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IdentifierFactory implementation based on the list of datasources authoritative for a given pid type

Browse Source
pull/104/head
Claudio Atzori 3 years ago
parent b3f3b895e5
commit 01630f638d
13 changed files with 289 additions and 58 deletions
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27
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java
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@ -14,6 +14,8 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
public class CleaningFunctions {
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10.)";
public static final String DOI_PREFIX = "10.";
public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
@ -263,6 +265,29 @@ public class CleaningFunctions {
classid, classname, scheme, scheme);
}
/**
* Utility method that filter PID values on a per-type basis.
* @param pid the PID whose value will be checked.
* @return true the PID containing the normalised value.
*/
private static boolean filterPid(StructuredProperty pid) {
String value = Optional
.ofNullable(pid.getValue())
.map(s -> StringUtils.replaceAll(s, "\\s", ""))
.orElse("");
if (StringUtils.isBlank(value)) {
return false;
}
switch (pid.getQualifier().getClassid()) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.startsWith(DOI_PREFIX);
default:
return true;
}
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
@ -277,7 +302,7 @@ public class CleaningFunctions {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10."));
pid.setValue(value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX));
break;
}
return pid;

2
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java
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@ -9,9 +9,9 @@ import java.util.function.Function;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.utils.DHPUtils;

116
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
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@ -1,23 +1,23 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.HashBiMap;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.DHPUtils;
/**
@ -35,44 +35,37 @@ public class IdentifierFactory implements Serializable {
public static final int ID_PREFIX_LEN = 12;
public static final HashBiMap<String, String> PID_AUTHORITY = HashBiMap.create(2);
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID
*/
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
static {
PID_AUTHORITY.put(ModelConstants.CROSSREF_ID, "Crossref");
PID_AUTHORITY.put(ModelConstants.DATACITE_ID, "Datacite");
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
}
/**
* Creates an identifier from the most relevant PID (if available) in the given entity T. Returns entity.id
* when no PID is available
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
*
* @param entity the entity providing PIDs and a default ID.
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
* @param md5 indicates whether should hash the PID value or not.
* @return an identifier from the most relevant PID, entity.id otherwise
*/
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
if (Objects.isNull(entity.getPid()) || entity.getPid().isEmpty()) {
return entity.getId();
}
if (Optional.ofNullable(
entity.getCollectedfrom())
.map(c -> c.stream()
.noneMatch(cf -> PID_AUTHORITY.containsKey(cf.getKey()) || PID_AUTHORITY.containsValue(cf.getValue())))
.orElse(true)) {
return entity.getId();
}
Map<String, List<StructuredProperty>> pids = entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(IdentifierFactory::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toList())));
final Map<String, List<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
@ -93,6 +86,57 @@ public class IdentifierFactory implements Serializable {
.orElseGet(entity::getId);
}
private static <T extends OafEntity> Map<String, List<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(
instance -> instance
.stream()
.map(
i -> Optional
.ofNullable(i.getPid())
.map(
pp -> pp
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
return Optional.ofNullable(i.getCollectedfrom()).isPresent() &&
Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(authorities -> {
final KeyValue cf = i.getCollectedfrom();
return authorities.containsKey(cf.getKey())
|| authorities.containsValue(cf.getValue());
})
.orElse(false);
})
.map(CleaningFunctions::normalizePidValue)
.filter(IdentifierFactory::pidFilter))
.orElse(Stream.empty()))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toList()))))
.orElse(new HashMap<>());
} else {
return entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(IdentifierFactory::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toList())));
}
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/

6
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java
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@ -1,6 +1,8 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
@ -12,6 +14,8 @@ public class BlackListProviderTest {
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
Assertions.assertNull(PidBlacklistProvider.getBlacklist("xxx"));
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
Assertions.assertNotNull(xxx);
Assertions.assertEquals(0, xxx.size());
}
}

23
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
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@ -23,28 +23,35 @@ public class IdentifierFactoryTest {
public void testCreateIdentifierForPublication() throws IOException {
verifyIdentifier(
"publication_doi1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::" + DHPUtils.md5("10.1016/j.cmet.2010.03.013"), true);
verifyIdentifier("publication_pmc1.json", "50|pmc_________::" + DHPUtils.md5("21459329"), true);
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_urn1.json",
"50|urn_________::" + DHPUtils.md5("urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"), true);
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, true);
verifyIdentifier("publication_4.json", defaultID, true);
verifyIdentifier("publication_5.json", defaultID, true);
}
@Test
public void testCreateIdentifierForPublicationNoHash() throws IOException {
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2011.03.013", false);
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_pmc1.json", "50|pmc_________::21459329", false);
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
verifyIdentifier(
"publication_urn1.json", "50|urn_________::urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2", false);
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, false);

34
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi1.json
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@ -1 +1,33 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[ {"qualifier":{"classid":"doi"},"value":"10.12739/10.12739"},{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]}
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
"value": "Crossref"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

38
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi2.json
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@ -1 +1,37 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2010.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}],"collectedfrom":[{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"}]}
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
"value": "Crossref"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

37
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
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@ -0,0 +1,37 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::1234",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

21
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
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@ -0,0 +1,21 @@
{
"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier":{"classid":"pmc"},
"value":"21459329"
}
]
}
]
}

24
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json
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@ -1 +1,23 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmcid"},"value":"21459329"}]}
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"pid": [
{
"qualifier": {
"classid": "urn"
},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {
"classid": "scp-number"
},
"value": "79953761260"
},
{
"qualifier": {
"classid": "pmcid"
},
"value": "21459329"
}
]
}

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
Unescape Escape View File

@ -14,6 +14,9 @@ public class ModelConstants {
public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
public static String EUROPE_PUBMED_CENTRAL_ID = "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c";
public static String PUBMED_CENTRAL_ID = "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357";
public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource";

12
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
Unescape Escape View File

@ -236,11 +236,11 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
@ -250,7 +250,7 @@ public abstract class AbstractMdRecordToOafMapper {
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
final String validationDate) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);

4
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
Unescape Escape View File

@ -71,7 +71,7 @@ public class MappersTest {
assertValidId(p.getId());
assertEquals(2, p.getOriginalId().size());
assertEquals(1, p.getOriginalId().size());
assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718"));
assertValidId(p.getCollectedfrom().get(0).getKey());
@ -186,7 +186,7 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
assertEquals(2, d.getOriginalId().size());
assertEquals(1, d.getOriginalId().size());
assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526"));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));

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