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Feature/fdo update #116

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merged 5 commits into from
Dec 10, 2024
Merged

Feature/fdo update #116

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a0934a9
fix fdo profile
southeo Dec 9, 2024
51585cc
Merge remote-tracking branch 'origin/main' into feature/fdo-update
southeo Dec 9, 2024
0ce2cbf
fix fdo profile
southeo Dec 9, 2024
0d058ff
remove license from request
southeo Dec 10, 2024
1a07390
fix test
southeo Dec 10, 2024
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3 changes: 1 addition & 2 deletions src/main/java/eu/dissco/core/handlemanager/domain/datacite/EventType.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,12 @@
package eu.dissco.core.handlemanager.domain.datacite;

import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
import eu.dissco.core.handlemanager.Profiles;
import org.springframework.context.annotation.Profile;

@Profile(Profiles.DOI)
public enum EventType {

@JsonProperty("create") CREATE,
@JsonPropertyOrder("update") UPDATE;
@JsonProperty("update") UPDATE;
}
14 changes: 8 additions & 6 deletions src/main/java/eu/dissco/core/handlemanager/domain/fdo/FdoProfile.java
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Expand Up @@ -41,7 +41,7 @@ public enum FdoProfile {
LIVING_OR_PRESERVED("livingOrPreserved", 208),
MATERIAL_SAMPLE_TYPE("materialSampleType", 209),
MARKED_AS_TYPE("markedAsType", 210),
CATALOG_IDENTIFIER("catalogIdentifier", 211),
CATALOG_NUMBER("catalogNumber", 211),

// Media
MEDIA_HOST("mediaHost", 400),
Expand All @@ -54,9 +54,9 @@ public enum FdoProfile {
MEDIA_TYPE("mediaType", 408),
MIME_TYPE("mimeType", 409),
LICENSE_NAME("licenseName", 410),
LICENSE_ID("licenseId", 411),
RIGHTS_HOLDER_NAME("rightsHolderName", 412),
RIGHTS_HOLDER_PID("rightsHolderId", 413),
LICENSE_URL("licenseUrl", 411),
RIGHTS_HOLDER_NAME("rightsHolder", 412),
RIGHTS_HOLDER_PID("rightsHolderPid", 413),

// Annotation
TARGET_PID("targetPid", 500),
Expand All @@ -76,7 +76,9 @@ public enum FdoProfile {

// Administration
HS_ADMIN("HS_ADMIN", 100),
LOC("10320/loc", 101);
LOC("10320/loc", 101),
UNRECOGNIZED("Unrecognized", 900);


private static final Map<String, FdoProfile> LOOKUP;

Expand All @@ -88,7 +90,7 @@ public enum FdoProfile {
}

public static FdoProfile fromString(String attributeName) {
return LOOKUP.get(attributeName);
return LOOKUP.getOrDefault(attributeName, UNRECOGNIZED);
}

private final String attribute;
Expand Down
11 changes: 6 additions & 5 deletions src/main/java/eu/dissco/core/handlemanager/repository/MongoRepository.java
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Expand Up @@ -111,11 +111,12 @@ private List<FdoRecord> formatResults(FindIterable<Document> results)

private static Map<FdoProfile, FdoAttribute> buildAttributeMap(
Collection<FdoAttribute> attributeList) {
return attributeList.stream().collect(Collectors.toMap(
a -> FdoProfile.fromString(a.getType()),
Function.identity(),
(oldVal, newVal) -> oldVal
));
return attributeList.stream()
.collect(Collectors.toMap(
a -> FdoProfile.fromString(a.getType()),
Function.identity(),
(oldVal, newVal) -> oldVal
));
}

private String getLocalId(JsonNode jsonRecord, FdoType fdoType) {
Expand Down
25 changes: 13 additions & 12 deletions src/main/java/eu/dissco/core/handlemanager/service/FdoRecordService.java
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Expand Up @@ -3,7 +3,7 @@

import static eu.dissco.core.handlemanager.configuration.AppConfig.DATE_STRING;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ANNOTATION_HASH;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_IDENTIFIER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_NUMBER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.DIGITAL_OBJECT_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.DIGITAL_OBJECT_TYPE;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.FDO_PROFILE;
Expand All @@ -13,8 +13,8 @@
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.HS_ADMIN;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ISSUED_FOR_AGENT;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ISSUED_FOR_AGENT_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_ID;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_URL;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LINKED_DO_PID;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LINKED_DO_TYPE;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LIVING_OR_PRESERVED;
Expand Down Expand Up @@ -366,7 +366,7 @@ private Map<FdoProfile, FdoAttribute> prepareDigitalSpecimenAttributes(
throws InvalidRequestException, JsonProcessingException {
var handleAttributeList = new EnumMap<FdoProfile, FdoAttribute>(FdoProfile.class);
// 101: 10320/Loc
var keyAttribute = getSpecimenResolvableId(request.getCatalogIdentifier(),
var keyAttribute = getSpecimenResolvableId(request.getCatalogNumber(),
request.getOtherSpecimenIds());
handleAttributeList.put(LOC,
new FdoAttribute(LOC, timestamp,
Expand Down Expand Up @@ -416,8 +416,8 @@ private Map<FdoProfile, FdoAttribute> prepareDigitalSpecimenAttributes(
handleAttributeList.put(MARKED_AS_TYPE,
new FdoAttribute(MARKED_AS_TYPE, timestamp, request.getMarkedAsType()));
// 211 Catalog Number
handleAttributeList.put(CATALOG_IDENTIFIER,
new FdoAttribute(CATALOG_IDENTIFIER, timestamp, request.getCatalogIdentifier()));
handleAttributeList.put(CATALOG_NUMBER,
new FdoAttribute(CATALOG_NUMBER, timestamp, request.getCatalogNumber()));
return handleAttributeList;
}

Expand Down Expand Up @@ -552,15 +552,16 @@ public Map<FdoProfile, FdoAttribute> prepareDigitalMediaAttributes(
handleAttributeList.put(LICENSE_NAME,
new FdoAttribute(LICENSE_NAME, timestamp, request.getLicenseName()));
// 410 License Id
handleAttributeList.put(LICENSE_ID,
new FdoAttribute(LICENSE_ID, timestamp, request.getLicenseId()));
// 411 Rights Holder Id
handleAttributeList.put(LICENSE_URL,
new FdoAttribute(LICENSE_URL, timestamp, request.getLicenseUrl()));
// 411 Rights Holder Pid
var rightsHolder =
request.getRightsHolderId() == null ? request.getMediaHost() : request.getRightsHolderId();
request.getRightsHolderPid() == null ? request.getMediaHost()
: request.getRightsHolderPid();
handleAttributeList.put(RIGHTS_HOLDER_PID,
new FdoAttribute(RIGHTS_HOLDER_PID, timestamp, rightsHolder));
String rightsHolderName = request.getRightsHolderName() != null ?
getObjectName(request.getRightsHolderId(), request.getRightsHolderName()) : mediaHostName;
String rightsHolderName = request.getRightsHolder() != null ?
getObjectName(request.getRightsHolderPid(), request.getRightsHolder()) : mediaHostName;
// 412 Rights Holder Name
handleAttributeList.put(RIGHTS_HOLDER_NAME,
new FdoAttribute(RIGHTS_HOLDER_NAME, timestamp, rightsHolderName));
Expand Down Expand Up @@ -812,7 +813,7 @@ private String getKeyLocationFromPidRecord(Map<FdoProfile, FdoAttribute> fdoAttr
try {
switch (fdoType) {
case DIGITAL_SPECIMEN -> {
var catalogIdValue = fdoAttributes.get(CATALOG_IDENTIFIER);
var catalogIdValue = fdoAttributes.get(CATALOG_NUMBER);
var catalogId = catalogIdValue == null ? null : catalogIdValue.getValue();
var otherSpecimenIdsField = fdoAttributes.get(OTHER_SPECIMEN_IDS);
var otherSpecimenIds =
Expand Down
19 changes: 14 additions & 5 deletions src/main/resources/json-schema/digital-media-request-attributes.json
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Expand Up @@ -61,35 +61,44 @@
"type": "string",
"description": "Only mimetypes for audio, image, model, video, text should be provided. https://www.iana.org/assignments/media-types/media-types.xhtml"
},
"license": {
"type": "string",
"description": "Maps to dcterms:license, unenforced value that may or may not be machine actionable. http://purl.org/dc/terms/license.",
"example": "CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
"$comment": "idx = 409"
},
"licenseName": {
"type": "string",
"description": "Human-readable name of the license",
"example": "CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
"$comment": "idx = 409"
},
"licenseId": {
"licenseUrl": {
"type": "string",
"description": "Machine-actionable licensing information. Uses SPDX Identifiers.",
"example": "https://spdx.org/licenses/CC0-1.0",
"$comment": "idx = 410"
},
"rightsHolderName": {
"rightsHolder": {
"type": "string",
"description": "If not present, defaults to mediaHost, https://purl.org/dc/terms/rightsHolder",
"example": "https://ror.org/0566bfb96"
},
"rightsHolderId": {
"rightsHolderPid": {
"type": "string",
"description": "Resolvable identifier of the rights holder",
"example": "https://ror.org/0566bfb96"
}
},
"required": [
"referentName",
"mediaHost",
"mediaHostName",
"linkedDigitalObjectPid",
"linkedDigitalObjectType",
"primaryMediaId"
"primaryMediaId",
"license",
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license is a required field but in the Service I don't think we actually set license. Couldn't that create a potential issue?

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Ok this should be removed, also made a pr on opends. If we don't have a license in the FDO record I think we'll somehow survive

"rightsHolder"
],
"additionalProperties": false
}
}
31 changes: 9 additions & 22 deletions src/main/resources/json-schema/digital-specimen-request-attributes.json
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Expand Up @@ -2,7 +2,7 @@
"$id": "https://schemas.dissco.tech/schemas/fdo-profile/digital-specimen/0.1.0/digital-specimen-request-attributes.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Attributes of a request to the DiSSCo PID API to create a FDO Record for a digital specimen",
"$comment": "FDO Profile Version 1.0.0",
"$comment": "FDO Profile Version 0.1.0",
"properties": {
"locations": {
"type": "array",
Expand Down Expand Up @@ -94,7 +94,7 @@
"enum": [
"Human remains",
"Hominid remains",
"Macrofungi, Lichens & Myxomycetes",
"Mycology",
"Algae",
"Bryophytes",
"Pteridophytes",
Expand Down Expand Up @@ -128,18 +128,13 @@
"Other Palaeontology Objects",
"Minerals and Gems",
"Loose Sediment Sample",
"Mixed Solid Matter Sample",
"Mixed Solid Mater Sample",
"Water-Ice Sample",
"Liquid or Gaseous Matter Sample",
"Mixed Geology Objects",
"Terrestrial Finds/Falls",
"Terrestrial Impacta",
"Sample Returns",
"Sedimentary Rock",
"Metamorphic or Igneous Rock",
"Plant Genetic Resource",
"Floral and Faunal remains",
"Other Anthropology Objects",
"Unclassified"
],
"description": "Countable things (objects) served as a more detailed classification of each of the disciplines."
Expand All @@ -153,28 +148,20 @@
},
"materialSampleType": {
"enum": [
"Whole organism specimen",
"Organism part",
"Organism product",
"Biome aggregation",
"Bundle biome aggregation",
"Fossil",
"Any biological specimen",
"Aggregation",
"Slurry biome aggregation",
"Other solid object",
"Biological material sample",
"Fluid in container",
"Anthropogenic aggregation",
"Artefact",
"Any aggregation specimen"
"Fluid in container",
"Non biologic solid object",
"Research product"
],
"description": "https://isamplesorg.github.io/models/generated/vocabularies/specimenType.html"
},
"markedAsType": {
"type": "boolean",
"description": "TRUE if the specimen is marked as type with a stamp or label."
},
"catalogIdentifier": {
"catalogNumber": {
"type": "string",
"description": "Identifier of source system catalog"
}
Expand All @@ -184,4 +171,4 @@
"normalisedPrimarySpecimenObjectId"
],
"additionalProperties": false
}
}
10 changes: 5 additions & 5 deletions src/test/java/eu/dissco/core/handlemanager/service/FdoRecordServiceTest.java
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@@ -1,6 +1,6 @@
package eu.dissco.core.handlemanager.service;

import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_IDENTIFIER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_NUMBER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LOC;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.OTHER_SPECIMEN_IDS;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.PID_RECORD_ISSUE_NUMBER;
Expand Down Expand Up @@ -347,10 +347,10 @@ void testPrepareNewDigitalSpecimenRecord() throws Exception {
@Test
void testPrepareNewDigitalSpecimenRecordNoOtherSpecimen() throws Exception {
// Given
var request = givenDigitalSpecimen().withCatalogIdentifier(null);
var request = givenDigitalSpecimen().withCatalogNumber(null);
var expectedAttributes = new EnumMap<>(givenDigitalSpecimenFdoRecord(HANDLE).attributes());
expectedAttributes.replace(CATALOG_IDENTIFIER,
new FdoAttribute(CATALOG_IDENTIFIER, CREATED, null));
expectedAttributes.replace(CATALOG_NUMBER,
new FdoAttribute(CATALOG_NUMBER, CREATED, null));
expectedAttributes.replace(LOC,
new FdoAttribute(LOC, CREATED, setLocations(HANDLE, FdoType.DIGITAL_SPECIMEN, false)));

Expand All @@ -373,7 +373,7 @@ void testPrepareNewDigitalSpecimenRecordNoOtherSpecimen() throws Exception {
void testGetSpecimenResolvableIdOtherId(String catalogId) throws Exception {
// Given
var keyLoc = CATALOG_ID_TEST + "A";
var request = givenDigitalSpecimen().withCatalogIdentifier(catalogId).withOtherSpecimenIds(
var request = givenDigitalSpecimen().withCatalogNumber(catalogId).withOtherSpecimenIds(
List.of(new OtherspecimenIds().withIdentifierType("Local id").withIdentifierValue("ABC")
.withResolvable(false),
new OtherspecimenIds().withIdentifierType("Resolvable id").withIdentifierValue(keyLoc)
Expand Down
17 changes: 9 additions & 8 deletions src/test/java/eu/dissco/core/handlemanager/testUtils/TestUtils.java
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@@ -1,7 +1,7 @@
package eu.dissco.core.handlemanager.testUtils;

import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ANNOTATION_HASH;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_IDENTIFIER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.CATALOG_NUMBER;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.DIGITAL_OBJECT_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.DIGITAL_OBJECT_TYPE;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.FDO_PROFILE;
Expand All @@ -11,8 +11,8 @@
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.HS_ADMIN;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ISSUED_FOR_AGENT;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.ISSUED_FOR_AGENT_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_ID;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_NAME;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LICENSE_URL;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LINKED_DO_PID;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LINKED_DO_TYPE;
import static eu.dissco.core.handlemanager.domain.fdo.FdoProfile.LIVING_OR_PRESERVED;
Expand Down Expand Up @@ -382,8 +382,8 @@ public static Map<FdoProfile, FdoAttribute> genDigitalSpecimenAttributes(String
fdoRecord.put(MATERIAL_SAMPLE_TYPE, new FdoAttribute(MATERIAL_SAMPLE_TYPE, timestamp, null));
fdoRecord.put(MARKED_AS_TYPE,
new FdoAttribute(MARKED_AS_TYPE, timestamp, null));
fdoRecord.put(CATALOG_IDENTIFIER,
new FdoAttribute(CATALOG_IDENTIFIER, timestamp, CATALOG_ID_TEST));
fdoRecord.put(CATALOG_NUMBER,
new FdoAttribute(CATALOG_NUMBER, timestamp, CATALOG_ID_TEST));
return fdoRecord;
}

Expand Down Expand Up @@ -426,7 +426,7 @@ public static Map<FdoProfile, FdoAttribute> genDigitalMediaAttributes(String han
fdoRecord.put(MEDIA_TYPE, new FdoAttribute(MEDIA_TYPE, timestamp, null));
fdoRecord.put(MIME_TYPE, new FdoAttribute(MIME_TYPE, timestamp, null));
fdoRecord.put(LICENSE_NAME, new FdoAttribute(LICENSE_NAME, timestamp, null));
fdoRecord.put(LICENSE_ID, new FdoAttribute(LICENSE_ID, timestamp, null));
fdoRecord.put(LICENSE_URL, new FdoAttribute(LICENSE_URL, timestamp, null));
fdoRecord.put(RIGHTS_HOLDER_NAME,
new FdoAttribute(RIGHTS_HOLDER_NAME, timestamp, SPECIMEN_HOST_NAME_TESTVAL));
fdoRecord.put(RIGHTS_HOLDER_PID,
Expand Down Expand Up @@ -605,7 +605,7 @@ public static DoiKernelRequestAttributes givenDoiKernelUpdated() {

public static DigitalSpecimenRequestAttributes givenDigitalSpecimen() {
return new DigitalSpecimenRequestAttributes()
.withCatalogIdentifier(CATALOG_ID_TEST)
.withCatalogNumber(CATALOG_ID_TEST)
.withReferentName(REFERENT_NAME_TESTVAL)
.withSpecimenHost(SPECIMEN_HOST_TESTVAL)
.withSpecimenHostName(SPECIMEN_HOST_NAME_TESTVAL)
Expand All @@ -624,9 +624,10 @@ public static DigitalMediaRequestAttributes givenDigitalMedia() {
.withMediaHostName(MEDIA_HOST_NAME_TESTVAL)
.withLinkedDigitalObjectPid(LINKED_DO_PID_TESTVAL)
.withLinkedDigitalObjectType(DIGITAL_SPECIMEN.getDigitalObjectType())
.withRightsHolderId(SPECIMEN_HOST_TESTVAL)
.withRightsHolderPid(SPECIMEN_HOST_TESTVAL)
.withPrimaryMediaId(PRIMARY_MEDIA_ID_TESTVAL)
.withRightsHolderName(SPECIMEN_HOST_NAME_TESTVAL);
.withRightsHolder(SPECIMEN_HOST_NAME_TESTVAL)
.withLicense("https://spdx.org/licenses/CC0-1.0.json");
}

public static DigitalMediaRequestAttributes givenDigitalMediaUpdated() {
Expand Down
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