forked from D-Net/dnet-hadoop
New propagation of ORCID to result exploiting the semantic relation connecting them. R has author with orcid o, R is bounf by strong semantic relationship with R1 that has the same author withouth orcid, then o is also associated to the author in R1
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@ -3,19 +3,26 @@ package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.TypedRow;
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import eu.dnetlib.dhp.TypedRow;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.io.File;
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import java.io.File;
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import java.util.Arrays;
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import java.util.Arrays;
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import java.util.List;
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import java.util.List;
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import java.util.Set;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import static eu.dnetlib.dhp.PropagationConstant.getResultResultSemRel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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public class SparkOrcidToResultFromSemRelJob {
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public class SparkOrcidToResultFromSemRelJob {
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public static void main(String[] args) throws Exception {
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public static void main(String[] args) throws Exception {
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@ -46,78 +53,198 @@ public class SparkOrcidToResultFromSemRelJob {
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache();
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache();
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JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
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JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
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}
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}
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/*
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public class PropagationOrcidToResultMapper extends TableMapper<ImmutableBytesWritable, Text> {
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private static final Log log = LogFactory.getLog(PropagationOrcidToResultMapper.class); // NOPMD by marko on 11/24/08 5:02 PM
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private Text valueOut;
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private ImmutableBytesWritable keyOut;
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private String[] sem_rels;
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private String trust;
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@Override
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JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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protected void setup(final Context context) throws IOException, InterruptedException {
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class));
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super.setup(context);
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JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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valueOut = new Text();
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class));
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keyOut = new ImmutableBytesWritable();
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JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class));
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JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class));
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sem_rels = context.getConfiguration().getStrings("propagatetoorcid.semanticrelations", DEFAULT_RESULT_RELATION_SET);
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//get the results having at least one author pid we are interested in
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trust = context.getConfiguration().get("propagatetoorcid.trust","0.85");
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JavaPairRDD<String, TypedRow> resultswithorcid = publications.map(p -> getTypedRow(p))
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.filter(p -> !(p == null))
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}
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.mapToPair(toPair())
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.union(datasets.map(p -> getTypedRow(p))
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@Override
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.filter(p -> !(p == null))
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protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {
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.mapToPair(toPair()))
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final TypeProtos.Type type = OafRowKeyDecoder.decode(keyIn.copyBytes()).getType();
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.union(software.map(p -> getTypedRow(p))
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final OafProtos.OafEntity entity = getEntity(value, type);//getEntity already verified that it is not delByInference
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.filter(p -> !(p == null))
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.mapToPair(toPair()))
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.union(other.map(p -> getTypedRow(p))
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.filter(p -> !(p == null))
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.mapToPair(toPair()));
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if (entity != null) {
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JavaPairRDD<String, TypedRow> to_add_orcid_to_result = resultswithorcid.join(result_result)
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.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)
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.mapToPair(toPair());
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if (type == TypeProtos.Type.result){
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JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
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Set<String> result_result = new HashSet<>();
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JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
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//verifico se il risultato ha una relazione semantica verso uno o piu' risultati.
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JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
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//per ogni risultato linkato con issupplementto o issupplementedby emetto:
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JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
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// id risultato linkato come chiave,
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// id risultato oggetto del mapping e lista degli autori del risultato oggetto del mapper come value
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for(String sem : sem_rels){
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result_result.addAll(getRelationTarget(value, sem, context, COUNTER_PROPAGATION));
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}
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if(!result_result.isEmpty()){
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List<String> authorlist = getAuthorList(entity.getResult().getMetadata().getAuthorList());
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Emit e = new Emit();
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e.setId(Bytes.toString(keyIn.get()));
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e.setAuthor_list(authorlist);
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valueOut.set(Value.newInstance(new Gson().toJson(e, Emit.class),
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trust,
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Type.fromsemrel).toJson());
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for (String result: result_result){
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keyOut.set(Bytes.toBytes(result));
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context.write(keyOut,valueOut);
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context.getCounter(COUNTER_PROPAGATION,"emit for sem_rel").increment(1);
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}
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//emetto anche id dell'oggetto del mapper come chiave e lista degli autori come valore
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updateResult(pubs, to_add_orcid_to_result, outputPath, "publication");
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e.setId(keyIn.toString());
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updateResult(dss, to_add_orcid_to_result, outputPath, "dataset");
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e.setAuthor_list(authorlist);
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updateResult(sfw, to_add_orcid_to_result, outputPath, "software");
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valueOut.set(Value.newInstance(new Gson().toJson(e, Emit.class), trust, Type.fromresult).toJson());
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updateResult(orp, to_add_orcid_to_result, outputPath, "otherresearchproduct");
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context.write(keyIn, valueOut);
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context.getCounter(COUNTER_PROPAGATION,"emit for result with orcid").increment(1);
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}
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}
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}
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}
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private List<String> getAuthorList(List<FieldTypeProtos.Author> author_list){
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return author_list.stream().map(a -> new JsonFormat().printToString(a)).collect(Collectors.toList());
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}
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}
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private static Author enrichAutor(Author autoritative_author, Author author) {
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boolean toaddpid = false;
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if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
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if (StringUtils.isNoneEmpty(author.getSurname())) {
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if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
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//have the same surname. Check the name
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if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
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if (StringUtils.isNoneEmpty(author.getName())) {
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if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
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toaddpid = true;
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}
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//they could be differently written (i.e. only the initials of the name in one of the two
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if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
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toaddpid = true;
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}
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}
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}
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}
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}
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}
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if (toaddpid){
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StructuredProperty pid = new StructuredProperty();
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for(StructuredProperty sp : autoritative_author.getPid()){
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if (PROPAGATION_AUTHOR_PID.equals(sp.getQualifier().getClassid())){
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pid.setValue(sp.getValue());
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pid.setQualifier(getQualifier(sp.getQualifier().getClassid(),sp.getQualifier().getClassname() ));
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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));
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if(author.getPid() == null){
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author.setPid(Arrays.asList(pid));
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}else{
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author.getPid().add(pid);
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}
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}
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}
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return author;
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}
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return null;
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}
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private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
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results.leftOuterJoin(toupdateresult)
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.map(p -> {
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Result r = p._2()._1();
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if (p._2()._2().isPresent()){
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List<Author> autoritative_authors = p._2()._2().get().getAuthors();
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List<Author> to_enrich_authors = r.getAuthor();
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//.stream().filter(a -> !containsAllowedPid(a))
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//.collect(Collectors.toList());
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r.setAuthor(to_enrich_authors
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.stream()
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.map(a -> {
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if (containsAllowedPid(a)) {
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return a;
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}
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List<Author> lst = autoritative_authors.stream()
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.map(aa -> enrichAutor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
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if(lst.size() == 0){
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return a;
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}
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return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
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}).collect(Collectors.toList()));
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}
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return r;
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})
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath+"/"+type);
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}
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private static TypedRow getTypedRow(Result p) {
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TypedRow tp = new TypedRow();
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tp.setSourceId(p.getId());
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List<Author> authorList = p.getAuthor()
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.stream()
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.map(a -> {
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if (a.getPid().stream().map(pid -> {
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if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
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return a;
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}
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return null;
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}).filter(aut -> !(aut == null)).collect(Collectors.toList()).size() > 0){
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return a;
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}
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return null;
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}).filter(a -> !(a == null)).collect(Collectors.toList());
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tp.setAuthors(authorList);
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if(authorList.size() > 0){
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return tp;
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}
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return null;
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}
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private static boolean containsAllowedPid(Author a){
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return (a.getPid().stream().map(pid -> {
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if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
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return true;
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}
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return false;
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}).filter(aut -> (aut == true)).collect(Collectors.toList()).size()) > 0;
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}
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}
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/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
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ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
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boolean updated = false;
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for (FieldTypeProtos.Author a: author_list){
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FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
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if(author != null){
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updated = true;
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metadataBuilder.addAuthor(author);
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}else{
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metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
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}
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}
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if(updated)
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return metadataBuilder;
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return null;
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}
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private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
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if(containsOrcid(a.getPidList()))
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return null;
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for(FieldTypeProtos.Author autoritative_author : author_list) {
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if (equals(autoritative_author, a)) {
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if(!containsOrcid(a.getPidList()))
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return update(a, autoritative_author);
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}
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}
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return null;
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}
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private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
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if(pidList == null)
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return false;
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return pidList
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.stream()
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.filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
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.collect(Collectors.toList()).size() > 0;
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}
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}
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*/
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*/
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