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1.0 fdo profile #138

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Oct 7, 2024
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1.0 fdo profile #138

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1.0 fdo profile
southeo Sep 3, 2024
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1.0 fdo profile
southeo Sep 3, 2024
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Merge remote-tracking branch 'refs/remotes/origin/master' into featur…
southeo Sep 16, 2024
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add digital specimen/media 1.0.0
southeo Sep 16, 2024
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add digital specimen/media 1.0.0
southeo Sep 17, 2024
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Merge remote-tracking branch 'refs/remotes/origin/master' into featur…
southeo Sep 24, 2024
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Merge remote-tracking branch 'refs/remotes/origin/master' into featur…
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code review
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32 changes: 20 additions & 12 deletions data-model/Dockerfile
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Expand Up @@ -8,29 +8,37 @@ COPY fdo-profile/digital-specimen/0.1.0/schema/ schema-root/schemas/fdo-profile/
COPY fdo-profile/doi-kernel/0.1.0/schema schema-root/schemas/fdo-profile/doi-kernel/0.1.0
COPY fdo-profile/handle-kernel/0.1.0/schema schema-root/schemas/fdo-profile/handle-kernel/0.1.0
COPY fdo-profile/data-mapping/0.1.0/schema schema-root/schemas/fdo-profile/data-mapping/0.1.0
COPY fdo-profile/mas/0.1.0/schema schema-root/schemas/fdo-profile/mas/0.1.0
COPY fdo-profile/machine-annotation-service/0.1.0/schema schema-root/schemas/fdo-profile/mas/0.1.0
COPY fdo-profile/digital-media/0.1.0/schema schema-root/schemas/fdo-profile/digital-media/0.1.0
COPY fdo-profile/organisation/0.1.0/schema schema-root/schemas/fdo-profile/organisation/0.1.0
COPY fdo-profile/source-system/0.1.0/schema schema-root/schemas/fdo-profile/source-system/0.1.0
COPY fdo-profile/tettris-service/0.1.0/schema schema-root/schemas/fdo-profile/tettris-service/0.1.0
COPY fdo-profile/tombstone/0.1.0/schema schema-root/schemas/fdo-profile/tombstone/0.1.0
COPY fdo-profile/virtual-collection/0.1.0/schema schema-root/schemas/fdo-profile/virtual-collection/0.1.0

COPY fdo-profile/annotation/1.0.0/schema schema-root/schemas/fdo-profile/annotation/1.0.0
COPY fdo-profile/handle-kernel/1.0.0/schema schema-root/schemas/fdo-profile/handle-kernel/1.0.0
COPY fdo-profile/data-mapping/1.0.0/schema schema-root/schemas/fdo-profile/data-mapping/1.0.0
COPY fdo-profile/machine-annotation-service/1.0.0/schema schema-root/schemas/fdo-profile/machine-annotation-service/1.0.0
COPY fdo-profile/doi-kernel/1.0.0/schema schema-root/schemas/fdo-profile/doi-kernel/1.0.0
COPY fdo-profile/source-system/1.0.0/schema schema-root/schemas/fdo-profile/source-system/1.0.0
COPY fdo-profile/digital-media/1.0.0/schema schema-root/schemas/fdo-profile/digital-media/1.0.0
COPY fdo-profile/digital-specimen/1.0.0/schema/ schema-root/schemas/fdo-profile/digital-specimen/1.0.0
COPY fdo-profile/tombstone/1.0.0/schema schema-root/schemas/fdo-profile/tombstone/1.0.0


# Latest FDO Profile schemas
COPY fdo-profile/annotation/0.1.0/schema schema-root/schemas/fdo-profile/annotation/latest
COPY fdo-profile/digital-specimen/0.1.0/schema/ schema-root/schemas/fdo-profile/digital-specimen/latest
COPY fdo-profile/doi-kernel/0.1.0/schema schema-root/schemas/fdo-profile/doi-kernel/latest
COPY fdo-profile/handle-kernel/0.1.0/schema schema-root/schemas/fdo-profile/handle-kernel/latest
COPY fdo-profile/data-mapping/0.1.0/schema schema-root/schemas/fdo-profile/data-mapping/latest
COPY fdo-profile/mas/0.1.0/schema schema-root/schemas/fdo-profile/mas/latest
COPY fdo-profile/digital-media/0.1.0/schema schema-root/schemas/fdo-profile/digital-media/latest
COPY fdo-profile/organisation/0.1.0/schema schema-root/schemas/fdo-profile/organisation/latest
COPY fdo-profile/source-system/0.1.0/schema schema-root/schemas/fdo-profile/source-system/latest
COPY fdo-profile/tettris-service/0.1.0/schema schema-root/schemas/fdo-profile/tettris-service/latest
COPY fdo-profile/annotation/1.0.0/schema schema-root/schemas/fdo-profile/annotation/latest
COPY fdo-profile/doi-kernel/1.0.0/schema schema-root/schemas/fdo-profile/doi-kernel/latest
COPY fdo-profile/handle-kernel/1.0.0/schema schema-root/schemas/fdo-profile/handle-kernel/latest
COPY fdo-profile/data-mapping/1.0.0/schema schema-root/schemas/fdo-profile/data-mapping/latest
COPY fdo-profile/machine-annotation-service/1.0.0/schema schema-root/schemas/fdo-profile/mas/latest
COPY fdo-profile/source-system/1.0.0/schema schema-root/schemas/fdo-profile/source-system/latest
COPY fdo-profile/digital-media/1.0.0/schema schema-root/schemas/fdo-profile/digital-media/latest
COPY fdo-profile/digital-specimen/1.0.0/schema schema-root/schemas/fdo-profile/digital-specimen/latest
COPY fdo-profile/tombstone/1.0.0/schema schema-root/schemas/fdo-profile/tombstone/latest

COPY fdo-profile/tettris-service/0.1.0/schema schema-root/schemas/fdo-profile/tettris-service/latest
COPY fdo-profile/organisation/0.1.0/schema schema-root/schemas/fdo-profile/organisation/latest
COPY fdo-profile/virtual-collection/0.1.0/schema schema-root/schemas/fdo-profile/virtual-collection/latest

# Versioned FDO Type schemas
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14 changes: 14 additions & 0 deletions data-model/fdo-profile/annotation/1.0.0/examples/example-annotation-request.json
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{
"data": {
"type": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"attributes": {
"locations": [
"https://coldb.mnhn.fr/catalognumber/mnhn/ec/ec23946"
],
"targetPid": "https://hdl.handle.net/20.5000.10235/aaa-bbb-ccc",
"targetType": "https://doi.org/21.T11148/894b1e6cad57e921764e",
"targetTypeName": "DigitalSpecimen",
"annotationHash": "b3dada2d-396b-cab2-665e-125659fc7ae6"
}
}
}
17 changes: 17 additions & 0 deletions data-model/fdo-profile/annotation/1.0.0/examples/example-annotation.json
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add VIEW=JSON to 10320/loc for consistency (although we do not currently have a HTML view for the annotation)

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it is now implemented as ID=JSON but the ID should not change, a VIEW parameter should be added. ID attributes are given an integer in the Handle documentation, I am not sure that is actually required but people using Handles may expect an integer there so I would keep the ID integers. They may be handy if there are for example multiple URLS with VIEW=JSON, to display one of them with preference using a weight (e.g. one is served in Chine, the other in Europe and for traffic coming from Europe you may prefer the one served from a location in Europe).

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I'm not 100% sure if the handle system supports that. In their documentation, they say:

The currently defined selection methods are:

  • Locatt (select by id)
  • country
  • weight

However, they also say:

The attributes for the set of locations, as well as each location entry in the set, are open-ended to allow for future capabilities.

So it might support it, it might not. Will need to test. If it fails, using the id this way should work. There's nothing in the documentation that says that the id needs to be an integer.

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ok, how I read the documentation you should be able to add any attribute you like. If it does not work then please use the id instead but having both attributes would be more flexible.

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pidissuerName should be DiSSCo (DataCite does not issue Handles for our annotations), pidIssuer is the ROR for DiSSCo

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now pidIssuerName is changed to the ROR, but the ROR should be in pidIssuer and pidIssuerName should be DiSSCo

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{
"10320/loc": "<locations><location href=\"https://dev.dissco.tech/api/v1/annotations/TEST/FFR-RTL-B8K\" id=\"0\" view=\"JSON\" weight=\"1\"/></locations>",
"fdoProfile": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"fdoRecordLicenseId": "https://spdx.org/licenses/CC0-1.0.json",
"fdoRecordLicenseName": "CC0 1.0 Universal",
"digitalObjectType": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"digitalObjectName": "Annotation",
"pid": "https://hdl.handle.net/TEST/FFR-RTL-B8K",
"pidIssuer": "https://ror.org/04wxnsj81",
"pidIssuerName": "Distributed System of Scientific Collections",
"pidRecordIssueDate": "2023-11-17T11:57:02.933Z",
"pidRecordIssueNumber": 1,
"pidStatus": "ACTIVE",
"targetPid": "https://hdl.handle.net/20.500.125/1111111",
"targetType": "DigitalSpecimen",
"annotationHash": "faab142f-40a5-fc15-7085-49c23301c608"
}
38 changes: 38 additions & 0 deletions data-model/fdo-profile/annotation/1.0.0/schema/annotation-request-attributes.json
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{
"$id": "https://schemas.dissco.tech/schemas/fdo-profile/annotation/1.0.0/annotation-request-attributes.json",
"$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 an annotation",
"$comment": "FDO Profile Version 1.0.0",
"properties": {
"locations": {
"type": "array",
"items": {
"type": "string"
},
"description": "Additional URLs to be appended to the 10320/loc field"
},
"targetPid": {
"type": "string",
"pattern": "https:\/\/(doi\\.org\/10\\.\\w+/\\w+$|hdl\\.handle\\.net\/[\\w.]+\/[\\w-]+$)",
"description": "A Handle or DOI of the object that is being annotated"
},
"targetType": {
"type": "string",
"description": "Map to ods:type in annotation model"
},
"targetTypeName": {
"type": "string",
"description": "Human-readable name of the above target type."
},
"annotationHash": {
"type": "string",
"format": "uuid",
"description": "MD5 hash based on target, motivation, and creator. Internally generated by DiSSCo Annotation Processing Service for machine annotations"
}
},
"required": [
"targetPid",
"targetType"
],
"additionalProperties": false
}
31 changes: 31 additions & 0 deletions data-model/fdo-profile/annotation/1.0.0/schema/annotation-request.json
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{
"$id": "https://schemas.dissco.tech/schemas/fdo-profile/annotation/1.0.0/annotation-request.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"type": "object",
"description": "Schema for making annotation-creation requests to the DiSSCo Handle Manager",
"$comment": "FDO Profile Version 1.0.0",
"properties": {
"data": {
"type": "object",
"properties": {
"type": {
"const": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"description": "PID of the Digital Object Type"
},
"attributes": {
"type": "object",
"$ref": "https://schemas.dissco.tech/schemas/fdo-profile/annotation/1.0.0/anotation-request-attributes.json"
}
},
"required": [
"type",
"attributes"
],
"additionalProperties": false
}
},
"required": [
"data"
],
"additionalProperties": false
}
172 changes: 172 additions & 0 deletions data-model/fdo-profile/annotation/1.0.0/schema/annotation.json
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update idx6 example with 10.3535 prefix, add VIEW=JSON to10320/loc

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{
"$id": "https://schemas.dissco.tech/schemas/fdo-profile/annotation/1.0.0/annotation-fdo-profile.json",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "FDO Profile for DiSSCo Annotations",
"$comment": "FDO Profile Version 1.0.0",
"properties": {
"fdoProfile": {
"description": "PID to a machine readable description of the attributes in the FDO record",
"const": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"$comment": "idx = 1"
},
"fdoRecordLicenseId": {
"const": "https://spdx.org/licenses/CC0-1.0.json",
"description": "The licence for the FDO record, required to be always public domain",
"$comment": "idx = 2"
},
"fdoRecordLicenseName": {
"const": "CC0 1.0 Universal",
"description": "CC0 1.0 Universal",
"$comment": "idx = 3"
},
"digitalObjectType": {
"description": "PID to a description of the Type of digital object that defines the metadata, bit sequences (if any) and operations for the object",
"const": "https://doi.org/21.T11148/cf458ca9ee1d44a5608f",
"$comment": "idx = 4"
},
"digitalObjectName": {
"type": "string",
"description": "Name of the object type for humans",
"example": "digital specimen type 1",
"$comment": "idx = 5"
},
"pid": {
"type": "string",
"description": "The PID of which the FDO record is part, in DiSSCo this is a Handle or DOI. It is recommended to store this pid also in the local collection management system for the specimen.",
"example": "https://doi.org/10.22/GEE-W3J-HL2",
"$comment": "idx = 6"
},
"pidIssuer": {
"type": "string",
"description": "In case of a DOI, this is a PID for the DOI Registration Agency",
"example": "https://hdl.handle.net/10.17183",
"$comment": "idx = 7"
},
"pidIssuerName": {
"type": "string",
"description": "Human-readable name of the PID issuer",
"example": "DataCite",
"$comment": "idx = 8"
},
"pidRecordIssueDate": {
"type": "string",
"description": "Date the PID record was created",
"example": "2023-10-16T12:08:37.494Z",
"$comment": "idx = 9"
},
"pidRecordIssueNumber": {
"type": "integer",
"description": "Starts with 1 and is incrementally increased by 1 every time the pid record is updated. Compatible with DOI schema requirements.",
"example": "2",
"$comment": "idx = 10"
},
"pidStatus": {
"enum": [
"TOMBSTONE",
"DRAFT",
"ACTIVE"
],
"description": "A PID is considered to have a lifecycle, PID status indicates the status in the life cycle, e.g. draft, active, retired. PID statuses are described further in the PID infrastructure design.",
"$comment": "idx = 11"
},
"HS_ADMIN": {
"type": "string",
"description": "Administrative information for PID profile",
"$comment": "idx = 100"
},
"10320/loc": {
"type": "string",
"description": "XML document describing location(s) of the resource",
"$comment": "idx = 101",
"example": "<locations><location href=\"https://dev.dissco.tech/api/v1/annotations/TEST/FFR-RTL-B8K\" id=\"0\" weight=\"1\"/></locations>"
},
"tombstoneText": {
"type": "string",
"description": "A reason why the Digital Object was tombstoned",
"examples": [
"This is a duplicate of XXX",
"This object was made by mistake"
],
"$comment": "idx = 30"
},
"hasRelatedPid": {
"type": "array",
"description": "The PIDs of the object the tombstoned object is related to",
"items": {
"type": "object",
"items": {
"type": "object",
"properties": {
"pid": {
"type": "string",
"description": "The PID of the related object",
"examples": [
"https://doi.org/10.1234/abcd"
]
},
"relationshipType": {
"type": "string",
"description": "The type of relationship between the tombstoned object and the related object",
"examples": [
"isObsoletedBy",
"isIdenticalTo"
]
}
},
"additionalProperties": false
},
"$comment": "idx = 31"
}
},
"tombstoneDate": {
"type": "string",
"description": "Timestamp the Digital Object was tombstoned and no longer active.",
"format": "date-time",
"examples": [
"2021-06-01T12:00:000Z"
],
"$comment": "idx = 32"
},
"targetPid": {
"type": "string",
"description": "A Handle or DOI of the object that is being annotated",
"examples": [
"https:/hdl.handle.net/20.5000.1025/ABC-123-XYZ"
],
"pattern": "https://(doi\\.org/10\\.\\w+/\\w+$|hdl\\.handle\\.net/[\\w.]+/[\\w-]+$)",
"$comment": "idx = 500"
},
"targetType": {
"type": "string",
"description": "Map to ods:type in annotation model",
"$comment": "idx = 501"
},
"targetTypeName": {
"type": "string",
"description": "Human-readable name of the above target type",
"$comment": "idx = 502"
},
"annotationHash": {
"type": "string",
"description": "MD5 hash based on target, motivation, and creator. Internally generated by DiSSCo Annotation Processing Service for machine annotations",
"$comment": "idx = 502"
}
},
"additionalProperties": false,
"required": [
"fdoProfile",
"fdoRecordLicenseId",
"fdoRecordLicenseName",
"digitalObjectType",
"digitalObjectName",
"pid",
"pidIssuer",
"pidIssuerName",
"pidRecordIssueDate",
"pidRecordIssueNumber",
"10320/loc",
"pidStatus",
"targetPid",
"targetType"
]
}
2 changes: 1 addition & 1 deletion data-model/fdo-profile/data-mapping/0.1.0/schema/data-mapping.json
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Expand Up @@ -98,7 +98,7 @@
"type": "string",
"description": "XML document describing location(s) of the resource",
"$comment": "idx = 101",
"example": "<locations><location href=\"https://dev.dissco.tech/api/v1/annotations/TEST/FFR-RTL-B8K\" id=\"0\" weight=\"1\"/></locations>"
"example": "<locations><location href=\"https://dev.dissco.tech/api/v1/annotations/TEST/FFR-RTL-B8K\" id=\"JSON\" weight=\"1\"/></locations>"
},
"tombstoneText": {
"type": "string",
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8 changes: 8 additions & 0 deletions data-model/fdo-profile/data-mapping/1.0.0/examples/example-data-mapping-request.json
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{
"data": {
"type": "https://doi.org/21.T11148/ce794a6f4df42eb7e77e",
"attributes": {
"sourceDataStandard": "dwc"
}
}
}
13 changes: 13 additions & 0 deletions data-model/fdo-profile/data-mapping/1.0.0/examples/example-data-mapping.json
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{
"10320/loc": "<locations><location href=\"https://dev-orchestration.dissco.tech/api/v1/mapping/TEST/QDD-Y07-QK6\" id=\"0\" view=\"JSON\" weight=\"1\"/></locations>",
"fdoProfile": "https://doi.org/21.T11148/ce794a6f4df42eb7e77e",
"fdoRecordLicense": "https://spdx.org/licenses/CC0-1.0.json",
"fdoRecordLicenseName": "CC0 1.0 Universal",
"digitalObjectType": "https://doi.org/21.T11148/ce794a6f4df42eb7e77e",
"digitalObjectName": "Mapping",
"pid": "https://hdl.handle.net/TEST/QDD-Y07-QK6",
"pidRecordIssueDate": "2023-09-01T13:05:08.375Z",
"pidRecordIssueNumber": 1,
"pidStatus": "ACTIVE",
"sourceDataStandard": "dwc"
}
15 changes: 15 additions & 0 deletions data-model/fdo-profile/data-mapping/1.0.0/examples/example-tombstoned-data-mapping-fdo.json
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{
"10320/loc": "<locations><location href=\"https://dev-orchestration.dissco.tech/api/v1/mapping/TEST/QDD-Y07-QK6\" id=\"0\" view=\"JSON\" weight=\"1\"/></locations>",
"fdoProfile": "https://doi.org/21.T11148/ce794a6f4df42eb7e77e",
"fdoRecordLicenseId": "https://spdx.org/licenses/CC0-1.0.json",
"fdoRecordLicenseName": "CC0 1.0 Universal",
"digitalObjectType": "https://doi.org/21.T11148/ce794a6f4df42eb7e77e",
"digitalObjectName": "Mapping",
"pid": "https://hdl.handle.net/TEST/QDD-Y07-QK6",
"pidRecordIssueDate": "2023-09-01T13:05:08.375Z",
"pidRecordIssueNumber": 1,
"pidStatus": "ACTIVE",
"sourceDataStandard": "dwc",
"tombstoneText": "Resource deleted by admin",
"tombstoneDate": "2024-11-17T11:57:02.933Z"
}
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