Fix for missing collectedfrom after dedup #442

Merged
claudio.atzori merged 1 commits from fix_mergedcliquesort into beta_to_master_may2024 2024-06-03 15:34:01 +02:00
6 changed files with 239 additions and 120 deletions

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@ -0,0 +1,104 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
public class MergeEntitiesComparator implements Comparator<Oaf> {
static final List<String> PID_AUTHORITIES = Arrays
.asList(
ModelConstants.ARXIV_ID,
ModelConstants.PUBMED_CENTRAL_ID,
ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
ModelConstants.DATACITE_ID,
ModelConstants.CROSSREF_ID);
static final List<String> RESULT_TYPES = Arrays
.asList(
ModelConstants.ORP_RESULTTYPE_CLASSID,
ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
ModelConstants.DATASET_RESULTTYPE_CLASSID,
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
@Override
public int compare(Oaf left, Oaf right) {
if (left == null && right == null)
return 0;
if (left == null)
return -1;
if (right == null)
return 1;
int res = 0;
// pid authority
int cfp1 = left
.getCollectedfrom()
.stream()
.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
.max(Integer::compare)
.orElse(-1);
int cfp2 = right
.getCollectedfrom()
.stream()
.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
.max(Integer::compare)
.orElse(-1);
if (cfp1 >= 0 && cfp1 > cfp2) {
return 1;
} else if (cfp2 >= 0 && cfp2 > cfp1) {
return -1;
}
// trust
if (left.getDataInfo() != null && right.getDataInfo() != null) {
res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
}
// result type
if (res == 0) {
if (left instanceof Result && right instanceof Result) {
Result r1 = (Result) left;
Result r2 = (Result) right;
if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
return -1;
}
} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
return 1;
}
int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
if (rt1 >= 0 && rt1 > rt2) {
return 1;
} else if (rt2 >= 0 && rt2 > rt1) {
return -1;
}
}
}
// id
if (res == 0) {
if (left instanceof OafEntity && right instanceof OafEntity) {
res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
}
}
return res;
}
}

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@ -40,27 +40,12 @@ public class MergeUtils {
public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
boolean checkDelegateAuthority) {
TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
int res = 0;
if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
}
ArrayList<T> sortedEntities = new ArrayList<>();
oafEntityIterator.forEachRemaining(sortedEntities::add);
sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
if (res == 0) {
if (o1 instanceof Result && o2 instanceof Result) {
return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
}
}
return res;
});
while (oafEntityIterator.hasNext()) {
sortedEntities.add(oafEntityIterator.next());
}
Iterator<T> it = sortedEntities.descendingIterator();
Iterator<T> it = sortedEntities.iterator();
T merged = it.next();
while (it.hasNext()) {
@ -143,7 +128,7 @@ public class MergeUtils {
* https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
* such version.
* <p>
* Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
* Otherwise, it considers a resulttype priority order implemented in {@link MergeEntitiesComparator}
* and proceeds with the canonical property merging.
*
* @param left
@ -161,8 +146,9 @@ public class MergeUtils {
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
// TODO: raise trust to have preferred fields from one or the other??
if (new ResultTypeComparator().compare(left, right) < 0) {
if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
return mergeResultFields(left, right);
} else {
return mergeResultFields(right, left);
@ -225,9 +211,9 @@ public class MergeUtils {
private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
Function<T, K> keyExtractor, BinaryOperator<T> merger) {
if (left == null) {
return right;
} else if (right == null) {
if (left == null || left.isEmpty()) {
return right != null ? right : new ArrayList<>();
} else if (right == null || right.isEmpty()) {
return left;
}
@ -405,7 +391,7 @@ public class MergeUtils {
}
// should be an instance attribute, get the first non-null value
merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
// distinct countries, do not manage datainfo
merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@ -575,6 +561,13 @@ public class MergeUtils {
return m != null ? m : e;
}
private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
return e;
}
return m;
}
private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
List<List<Author>> authors = new ArrayList<>();
if (author != null) {
@ -587,6 +580,10 @@ public class MergeUtils {
}
private static String instanceKeyExtractor(Instance i) {
// three levels of concatenating:
// 1. ::
// 2. @@
// 3. ||
return String
.join(
"::",
@ -594,10 +591,10 @@ public class MergeUtils {
kvKeyExtractor(i.getCollectedfrom()),
qualifierKeyExtractor(i.getAccessright()),
qualifierKeyExtractor(i.getInstancetype()),
Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
Optional
.ofNullable(i.getPid())
.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
.orElse(null));
}
@ -706,7 +703,7 @@ public class MergeUtils {
private static String spKeyExtractor(StructuredProperty sp) {
return Optional
.ofNullable(sp)
.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
.orElse(null);
}

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@ -1,87 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
return 0;
}
return 1;
} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
return -1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
if (!lClass.equals(rClass)) {
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
}
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

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@ -0,0 +1,103 @@
package eu.dnetlib.dhp.oa.dedup;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
class DatasetMergerTest implements Serializable {
private List<Tuple2<String, Dataset>> datasets;
private String testEntityBasePath;
private DataInfo dataInfo;
private final String dedupId = "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148";
private Dataset dataset_top;
@BeforeEach
public void setUp() throws Exception {
testEntityBasePath = Paths
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
.toFile()
.getAbsolutePath();
datasets = readSample(testEntityBasePath + "/dataset_merge.json", Dataset.class);
dataset_top = getTopPub(datasets);
dataInfo = setDI();
}
@Test
void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
// verify id
assertEquals(dedupId, pub_merged.getId());
assertEquals(2, pub_merged.getInstance().size());
}
public DataInfo setDI() {
DataInfo dataInfo = new DataInfo();
dataInfo.setTrust("0.9");
dataInfo.setDeletedbyinference(false);
dataInfo.setInferenceprovenance("testing");
dataInfo.setInferred(true);
return dataInfo;
}
public Dataset getTopPub(List<Tuple2<String, Dataset>> publications) {
Double maxTrust = 0.0;
Dataset maxPub = new Dataset();
for (Tuple2<String, Dataset> publication : publications) {
Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
if (pubTrust > maxTrust) {
maxTrust = pubTrust;
maxPub = publication._2();
}
}
return maxPub;
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
}

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@ -93,14 +93,14 @@ class EntityMergerTest implements Serializable {
assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
assertEquals(pub_top.getResulttype().getClassid(), pub_merged.getResulttype().getClassid());
assertEquals(pub_top.getLanguage().getClassid(), pub_merged.getLanguage().getClassid());
assertEquals("Elsevier BV", pub_merged.getPublisher().getValue());
assertEquals(pub_top.getEmbargoenddate().getValue(), pub_merged.getEmbargoenddate().getValue());
assertEquals(pub_top.getResourcetype().getClassid(), "");
assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
// assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
assertEquals(3, pub_merged.getInstance().size());
assertEquals(2, pub_merged.getCountry().size());
assertEquals(0, pub_merged.getSubject().size());

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