forked from D-Net/dnet-hadoop
fixed issues while running on cluster
This commit is contained in:
parent
56e70573c2
commit
f96ca900e1
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@ -1,7 +1,8 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.Serializable;
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import java.util.HashMap;
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public class CommunityMap extends HashMap<String, String> {
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public class CommunityMap extends HashMap<String, String> implements Serializable {
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}
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@ -1,18 +1,29 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import com.google.common.collect.Maps;
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import java.util.Map;
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import com.google.common.collect.Maps;
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public class Constants {
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public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
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public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
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public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
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static {
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accessRightsCoarMap.put("OPEN", "http://purl.org/coar/access_right/c_abf2");
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accessRightsCoarMap.put("RESTRICTED", "http://purl.org/coar/access_right/c_16ec");
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accessRightsCoarMap.put("OPEN SOURCE", "http://purl.org/coar/access_right/c_abf2");
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accessRightsCoarMap.put("CLOSED", "http://purl.org/coar/access_right/c_14cb //metadataonly for coar");
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accessRightsCoarMap.put("EMBARGO", "http://purl.org/coar/access_right/c_f1cf");
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accessRightsCoarMap.put("OPEN", "c_abf2");
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accessRightsCoarMap.put("RESTRICTED", "c_16ec");
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accessRightsCoarMap.put("OPEN SOURCE", "c_abf2");
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accessRightsCoarMap.put("CLOSED", "c_14cb");
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accessRightsCoarMap.put("EMBARGO", "c_f1cf");
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}
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static {
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coarCodeLabelMap.put("c_abf2", "OPEN");
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coarCodeLabelMap.put("c_16ec", "RESTRICTED");
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coarCodeLabelMap.put("c_14cb", "CLOSED");
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coarCodeLabelMap.put("c_f1cf", "EMBARGO");
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}
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}
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@ -1,26 +1,34 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import scala.collection.immutable.Stream;
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import javax.swing.text.html.Option;
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import org.apache.avro.generic.GenericData;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class Mapper implements Serializable {
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public static <I extends eu.dnetlib.dhp.schema.oaf.Result, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> O map(
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I input, Map<String,String> communityMap){
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I input, Map<String, String> communityMap) {
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O out = null;
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switch (input.getResulttype().getClassid()){
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
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if (ort.isPresent()) {
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switch (ort.get().getClassid()) {
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case "publication":
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out = (O)new Publication();
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Optional<Journal> journal = Optional.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
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if(journal.isPresent()){
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out = (O) new Publication();
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Optional<Journal> journal = Optional
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.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
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if (journal.isPresent()) {
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Journal j = journal.get();
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Container c = new Container();
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c.setConferencedate(j.getConferencedate());
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@ -39,12 +47,17 @@ public class Mapper implements Serializable {
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break;
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case "dataset":
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Dataset d = new Dataset();
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eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset)input;
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d.setSize(id.getSize().getValue());
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d.setVersion(id.getVersion().getValue());
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eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input;
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Optional.ofNullable(id.getSize()).ifPresent(v -> d.setSize(v.getValue()));
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Optional.ofNullable(id.getVersion()).ifPresent(v -> d.setVersion(v.getValue()));
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List<eu.dnetlib.dhp.schema.oaf.GeoLocation> igl = id.getGeolocation();
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d.setGeolocation(igl.stream()
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d
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.setGeolocation(
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Optional
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.ofNullable(id.getGeolocation())
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.map(
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igl -> igl
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.stream()
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.filter(Objects::nonNull)
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.map(gli -> {
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GeoLocation gl = new GeoLocation();
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@ -52,172 +65,343 @@ public class Mapper implements Serializable {
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gl.setPlace(gli.getPlace());
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gl.setPoint(gli.getPoint());
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return gl;
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}).collect(Collectors.toList()));
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out = (O)d;
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})
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.collect(Collectors.toList()))
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.orElse(null));
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out = (O) d;
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break;
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case "software":
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Software s = new Software();
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eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software)input;
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s.setCodeRepositoryUrl(is.getCodeRepositoryUrl().getValue());
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s.setDocumentationUrl(is.getDocumentationUrl()
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eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
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Optional
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.ofNullable(is.getCodeRepositoryUrl())
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.ifPresent(value -> s.setCodeRepositoryUrl(value.getValue()));
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Optional
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.ofNullable(is.getDocumentationUrl())
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.ifPresent(
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value -> s
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.setDocumentationUrl(
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value
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.stream()
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.map(du -> du.getValue()).collect(Collectors.toList()));
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s.setProgrammingLanguage(is.getProgrammingLanguage().getClassid());
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.map(v -> v.getValue())
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.collect(Collectors.toList())));
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Optional
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.ofNullable(is.getProgrammingLanguage())
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.ifPresent(value -> s.setProgrammingLanguage(value.getClassid()));
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out = (O) s;
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break;
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case "otherresearchproduct":
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case "other":
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OtherResearchProduct or = new OtherResearchProduct();
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eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct)input;
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or.setContactgroup(ir.getContactgroup().stream().map(cg -> cg.getValue()).collect(Collectors.toList()));
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or.setContactperson(ir.getContactperson().stream().map(cp->cp.getValue()).collect(Collectors.toList()));
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or.setTool(ir.getTool().stream().map(t -> t.getValue()).collect(Collectors.toList()));
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eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
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or
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.setContactgroup(
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Optional
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.ofNullable(ir.getContactgroup())
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.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
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.orElse(null));
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or
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.setContactperson(
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Optional
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.ofNullable(ir.getContactperson())
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.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
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.orElse(null));
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or
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.setTool(
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Optional
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.ofNullable(ir.getTool())
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.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
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.orElse(null));
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out = (O) or;
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break;
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}
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out.setAuthor(input.getAuthor()
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Optional<List<eu.dnetlib.dhp.schema.oaf.Author>> oAuthor = Optional.ofNullable(input.getAuthor());
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if (oAuthor.isPresent()) {
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// List<eu.dnetlib.dhp.schema.dump.oaf.Author> authorList = new ArrayList<>();
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out
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.setAuthor(
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oAuthor
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.get()
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.stream()
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.map(oa -> {
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Author a = new Author();
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a.setAffiliation(oa.getAffiliation().stream().map(aff -> aff.getValue()).collect(Collectors.toList()));
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a.setFullname(oa.getFullname());
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a.setName(oa.getName());
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a.setSurname(oa.getSurname());
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a.setRank(oa.getRank());
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a.setPid(oa.getPid().stream().map(p -> {
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ControlledField cf = new ControlledField();
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cf.setScheme( p.getQualifier().getClassid());
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cf.setValue( p.getValue());
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return cf;
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}).collect(Collectors.toList()));
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return a;
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}).collect(Collectors.toList()));
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//I do not map Access Right UNKNOWN or OTHER
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if (Constants.accessRightsCoarMap.containsKey(input.getBestaccessright().getClassid())){
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AccessRight ar = new AccessRight();
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ar.setSchema(Constants.accessRightsCoarMap.get(input.getBestaccessright().getClassid()));
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ar.setCode(input.getBestaccessright().getClassid());
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ar.setLabel(input.getBestaccessright().getClassname());
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out.setBestaccessright(ar);
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.map(oa -> getAuthor(oa))
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.collect(Collectors.toList()));
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}
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out.setCollectedfrom(input.getCollectedfrom().stream().map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
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// I do not map Access Right UNKNOWN or OTHER
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
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if (oar.isPresent()) {
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if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
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String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
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out
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.setBestaccessright(
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AccessRight
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.newInstance(
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code,
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Constants.coarCodeLabelMap.get(code),
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Constants.COAR_ACCESS_RIGHT_SCHEMA));
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}
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}
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out
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.setCollectedfrom(
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input
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.getCollectedfrom()
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.stream()
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.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
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.collect(Collectors.toList()));
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Set<String> communities = communityMap.keySet();
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List<Context> contextList = input.getContext()
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List<Context> contextList = input
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.getContext()
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.stream()
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.map(c -> {
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if(communities.contains(c.getId())){
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if (communities.contains(c.getId())
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|| communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
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Context context = new Context();
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if (!communityMap.containsKey(c.getId())) {
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context.setCode(c.getId().substring(0, c.getId().indexOf("::")));
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context.setLabel(communityMap.get(context.getCode()));
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} else {
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context.setCode(c.getId());
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context.setLabel(communityMap.get(c.getId()));
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}
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Optional<List<DataInfo>> dataInfo = Optional.ofNullable(c.getDataInfo());
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if(dataInfo.isPresent()){
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context.setProvenance(dataInfo.get().stream()
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if (dataInfo.isPresent()) {
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List<String> provenance = new ArrayList<>();
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provenance
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.addAll(
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dataInfo
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.get()
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.stream()
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.map(di -> {
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if (di.getInferred()){
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return di.getProvenanceaction().getClassid();
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if (di.getInferred()) {
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return di.getProvenanceaction().getClassname();
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}
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return null;
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}).filter(Objects::nonNull)
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.collect(Collectors.toList()));
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})
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.filter(Objects::nonNull)
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.collect(Collectors.toSet()));
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context.setProvenance(provenance);
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}
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return context;
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}
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return null;
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}
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).filter(Objects::nonNull)
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})
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.filter(Objects::nonNull)
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.collect(Collectors.toList());
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if(contextList.size() > 0){
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if (contextList.size() > 0) {
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out.setContext(contextList);
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}
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out.setContributor(input.getContributor()
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final List<String> contributorList = new ArrayList<>();
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Optional
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.ofNullable(input.getContributor())
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.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
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out.setContributor(contributorList);
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List<Country> countryList = new ArrayList<>();
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Optional
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.ofNullable(input.getCountry())
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.ifPresent(
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value -> value
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.stream()
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.map(c -> c.getValue()).collect(Collectors.toList()));
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out.setCountry(input.getCountry()
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.stream()
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.map(c -> {
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.forEach(
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c -> {
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Country country = new Country();
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country.setCode(c.getClassid());
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country.setLabel(c.getClassname());
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Optional<DataInfo> dataInfo = Optional.ofNullable(c.getDataInfo());
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if(dataInfo.isPresent()){
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country.setProvenance(dataInfo.get().getProvenanceaction().getClassid());
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}
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return country;
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}).collect(Collectors.toList()));
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out.setCoverage(input.getCoverage().stream().map(c->c.getValue()).collect(Collectors.toList()));
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Optional
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.ofNullable(c.getDataInfo())
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.ifPresent(
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provenance -> country
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.setProvenance(
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provenance
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.getProvenanceaction()
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.getClassname()));
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countryList
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.add(country);
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}));
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out.setCountry(countryList);
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final List<String> coverageList = new ArrayList<>();
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Optional
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.ofNullable(input.getCoverage())
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.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
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out.setCoverage(coverageList);
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out.setDateofcollection(input.getDateofcollection());
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out.setDescription(input.getDescription().stream().map(d->d.getValue()).collect(Collectors.toList()));
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out.setEmbargoenddate(input.getEmbargoenddate().getValue());
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out.setFormat(input.getFormat().stream().map(f->f.getValue()).collect(Collectors.toList()));
|
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|
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final List<String> descriptionList = new ArrayList<>();
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Optional
|
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.ofNullable(input.getDescription())
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.ifPresent(value -> value.stream().forEach(d -> descriptionList.add(d.getValue())));
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out.setDescription(descriptionList);
|
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Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
|
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if (oStr.isPresent()) {
|
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out.setEmbargoenddate(oStr.get().getValue());
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}
|
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|
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final List<String> formatList = new ArrayList<>();
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Optional
|
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.ofNullable(input.getFormat())
|
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.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
|
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out.setFormat(formatList);
|
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out.setId(input.getId());
|
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out.setOriginalId(input.getOriginalId());
|
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out.setInstance(input.getInstance()
|
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|
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final List<Instance> instanceList = new ArrayList<>();
|
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Optional
|
||||
.ofNullable(input.getInstance())
|
||||
.ifPresent(
|
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inst -> inst
|
||||
.stream()
|
||||
.map(i -> {
|
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.forEach(i -> {
|
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Instance instance = new Instance();
|
||||
AccessRight ar = new AccessRight();
|
||||
ar.setCode(i.getAccessright().getClassid());
|
||||
ar.setLabel(i.getAccessright().getClassname());
|
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if(Constants.accessRightsCoarMap.containsKey(i.getAccessright().getClassid())){
|
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ar.setSchema(Constants.accessRightsCoarMap.get(i.getAccessright().getClassid()));
|
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|
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Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
|
||||
.ofNullable(i.getAccessright());
|
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if (opAr.isPresent()) {
|
||||
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
|
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String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
|
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instance
|
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.setAccessright(
|
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AccessRight
|
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.newInstance(
|
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code,
|
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Constants.coarCodeLabelMap.get(code),
|
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Constants.COAR_ACCESS_RIGHT_SCHEMA));
|
||||
}
|
||||
}
|
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instance.setAccessright(ar);
|
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instance.setCollectedfrom(KeyValue.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
|
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instance.setHostedby(KeyValue.newInstance(i.getHostedby().getKey(),i.getHostedby().getValue()));
|
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instance.setLicense(i.getLicense().getValue());
|
||||
instance.setPublicationdata(i.getDateofacceptance().getValue());
|
||||
instance.setRefereed(i.getRefereed().getValue());
|
||||
instance.setType(i.getInstancetype().getClassid());
|
||||
instance.setUrl(i.getUrl());
|
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return instance;
|
||||
}).collect(Collectors.toList()));
|
||||
|
||||
out.setLanguage(Qualifier.newInstance(input.getLanguage().getClassid(), input.getLanguage().getClassname()));
|
||||
out.setLastupdatetimestamp(input.getLastupdatetimestamp());
|
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instance
|
||||
.setCollectedfrom(
|
||||
KeyValue
|
||||
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
|
||||
instance
|
||||
.setHostedby(
|
||||
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getLicense())
|
||||
.ifPresent(value -> instance.setLicense(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getDateofacceptance())
|
||||
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getRefereed())
|
||||
.ifPresent(value -> instance.setRefereed(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getInstancetype())
|
||||
.ifPresent(value -> instance.setType(value.getClassname()));
|
||||
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
|
||||
instanceList.add(instance);
|
||||
}));
|
||||
out
|
||||
.setInstance(instanceList);
|
||||
|
||||
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
|
||||
if (oL.isPresent()) {
|
||||
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
|
||||
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
|
||||
}
|
||||
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
|
||||
if (oLong.isPresent()) {
|
||||
out.setLastupdatetimestamp(oLong.get());
|
||||
}
|
||||
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
|
||||
if(otitle.isPresent()){
|
||||
List<StructuredProperty> iTitle = otitle.get()
|
||||
if (otitle.isPresent()) {
|
||||
List<StructuredProperty> iTitle = otitle
|
||||
.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
|
||||
.collect(Collectors.toList());
|
||||
if(iTitle.size() > 0 ){
|
||||
if (iTitle.size() > 0) {
|
||||
out.setMaintitle(iTitle.get(0).getValue());
|
||||
}
|
||||
|
||||
iTitle = otitle.get()
|
||||
iTitle = otitle
|
||||
.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
|
||||
.collect(Collectors.toList());
|
||||
if(iTitle.size() > 0){
|
||||
if (iTitle.size() > 0) {
|
||||
out.setSubtitle(iTitle.get(0).getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
out.setPid(input.getPid().stream().map(p -> {
|
||||
ControlledField pid = new ControlledField();
|
||||
pid.setScheme(p.getQualifier().getClassid());
|
||||
pid.setValue(p.getValue());
|
||||
return pid;
|
||||
}).collect(Collectors.toList()));
|
||||
out.setPublicationdata(input.getDateofacceptance().getValue());
|
||||
out.setPublisher(input.getPublisher().getValue());
|
||||
out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
|
||||
out.setSubject(input.getSubject().stream().map(s->{
|
||||
ControlledField subject = new ControlledField();
|
||||
subject.setScheme(s.getQualifier().getClassid());
|
||||
subject.setValue(s.getValue());
|
||||
return subject;
|
||||
}).collect(Collectors.toList()));
|
||||
List<ControlledField> pids = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getPid())
|
||||
.ifPresent(
|
||||
value -> value
|
||||
.stream()
|
||||
.forEach(
|
||||
p -> pids
|
||||
.add(
|
||||
ControlledField
|
||||
.newInstance(p.getQualifier().getClassid(), p.getValue()))));
|
||||
out.setPid(pids);
|
||||
oStr = Optional.ofNullable(input.getDateofacceptance());
|
||||
if (oStr.isPresent()) {
|
||||
out.setPublicationdate(oStr.get().getValue());
|
||||
}
|
||||
oStr = Optional.ofNullable(input.getPublisher());
|
||||
if (oStr.isPresent()) {
|
||||
out.setPublisher(oStr.get().getValue());
|
||||
}
|
||||
|
||||
List<String> sourceList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getSource())
|
||||
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
|
||||
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
|
||||
List<ControlledField> subjectList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getSubject())
|
||||
.ifPresent(
|
||||
value -> value
|
||||
.stream()
|
||||
.forEach(
|
||||
s -> subjectList
|
||||
.add(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()))));
|
||||
out.setSubject(subjectList);
|
||||
|
||||
out.setType(input.getResulttype().getClassid());
|
||||
}
|
||||
|
||||
return out;
|
||||
}
|
||||
|
||||
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
|
||||
Author a = new Author();
|
||||
Optional
|
||||
.ofNullable(oa.getAffiliation())
|
||||
.ifPresent(
|
||||
value -> a
|
||||
.setAffiliation(
|
||||
value
|
||||
.stream()
|
||||
.map(aff -> aff.getValue())
|
||||
.collect(Collectors.toList())));
|
||||
a.setFullname(oa.getFullname());
|
||||
a.setName(oa.getName());
|
||||
a.setSurname(oa.getSurname());
|
||||
a.setRank(oa.getRank());
|
||||
Optional
|
||||
.ofNullable(oa.getPid())
|
||||
.ifPresent(
|
||||
value -> a
|
||||
.setPid(
|
||||
value
|
||||
.stream()
|
||||
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
|
||||
.collect(Collectors.toList())));
|
||||
return a;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,24 +1,24 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import java.io.StringReader;
|
||||
import java.util.List;
|
||||
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.io.SAXReader;
|
||||
|
||||
import java.io.StringReader;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class QueryInformationSystem {
|
||||
|
||||
private ISLookUpService isLookUp;
|
||||
|
||||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " +
|
||||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
|
||||
+
|
||||
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
||||
" return " +
|
||||
"<community> " +
|
||||
|
|
@ -26,9 +26,7 @@ public class QueryInformationSystem {
|
|||
"{$x//CONFIGURATION/context/@label}" +
|
||||
"</community>";
|
||||
|
||||
|
||||
|
||||
public Map<String,String> getCommunityMap()
|
||||
public CommunityMap getCommunityMap()
|
||||
throws ISLookUpException {
|
||||
return getMap(isLookUp.quickSearchProfile(XQUERY));
|
||||
|
||||
|
|
@ -42,12 +40,8 @@ public class QueryInformationSystem {
|
|||
this.isLookUp = isLookUpService;
|
||||
}
|
||||
|
||||
public void set(String isLookUpUrl){
|
||||
isLookUpUrl = get(isLookUpUrl);
|
||||
}
|
||||
public ISLookUpService
|
||||
private static Map<String, String> getMap(List<String> communityMap) {
|
||||
final Map<String, String> map = new HashMap<>();
|
||||
public static CommunityMap getMap(List<String> communityMap) {
|
||||
final CommunityMap map = new CommunityMap();
|
||||
|
||||
communityMap.stream().forEach(xml -> {
|
||||
final Document doc;
|
||||
|
|
@ -59,7 +53,6 @@ public void set(String isLookUpUrl){
|
|||
e.printStackTrace();
|
||||
}
|
||||
|
||||
|
||||
});
|
||||
|
||||
return map;
|
||||
|
|
|
|||
|
|
@ -1,10 +1,11 @@
|
|||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Projects;
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Projects;
|
||||
|
||||
public class ResultProject implements Serializable {
|
||||
private String resultId;
|
||||
private List<Projects> projectsList;
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
|
@ -6,10 +7,8 @@ import java.io.Serializable;
|
|||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import javax.management.Query;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
|
|
@ -19,17 +18,19 @@ import org.apache.spark.sql.SparkSession;
|
|||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
import javax.management.Query;
|
||||
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class SparkDumpCommunityProducts implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class);
|
||||
private QueryInformationSystem queryInformationSystem;
|
||||
|
||||
private static QueryInformationSystem queryInformationSystem;
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
|
|
@ -47,7 +48,6 @@ public class SparkDumpCommunityProducts implements Serializable {
|
|||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
|
|
@ -63,83 +63,84 @@ public class SparkDumpCommunityProducts implements Serializable {
|
|||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
log.info("isLookUpUrl: {}", isLookUpUrl);
|
||||
|
||||
final String resultType = parser.get("resultType");
|
||||
log.info("resultType: {}", resultType);
|
||||
// final String resultType = parser.get("resultType");
|
||||
// log.info("resultType: {}", resultType);
|
||||
|
||||
|
||||
SparkDumpCommunityProducts sdcp = new SparkDumpCommunityProducts();
|
||||
|
||||
sdcp.exec(isLookUpUrl, isSparkSessionManaged, outputPath,
|
||||
inputPath, resultClassName, dumpClassName);
|
||||
|
||||
}
|
||||
|
||||
public QueryInformationSystem getQueryInformationSystem() {
|
||||
return queryInformationSystem;
|
||||
}
|
||||
|
||||
public void setQueryInformationSystem(QueryInformationSystem queryInformationSystem) {
|
||||
this.queryInformationSystem = queryInformationSystem;
|
||||
}
|
||||
|
||||
public ISLookUpService getIsLookUpService(String isLookUpUrl){
|
||||
return ISLookupClientFactory.getLookUpService(isLookUpUrl);
|
||||
}
|
||||
|
||||
public void exec(String isLookUpUrl, Boolean isSparkSessionManaged, String outputPath, String inputPath,
|
||||
String resultClassName, String dumpClassName) throws ISLookUpException, ClassNotFoundException {
|
||||
SparkConf conf = new SparkConf();
|
||||
final Optional<String> cm = Optional.ofNullable(parser.get("communityMap"));
|
||||
|
||||
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> dumpClazz =
|
||||
(Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result>) Class.forName(dumpClassName);
|
||||
Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> dumpClazz = (Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result>) Class
|
||||
.forName(dumpClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
CommunityMap communityMap;
|
||||
|
||||
if (!isLookUpUrl.equals("BASEURL:8280/is/services/isLookUp")) {
|
||||
queryInformationSystem = new QueryInformationSystem();
|
||||
queryInformationSystem.setIsLookUp(getIsLookUpService(isLookUpUrl));
|
||||
Map<String,String>
|
||||
communityMap = queryInformationSystem.getCommunityMap();
|
||||
} else {
|
||||
communityMap = new Gson().fromJson(cm.get(), CommunityMap.class);
|
||||
}
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
execDump(spark, inputPath, outputPath , communityMap, inputClazz, dumpClazz);
|
||||
execDump(spark, inputPath, outputPath, communityMap, inputClazz, dumpClazz);
|
||||
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
|
||||
return ISLookupClientFactory.getLookUpService(isLookUpUrl);
|
||||
}
|
||||
|
||||
private <I extends Result, O extends eu.dnetlib.dhp.schema.dump.oaf.Result > void execDump(
|
||||
SparkSession spark,
|
||||
public static <I extends Result, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> void execDump(SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
Map<String,String> communityMap,
|
||||
CommunityMap communityMap,
|
||||
Class<I> inputClazz,
|
||||
Class<O> dumpClazz) {
|
||||
|
||||
Set<String> communities = communityMap.keySet();
|
||||
// Set<String> communities = communityMap.keySet();
|
||||
Dataset<I> tmp = Utils.readPath(spark, inputPath, inputClazz);
|
||||
tmp.map(value -> {
|
||||
|
||||
tmp
|
||||
.map(value -> execMap(value, communityMap), Encoders.bean(dumpClazz))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
|
||||
}
|
||||
|
||||
private static <O extends eu.dnetlib.dhp.schema.dump.oaf.Result, I extends Result> O execMap(I value,
|
||||
CommunityMap communityMap) {
|
||||
{
|
||||
Set<String> communities = communityMap.keySet();
|
||||
Optional<List<Context>> inputContext = Optional.ofNullable(value.getContext());
|
||||
if(!inputContext.isPresent()){
|
||||
if (!inputContext.isPresent()) {
|
||||
return null;
|
||||
}
|
||||
List<String> toDumpFor = inputContext.get().stream().map(c -> {
|
||||
if (communities.contains(c.getId())) {
|
||||
return c.getId();
|
||||
}
|
||||
if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
|
||||
return c.getId().substring(0, 3);
|
||||
}
|
||||
return null;
|
||||
}).filter(Objects::nonNull).collect(Collectors.toList());
|
||||
if(toDumpFor.size() == 0){
|
||||
if (toDumpFor.size() == 0) {
|
||||
return null;
|
||||
}
|
||||
return Mapper.map(value, communityMap);
|
||||
},Encoders.bean(dumpClazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,11 +1,13 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Projects;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.io.StringReader;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -14,22 +16,28 @@ import org.apache.spark.sql.Dataset;
|
|||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.Node;
|
||||
import org.dom4j.io.SAXReader;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Funder;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Projects;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class SparkPrepareResultProject implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class);
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
|
|
@ -52,7 +60,6 @@ public class SparkPrepareResultProject implements Serializable {
|
|||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
|
|
@ -65,35 +72,109 @@ public class SparkPrepareResultProject implements Serializable {
|
|||
}
|
||||
|
||||
private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) {
|
||||
Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation" , Relation.class)
|
||||
Dataset<Relation> relation = Utils
|
||||
.readPath(spark, inputPath + "/relation", Relation.class)
|
||||
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
|
||||
Dataset<Project> projects = Utils.readPath(spark, inputPath + "/project" , Project.class);
|
||||
Dataset<Project> projects = Utils.readPath(spark, inputPath + "/project", Project.class);
|
||||
|
||||
projects.joinWith(relation, projects.col("id").equalTo(relation.col("source")))
|
||||
.groupByKey((MapFunction<Tuple2<Project,Relation>,String>)value -> value._2().getTarget(), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Tuple2<Project,Relation>, ResultProject>) (s, it) ->
|
||||
{
|
||||
projects
|
||||
.joinWith(relation, projects.col("id").equalTo(relation.col("source")))
|
||||
.groupByKey(
|
||||
(MapFunction<Tuple2<Project, Relation>, String>) value -> value._2().getTarget(), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Tuple2<Project, Relation>, ResultProject>) (s, it) -> {
|
||||
Set<String> projectSet = new HashSet<>();
|
||||
Tuple2<Project, Relation> first = it.next();
|
||||
ResultProject rp = new ResultProject();
|
||||
rp.setResultId(first._2().getTarget());
|
||||
Project p = first._1();
|
||||
Projects ps = Projects.newInstance(p.getId(), p.getCode().getValue(), p.getAcronym().getValue(),
|
||||
p.getTitle().getValue(), p.getFundingtree()
|
||||
projectSet.add(p.getId());
|
||||
Projects ps = Projects
|
||||
.newInstance(
|
||||
p.getId(), p.getCode().getValue(),
|
||||
Optional
|
||||
.ofNullable(p.getAcronym())
|
||||
.map(a -> a.getValue())
|
||||
.orElse(null),
|
||||
Optional
|
||||
.ofNullable(p.getTitle())
|
||||
.map(v -> v.getValue())
|
||||
.orElse(null),
|
||||
Optional
|
||||
.ofNullable(p.getFundingtree())
|
||||
.map(
|
||||
value -> value
|
||||
.stream()
|
||||
.map(ft -> ft.getValue()).collect(Collectors.toList()));
|
||||
List<Projects> projList = Arrays.asList(ps);
|
||||
.map(ft -> getFunder(ft.getValue()))
|
||||
.collect(Collectors.toList())
|
||||
.get(0))
|
||||
.orElse(null));
|
||||
List<Projects> projList = new ArrayList<>();
|
||||
projList.add(ps);
|
||||
rp.setProjectsList(projList);
|
||||
it.forEachRemaining(c -> {
|
||||
Project op = c._1();
|
||||
projList.add(Projects.newInstance(op.getId(), op.getCode().getValue(),
|
||||
op.getAcronym().getValue(), op.getTitle().getValue(),
|
||||
op.getFundingtree().stream().map(ft -> ft.getValue()).collect(Collectors.toList())));
|
||||
if (!projectSet.contains(op.getId())) {
|
||||
projList
|
||||
.add(
|
||||
Projects
|
||||
.newInstance(
|
||||
op.getId(),
|
||||
op.getCode().getValue(),
|
||||
Optional
|
||||
.ofNullable(op.getAcronym())
|
||||
.map(a -> a.getValue())
|
||||
.orElse(null),
|
||||
Optional
|
||||
.ofNullable(op.getTitle())
|
||||
.map(v -> v.getValue())
|
||||
.orElse(null),
|
||||
Optional
|
||||
.ofNullable(op.getFundingtree())
|
||||
.map(
|
||||
value -> value
|
||||
.stream()
|
||||
.map(ft -> getFunder(ft.getValue()))
|
||||
.collect(Collectors.toList())
|
||||
.get(0))
|
||||
.orElse(null)));
|
||||
projectSet.add(op.getId());
|
||||
|
||||
}
|
||||
|
||||
});
|
||||
return rp;
|
||||
} ,Encoders.bean(ResultProject.class))
|
||||
}, Encoders.bean(ResultProject.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
private static Funder getFunder(String fundingtree) {
|
||||
// ["<fundingtree><funder><id>nsf_________::NSF</id><shortname>NSF</shortname><name>National Science
|
||||
// Foundation</name><jurisdiction>US</jurisdiction></funder><funding_level_1><id>nsf_________::NSF::CISE/OAD::CISE/CCF</id><description>Division
|
||||
// of Computing and Communication Foundations</description><name>Division of Computing and Communication
|
||||
// Foundations</name><parent><funding_level_0><id>nsf_________::NSF::CISE/OAD</id><description>Directorate for
|
||||
// Computer & Information Science & Engineering</description><name>Directorate for Computer &
|
||||
// Information Science &
|
||||
// Engineering</name><parent/><class>nsf:fundingStream</class></funding_level_0></parent></funding_level_1></fundingtree>"]
|
||||
Funder f = new Funder();
|
||||
final Document doc;
|
||||
try {
|
||||
doc = new SAXReader().read(new StringReader(fundingtree));
|
||||
f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
|
||||
f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText());
|
||||
f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
|
||||
for (Object o : doc.selectNodes("//funding_level_0")) {
|
||||
List node = ((Node) o).selectNodes("./name");
|
||||
f.setFundingStream(((Node) node.get(0)).getText());
|
||||
|
||||
}
|
||||
|
||||
return f;
|
||||
} catch (DocumentException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return f;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,29 +1,36 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.io.StringReader;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.io.SAXReader;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
import com.google.gson.Gson;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class SparkSplitForCommunity implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class);
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
|
|
@ -40,7 +47,6 @@ public class SparkSplitForCommunity implements Serializable {
|
|||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
|
|
@ -53,45 +59,63 @@ public class SparkSplitForCommunity implements Serializable {
|
|||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
log.info("isLookUpUrl: {}", isLookUpUrl);
|
||||
|
||||
final Optional<String> cm = Optional.ofNullable(parser.get("communityMap"));
|
||||
|
||||
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
Map<String,String>
|
||||
communityMap = QueryInformationSystem.getCommunityMap(isLookUpUrl);
|
||||
CommunityMap communityMap;
|
||||
|
||||
if (!isLookUpUrl.equals("BASEURL:8280/is/services/isLookUp")) {
|
||||
QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
|
||||
queryInformationSystem.setIsLookUp(getIsLookUpService(isLookUpUrl));
|
||||
communityMap = queryInformationSystem.getCommunityMap();
|
||||
} else {
|
||||
communityMap = new Gson().fromJson(cm.get(), CommunityMap.class);
|
||||
}
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
execSplit(spark, inputPath, outputPath , communityMap.keySet(), inputClazz);
|
||||
execSplit(spark, inputPath, outputPath, communityMap.keySet(), inputClazz);
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result> void execSplit(SparkSession spark, String inputPath, String outputPath, Set<String> communities
|
||||
, Class<R> inputClazz) {
|
||||
public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
|
||||
return ISLookupClientFactory.getLookUpService(isLookUpUrl);
|
||||
}
|
||||
|
||||
private static <R extends Result> void execSplit(SparkSession spark, String inputPath, String outputPath,
|
||||
Set<String> communities, Class<R> inputClazz) {
|
||||
|
||||
Dataset<R> result = Utils.readPath(spark, inputPath, inputClazz);
|
||||
|
||||
communities.stream()
|
||||
communities
|
||||
.stream()
|
||||
.forEach(c -> printResult(c, result, outputPath));
|
||||
|
||||
}
|
||||
|
||||
private static <R extends Result> void printResult(String c, Dataset<R> result, String outputPath) {
|
||||
result.filter(r -> containsCommunity(r, c))
|
||||
result
|
||||
.filter(r -> containsCommunity(r, c))
|
||||
.write()
|
||||
.option("compression","gzip")
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Append)
|
||||
.json(outputPath + "/" + c);
|
||||
}
|
||||
|
||||
private static <R extends Result> boolean containsCommunity(R r, String c) {
|
||||
if(Optional.ofNullable(r.getContext()).isPresent()) {
|
||||
return r.getContext().stream().filter(con -> con.getCode().equals(c)).collect(Collectors.toList()).size() > 0;
|
||||
if (Optional.ofNullable(r.getContext()).isPresent()) {
|
||||
return r
|
||||
.getContext()
|
||||
.stream()
|
||||
.filter(con -> con.getCode().equals(c))
|
||||
.collect(Collectors.toList())
|
||||
.size() > 0;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,11 +1,11 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -16,13 +16,15 @@ import org.apache.spark.sql.SaveMode;
|
|||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class SparkUpdateProjectInfo implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class);
|
||||
|
|
@ -53,7 +55,6 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
|
||||
final String preparedInfoPath = parser.get("preparedInfoPath");
|
||||
log.info("preparedInfoPath: {}", preparedInfoPath);
|
||||
|
||||
|
|
@ -66,20 +67,22 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
extend(spark, inputPath, outputPath , preparedInfoPath, inputClazz);
|
||||
extend(spark, inputPath, outputPath, preparedInfoPath, inputClazz);
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result > void extend(
|
||||
private static <R extends Result> void extend(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
String preparedInfoPath,
|
||||
Class<R> inputClazz) {
|
||||
|
||||
Dataset<R> result = Utils.readPath(spark, inputPath , inputClazz);
|
||||
Dataset<R> result = Utils.readPath(spark, inputPath, inputClazz);
|
||||
Dataset<ResultProject> resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class);
|
||||
result.joinWith(resultProject, result.col("id").equalTo(resultProject.col("resultId")),
|
||||
result
|
||||
.joinWith(
|
||||
resultProject, result.col("id").equalTo(resultProject.col("resultId")),
|
||||
"left")
|
||||
.map(value -> {
|
||||
R r = value._1();
|
||||
|
|
@ -87,13 +90,12 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
r.setProjects(rp.getProjectsList());
|
||||
});
|
||||
return r;
|
||||
},Encoders.bean(inputClazz))
|
||||
}, Encoders.bean(inputClazz))
|
||||
.write()
|
||||
.option("compression","gzip")
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,14 +1,18 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
|
||||
public class Utils {
|
||||
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue