forked from D-Net/dnet-hadoop
new implementation that exploits prepared information (the list of possible updates: resultId - possible list of orcid to be added
This commit is contained in:
parent
f077f22f73
commit
d6cd700a32
|
|
@ -9,131 +9,115 @@ import org.apache.hadoop.fs.FileSystem;
|
|||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
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 org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
|
||||
public class SparkOrcidToResultFromSemRelJob3 {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob3.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public class SparkOrcidToResultFromSemRelJob2 {
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
jsonConfiguration);
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String possibleUpdates = parser.get("possibleUpdatesPath");
|
||||
log.info("possibleUpdatesPath: {}", possibleUpdates);
|
||||
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
|
||||
log.info("resultType: {}", resultType);
|
||||
|
||||
final Boolean saveGraph = Optional
|
||||
.ofNullable(parser.get("saveGraph"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("saveGraph: {}", saveGraph);
|
||||
|
||||
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkOrcidToResultFromSemRelJob2.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/orcidtoresult";
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
|
||||
boolean writeUpdate = TRUE.equals(parser.get("writeUpdate"));
|
||||
boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
|
||||
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
|
||||
Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
|
||||
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
|
||||
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
|
||||
|
||||
|
||||
relation.createOrReplaceTempView("relation");
|
||||
String query = "Select source, target " +
|
||||
"from relation " +
|
||||
"where datainfo.deletedbyinference = false " + getConstraintList(" relclass = '" , allowedsemrel);
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> result_result = spark.sql(query);
|
||||
|
||||
publication.createOrReplaceTempView("publication");
|
||||
org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid = getResultWithOrcid("publication", spark)
|
||||
.as(Encoders.bean(ResultWithOrcid.class));
|
||||
|
||||
dataset.createOrReplaceTempView("dataset");
|
||||
org.apache.spark.sql.Dataset<ResultWithOrcid> dats_with_orcid = getResultWithOrcid("dataset", spark)
|
||||
.as(Encoders.bean(ResultWithOrcid.class));
|
||||
|
||||
other.createOrReplaceTempView("orp");
|
||||
org.apache.spark.sql.Dataset<ResultWithOrcid> orp_with_orcid = getResultWithOrcid("orp", spark)
|
||||
.as(Encoders.bean(ResultWithOrcid.class));
|
||||
|
||||
dataset.createOrReplaceTempView("software");
|
||||
org.apache.spark.sql.Dataset<ResultWithOrcid> software_with_orcid = getResultWithOrcid("software", spark)
|
||||
.as(Encoders.bean(ResultWithOrcid.class));
|
||||
//get the results having at least one author pid we are interested in
|
||||
|
||||
//target of the relation from at least one source with orcid.
|
||||
//the set of authors contains all those that have orcid and are related to target
|
||||
//from any source with allowed semantic relationship
|
||||
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_pubs = getTargetAutoritativeAuthorList(pubs_with_orcid);
|
||||
|
||||
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_dats = getTargetAutoritativeAuthorList(dats_with_orcid);
|
||||
|
||||
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_orp = getTargetAutoritativeAuthorList(orp_with_orcid);
|
||||
|
||||
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_sw = getTargetAutoritativeAuthorList(software_with_orcid);
|
||||
|
||||
if(writeUpdate){
|
||||
target_authorlist_from_dats.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/" + "update_dats");
|
||||
target_authorlist_from_pubs.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/" + "update_pubs");
|
||||
target_authorlist_from_orp.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/" + "update_orp");
|
||||
target_authorlist_from_sw.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath + "/" + "update_sw");
|
||||
}
|
||||
|
||||
if(saveGraph){
|
||||
sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class))
|
||||
.mapToPair(p -> new Tuple2<>(p.getId(),p))
|
||||
.leftOuterJoin(target_authorlist_from_pubs)
|
||||
.map(c -> {
|
||||
Result r = c._2()._1();
|
||||
if(!c._2()._2().isPresent()){
|
||||
return r;
|
||||
}
|
||||
List<eu.dnetlib.dhp.schema.oaf.Author> toenrich_author = r.getAuthor();
|
||||
List<AutoritativeAuthor> autoritativeAuthors = c._2()._2().get();
|
||||
for(eu.dnetlib.dhp.schema.oaf.Author author: toenrich_author){
|
||||
if (!containsAllowedPid(author)){
|
||||
enrichAuthor(author, autoritativeAuthors);
|
||||
}
|
||||
}
|
||||
return r;
|
||||
});
|
||||
|
||||
}
|
||||
runWithSparkHiveSession(conf, isSparkSessionManaged,
|
||||
spark -> {
|
||||
if(isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
if(saveGraph)
|
||||
execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
|
||||
|
||||
private static <R extends Result> void execPropagation(SparkSession spark, String possibleUpdatesPath, String inputPath,
|
||||
String outputPath, Class<R> resultClazz ) {
|
||||
|
||||
//read possible updates (resultId and list of possible orcid to add
|
||||
Dataset<ResultOrcidList> possible_updates = readAssocResultOrcidList(spark, possibleUpdatesPath);
|
||||
//read the result we have been considering
|
||||
Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
|
||||
//make join result left_outer with possible updates
|
||||
|
||||
result.joinWith(possible_updates, result.col("id").equalTo(possible_updates.col("resultId")),
|
||||
"left_outer")
|
||||
.map(value -> {
|
||||
R ret = value._1();
|
||||
Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
|
||||
if(rol.isPresent()) {
|
||||
List<Author> toenrich_author = ret.getAuthor();
|
||||
List<AutoritativeAuthor> autoritativeAuthors = rol.get().getAuthorList();
|
||||
for(Author author: toenrich_author){
|
||||
if (!containsAllowedPid(author)){
|
||||
enrichAuthor(author, autoritativeAuthors);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return ret;
|
||||
}, Encoders.bean(resultClazz))
|
||||
.toJSON()
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.text(outputPath);
|
||||
|
||||
|
||||
}
|
||||
|
||||
private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
|
||||
return spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
|
||||
}
|
||||
|
||||
private static void enrichAuthor(Author a, List<AutoritativeAuthor> au){
|
||||
for (AutoritativeAuthor aa: au){
|
||||
if(enrichAuthor(aa, a)){
|
||||
return;
|
||||
|
|
@ -142,77 +126,9 @@ public class SparkOrcidToResultFromSemRelJob2 {
|
|||
|
||||
}
|
||||
|
||||
// private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
|
||||
// return pubs_with_orcid
|
||||
// .toJavaRDD()
|
||||
// .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
|
||||
// .join(result_result.toJavaRDD().mapToPair(rel -> new Tuple2<>(rel.getString(0), rel.getString(1))))
|
||||
// .mapToPair(c -> new Tuple2<>(c._2._2(), c._2()._1()))
|
||||
// .reduceByKey((a, b) -> {
|
||||
// if(a == null){
|
||||
// return b;
|
||||
// }
|
||||
// if(b==null){
|
||||
// return a;
|
||||
// }
|
||||
//
|
||||
// Set<String> authSet = new HashSet<>();
|
||||
// a.stream().forEach(au -> authSet.add(au.getOrcid()));
|
||||
//
|
||||
// b.stream().forEach(au -> {
|
||||
// if (!authSet.contains(au.getOrcid())) {
|
||||
// a.add(au);
|
||||
// }
|
||||
// }
|
||||
// );
|
||||
// return a;
|
||||
// });
|
||||
// }
|
||||
private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList( org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
|
||||
return pubs_with_orcid
|
||||
.toJavaRDD()
|
||||
.mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
|
||||
.reduceByKey((a, b) -> {
|
||||
if(a == null){
|
||||
return b;
|
||||
}
|
||||
if(b==null){
|
||||
return a;
|
||||
}
|
||||
Set<String> authSet = new HashSet<>();
|
||||
a.stream().forEach(au -> authSet.add(au.getOrcid()));
|
||||
|
||||
b.stream().forEach(au -> {
|
||||
if (!authSet.contains(au.getOrcid())) {
|
||||
a.add(au);
|
||||
}
|
||||
}
|
||||
);
|
||||
return a;
|
||||
});
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getResultWithOrcid(String table, SparkSession spark){
|
||||
String query = " select target, author " +
|
||||
" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
|
||||
" from ( " +
|
||||
" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
|
||||
" from " + table +
|
||||
" lateral view explode (author) a as MyT " +
|
||||
" lateral view explode (MyT.pid) p as MyP " +
|
||||
" where MyP.qualifier.classid = 'ORCID') tmp " +
|
||||
" group by id) r_t " +
|
||||
" join (" +
|
||||
" select source, target " +
|
||||
" from relation " +
|
||||
" where datainfo.deletedbyinference = false and (relclass = 'isSupplementedBy' or relclass = 'isSupplementTo') rel_rel " +
|
||||
" on source = id";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
|
||||
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
|
||||
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) {
|
||||
boolean toaddpid = false;
|
||||
|
||||
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
|
||||
|
|
@ -252,100 +168,9 @@ private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritati
|
|||
}
|
||||
|
||||
|
||||
// private static List<Author> enrichAuthors(List<Author> autoritative_authors, List<Author> to_enrich_authors, boolean filter){
|
||||
//// List<Author> autoritative_authors = p._2()._2().get().getAuthors();
|
||||
//// List<Author> to_enrich_authors = r.getAuthor();
|
||||
//
|
||||
// return to_enrich_authors
|
||||
// .stream()
|
||||
// .map(a -> {
|
||||
// if (filter) {
|
||||
// if (containsAllowedPid(a)) {
|
||||
// return a;
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// List<Author> lst = autoritative_authors.stream()
|
||||
// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||
// if (lst.size() == 0) {
|
||||
// return a;
|
||||
// }
|
||||
// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||
//
|
||||
// }).collect(Collectors.toList());
|
||||
// }
|
||||
//
|
||||
// private static void writeResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
|
||||
// String outputPath, String type) {
|
||||
//
|
||||
// results.join(toupdateresult)
|
||||
// .map(p -> {
|
||||
// Result r = p._2()._1();
|
||||
//
|
||||
// List<Author> autoritative_authors = p._2()._2().getAuthors();
|
||||
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
||||
//
|
||||
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, false));
|
||||
//// .stream()
|
||||
//// .map(a -> {
|
||||
//// if(filter) {
|
||||
//// if (containsAllowedPid(a)) {
|
||||
//// return a;
|
||||
//// }
|
||||
//// }
|
||||
////
|
||||
//// List<Author> lst = autoritative_authors.stream()
|
||||
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||
//// if(lst.size() == 0){
|
||||
//// return a;
|
||||
//// }
|
||||
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||
////
|
||||
//// }).collect(Collectors.toList()));
|
||||
//
|
||||
// return r;
|
||||
// })
|
||||
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
// .saveAsTextFile(outputPath + "/" + type + "_update");
|
||||
// }
|
||||
|
||||
|
||||
// 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()){
|
||||
// List<AutoritativeAuthor> autoritative_authors = p._2()._2().get().getAuthors();
|
||||
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
||||
//
|
||||
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, true));
|
||||
//// .stream()
|
||||
//// .map(a -> {
|
||||
//// if(filter) {
|
||||
//// if (containsAllowedPid(a)) {
|
||||
//// return a;
|
||||
//// }
|
||||
//// }
|
||||
////
|
||||
//// List<Author> lst = autoritative_authors.stream()
|
||||
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||
//// if(lst.size() == 0){
|
||||
//// return a;
|
||||
//// }
|
||||
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||
////
|
||||
//// }).collect(Collectors.toList()));
|
||||
// }
|
||||
// return r;
|
||||
// })
|
||||
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
// .saveAsTextFile(outputPath+"/"+type);
|
||||
// }
|
||||
|
||||
|
||||
|
||||
private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a) {
|
||||
private static boolean containsAllowedPid(Author a) {
|
||||
for (StructuredProperty pid : a.getPid()) {
|
||||
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
||||
return true;
|
||||
|
|
@ -355,44 +180,3 @@ private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritati
|
|||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
|
||||
ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
|
||||
boolean updated = false;
|
||||
|
||||
for (FieldTypeProtos.Author a: author_list){
|
||||
FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
|
||||
if(author != null){
|
||||
updated = true;
|
||||
metadataBuilder.addAuthor(author);
|
||||
}else{
|
||||
metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
|
||||
}
|
||||
}
|
||||
if(updated)
|
||||
return metadataBuilder;
|
||||
return null;
|
||||
}
|
||||
private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
|
||||
if(containsOrcid(a.getPidList()))
|
||||
return null;
|
||||
for(FieldTypeProtos.Author autoritative_author : author_list) {
|
||||
if (equals(autoritative_author, a)) {
|
||||
if(!containsOrcid(a.getPidList()))
|
||||
return update(a, autoritative_author);
|
||||
}
|
||||
}
|
||||
return null;
|
||||
|
||||
}
|
||||
|
||||
private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
|
||||
if(pidList == null)
|
||||
return false;
|
||||
return pidList
|
||||
.stream()
|
||||
.filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
|
||||
.collect(Collectors.toList()).size() > 0;
|
||||
}
|
||||
*/
|
||||
Loading…
Reference in New Issue