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Merge branch 'master' into datasource_model_eosc

This commit is contained in:
Claudio Atzori 2021-07-29 17:27:30 +02:00
parent 97c5fe44d8 269e166661
commit 00693d6f9b
7 changed files with 102 additions and 9 deletions
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15
src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
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@ -1,7 +1,10 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
@ -13,6 +16,9 @@ public class ModelConstants {
public static final String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
public static final String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
public static final String ZENODO_OD_ID = "10|opendoar____::358aee4cc897452c00244351e4d91f69";
public static final String ZENODO_R3_ID = "10|re3data_____::7b0ad08687b2c960d5aeef06f811d5e6";
public static final String EUROPE_PUBMED_CENTRAL_ID = "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c";
public static final String PUBMED_CENTRAL_ID = "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357";
public static final String ARXIV_ID = "10|opendoar____::6f4922f45568161a8cdf4ad2299f6d23";
@ -21,6 +27,9 @@ public class ModelConstants {
// VOCABULARY VALUE
public static final String ACCESS_RIGHT_OPEN = "OPEN";
public static final String ACCESS_RIGHT_EMBARGO = "EMBARGO";
public static final String ACCESS_RIGHT_CLOSED = "CLOSED";
public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
@ -194,8 +203,8 @@ public class ModelConstants {
return q;
}
private static KeyValue keyValue(String key, String value) {
KeyValue kv = new KeyValue();
private static KeyValue keyValue(final String key, final String value) {
final KeyValue kv = new KeyValue();
kv.setKey(key);
kv.setValue(value);
kv.setDataInfo(new DataInfo());

34
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
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@ -40,6 +40,8 @@ public class IdentifierFactory implements Serializable {
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.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
@ -53,6 +55,18 @@ public class IdentifierFactory implements Serializable {
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
*/
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
static {
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
}
@ -164,24 +178,38 @@ public class IdentifierFactory implements Serializable {
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> shouldFilterPid(collectedFrom, p, mapHandles))
.filter(p -> shouldFilterPidByAuthority(collectedFrom, p, mapHandles))
.map(CleaningFunctions::normalizePidValue)
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPid(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
private static boolean shouldFilterPidByAuthority(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
return (mapHandles && pType.equals(PidType.handle)) || Optional.ofNullable(collectedFrom).isPresent() &&
Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(authorities -> {
return authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue());
|| authorities.containsValue(collectedFrom.getValue());
})
.orElse(false);
}
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
if (Objects.isNull(da)) {
return true;
}
if (!da.containsKey(collectedFrom.getKey())) {
return true;
}
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/

3
src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
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@ -34,6 +34,9 @@ public class IdentifierFactoryTest {
verifyIdentifier(
"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
verifyIdentifier(
"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);

2
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
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@ -3,7 +3,7 @@
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::1234",
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [

2
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi4.json
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@ -3,7 +3,7 @@
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::1234",
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [

37
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi5.json Normal file
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@ -0,0 +1,37 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.5281/zenodo.5121485"
}
]
},
{
"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"
}
]
}
]
}

18
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc1.json
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@ -1 +1,17 @@
{"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":"pmc"},"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": "pmc"},
"value": "21459329"
}
]
}