D-Net
/
dnet-hadoop
14
5
Fork 11
Code Issues 14 Pull Requests 13 Projects 2 Releases 2 Wiki Activity

master #11

Manually merged
claudio.atzori merged 275 commits from :master into enrichment_wfs 2020-05-11 15:14:56 +02:00
Conversation 1 Commits 275 Files Changed 156 +288
2 changed files with 288 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files
Showing only changes of commit 90469789b9 - Show all commits

69
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareResultProjectAssociation.java Normal file
View File

@ -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()));
});
}
}

219
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob3.java Normal file
View File

@ -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");
}
}