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code formatting

This commit is contained in:
Claudio Atzori 2020-05-22 12:34:00 +02:00
parent dc4621b3cb
commit 3cf2796ac6
6 changed files with 315 additions and 244 deletions
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259
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java
View File

@ -1,159 +1,164 @@
package eu.dnetlib.dhp.oa.dedup;
import com.wcohen.ss.JaroWinkler; package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.model.Person;
import org.apache.commons.lang3.StringUtils;
import scala.Tuple2;
import java.text.Normalizer; import java.text.Normalizer;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.model.Person;
import scala.Tuple2;
public class AuthorMerger { public class AuthorMerger {
private static final Double THRESHOLD = 0.95; private static final Double THRESHOLD = 0.95;
public static List<Author> merge(List<List<Author>> authors){ public static List<Author> merge(List<List<Author>> authors) {
authors.sort(new Comparator<List<Author>>() { authors.sort(new Comparator<List<Author>>() {
@Override @Override
public int compare(List<Author> o1, List<Author> o2) { public int compare(List<Author> o1, List<Author> o2) {
return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2));
} }
}); });
List<Author> author = new ArrayList<>(); List<Author> author = new ArrayList<>();
for(List<Author> a : authors){ for (List<Author> a : authors) {
author = mergeAuthor(author, a); author = mergeAuthor(author, a);
} }
return author; return author;
} }
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) { public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
int pa = countAuthorsPids(a); int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b); int pb = countAuthorsPids(b);
List<Author> base, enrich; List<Author> base, enrich;
int sa = authorsSize(a); int sa = authorsSize(a);
int sb = authorsSize(b); int sb = authorsSize(b);
if (pa == pb) { if (pa == pb) {
base = sa > sb ? a : b; base = sa > sb ? a : b;
enrich = sa > sb ? b : a; enrich = sa > sb ? b : a;
} else { } else {
base = pa > pb ? a : b; base = pa > pb ? a : b;
enrich = pa > pb ? b : a; enrich = pa > pb ? b : a;
} }
enrichPidFromList(base, enrich); enrichPidFromList(base, enrich);
return base; return base;
} }
private static void enrichPidFromList(List<Author> base, List<Author> enrich) { private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
if (base == null || enrich == null) if (base == null || enrich == null)
return; return;
final Map<String, Author> basePidAuthorMap = base final Map<String, Author> basePidAuthorMap = base
.stream() .stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0) .filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap( .flatMap(
a -> a a -> a
.getPid() .getPid()
.stream() .stream()
.map(p -> new Tuple2<>(pidToComparableString(p), a))) .map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream() .stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0) .filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap( .flatMap(
a -> a a -> a
.getPid() .getPid()
.stream() .stream()
.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
.map(p -> new Tuple2<>(p, a))) .map(p -> new Tuple2<>(p, a)))
.collect(Collectors.toList()); .collect(Collectors.toList());
pidToEnrich pidToEnrich
.forEach( .forEach(
a -> { a -> {
Optional<Tuple2<Double, Author>> simAuthor = base Optional<Tuple2<Double, Author>> simAuthor = base
.stream() .stream()
.map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) .map(ba -> new Tuple2<>(sim(ba, a._2()), ba))
.max(Comparator.comparing(Tuple2::_1)); .max(Comparator.comparing(Tuple2::_1));
if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) {
Author r = simAuthor.get()._2(); Author r = simAuthor.get()._2();
if (r.getPid() == null) { if (r.getPid() == null) {
r.setPid(new ArrayList<>()); r.setPid(new ArrayList<>());
} }
r.getPid().add(a._1()); r.getPid().add(a._1());
} }
}); });
} }
public static String pidToComparableString(StructuredProperty pid){ public static String pidToComparableString(StructuredProperty pid) {
return (pid.getQualifier()!=null? pid.getQualifier().getClassid()!=null?pid.getQualifier().getClassid().toLowerCase():"":"") + (pid.getValue()!=null? pid.getValue().toLowerCase():""); return (pid.getQualifier() != null
} ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
: "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
}
public static int countAuthorsPids(List<Author> authors) { public static int countAuthorsPids(List<Author> authors) {
if (authors == null) if (authors == null)
return 0; return 0;
return (int) authors.stream().filter(AuthorMerger::hasPid).count(); return (int) authors.stream().filter(AuthorMerger::hasPid).count();
} }
private static int authorsSize(List<Author> authors) { private static int authorsSize(List<Author> authors) {
if (authors == null) if (authors == null)
return 0; return 0;
return authors.size(); return authors.size();
} }
private static Double sim(Author a, Author b) { private static Double sim(Author a, Author b) {
final Person pa = parse(a); final Person pa = parse(a);
final Person pb = parse(b); final Person pb = parse(b);
if (pa.isAccurate() & pb.isAccurate()) { if (pa.isAccurate() & pb.isAccurate()) {
return new JaroWinkler() return new JaroWinkler()
.score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString()));
} else { } else {
return new JaroWinkler() return new JaroWinkler()
.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
} }
} }
private static boolean hasPid(Author a) { private static boolean hasPid(Author a) {
if (a == null || a.getPid() == null || a.getPid().size() == 0) if (a == null || a.getPid() == null || a.getPid().size() == 0)
return false; return false;
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
} }
private static Person parse(Author author) { private static Person parse(Author author) {
if (StringUtils.isNotBlank(author.getSurname())) { if (StringUtils.isNotBlank(author.getSurname())) {
return new Person(author.getSurname() + ", " + author.getName(), false); return new Person(author.getSurname() + ", " + author.getName(), false);
} else { } else {
return new Person(author.getFullname(), false); return new Person(author.getFullname(), false);
} }
} }
private static String normalize(final String s) { private static String normalize(final String s) {
return nfd(s) return nfd(s)
.toLowerCase() .toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError // do not compact the regexes in a single expression, would cause StackOverflowError
// in case // in case
// of large input strings // of large input strings
.replaceAll("(\\W)+", " ") .replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ") .replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ") .replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ") .replaceAll("(\\n)+", " ")
.trim(); .trim();
} }
private static String nfd(final String s) { private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD); return Normalizer.normalize(s, Normalizer.Form.NFD);
} }
} }

8
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.dedup; package eu.dnetlib.dhp.oa.dedup;
import java.io.Serializable; import java.io.Serializable;
@ -73,7 +74,8 @@ public class DedupRecordFactory {
} }
public static <T extends OafEntity> T entityMerger( public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) throws IllegalAccessException, InstantiationException { String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
throws IllegalAccessException, InstantiationException {
T entity = clazz.newInstance(); T entity = clazz.newInstance();
@ -87,14 +89,14 @@ public class DedupRecordFactory {
entity.mergeFrom(duplicate); entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) { if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate; Result r1 = (Result) duplicate;
if (r1.getAuthor() != null && r1.getAuthor().size()>0) if (r1.getAuthor() != null && r1.getAuthor().size() > 0)
authors.add(r1.getAuthor()); authors.add(r1.getAuthor());
if (r1.getDateofacceptance() != null) if (r1.getDateofacceptance() != null)
dates.add(r1.getDateofacceptance().getValue()); dates.add(r1.getDateofacceptance().getValue());
} }
}); });
//set authors and date // set authors and date
if (ModelSupport.isSubClass(entity, Result.class)) { if (ModelSupport.isSubClass(entity, Result.class)) {
((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setDateofacceptance(DatePicker.pick(dates));
((Result) entity).setAuthor(AuthorMerger.merge(authors)); ((Result) entity).setAuthor(AuthorMerger.merge(authors));

69
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -1,5 +1,8 @@
package eu.dnetlib.dhp.oa.dedup; package eu.dnetlib.dhp.oa.dedup;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.BufferedReader; import java.io.BufferedReader;
import java.io.FileReader; import java.io.FileReader;
import java.io.IOException; import java.io.IOException;
@ -7,15 +10,13 @@ import java.io.Serializable;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.*; import java.util.*;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.codehaus.jackson.map.ObjectMapper; import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import scala.Tuple2;
import static org.junit.jupiter.api.Assertions.assertEquals; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class EntityMergerTest implements Serializable { public class EntityMergerTest implements Serializable {
@ -30,9 +31,9 @@ public class EntityMergerTest implements Serializable {
public void setUp() throws Exception { public void setUp() throws Exception {
testEntityBasePath = Paths testEntityBasePath = Paths
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
.toFile() .toFile()
.getAbsolutePath(); .getAbsolutePath();
publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class);
@ -45,7 +46,8 @@ public class EntityMergerTest implements Serializable {
@Test @Test
public void publicationMergerTest() throws InstantiationException, IllegalAccessException { public void publicationMergerTest() throws InstantiationException, IllegalAccessException {
Publication pub_merged = DedupRecordFactory.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
assertEquals(dedupId, pub_merged.getId()); assertEquals(dedupId, pub_merged.getId());
@ -59,36 +61,36 @@ public class EntityMergerTest implements Serializable {
assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation()); assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation());
assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance()); assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance());
assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection()); assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection());
assertEquals(pub_merged.getInstance().size(),3); assertEquals(pub_merged.getInstance().size(), 3);
assertEquals(pub_merged.getCountry().size(), 2); assertEquals(pub_merged.getCountry().size(), 2);
assertEquals(pub_merged.getSubject().size(), 0); assertEquals(pub_merged.getSubject().size(), 0);
assertEquals(pub_merged.getTitle().size(), 2); assertEquals(pub_merged.getTitle().size(), 2);
assertEquals(pub_merged.getRelevantdate().size(),0); assertEquals(pub_merged.getRelevantdate().size(), 0);
assertEquals(pub_merged.getDescription().size(),0); assertEquals(pub_merged.getDescription().size(), 0);
assertEquals(pub_merged.getSource().size(),0); assertEquals(pub_merged.getSource().size(), 0);
assertEquals(pub_merged.getFulltext().size(),0); assertEquals(pub_merged.getFulltext().size(), 0);
assertEquals(pub_merged.getFormat().size(),0); assertEquals(pub_merged.getFormat().size(), 0);
assertEquals(pub_merged.getContributor().size(),0); assertEquals(pub_merged.getContributor().size(), 0);
assertEquals(pub_merged.getCoverage().size(),0); assertEquals(pub_merged.getCoverage().size(), 0);
assertEquals(pub_merged.getContext().size(),0); assertEquals(pub_merged.getContext().size(), 0);
assertEquals(pub_merged.getExternalReference().size(),0); assertEquals(pub_merged.getExternalReference().size(), 0);
assertEquals(pub_merged.getOriginalId().size(),3); assertEquals(pub_merged.getOriginalId().size(), 3);
assertEquals(pub_merged.getCollectedfrom().size(),3); assertEquals(pub_merged.getCollectedfrom().size(), 3);
assertEquals(pub_merged.getPid().size(),1); assertEquals(pub_merged.getPid().size(), 1);
assertEquals(pub_merged.getExtraInfo().size(),0); assertEquals(pub_merged.getExtraInfo().size(), 0);
//verify datainfo // verify datainfo
assertEquals(pub_merged.getDataInfo(), dataInfo); assertEquals(pub_merged.getDataInfo(), dataInfo);
//verify datepicker // verify datepicker
assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
//verify authors // verify authors
assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(pub_merged.getAuthor().size(), 9);
assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
} }
public DataInfo setDI(){ public DataInfo setDI() {
DataInfo dataInfo = new DataInfo(); DataInfo dataInfo = new DataInfo();
dataInfo.setTrust("0.9"); dataInfo.setTrust("0.9");
dataInfo.setDeletedbyinference(false); dataInfo.setDeletedbyinference(false);
@ -97,13 +99,13 @@ public class EntityMergerTest implements Serializable {
return dataInfo; return dataInfo;
} }
public Publication getTopPub(List<Tuple2<String, Publication>> publications){ public Publication getTopPub(List<Tuple2<String, Publication>> publications) {
Double maxTrust = 0.0; Double maxTrust = 0.0;
Publication maxPub = new Publication(); Publication maxPub = new Publication();
for (Tuple2<String, Publication> publication : publications) { for (Tuple2<String, Publication> publication : publications) {
Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust()); Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
if(pubTrust > maxTrust){ if (pubTrust > maxTrust) {
maxTrust = pubTrust; maxTrust = pubTrust;
maxPub = publication._2(); maxPub = publication._2();
} }
@ -118,11 +120,11 @@ public class EntityMergerTest implements Serializable {
reader = new BufferedReader(new FileReader(path)); reader = new BufferedReader(new FileReader(path));
String line = reader.readLine(); String line = reader.readLine();
while (line != null) { while (line != null) {
res.add( res
.add(
new Tuple2<>( new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line), MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)) new ObjectMapper().readValue(line, clazz)));
);
// read next line // read next line
line = reader.readLine(); line = reader.readLine();
} }
@ -134,5 +136,4 @@ public class EntityMergerTest implements Serializable {
return res; return res;
} }
} }

141
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -59,8 +59,10 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Qualifier ORCID_PID_TYPE = qualifier(
protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier MAG_PID_TYPE = qualifier(
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Map<String, String> nsContext = new HashMap<>(); protected static final Map<String, String> nsContext = new HashMap<>();
@ -74,7 +76,8 @@ public abstract class AbstractMdRecordToOafMapper {
nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
} }
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) { protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name; this.code2name = code2name;
@ -88,15 +91,20 @@ public abstract class AbstractMdRecordToOafMapper {
.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); .parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
final String type = doc.valueOf("//dr:CobjCategory/@type"); final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); final KeyValue collectedFrom = getProvenanceDatasource(
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
if (collectedFrom == null) { return null; } if (collectedFrom == null) {
return null;
}
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom ? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
if (hostedBy == null) { return null; } if (hostedBy == null) {
return null;
}
final DataInfo info = prepareDataInfo(doc); final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime(); final long lastUpdateTimestamp = new Date().getTime();
@ -111,7 +119,9 @@ public abstract class AbstractMdRecordToOafMapper {
final String dsId = doc.valueOf(xpathId); final String dsId = doc.valueOf(xpathId);
final String dsName = doc.valueOf(xpathName); final String dsName = doc.valueOf(xpathName);
if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
return null;
}
return keyValue(createOpenaireId(10, dsId, true), dsName); return keyValue(createOpenaireId(10, dsId, true), dsName);
} }
@ -127,47 +137,47 @@ public abstract class AbstractMdRecordToOafMapper {
final List<Oaf> oafs = new ArrayList<>(); final List<Oaf> oafs = new ArrayList<>();
switch (type.toLowerCase()) { switch (type.toLowerCase()) {
case "publication": case "publication":
final Publication p = new Publication(); final Publication p = new Publication();
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
p.setJournal(prepareJournal(doc, info)); p.setJournal(prepareJournal(doc, info));
oafs.add(p); oafs.add(p);
break; break;
case "dataset": case "dataset":
final Dataset d = new Dataset(); final Dataset d = new Dataset();
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setResulttype(DATASET_DEFAULT_RESULTTYPE); d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info)); d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info)); d.setSize(prepareDatasetSize(doc, info));
d.setVersion(prepareDatasetVersion(doc, info)); d.setVersion(prepareDatasetVersion(doc, info));
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
d.setGeolocation(prepareDatasetGeoLocations(doc, info)); d.setGeolocation(prepareDatasetGeoLocations(doc, info));
oafs.add(d); oafs.add(d);
break; break;
case "software": case "software":
final Software s = new Software(); final Software s = new Software();
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
oafs.add(s); oafs.add(s);
break; break;
case "": case "":
case "otherresearchproducts": case "otherresearchproducts":
default: default:
final OtherResearchProduct o = new OtherResearchProduct(); final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
o.setResulttype(ORP_DEFAULT_RESULTTYPE); o.setResulttype(ORP_DEFAULT_RESULTTYPE);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info));
oafs.add(o); oafs.add(o);
break; break;
} }
if (!oafs.isEmpty()) { if (!oafs.isEmpty()) {
@ -196,9 +206,15 @@ public abstract class AbstractMdRecordToOafMapper {
final String projectId = createOpenaireId(40, originalId, true); final String projectId = createOpenaireId(40, originalId, true);
res res
.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
lastUpdateTimestamp));
res res
.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
lastUpdateTimestamp));
} }
} }
@ -244,7 +260,9 @@ public abstract class AbstractMdRecordToOafMapper {
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setCollectedfrom(Arrays.asList(collectedFrom));
r r
.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); .setPid(
prepareListStructProps(
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@ -362,7 +380,9 @@ public abstract class AbstractMdRecordToOafMapper {
final String sp = n.valueOf("@sp"); final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol"); final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition"); final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } if (StringUtils.isNotBlank(name)) {
return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
}
} }
return null; return null;
} }
@ -415,7 +435,10 @@ public abstract class AbstractMdRecordToOafMapper {
for (final Object o : node.selectNodes(xpath)) { for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o; final Node n = (Node) o;
res res
.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); .add(
structuredProperty(
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
n.valueOf("@schemename"), info));
} }
return res; return res;
} }
@ -423,7 +446,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected OAIProvenance prepareOAIprovenance(final Document doc) { protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) { return null; } if (n == null) {
return null;
}
final String identifier = n.valueOf("./*[local-name()='identifier']"); final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']");
@ -438,7 +463,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected DataInfo prepareDataInfo(final Document doc) { protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo"); final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@ -450,7 +477,9 @@ public abstract class AbstractMdRecordToOafMapper {
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf:trust"); final String trust = n.valueOf("./oaf:trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); return dataInfo(
deletedbyinference, inferenceprovenance, inferred, false,
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
} }
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) { protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {

35
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -56,7 +56,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
} }
final String pid = e.valueOf("./@nameIdentifier"); final String pid = e.valueOf("./@nameIdentifier");
final String type = e.valueOf("./@nameIdentifierScheme") final String type = e
.valueOf("./@nameIdentifierScheme")
.trim() .trim()
.toUpperCase() .toUpperCase()
.replaceAll(" ", "") .replaceAll(" ", "")
@ -66,7 +67,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
if (StringUtils.isNotBlank(pid)) { if (StringUtils.isNotBlank(pid)) {
if (type.startsWith("ORCID")) { if (type.startsWith("ORCID")) {
final String cleanedId = pid.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", ""); final String cleanedId = pid
.replaceAll("http://orcid.org/", "")
.replaceAll("https://orcid.org/", "");
author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info)); author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info));
} else if (type.startsWith("MAGID")) { } else if (type.startsWith("MAGID")) {
author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info)); author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info));
@ -127,7 +130,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance(); final Instance instance = new Instance();
instance instance
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); .setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom); instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby); instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@ -143,13 +147,14 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
instance instance
.setUrl(nodes .setUrl(
.stream() nodes
.filter(n -> StringUtils.isNotBlank(n.getText())) .stream()
.map(n -> n.getText().trim()) .filter(n -> StringUtils.isNotBlank(n.getText()))
.filter(u -> u.startsWith("http")) .map(n -> n.getText().trim())
.distinct() .filter(u -> u.startsWith("http"))
.collect(Collectors.toCollection(ArrayList::new))); .distinct()
.collect(Collectors.toCollection(ArrayList::new)));
return Lists.newArrayList(instance); return Lists.newArrayList(instance);
} }
@ -274,9 +279,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final String otherId = createOpenaireId(50, originalId, false); final String otherId = createOpenaireId(50, originalId, false);
res res
.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
res res
.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
} }
} }
return res; return res;

47
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -94,7 +94,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
for (final Object o : n.selectNodes("./datacite:nameIdentifier")) { for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
final String id = ((Node) o).getText(); final String id = ((Node) o).getText();
final String type = ((Node) o).valueOf("./@nameIdentifierScheme") final String type = ((Node) o)
.valueOf("./@nameIdentifierScheme")
.trim() .trim()
.toUpperCase() .toUpperCase()
.replaceAll(" ", "") .replaceAll(" ", "")
@ -119,7 +120,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance(); final Instance instance = new Instance();
instance instance
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); .setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom); instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby); instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@ -168,7 +170,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
&& !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Updated")
&& !dateType.equalsIgnoreCase("Available")) { && !dateType.equalsIgnoreCase("Available")) {
res res
.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info)); .add(
structuredProperty(
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
info));
} }
} }
return res; return res;
@ -220,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
protected List<Field<String>> prepareOtherResearchProductContactGroups( protected List<Field<String>> prepareOtherResearchProductContactGroups(
final Document doc, final Document doc,
final DataInfo info) { final DataInfo info) {
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info); return prepareListFields(
doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
} }
@Override @Override
protected List<Field<String>> prepareOtherResearchProductContactPersons( protected List<Field<String>> prepareOtherResearchProductContactPersons(
final Document doc, final Document doc,
final DataInfo info) { final DataInfo info) {
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info); return prepareListFields(
doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
} }
@Override @Override
@ -253,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
protected List<Field<String>> prepareSoftwareDocumentationUrls( protected List<Field<String>> prepareSoftwareDocumentationUrls(
final Document doc, final Document doc,
final DataInfo info) { final DataInfo info) {
return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); return prepareListFields(
doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
} }
// DATASETS // DATASETS
@ -327,16 +335,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
if (type.equalsIgnoreCase("IsSupplementTo")) { if (type.equalsIgnoreCase("IsSupplementTo")) {
res res
.add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info,
lastUpdateTimestamp));
res res
.add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
lastUpdateTimestamp));
} else if (type.equals("IsPartOf")) { } else if (type.equals("IsPartOf")) {
res res
.add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp)); .add(
getRelation(
docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info,
lastUpdateTimestamp));
res res
.add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp)); .add(
} else {} getRelation(
otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
lastUpdateTimestamp));
} else {
}
} }
} }
return res; return res;
@ -344,6 +365,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override @Override
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE); return prepareQualifier(
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
DNET_DATA_CITE_RESOURCE);
} }
} }