diff --git a/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 3632cf745..adc92aa75 100644 --- a/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -3,19 +3,26 @@ 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.Relation; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.Text; 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.api.java.function.Function; +import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.SparkSession; +import scala.Tuple2; import java.io.File; import java.util.Arrays; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; +import java.util.stream.Stream; -import static eu.dnetlib.dhp.PropagationConstant.getResultResultSemRel; +import static eu.dnetlib.dhp.PropagationConstant.*; public class SparkOrcidToResultFromSemRelJob { public static void main(String[] args) throws Exception { @@ -46,78 +53,198 @@ public class SparkOrcidToResultFromSemRelJob { .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache(); JavaPairRDD result_result = getResultResultSemRel(allowedsemrel, relations); - } -} -/* -public class PropagationOrcidToResultMapper extends TableMapper { - private static final Log log = LogFactory.getLog(PropagationOrcidToResultMapper.class); // NOPMD by marko on 11/24/08 5:02 PM - private Text valueOut; - private ImmutableBytesWritable keyOut; - private String[] sem_rels; - private String trust; - @Override - protected void setup(final Context context) throws IOException, InterruptedException { - super.setup(context); - valueOut = new Text(); - keyOut = new ImmutableBytesWritable(); + JavaRDD publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class) + .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class)); + JavaRDD datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class) + .map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class)); + JavaRDD software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class) + .map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class)); + JavaRDD other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class) + .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class)); - sem_rels = context.getConfiguration().getStrings("propagatetoorcid.semanticrelations", DEFAULT_RESULT_RELATION_SET); - trust = context.getConfiguration().get("propagatetoorcid.trust","0.85"); + //get the results having at least one author pid we are interested in + JavaPairRDD 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 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 pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p)); + JavaPairRDD dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p)); + JavaPairRDD sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p)); + JavaPairRDD orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p)); + + 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"); } - @Override - protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException { - final TypeProtos.Type type = OafRowKeyDecoder.decode(keyIn.copyBytes()).getType(); - final OafProtos.OafEntity entity = getEntity(value, type);//getEntity already verified that it is not delByInference + private static Author enrichAutor(Author autoritative_author, Author author) { + boolean toaddpid = false; - if (entity != null) { + if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) { + if (StringUtils.isNoneEmpty(author.getSurname())) { + if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) { - if (type == TypeProtos.Type.result){ - Set result_result = new HashSet<>(); - //verifico se il risultato ha una relazione semantica verso uno o piu' risultati. - //per ogni risultato linkato con issupplementto o issupplementedby emetto: - // id risultato linkato come chiave, - // id risultato oggetto del mapping e lista degli autori del risultato oggetto del mapper come value - for(String sem : sem_rels){ - result_result.addAll(getRelationTarget(value, sem, context, COUNTER_PROPAGATION)); - } - if(!result_result.isEmpty()){ - List authorlist = getAuthorList(entity.getResult().getMetadata().getAuthorList()); - Emit e = new Emit(); - e.setId(Bytes.toString(keyIn.get())); - e.setAuthor_list(authorlist); - valueOut.set(Value.newInstance(new Gson().toJson(e, Emit.class), - trust, - Type.fromsemrel).toJson()); - for (String result: result_result){ - keyOut.set(Bytes.toBytes(result)); - context.write(keyOut,valueOut); - context.getCounter(COUNTER_PROPAGATION,"emit for sem_rel").increment(1); + //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; + } + } } - - //emetto anche id dell'oggetto del mapper come chiave e lista degli autori come valore - e.setId(keyIn.toString()); - e.setAuthor_list(authorlist); - valueOut.set(Value.newInstance(new Gson().toJson(e, Emit.class), trust, Type.fromresult).toJson()); - context.write(keyIn, valueOut); - context.getCounter(COUNTER_PROPAGATION,"emit for result with orcid").increment(1); - } } - } - } - - private List getAuthorList(List author_list){ - - return author_list.stream().map(a -> new JsonFormat().printToString(a)).collect(Collectors.toList()); - + 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 void updateResult(JavaPairRDD results, JavaPairRDD toupdateresult, String outputPath, String type) { + results.leftOuterJoin(toupdateresult) + .map(p -> { + Result r = p._2()._1(); + if (p._2()._2().isPresent()){ + List autoritative_authors = p._2()._2().get().getAuthors(); + List to_enrich_authors = r.getAuthor(); + //.stream().filter(a -> !containsAllowedPid(a)) + //.collect(Collectors.toList()); + + r.setAuthor(to_enrich_authors + .stream() + .map(a -> { + if (containsAllowedPid(a)) { + return a; + } + + List 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 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(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; + } + } - */ \ No newline at end of file + + +/*private ResultProtos.Result.Metadata.Builder searchMatch(List 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 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 pidList){ + if(pidList == null) + return false; + return pidList + .stream() + .filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID)) + .collect(Collectors.toList()).size() > 0; + } + */ \ No newline at end of file