removed unuseful classes

This commit is contained in:
Miriam Baglioni 2020-04-16 16:11:44 +02:00
parent 5e72a51f11
commit 4d89f3dfed
2 changed files with 0 additions and 710 deletions

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@ -1,312 +0,0 @@
package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.TypedRow;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Author;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
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.SparkSession;
import scala.Tuple2;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.PropagationConstant.*;
public class SparkOrcidToResultFromSemRelJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkOrcidToResultFromSemRelJob.class.getSimpleName())
.master(parser.get("master"))
.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()));
JavaRDD<Relation> relations = sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class)).cache();
JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
JavaRDD<Publication> publications = sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, Publication.class));
JavaRDD<Dataset> datasets = sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, Dataset.class));
JavaRDD<Software> software = sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, Software.class));
JavaRDD<OtherResearchProduct> other = sc.textFile(inputPath + "/otherresearchproduct")
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
//get the results having at least one author pid we are interested in
JavaPairRDD<String, TypedRow> resultswithorcid = publications.map(p -> getTypedRow(p))
.filter(p -> !(p == null))
.mapToPair(toPair())
.union(datasets.map(p -> getTypedRow(p))
.filter(p -> !(p == null))
.mapToPair(toPair()))
.union(software.map(p -> getTypedRow(p))
.filter(p -> !(p == null))
.mapToPair(toPair()))
.union(other.map(p -> getTypedRow(p))
.filter(p -> !(p == null))
.mapToPair(toPair()));
JavaPairRDD<String, TypedRow> to_add_orcid_to_result = resultswithorcid.join(result_result)
.map(p -> p._2()._1().setSourceId(p._2()._2().getTargetId())) //associate the pid of the result (target) which should get the orcid to the typed row containing the authors with the orcid from the result(source)
.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));
if(writeUpdate){
writeResult(pubs, to_add_orcid_to_result, outputPath, "publication");
writeResult(dss, to_add_orcid_to_result, outputPath, "dataset");
writeResult(sfw, to_add_orcid_to_result, outputPath, "software");
writeResult(orp, to_add_orcid_to_result, outputPath, "otherresearchproduct");
}
if (saveGraph){
updateResult(pubs, to_add_orcid_to_result, outputPath, "publication");
updateResult(dss, to_add_orcid_to_result, outputPath, "dataset");
updateResult(sfw, to_add_orcid_to_result, outputPath, "software");
updateResult(orp, to_add_orcid_to_result, outputPath, "otherresearchproduct");
}
}
public static eu.dnetlib.dhp.schema.oaf.Author enrichAutor(eu.dnetlib.dhp.schema.oaf.Author autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
boolean toaddpid = false;
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
if (StringUtils.isNoneEmpty(author.getSurname())) {
if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
//have the same surname. Check the name
if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
if (StringUtils.isNoneEmpty(author.getName())) {
if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
toaddpid = true;
}
//they could be differently written (i.e. only the initials of the name in one of the two
if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
toaddpid = true;
}
}
}
}
}
}
if (toaddpid){
StructuredProperty pid = new StructuredProperty();
for(StructuredProperty sp : autoritative_author.getPid()){
if (PROPAGATION_AUTHOR_PID.equals(sp.getQualifier().getClassid())){
pid.setValue(sp.getValue());
pid.setQualifier(getQualifier(sp.getQualifier().getClassid(),sp.getQualifier().getClassname() ));
pid.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
if(author.getPid() == null){
author.setPid(Arrays.asList(pid));
}else{
author.getPid().add(pid);
}
}
}
return author;
}
return null;
}
private static List<eu.dnetlib.dhp.schema.oaf.Author> enrichAutors(List<eu.dnetlib.dhp.schema.oaf.Author> autoritative_authors,
List<eu.dnetlib.dhp.schema.oaf.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<eu.dnetlib.dhp.schema.oaf.Author> lst = autoritative_authors.stream()
.map(aa -> enrichAutor(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<eu.dnetlib.dhp.schema.oaf.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 -> enrichAutor(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<eu.dnetlib.dhp.schema.oaf.Author> 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 -> enrichAutor(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 TypedRow getTypedRow(Result p) {
TypedRow tp = new TypedRow();
tp.setSourceId(p.getId());
List<Author> authorList = p.getAuthor()
.stream()
.map(a -> {
if (a.getPid().stream().map(pid -> {
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
return a;
}
return null;
}).filter(aut -> !(aut == null)).collect(Collectors.toList()).size() > 0){
return a;
}
return null;
}).filter(a -> !(a == null)).collect(Collectors.toList());
tp.setAuthors(authorList);
if(authorList.size() > 0){
return tp;
}
return null;
}
private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a){
return (a.getPid().stream().map(pid -> {
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
return true;
}
return false;
}).filter(aut -> (aut == true)).collect(Collectors.toList()).size()) > 0;
}
}
/*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;
}
*/

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
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 scala.Tuple2;
import java.util.*;
import static eu.dnetlib.dhp.PropagationConstant.*;
public class SparkOrcidToResultFromSemRelJob2 {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_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(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<ResultOrcidList> pubs_with_orcid = getResultWithOrcid("publication", spark)
.as(Encoders.bean(ResultOrcidList.class));
dataset.createOrReplaceTempView("dataset");
org.apache.spark.sql.Dataset<ResultOrcidList> dats_with_orcid = getResultWithOrcid("dataset", spark)
.as(Encoders.bean(ResultOrcidList.class));
other.createOrReplaceTempView("orp");
org.apache.spark.sql.Dataset<ResultOrcidList> orp_with_orcid = getResultWithOrcid("orp", spark)
.as(Encoders.bean(ResultOrcidList.class));
dataset.createOrReplaceTempView("software");
org.apache.spark.sql.Dataset<ResultOrcidList> software_with_orcid = getResultWithOrcid("software", spark)
.as(Encoders.bean(ResultOrcidList.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;
});
}
}
private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
for (AutoritativeAuthor aa: au){
if(enrichAuthor(aa, a)){
return;
}
}
}
// private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultOrcidList> 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<ResultOrcidList> pubs_with_orcid) {
return pubs_with_orcid
.toJavaRDD()
.mapToPair(p -> new Tuple2<>(p.getResultId(), 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) {
boolean toaddpid = false;
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
if (StringUtils.isNoneEmpty(author.getSurname())) {
if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
//have the same surname. Check the name
if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
if (StringUtils.isNoneEmpty(author.getName())) {
if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
toaddpid = true;
}
//they could be differently written (i.e. only the initials of the name in one of the two
if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
toaddpid = true;
}
}
}
}
}
}
if (toaddpid){
StructuredProperty pid = new StructuredProperty();
String aa_pid = autoritative_author.getOrcid();
pid.setValue(aa_pid);
pid.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID ));
pid.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
if(author.getPid() == null){
author.setPid(Arrays.asList(pid));
}else{
author.getPid().add(pid);
}
}
return toaddpid;
}
// 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) {
for (StructuredProperty pid : a.getPid()) {
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
return true;
}
}
return false;
}
}
/*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;
}
*/