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removed unuseful classes

This commit is contained in:
Miriam Baglioni 2020-04-23 12:59:43 +02:00
parent edb00db86a
commit 0e447add66
3 changed files with 0 additions and 2032 deletions
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690
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java
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@ -1,690 +0,0 @@
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;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
public class SparkResultToCommunityThroughSemRelJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
SparkResultToCommunityThroughSemRelJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
parser.parseArgument(args);
for (String key : parser.getObjectMap().keySet()) {
System.out.println(key + " = " + parser.get(key));
}
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final SparkSession spark =
SparkSession.builder()
.appName(SparkResultToCommunityThroughSemRelJob.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/resulttocommunityfromsemrel";
// final List<String> allowedsemrel =
// Arrays.asList(parser.get("allowedsemrels").split(";"));
final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
// final List<String> communityIdList =
// QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
final List<String> communityIdList =
QueryInformationSystem.getCommunityList(
"http://beta.services.openaire.eu:8280/is/services/isLookUp");
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
JavaRDD<Publication> all_publication_rdd =
sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, Publication.class))
.filter(p -> !p.getDataInfo().getDeletedbyinference())
.cache();
JavaRDD<Publication> publication_rdd =
all_publication_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
JavaRDD<Dataset> all_dataset_rdd =
sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, Dataset.class))
.filter(p -> !p.getDataInfo().getDeletedbyinference())
.cache();
JavaRDD<Dataset> dataset_rdd =
all_dataset_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
JavaRDD<OtherResearchProduct> all_orp_rdd =
sc.textFile(inputPath + "/otherresearchproduct")
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
.filter(p -> !p.getDataInfo().getDeletedbyinference())
.cache();
JavaRDD<OtherResearchProduct> orp_rdd =
all_orp_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
JavaRDD<Software> all_software_rdd =
sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, Software.class))
.filter(p -> !p.getDataInfo().getDeletedbyinference())
.cache();
JavaRDD<Software> software_rdd =
all_software_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
JavaRDD<Relation> relation_rdd =
sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class))
.filter(r -> !r.getDataInfo().getDeletedbyinference())
.filter(
r ->
allowedsemrel.contains(r.getRelClass())
&& RELATION_RESULTRESULT_REL_TYPE.equals(
r.getRelType()))
.cache();
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<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<Relation> relation =
spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
publication.createOrReplaceTempView("publication");
relation.createOrReplaceTempView("relation");
dataset.createOrReplaceTempView("dataset");
software.createOrReplaceTempView("software");
other.createOrReplaceTempView("other");
// org.apache.spark.sql.Dataset<Row> publication_context = getContext(spark,
// "publication");
// publication_context.createOrReplaceTempView("publication_context");
org.apache.spark.sql.Dataset<Row> publication_context =
spark.sql(
"SELECT relation.source, "
+ "publication.context , relation.target "
+ "FROM publication "
+ " JOIN relation "
+ "ON id = source");
org.apache.spark.sql.Dataset<Row> dataset_context = getContext(spark, "dataset");
dataset_context.createOrReplaceTempView("dataset_context");
org.apache.spark.sql.Dataset<Row> software_context = getContext(spark, "software");
software_context.createOrReplaceTempView("software_context");
org.apache.spark.sql.Dataset<Row> other_context = getContext(spark, "other");
other_context.createOrReplaceTempView("other_context");
publication =
spark.createDataset(all_publication_rdd.rdd(), Encoders.bean(Publication.class));
publication.createOrReplaceTempView("publication");
dataset = spark.createDataset(all_dataset_rdd.rdd(), Encoders.bean(Dataset.class));
dataset.createOrReplaceTempView("dataset");
other = spark.createDataset(all_orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
other.createOrReplaceTempView("other");
software = spark.createDataset(all_software_rdd.rdd(), Encoders.bean(Software.class));
software.createOrReplaceTempView("software");
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> toupdatepublicationreresult =
getUpdateCommunitiesForTable(spark, "publication");
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(
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(
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);
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);
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"))
.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, 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
*/
}
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);
}
}
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 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 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();
}
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<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 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";
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());
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
return true;
}
}
return false;
}
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());
}
}
}
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;
})
.map(p -> new ObjectMapper().writeValueAsString(p))
.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());
TypedRow tp = new TypedRow();
tp.setSourceId(id);
tp.setType(type);
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
tp.add(communityId);
}
}
if (tp.getAccumulator() != null) {
return tp;
}
return null;
}
}

682
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob2.java
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@ -1,682 +0,0 @@
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;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
public class SparkResultToCommunityThroughSemRelJob2 {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
SparkResultToCommunityThroughSemRelJob2.class.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_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(SparkResultToCommunityThroughSemRelJob2.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/resulttocommunityfromsemrel";
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
// final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
final List<String> communityIdList =
QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
// final List<String> communityIdList =
// QueryInformationSystem.getCommunityList("http://beta.services.openaire.eu:8280/is/services/isLookUp");
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
JavaRDD<Publication> publication_rdd =
sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, Publication.class));
System.out.println(publication_rdd.count());
// 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<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));
System.out.println(relation_rdd.count());
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
// .filter(r -> allowedsemrel.contains(r.getRelClass()) &&
// RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType())).cache();
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<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<Relation> relation =
// spark.createDataset(relation_rdd.rdd(),
// Encoders.bean(Relation.class));
publication.createOrReplaceTempView("publication");
relation.createOrReplaceTempView("relation");
// relation.createOrReplaceTempView("relation");
// dataset.createOrReplaceTempView("dataset");
// software.createOrReplaceTempView("software");
// other.createOrReplaceTempView("other");
String communitylist = getConstraintList(" co.id = '", communityIdList);
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 and (relClass = 'isSupplementedBy' OR relClass = 'isSupplementTo')) r "
+ "ON p.id = r.source";
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";
org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
System.out.println(toupdatepublicationreresult.count());
toupdatepublicationreresult
.toJavaRDD()
.map(
r -> {
TypedRow tp = new TypedRow();
tp.setSourceId(r.getString(0));
r.getList(1).stream().forEach(c -> tp.add((String) c));
return tp;
})
.map(tr -> new ObjectMapper().writeValueAsString(tr))
.saveAsTextFile(outputPath + "/community2semrelonpublication");
// toupdatepublicationreresult.toJavaRDD().flatMap(c -> {
//
// String source = c.getString(0);
// List<Relation> relation_list = new ArrayList<>();
// c.getList(1).stream()
// .forEach(res -> {
// Relation r = new Relation();
// r.setSource(source);
// r.setTarget((String)res);
// r.setRelClass("produces");
// relation_list.add(r);
// r = new Relation();
// r.setSource((String)res);
// r.setTarget(source);
// r.setRelClass("isProducedBy");
// relation_list.add(r);
// });
// return relation_list.iterator();
// }).map(tr -> new ObjectMapper().writeValueAsString(tr))
// .saveAsTextFile(outputPath + "/community2semrel");
//
// 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> toupdatepublicationreresult =
// getUpdateCommunitiesForTable(spark, "publication");
// 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(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(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);
//
// 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);
//
// 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"))
.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, 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
*/
}
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);
}
}
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 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 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();
}
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<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 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";
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());
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
return true;
}
}
return false;
}
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());
}
}
}
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;
})
.map(p -> new ObjectMapper().writeValueAsString(p))
.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());
TypedRow tp = new TypedRow();
tp.setSourceId(id);
tp.setType(type);
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
tp.add(communityId);
}
}
if (tp.getAccumulator() != null) {
return tp;
}
return null;
}
}

660
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob3.java
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@ -1,660 +0,0 @@
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;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
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_communitytoresult_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(SparkResultToCommunityThroughSemRelJob3.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/resulttocommunityfromsemrel";
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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<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<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));
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<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));
publication.createOrReplaceTempView("publication");
relation.createOrReplaceTempView("relation");
dataset.createOrReplaceTempView("dataset");
software.createOrReplaceTempView("software");
other.createOrReplaceTempView("other");
String communitylist = getConstraintList(" co.id = '", communityIdList);
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";
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";
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");
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(
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);
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);
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);
//
/*
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"))
.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, 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
*/
}
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);
}
}
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 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 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();
}
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<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 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";
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());
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
return true;
}
}
return false;
}
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());
}
}
}
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;
})
.map(p -> new ObjectMapper().writeValueAsString(p))
.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());
TypedRow tp = new TypedRow();
tp.setSourceId(id);
tp.setType(type);
for (String communityId : result_communities) {
if (communityIdList.contains(communityId)) {
tp.add(communityId);
}
}
if (tp.getAccumulator() != null) {
return tp;
}
return null;
}
}