two new classes fro new implementation of project to result propagation
This commit is contained in:
parent
627ad58a8b
commit
90469789b9
|
|
@ -0,0 +1,69 @@
|
|||
package eu.dnetlib.dhp.projecttoresult;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.gson.Gson;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.TaskResultLost;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.TRUE;
|
||||
import static eu.dnetlib.dhp.PropagationConstant.createOutputDirs;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
|
||||
public class PrepareResultProjectAssociation {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception{
|
||||
|
||||
String jsonConfiguration = IOUtils.toString(PrepareDatasourceCountryAssociation.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_projecttoresult_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
jsonConfiguration);
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath {}: ", outputPath);
|
||||
|
||||
boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
|
||||
log.info("writeUpdates: {} ", writeUpdates);
|
||||
|
||||
boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
|
||||
log.info("saveGraph {}", saveGraph);
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
|
||||
log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
|
||||
runWithSparkHiveSession(conf, isSparkSessionManaged,
|
||||
spark -> {
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
});
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,219 @@
|
|||
package eu.dnetlib.dhp.projecttoresult;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
|
||||
public class SparkResultToProjectThroughSemRelJob3 {
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(SparkResultToProjectThroughSemRelJob3.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkResultToProjectThroughSemRelJob3.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/propagation/projecttoresult";
|
||||
boolean writeUpdates = "true".equals(parser.get("writeUpdate"));
|
||||
boolean saveGraph = "true".equals(parser.get("saveGraph"));
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
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");
|
||||
|
||||
String query = "Select source, target " +
|
||||
"from relation " +
|
||||
"where datainfo.deletedbyinference = false and relClass = '" + RELATION_RESULT_PROJECT_REL_CLASS + "'";
|
||||
|
||||
Dataset<Row> resproj_relation = spark.sql(query);
|
||||
|
||||
query = "Select source, target " +
|
||||
"from relation " +
|
||||
"where datainfo.deletedbyinference = false " + getConstraintList(" relClass = '", allowedsemrel );
|
||||
|
||||
Dataset<Row> resres_relation = spark.sql(query);
|
||||
resres_relation.createOrReplaceTempView("resres_relation");
|
||||
resproj_relation.createOrReplaceTempView("resproj_relation");
|
||||
|
||||
query ="SELECT proj, collect_set(r1target) result_set " +
|
||||
"FROM (" +
|
||||
" SELECT r1.source as source, r1.target as r1target, r2.target as proj " +
|
||||
" FROM resres_relation r1 " +
|
||||
" JOIN resproj_relation r2 " +
|
||||
" ON r1.source = r2.source " +
|
||||
" ) tmp " +
|
||||
"GROUP BY proj ";
|
||||
|
||||
Dataset<Row> toaddrelations = spark.sql(query);
|
||||
|
||||
query = "select target, collect_set(source) result_list from " +
|
||||
"resproj_relation " +
|
||||
"group by target";
|
||||
|
||||
Dataset<Row> project_resultlist = spark.sql(query);
|
||||
|
||||
//if (writeUpdaes){
|
||||
toaddrelations.toJavaRDD().map(r->new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/toupdaterelations");
|
||||
//}
|
||||
|
||||
if(saveGraph){
|
||||
JavaRDD<Relation> new_relations = toaddrelations.toJavaRDD().mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
|
||||
.leftOuterJoin(project_resultlist.toJavaRDD().mapToPair(pr -> new Tuple2<>(pr.getString(0), pr.getList(1))))
|
||||
.flatMap(c -> {
|
||||
List<Object> toAddRel = new ArrayList<>();
|
||||
toAddRel.addAll(c._2()._1());
|
||||
if (c._2()._2().isPresent()) {
|
||||
List<Object> originalRels = c._2()._2().get();
|
||||
for (Object o : originalRels) {
|
||||
if (toAddRel.contains(o)) {
|
||||
toAddRel.remove(o);
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Relation> relationList = new ArrayList<>();
|
||||
String projId = c._1();
|
||||
for (Object r : toAddRel) {
|
||||
String rId = (String) r;
|
||||
relationList.add(getRelation(rId, projId, RELATION_RESULT_PROJECT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
|
||||
RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
|
||||
relationList.add(getRelation(projId, rId, RELATION_PROJECT_RESULT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
|
||||
RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
|
||||
|
||||
}
|
||||
if(relationList.size()==0){
|
||||
return null;
|
||||
}
|
||||
return relationList.iterator();
|
||||
}).filter(r -> !(r==null));
|
||||
|
||||
|
||||
new_relations.map(r-> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/new_relations" );
|
||||
|
||||
sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class))
|
||||
.union(new_relations)
|
||||
.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/relation");
|
||||
|
||||
}
|
||||
|
||||
|
||||
//JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
|
||||
|
||||
// JavaPairRDD<String, TypedRow> result_project = relations
|
||||
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
// .filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass())
|
||||
// && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
|
||||
// .map(rel ->{
|
||||
//
|
||||
// TypedRow tr = new TypedRow();
|
||||
// tr.setSourceId(rel.getSource());
|
||||
// tr.setTargetId(rel.getTarget());
|
||||
// return tr;
|
||||
// })
|
||||
// .mapToPair(toPair());
|
||||
//
|
||||
// //relationships from project to result. One pair for each relationship for results having allowed semantics relation with another result
|
||||
// JavaPairRDD<String, TypedRow> project_result = result_project.join(result_result)
|
||||
// .map(c -> {
|
||||
// String projectId = c._2()._1().getTargetId();
|
||||
// String resultId = c._2()._2().getTargetId();
|
||||
// TypedRow tr = new TypedRow(); tr.setSourceId(projectId); tr.setTargetId(resultId);
|
||||
// return tr;
|
||||
// })
|
||||
// .mapToPair(toPair());
|
||||
//
|
||||
// //relationships from project to result. One Pair for each project => project id list of results related to the project
|
||||
// JavaPairRDD<String, TypedRow> project_results = relations
|
||||
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
// .filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
|
||||
// .map(r -> {
|
||||
// TypedRow tr = new TypedRow(); tr.setSourceId(r.getSource()); tr.setTargetId(r.getTarget());
|
||||
// return tr;
|
||||
// })
|
||||
// .mapToPair(toPair())
|
||||
// .reduceByKey((a, b) -> {
|
||||
// if (a == null) {
|
||||
// return b;
|
||||
// }
|
||||
// if (b == null) {
|
||||
// return a;
|
||||
// }
|
||||
// a.addAll(b.getAccumulator());
|
||||
// return a;
|
||||
// });
|
||||
//
|
||||
//
|
||||
//
|
||||
// JavaRDD<Relation> newRels = project_result.join(project_results)
|
||||
// .flatMap(c -> {
|
||||
// String resId = c._2()._1().getTargetId();
|
||||
//
|
||||
// if (c._2()._2().getAccumulator().contains(resId)) {
|
||||
// return null;
|
||||
// }
|
||||
// String progId = c._2()._1().getSourceId();
|
||||
// List<Relation> rels = new ArrayList();
|
||||
//
|
||||
// rels.add(getRelation(progId, resId, RELATION_PROJECT_RESULT_REL_CLASS,
|
||||
// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
|
||||
// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
|
||||
// rels.add(getRelation(resId, progId, RELATION_RESULT_PROJECT_REL_CLASS,
|
||||
// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
|
||||
// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
|
||||
// return rels.iterator();
|
||||
// })
|
||||
// .cache();
|
||||
//
|
||||
// newRels.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
// .saveAsTextFile(outputPath + "/relation_new");
|
||||
//
|
||||
// newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
// .saveAsTextFile(outputPath + "/relation");
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue