSession(conf, isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
prepareInfo(spark, inputPath, outputPath, resultClazz, resultType, allowedsemrel);
|
||||
mergeInfo(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result> void prepareInfo(SparkSession spark, String inputPath,
|
||||
String outputPath, Class<R> resultClazz,
|
||||
String resultType,
|
||||
List<String> allowedsemrel) {
|
||||
private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
|
||||
|
||||
//read the relation table and the table related to the result it is using
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
|
||||
relation.createOrReplaceTempView("relation");
|
||||
Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath);
|
||||
|
||||
log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
|
||||
Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
|
||||
|
||||
result.createOrReplaceTempView("result");
|
||||
|
||||
getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
|
||||
resultOrcidAssoc
|
||||
.toJavaRDD()
|
||||
.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
|
||||
.reduceByKey((a, b) -> {
|
||||
if (a == null) {
|
||||
return b;
|
||||
}
|
||||
if (b == null) {
|
||||
return a;
|
||||
}
|
||||
Set<String> orcid_set = new HashSet<>();
|
||||
a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
|
||||
|
||||
b.getAuthorList().stream().forEach(aa -> {
|
||||
if (!orcid_set.contains(aa.getOrcid())) {
|
||||
a.getAuthorList().add(aa);
|
||||
orcid_set.add(aa.getOrcid());
|
||||
}
|
||||
});
|
||||
return a;
|
||||
})
|
||||
.map(c -> c._2())
|
||||
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
private static void getPossibleResultOrcidAssociation(SparkSession spark, List<String> allowedsemrel, String outputPath){
|
||||
String query = " select target resultId, author authorList" +
|
||||
" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
|
||||
" from ( " +
|
||||
" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
|
||||
" from result " +
|
||||
" lateral view explode (author) a as MyT " +
|
||||
" lateral view explode (MyT.pid) p as MyP " +
|
||||
" where MyP.qualifier.classid = 'ORCID') tmp " +
|
||||
" group by id) r_t " +
|
||||
" join (" +
|
||||
" select source, target " +
|
||||
" from relation " +
|
||||
" where datainfo.deletedbyinference = false " +
|
||||
getConstraintList(" relclass = '" ,allowedsemrel) + ") rel_rel " +
|
||||
" on source = id";
|
||||
|
||||
spark.sql(query)
|
||||
.as(Encoders.bean(ResultOrcidList.class))
|
||||
.toJSON()
|
||||
.write()
|
||||
.mode(SaveMode.Append)
|
||||
.option("compression","gzip")
|
||||
.text(outputPath)
|
||||
;
|
||||
private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
|
||||
return spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue