This commit is contained in:
Miriam Baglioni 2020-04-23 12:42:07 +02:00
parent 769aa8178a
commit 44fab140de
3 changed files with 1626 additions and 1081 deletions

View File

@ -1,10 +1,14 @@
package eu.dnetlib.dhp.resulttocommunityfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.QueryInformationSystem;
import eu.dnetlib.dhp.TypedRow;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.spark.SparkConf;
@ -16,28 +20,25 @@ import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
import java.util.*;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.PropagationConstant.*;
public class SparkResultToCommunityThroughSemRelJob3 {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils
.toString(SparkResultToCommunityThroughSemRelJob3.class
.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_propagationresultcommunityfromsemrel_parameters.json")));
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
SparkResultToCommunityThroughSemRelJob3.class.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf();
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final SparkSession spark = SparkSession
.builder()
.appName(SparkResultToCommunityThroughSemRelJob3.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
final SparkSession spark =
SparkSession.builder()
.appName(SparkResultToCommunityThroughSemRelJob3.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String inputPath = parser.get("sourcePath");
@ -45,42 +46,48 @@ public class SparkResultToCommunityThroughSemRelJob3 {
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
final List<String> communityIdList = QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
final List<String> communityIdList =
QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
JavaRDD<Publication> publication_rdd =
sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, Publication.class));
JavaRDD<Publication> publication_rdd = sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, Publication.class));
JavaRDD<Dataset> dataset_rdd =
sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, Dataset.class));
JavaRDD<Dataset> dataset_rdd = sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, Dataset.class));
JavaRDD<OtherResearchProduct> orp_rdd =
sc.textFile(inputPath + "/otherresearchproduct")
.map(
item ->
new ObjectMapper()
.readValue(item, OtherResearchProduct.class));
JavaRDD<OtherResearchProduct> orp_rdd = sc.textFile(inputPath + "/otherresearchproduct")
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
JavaRDD<Software> software_rdd =
sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, Software.class));
JavaRDD<Software> software_rdd = sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, Software.class));
JavaRDD<Relation> relation_rdd =
sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class));
JavaRDD<Relation> relation_rdd = sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class));
org.apache.spark.sql.Dataset<Publication> publication =
spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
org.apache.spark.sql.Dataset<Relation> relation =
spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(publication_rdd.rdd(),
Encoders.bean(Publication.class));
org.apache.spark.sql.Dataset<Dataset> dataset =
spark.createDataset(dataset_rdd.rdd(), Encoders.bean(Dataset.class));
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(),
Encoders.bean(Relation.class));
org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(dataset_rdd.rdd(),
Encoders.bean(Dataset.class));
org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(orp_rdd.rdd(),
Encoders.bean(OtherResearchProduct.class));
org.apache.spark.sql.Dataset<Software> software = spark.createDataset(software_rdd.rdd(),
Encoders.bean(Software.class));
org.apache.spark.sql.Dataset<OtherResearchProduct> other =
spark.createDataset(orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
org.apache.spark.sql.Dataset<Software> software =
spark.createDataset(software_rdd.rdd(), Encoders.bean(Software.class));
publication.createOrReplaceTempView("publication");
relation.createOrReplaceTempView("relation");
@ -90,327 +97,490 @@ public class SparkResultToCommunityThroughSemRelJob3 {
String communitylist = getConstraintList(" co.id = '", communityIdList);
String semrellist = getConstraintList(" relClass = '", allowedsemrel );
String semrellist = getConstraintList(" relClass = '", allowedsemrel);
String query =
"Select source, community_context, target "
+ "from (select id, collect_set(co.id) community_context "
+ "from publication "
+ "lateral view explode (context) c as co "
+ "where datainfo.deletedbyinference = false "
+ communitylist
+ " group by id) p "
+ "JOIN "
+ "(select * "
+ "from relation "
+ "where datainfo.deletedbyinference = false "
+ semrellist
+ ") r "
+ "ON p.id = r.source";
String query = "Select source, community_context, target " +
"from (select id, collect_set(co.id) community_context " +
"from publication " +
"lateral view explode (context) c as co " +
"where datainfo.deletedbyinference = false "+ communitylist +
" group by id) p " +
"JOIN " +
"(select * " +
"from relation " +
"where datainfo.deletedbyinference = false " + semrellist + ") r " +
"ON p.id = r.source";
org.apache.spark.sql.Dataset<Row> publication_context = spark.sql( query);
org.apache.spark.sql.Dataset<Row> publication_context = spark.sql(query);
publication_context.createOrReplaceTempView("publication_context");
//( source, (mes, dh-ch-, ni), target )
query = "select target , collect_set(co) " +
"from (select target, community_context " +
"from publication_context pc join publication p on " +
"p.id = pc.source) tmp " +
"lateral view explode (community_context) c as co " +
"group by target";
// ( source, (mes, dh-ch-, ni), target )
query =
"select target , collect_set(co) "
+ "from (select target, community_context "
+ "from publication_context pc join publication p on "
+ "p.id = pc.source) tmp "
+ "lateral view explode (community_context) c as co "
+ "group by target";
org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult = getUpdateCommunitiesForTable(spark, "software");
org.apache.spark.sql.Dataset<Row> toupdatedatasetresult = getUpdateCommunitiesForTable(spark, "dataset");
org.apache.spark.sql.Dataset<Row> toupdateotherresult = getUpdateCommunitiesForTable(spark, "other");
org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
getUpdateCommunitiesForTable(spark, "software");
org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
getUpdateCommunitiesForTable(spark, "dataset");
org.apache.spark.sql.Dataset<Row> toupdateotherresult =
getUpdateCommunitiesForTable(spark, "other");
createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath, "software_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
createUpdateForResultDatasetWrite(
toupdatesoftwareresult.toJavaRDD(),
outputPath,
"software_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(), outputPath, "dataset_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
createUpdateForResultDatasetWrite(
toupdatedatasetresult.toJavaRDD(),
outputPath,
"dataset_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(), outputPath, "publication_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
createUpdateForResultDatasetWrite(
toupdatepublicationreresult.toJavaRDD(),
outputPath,
"publication_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath, "other_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
createUpdateForResultDatasetWrite(
toupdateotherresult.toJavaRDD(),
outputPath,
"other_update",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(), outputPath, "dataset",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
updateForDatasetDataset(
toupdatedatasetresult.toJavaRDD(),
dataset.toJavaRDD(),
outputPath,
"dataset",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(), outputPath, "otherresearchproduct",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
updateForOtherDataset(
toupdateotherresult.toJavaRDD(),
other.toJavaRDD(),
outputPath,
"otherresearchproduct",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(), outputPath, "software",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
updateForSoftwareDataset(
toupdatesoftwareresult.toJavaRDD(),
software.toJavaRDD(),
outputPath,
"software",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(), publication.toJavaRDD(), outputPath, "publication",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
//
updateForPublicationDataset(
toupdatepublicationreresult.toJavaRDD(),
publication.toJavaRDD(),
outputPath,
"publication",
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
communityIdList);
//
/*
JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"publication"))
.filter(p -> !(p == null))
.mapToPair(toPair())
.union(datasets
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"dataset"))
/*
JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"publication"))
.filter(p -> !(p == null))
.mapToPair(toPair())
)
.union(software
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"software"))
.filter(p -> !(p == null))
.mapToPair(toPair())
)
.union(other
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"otherresearchproduct"))
.filter(p -> !(p == null))
.mapToPair(toPair())
);
.union(datasets
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"dataset"))
.filter(p -> !(p == null))
.mapToPair(toPair())
)
.union(software
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"software"))
.filter(p -> !(p == null))
.mapToPair(toPair())
)
.union(other
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"otherresearchproduct"))
.filter(p -> !(p == null))
.mapToPair(toPair())
);
JavaPairRDD<String, TypedRow> to_add_result_communities = resultLinkedToCommunities.join(result_result).map(r -> r._2()._1().setSourceId(r._2()._2().getTargetId()))
.mapToPair(toPair());
JavaPairRDD<String, TypedRow> to_add_result_communities = resultLinkedToCommunities.join(result_result).map(r -> r._2()._1().setSourceId(r._2()._2().getTargetId()))
.mapToPair(toPair());
JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
//leftouterjoin result.to_add_result_communities (result = java pair rdd result) [left outer join perche' li voglio tutti anche quelli che non ho aggiornato]
//per quelli che matchano cercare nel risultato se i context da aggiungere sono gia' presenti. Se non ci sono aggiungerli, altrimenti nulla
*/
updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
//leftouterjoin result.to_add_result_communities (result = java pair rdd result) [left outer join perche' li voglio tutti anche quelli che non ho aggiornato]
//per quelli che matchano cercare nel risultato se i context da aggiungere sono gia' presenti. Se non ci sono aggiungerli, altrimenti nulla
*/
}
private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(SparkSession spark, String table){
String query = "SELECT target_id, collect_set(co.id) context_id " +
" FROM (SELECT t.id target_id, s.context source_context " +
" FROM context_software s " +
" JOIN " + table + " t " +
" ON s.target = t.id " +
" UNION ALL " +
" SELECT t.id target_id, d.context source_context " +
" FROM dataset_context d " +
" JOIN " + table + " t" +
" ON s.target = t.id " +
" UNION ALL " +
" SELECT t.id target_id, p.context source_context " +
" FROM publication_context p" +
" JOIN " + table +" t " +
" on p.target = t.id " +
" UNION ALL " +
" SELECT t.id target_id, o.context source_context " +
" FROM other_context o " +
" JOIN " + table + " t " +
" ON o.target = t.id) TMP " +
" LATERAL VIEW EXPLODE(source_context) MyT as co " +
" GROUP BY target_id" ;
private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
SparkSession spark, String table) {
String query =
"SELECT target_id, collect_set(co.id) context_id "
+ " FROM (SELECT t.id target_id, s.context source_context "
+ " FROM context_software s "
+ " JOIN "
+ table
+ " t "
+ " ON s.target = t.id "
+ " UNION ALL "
+ " SELECT t.id target_id, d.context source_context "
+ " FROM dataset_context d "
+ " JOIN "
+ table
+ " t"
+ " ON s.target = t.id "
+ " UNION ALL "
+ " SELECT t.id target_id, p.context source_context "
+ " FROM publication_context p"
+ " JOIN "
+ table
+ " t "
+ " on p.target = t.id "
+ " UNION ALL "
+ " SELECT t.id target_id, o.context source_context "
+ " FROM other_context o "
+ " JOIN "
+ table
+ " t "
+ " ON o.target = t.id) TMP "
+ " LATERAL VIEW EXPLODE(source_context) MyT as co "
+ " GROUP BY target_id";
return spark.sql(query);
}
private static JavaRDD<Result> createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
return toupdateresult.map(r -> {
List<Context> contextList = new ArrayList();
List<String> toAddContext = r.getList(1);
for (String cId : toAddContext) {
if (communityIdList.contains(cId)) {
Context newContext = new Context();
newContext.setId(cId);
newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
contextList.add(newContext);
}
private static JavaRDD<Result> createUpdateForResultDatasetWrite(
JavaRDD<Row> toupdateresult,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
return toupdateresult
.map(
r -> {
List<Context> contextList = new ArrayList();
List<String> toAddContext = r.getList(1);
for (String cId : toAddContext) {
if (communityIdList.contains(cId)) {
Context newContext = new Context();
newContext.setId(cId);
newContext.setDataInfo(
Arrays.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
class_id,
class_name)));
contextList.add(newContext);
}
}
}
if (contextList.size() > 0) {
Result ret = new Result();
ret.setId(r.getString(0));
ret.setContext(contextList);
return ret;
}
return null;
}).filter(r -> r != null);
if (contextList.size() > 0) {
Result ret = new Result();
ret.setId(r.getString(0));
ret.setContext(contextList);
return ret;
}
return null;
})
.filter(r -> r != null);
}
private static void updateForSoftwareDataset(JavaRDD<Row> toupdateresult, JavaRDD<Software> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
.map(r -> (Software) r)
.map(s -> new ObjectMapper().writeValueAsString(s))
.saveAsTextFile(outputPath + "/" + type);
private static void updateForSoftwareDataset(
JavaRDD<Row> toupdateresult,
JavaRDD<Software> result,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(
toupdateresult,
tmp,
outputPath,
type,
class_id,
class_name,
communityIdList)
.map(r -> (Software) r)
.map(s -> new ObjectMapper().writeValueAsString(s))
.saveAsTextFile(outputPath + "/" + type);
}
private static void updateForDatasetDataset(JavaRDD<Row> toupdateresult, JavaRDD<Dataset> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
.map( r-> (Dataset)r)
private static void updateForDatasetDataset(
JavaRDD<Row> toupdateresult,
JavaRDD<Dataset> result,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(
toupdateresult,
tmp,
outputPath,
type,
class_id,
class_name,
communityIdList)
.map(r -> (Dataset) r)
.map(d -> new ObjectMapper().writeValueAsString(d))
.saveAsTextFile(outputPath + "/" + type);
}
private static void updateForPublicationDataset(JavaRDD<Row> toupdateresult, JavaRDD<Publication> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
.map(r -> (Publication)r)
.map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath + "/" + type);
private static void updateForPublicationDataset(
JavaRDD<Row> toupdateresult,
JavaRDD<Publication> result,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(
toupdateresult,
tmp,
outputPath,
type,
class_id,
class_name,
communityIdList)
.map(r -> (Publication) r)
.map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath + "/" + type);
}
private static void updateForOtherDataset(JavaRDD<Row> toupdateresult, JavaRDD<OtherResearchProduct> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
.map( r -> (OtherResearchProduct)r)
.map( o -> new ObjectMapper().writeValueAsString(o))
.saveAsTextFile(outputPath + "/" + type);
private static void updateForOtherDataset(
JavaRDD<Row> toupdateresult,
JavaRDD<OtherResearchProduct> result,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
getUpdateForResultDataset(
toupdateresult,
tmp,
outputPath,
type,
class_id,
class_name,
communityIdList)
.map(r -> (OtherResearchProduct) r)
.map(o -> new ObjectMapper().writeValueAsString(o))
.saveAsTextFile(outputPath + "/" + type);
}
private static JavaRDD<Result> getUpdateForResultDataset(
JavaRDD<Row> toupdateresult,
JavaPairRDD<String, Result> result,
String outputPath,
String type,
String class_id,
String class_name,
List<String> communityIdList) {
return result.leftOuterJoin(
toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
.map(
c -> {
if (!c._2()._2().isPresent()) {
return c._2()._1();
}
private static JavaRDD<Result> getUpdateForResultDataset(JavaRDD<Row> toupdateresult, JavaPairRDD<String, Result> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
return result.leftOuterJoin(toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
.map(c -> {
if(! c._2()._2().isPresent()){
return c._2()._1();
}
List<Object> toAddContext = c._2()._2().get();
Set<String> context_set = new HashSet<>();
for(Object cId: toAddContext){
String id = (String)cId;
if (communityIdList.contains(id)){
context_set.add(id);
}
}
for (Context context: c._2()._1().getContext()){
if(context_set.contains(context)){
context_set.remove(context);
}
}
List<Context> contextList = context_set.stream().map(co -> {
Context newContext = new Context();
newContext.setId(co);
newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
return newContext;
}).collect(Collectors.toList());
if(contextList.size() > 0 ){
Result r = new Result();
r.setId(c._1());
r.setContext(contextList);
return r;
}
return null;
}).filter(r -> r != null);
// return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
// .join(result)
// .map(c -> {
// List<Object> toAddContext = c._2()._1();
// Set<String> context_set = new HashSet<>();
// for(Object cId: toAddContext){
// String id = (String)cId;
// if (communityIdList.contains(id)){
// context_set.add(id);
// }
// }
// for (Context context: c._2()._2().getContext()){
// if(context_set.contains(context)){
// context_set.remove(context);
// }
// }
//
// List<Context> contextList = context_set.stream().map(co -> {
// Context newContext = new Context();
// newContext.setId(co);
// newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
// return newContext;
//
// }).collect(Collectors.toList());
//
// if(contextList.size() > 0 ){
// Result r = new Result();
// r.setId(c._1());
// r.setContext(contextList);
// return r;
// }
// return null;
// })
// .filter(r -> r != null);
}
private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, List<String> communityList,
JavaRDD<Software> result, String class_id, String class_name) {
return result
.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
.map(c -> {
Software oaf = c._2()._1();
if (c._2()._2().isPresent()) {
HashSet<String> contexts = new HashSet<>(c._2()._2().get());
for (Context context : oaf.getContext()) {
if (contexts.contains(context.getId())){
if (!context.getDataInfo().stream().map(di -> di.getInferenceprovenance())
.collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
context.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name));
//community id already in the context of the result. Remove it from the set that has to be added
contexts.remove(context.getId());
List<Object> toAddContext = c._2()._2().get();
Set<String> context_set = new HashSet<>();
for (Object cId : toAddContext) {
String id = (String) cId;
if (communityIdList.contains(id)) {
context_set.add(id);
}
}
for (Context context : c._2()._1().getContext()) {
if (context_set.contains(context)) {
context_set.remove(context);
}
}
}
List<Context> cc = oaf.getContext();
for(String cId: contexts){
Context context = new Context();
context.setId(cId);
context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
cc.add(context);
}
oaf.setContext(cc);
List<Context> contextList =
context_set.stream()
.map(
co -> {
Context newContext = new Context();
newContext.setId(co);
newContext.setDataInfo(
Arrays.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
class_id,
class_name)));
return newContext;
})
.collect(Collectors.toList());
if (contextList.size() > 0) {
Result r = new Result();
r.setId(c._1());
r.setContext(contextList);
return r;
}
return null;
})
.filter(r -> r != null);
// return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
// .join(result)
// .map(c -> {
// List<Object> toAddContext = c._2()._1();
// Set<String> context_set = new HashSet<>();
// for(Object cId: toAddContext){
// String id = (String)cId;
// if (communityIdList.contains(id)){
// context_set.add(id);
// }
// }
// for (Context context: c._2()._2().getContext()){
// if(context_set.contains(context)){
// context_set.remove(context);
// }
// }
//
// List<Context> contextList = context_set.stream().map(co -> {
// Context newContext = new Context();
// newContext.setId(co);
//
// newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
// class_name)));
// return newContext;
//
// }).collect(Collectors.toList());
//
// if(contextList.size() > 0 ){
// Result r = new Result();
// r.setId(c._1());
// r.setContext(contextList);
// return r;
// }
// return null;
// })
// .filter(r -> r != null);
}
private static JavaRDD<Software> createUpdateForSoftwareDataset(
JavaRDD<Row> toupdateresult,
List<String> communityList,
JavaRDD<Software> result,
String class_id,
String class_name) {
return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
.leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
.map(
c -> {
Software oaf = c._2()._1();
if (c._2()._2().isPresent()) {
HashSet<String> contexts = new HashSet<>(c._2()._2().get());
for (Context context : oaf.getContext()) {
if (contexts.contains(context.getId())) {
if (!context.getDataInfo().stream()
.map(di -> di.getInferenceprovenance())
.collect(Collectors.toSet())
.contains(PROPAGATION_DATA_INFO_TYPE)) {
context.getDataInfo()
.add(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
class_id,
class_name));
// community id already in the context of the result.
// Remove it from the set that has to be added
contexts.remove(context.getId());
}
}
}
List<Context> cc = oaf.getContext();
for (String cId : contexts) {
Context context = new Context();
context.setId(cId);
context.setDataInfo(
Arrays.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
class_id,
class_name)));
cc.add(context);
}
oaf.setContext(cc);
}
return oaf;
});
}
private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
JavaRDD<Row> toupdateresult, List<String> communityList) {
return toupdateresult.mapToPair(
c -> {
List<String> contextList = new ArrayList<>();
List<String> contexts = c.getList(1);
for (String context : contexts) {
if (communityList.contains(context)) {
contextList.add(context);
}
}
return oaf;
return new Tuple2<>(c.getString(0), contextList);
});
}
private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult, List<String> communityList) {
return toupdateresult.mapToPair(c -> {
List<String> contextList = new ArrayList<>();
List<String> contexts = c.getList(1);
for (String context : contexts) {
if (communityList.contains(context)) {
contextList.add(context);
}
}
return new Tuple2<>(c.getString(0) ,contextList);
});
}
private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table){
String query = "SELECT relation.source, " + table +".context , relation.target " +
"FROM " + table +
" JOIN relation " +
"ON id = source" ;
private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
String query =
"SELECT relation.source, "
+ table
+ ".context , relation.target "
+ "FROM "
+ table
+ " JOIN relation "
+ "ON id = source";
return spark.sql(query);
}
private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
Set<String> result_communities = r.getContext()
.stream()
.map(c -> c.getId())
.collect(Collectors.toSet());
Set<String> result_communities =
r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
return true;
@ -419,44 +589,61 @@ public class SparkResultToCommunityThroughSemRelJob3 {
return false;
}
private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
private static void updateResult(
JavaPairRDD<String, Result> results,
JavaPairRDD<String, TypedRow> toupdateresult,
String outputPath,
String type) {
results.leftOuterJoin(toupdateresult)
.map(p -> {
Result r = p._2()._1();
if (p._2()._2().isPresent()){
Set<String> communityList = p._2()._2().get().getAccumulator();
for(Context c: r.getContext()){
if (communityList.contains(c.getId())){
//verify if the datainfo for this context contains propagation
if (!c.getDataInfo().stream().map(di -> di.getInferenceprovenance()).collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
c.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
//community id already in the context of the result. Remove it from the set that has to be added
communityList.remove(c.getId());
.map(
p -> {
Result r = p._2()._1();
if (p._2()._2().isPresent()) {
Set<String> communityList = p._2()._2().get().getAccumulator();
for (Context c : r.getContext()) {
if (communityList.contains(c.getId())) {
// verify if the datainfo for this context contains
// propagation
if (!c.getDataInfo().stream()
.map(di -> di.getInferenceprovenance())
.collect(Collectors.toSet())
.contains(PROPAGATION_DATA_INFO_TYPE)) {
c.getDataInfo()
.add(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
// community id already in the context of the result.
// Remove it from the set that has to be added
communityList.remove(c.getId());
}
}
}
List<Context> cc = r.getContext();
for (String cId : communityList) {
Context context = new Context();
context.setId(cId);
context.setDataInfo(
Arrays.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
cc.add(context);
}
r.setContext(cc);
}
}
List<Context> cc = r.getContext();
for(String cId: communityList){
Context context = new Context();
context.setId(cId);
context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
cc.add(context);
}
r.setContext(cc);
}
return r;
})
return r;
})
.map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath+"/"+type);
.saveAsTextFile(outputPath + "/" + type);
}
private static TypedRow getTypedRow(List<String> communityIdList, List<Context> context, String id, String type) {
Set<String> result_communities = context
.stream()
.map(c -> c.getId())
.collect(Collectors.toSet());
private static TypedRow getTypedRow(
List<String> communityIdList, List<Context> context, String id, String type) {
Set<String> result_communities =
context.stream().map(c -> c.getId()).collect(Collectors.toSet());
TypedRow tp = new TypedRow();
tp.setSourceId(id);
tp.setType(type);