diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml new file mode 100644 index 0000000..814d185 --- /dev/null +++ b/.github/workflows/checks.yaml @@ -0,0 +1,35 @@ +name: crate_db checks + +on: [push, pull_request] + +jobs: + lint-and-test: + runs-on: ubuntu-latest + + strategy: + matrix: + python-version: [3.10, 3.11] + + steps: + - name: Checkout code + uses: actions/checkout@v3 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install poetry + poetry install + + - name: Lint with flake8 + run: | + pip install flake8 + flake8 crate_db tests + + - name: Run tests + run: | + poetry run pytest diff --git a/.gitignore b/.gitignore index 68bc17f..ae0eade 100644 --- a/.gitignore +++ b/.gitignore @@ -22,6 +22,7 @@ var/ wheels/ share/python-wheels/ *.egg-info/ +*.modified.yaml .installed.cfg *.egg MANIFEST diff --git a/README.md b/README.md index e69de29..8e43d1c 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,18 @@ +# ELIXIR Crate DB + +[![License][badge-license]][badge-url-license] +[![Docs][badge-docs]][badge-url-docs] +[![Build_status][badge-build-status]][badge-url-build-status] +[![Coverage][badge-coverage]][badge-url-coverage] + +## Description + +Various research artifacts are produced daily around the world, but managing +them is a tedious task for a researcher as any researcher will want to spend +more time researching new stuff rather than finding a way to efficiently store, +retrieve, or share them. The management of these research artifacts becomes a +problem, that's where exactly Crate DB comes into play. + +Crate DB mainly focuses on developing a versatile backend to +manage and share RO_Crates using various technologies. The end goal is to +make it easy for a user to manage any RO_Crate. \ No newline at end of file diff --git a/crate-db/api/crate-db-specs.modified.yaml b/crate-db/api/crate-db-specs.modified.yaml deleted file mode 100644 index d2b3863..0000000 --- a/crate-db/api/crate-db-specs.modified.yaml +++ /dev/null @@ -1,289 +0,0 @@ -components: - parameters: - rocrate_id: - description: ID of the ROCrate - in: path - name: rocrate_id - required: true - schema: - example: 609d4b156f6d1972e7f78c87 - type: string - schemas: - Error: - properties: - code: - format: int32 - type: integer - message: - type: string - required: - - code - - message - type: object - ROCrateBase: - description: The base schema for an ROCrate. - properties: - description: - description: A description of the ROCrate. - example: This is an example description of an ROCrate. - type: string - title: - description: The title of the ROCrate. - example: Example ROCrate - type: string - zenodo_info: - description: Additional information for Zenodo. - example: - doi: 10.1234/example.doi - metadata: - '...': null - type: object - required: - - title - - description - type: object - ROCrateRequest: - allOf: - - $ref: '#/components/schemas/ROCrateBase' - - properties: - rocrate: - description: The ROCrate file to upload. - example: rocrate.zip - format: binary - type: string - required: - - rocrate - type: object - ROCrateResponse: - allOf: - - $ref: '#/components/schemas/ROCrateBase' - - properties: - _id: - description: The unique identifier for the ROCrate. - example: 60b6c0f9f1d2c12a5c7d6b8e - type: string - created_at: - description: The creation date of the ROCrate. - example: 2023-01-01 12:00:00+00:00 - format: date-time - type: string - rocrate: - description: The link to the ROCrate file in MinIO. - example: https://minio.example.com/rocrates/rocrate.zip - type: string - updated_at: - description: The last update date of the ROCrate. - example: 2023-01-02 12:00:00+00:00 - format: date-time - type: string - user_id: - description: The user ID extracted from the access token. - example: 1234567890abcdef - type: string - type: object -info: - description: Microservice for managing ROCrates - title: Crate DB Microservice - version: 1.0.0 -openapi: 3.0.0 -paths: - /rocrates: - get: - description: Returns a list of all ROCrates stored in the database. - operationId: listROCrates - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/ROCrateResponse' - type: array - description: OK - '401': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The request is unauthorized. - '403': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The requester is not authorized to perform this action. - '404': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: Resource not found - default: - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: unexpected error - summary: Get all ROCrates - x-openapi-router-controller: ga4gh.controllers.server - post: - description: Stores a new crate in the database and uploads the zip file to - MinIO. - operationId: createROCrate - requestBody: - content: - multipart/form-data: - schema: - $ref: '#/components/schemas/ROCrateRequest' - x-body-name: rocrate_data - required: true - responses: - '201': - $ref: '#/components/schemas/ROCrateResponse' - '400': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: Bad Request - '401': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The request is unauthorized. - '403': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The requester is not authorized to perform this action. - default: - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: unexpected error - summary: Creates a new ROCrate - x-openapi-router-controller: ga4gh.controllers.server - /rocrates/{rocrate_id}: - delete: - description: Delete an existing ROCrate - operationId: deleteROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - responses: - '204': - description: No Content - '401': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The request is unauthorized. - '403': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The requester is not authorized to perform this action. - '404': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: Resource not found - default: - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: unexpected error - summary: Delete a specific ROCrate by ID - x-openapi-router-controller: ga4gh.controllers.server - get: - description: Returns a specific ROCrate stored in the database. - operationId: getROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ROCrateResponse' - description: OK - '401': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The request is unauthorized. - '403': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The requester is not authorized to perform this action. - '404': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: Resource not found - default: - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: unexpected error - summary: Get a specific ROCrate by ID - x-openapi-router-controller: ga4gh.controllers.server - put: - description: Updates an existing crate in the database and uploads the zip file - to MinIO. - operationId: updateROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - requestBody: - content: - multipart/form-data: - schema: - $ref: '#/components/schemas/ROCrateRequest' - x-body-name: rocrate - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ROCrateResponse' - description: Crate updated successfully - '401': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The request is unauthorized. - '403': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: The requester is not authorized to perform this action. - '404': - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: Resource not found - default: - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - description: unexpected error - summary: Update an existing RO-Crate - x-openapi-router-controller: ga4gh.controllers.server -servers: -- url: http://localhost/ diff --git a/crate-db/api/crate-db-specs.yaml b/crate-db/api/crate-db-specs.yaml deleted file mode 100644 index a9cc01f..0000000 --- a/crate-db/api/crate-db-specs.yaml +++ /dev/null @@ -1,374 +0,0 @@ -openapi: "3.0.0" -info: - title: "Crate DB Microservice" - description: "Microservice for managing ROCrates" - version: "1.0.0" -servers: - - url: "http://localhost/" - -paths: - /rocrates: - post: - summary: Creates a new ROCrate - description: |- - Stores a new crate in the database and uploads the zip file to MinIO. - operationId: createROCrate - requestBody: - required: true - content: - multipart/form-data: - schema: - x-body-name: rocrate_data - $ref: '#/components/schemas/ROCrateRequest' - responses: - '201': - $ref: '#/components/schemas/ROCrateResponse' - '400': - description: Bad Request - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '401': - description: The request is unauthorized. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '403': - description: The requester is not authorized to perform this action. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - default: - description: unexpected error - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - - get: - summary: Get all ROCrates - description: |- - Returns a list of all ROCrates stored in the database. - operationId: listROCrates - responses: - '200': - description: OK - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/ROCrateResponse" - '404': - description: Resource not found - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '401': - description: The request is unauthorized. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '403': - description: The requester is not authorized to perform this action. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - default: - description: unexpected error - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - - /rocrates/{rocrate_id}: - get: - summary: Get a specific ROCrate by ID - description: |- - Returns a specific ROCrate stored in the database. - operationId: getROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - responses: - '200': - description: OK - content: - application/json: - schema: - $ref: "#/components/schemas/ROCrateResponse" - '404': - description: Resource not found - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '401': - description: The request is unauthorized. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '403': - description: The requester is not authorized to perform this action. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - default: - description: unexpected error - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - - put: - summary: Update an existing RO-Crate - description: |- - Updates an existing crate in the database and uploads the zip file to MinIO. - operationId: updateROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - requestBody: - required: true - content: - multipart/form-data: - schema: - x-body-name: rocrate - $ref: '#/components/schemas/ROCrateRequest' - responses: - '200': - description: Crate updated successfully - content: - application/json: - schema: - $ref: '#/components/schemas/ROCrateResponse' - '404': - description: Resource not found - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '401': - description: The request is unauthorized. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '403': - description: The requester is not authorized to perform this action. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - default: - description: unexpected error - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - - - delete: - summary: Delete a specific ROCrate by ID - description: |- - Delete an existing ROCrate - operationId: deleteROCrate - parameters: - - $ref: '#/components/parameters/rocrate_id' - responses: - '204': - description: No Content - '404': - description: Resource not found - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '401': - description: The request is unauthorized. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - '403': - description: The requester is not authorized to perform this action. - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - default: - description: unexpected error - content: - application/json: - schema: - $ref: '#/components/schemas/Error' - -components: - schemas: - # ROCrateBase: - # description: The base schema for an ROCrate. - # type: object - # properties: - # title: - # type: string - # description: The title of the ROCrate. - # example: Example ROCrate - # description: - # type: string - # description: A description of the ROCrate. - # example: This is an example description of an ROCrate. - # zenodo_info: - # type: object - # description: Additional information for Zenodo. - # example: - # doi: 10.1234/example.doi - # metadata: {...} - # required: - # - title - # - description - - # ROCrateRequest: - # allOf: - # - $ref: '#/components/schemas/ROCrateBase' - # - type: object - # properties: - # rocrate: - # type: string - # format: binary - # description: The ROCrate file to upload. - # example: rocrate.zip - # required: - # - rocrate - - # ROCrateResponse: - # allOf: - # - $ref: '#/components/schemas/ROCrateBase' - # - type: object - # properties: - # _id: - # type: string - # description: The unique identifier for the ROCrate. - # example: 60b6c0f9f1d2c12a5c7d6b8e - # rocrate: - # type: string - # description: The link to the ROCrate file in MinIO. - # example: https://minio.example.com/rocrates/rocrate.zip - # created_at: - # type: string - # format: date-time - # description: The creation date of the ROCrate. - # example: 2023-01-01T12:00:00Z - # updated_at: - # type: string - # format: date-time - # description: The last update date of the ROCrate. - # example: 2023-01-02T12:00:00Z - # user_id: - # type: string - # description: The user ID extracted from the access token. - # example: 1234567890abcdef - - ROCrateRequest: - description: The base schema for an ROCrate. - type: object - properties: - rocrate: - type: string - format: binary - description: The ROCrate file to upload. - example: rocrate.zip - description: - type: string - description: A description of the ROCrate. - example: This is an example description of an ROCrate. - title: - type: string - description: The title of the ROCrate. - example: Example ROCrate - zenodo_info: - type: object - description: Additional information for Zenodo. - example: - doi: 10.1234/example.doi - metadata: {...} - required: - - rocrate - - title - - description - - ROCrateResponse: - description: The base schema for an ROCrate. - type: object - properties: - _id: - type: string - description: The unique identifier for the ROCrate. - example: 60b6c0f9f1d2c12a5c7d6b8e - rocrate: - type: string - description: The link to the ROCrate file in MinIO. - example: https://minio.example.com/rocrates/rocrate.zip - created_at: - type: string - format: date-time - description: The creation date of the ROCrate. - example: 2023-01-01T12:00:00Z - updated_at: - type: string - format: date-time - description: The last update date of the ROCrate. - example: 2023-01-02T12:00:00Z - user_id: - type: string - description: The user ID extracted from the access token. - example: 1234567890abcdef - title: - type: string - description: The title of the ROCrate. - example: Example ROCrate - description: - type: string - description: A description of the ROCrate. - example: This is an example description of an ROCrate - zenodo_info: - type: object - description: Additional information for Zenodo. - example: - doi: 10.1234/example.doi - metadata: {...} - required: - - _id - - rocrate - - created_at - - updated_at - - user_id - - title - - description - - Error: - type: object - required: - - code - - message - properties: - code: - type: integer - format: int32 - message: - type: string - - parameters: - rocrate_id: - name: rocrate_id - in: path - description: ID of the ROCrate - required: true - schema: - type: string - example: "609d4b156f6d1972e7f78c87" \ No newline at end of file diff --git a/crate-db/exceptions.py b/crate-db/exceptions.py deleted file mode 100644 index b561d42..0000000 --- a/crate-db/exceptions.py +++ /dev/null @@ -1,60 +0,0 @@ -"""Petstore exceptions.""" - -from connexion.exceptions import ( - BadRequestProblem, - ExtraParameterProblem, - Forbidden, - Unauthorized, - OAuthProblem, -) -from werkzeug.exceptions import ( - BadRequest, - InternalServerError, - NotFound, -) - -exceptions = { - Exception: { - "message": "Oops, something unexpected happened.", - "code": 500, - }, - BadRequestProblem: { - "message": "We don't quite understand what it is you are looking for.", - "code": 400, - }, - BadRequest: { - "message": "We don't quite understand what it is you are looking for.", - "code": 400, - }, - ExtraParameterProblem: { - "message": "We don't quite understand what it is you are looking for.", - "code": 400, - }, - OAuthProblem: { - "message": ( - "Unauthorized! You need to be logged in to" - "perform this action." - ), - "code": 401, - }, - Unauthorized: { - "message": ( - "Unauthorized!" - ), - "code": 401, - }, - Forbidden: { - "message": ( - "Not authorized to perform this action." - ), - "code": 403, - }, - NotFound: { - "message": "Not sure what you are looking for, but it's not here.", - "code": 404, - }, - InternalServerError: { - "message": "Oops, something unexpected happened.", - "code": 500, - }, -} \ No newline at end of file diff --git a/crate-db/ga4gh/__init__.py b/crate-db/ga4gh/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/crate-db/ga4gh/controllers/server.py b/crate-db/ga4gh/controllers/server.py deleted file mode 100644 index 605cc11..0000000 --- a/crate-db/ga4gh/controllers/server.py +++ /dev/null @@ -1,26 +0,0 @@ -from typing import Dict, List - - -def createROCrate(rocrate_data, rocrate) -> Dict: - print(rocrate_data) - print(rocrate) - return "Demo request" - - -def listROCrates() -> List: - return "Demo request" - - -def getROCrate(rocrate_id: str) -> Dict: - print(rocrate_id) - return "Demo request" - - -def updateROCrate(rocrate_id: str) -> Dict: - print(rocrate_id) - return "Demo request" - - -def deleteROCrate(rocrate_id: str) -> Dict: - print(rocrate_id) - return "Demo request" diff --git a/crate-db/version.py b/crate-db/version.py deleted file mode 100644 index e69de29..0000000 diff --git a/crate_db/__init__.py b/crate_db/__init__.py new file mode 100644 index 0000000..772d776 --- /dev/null +++ b/crate_db/__init__.py @@ -0,0 +1 @@ +"""Crate DB root package""" diff --git a/crate-db/__init__.py b/crate_db/api/__init__.py similarity index 100% rename from crate-db/__init__.py rename to crate_db/api/__init__.py diff --git a/crate_db/api/crate_db_specs.yaml b/crate_db/api/crate_db_specs.yaml new file mode 100644 index 0000000..9efa5bf --- /dev/null +++ b/crate_db/api/crate_db_specs.yaml @@ -0,0 +1,454 @@ +openapi: "3.1.0" +info: + title: "OpenAPI specification for managing RO-Crates" + description: "Microservice for managing RO-Crates" + version: "0.1.0" +servers: + - url: /elixircloud/roc/v1 + +paths: + /service-info: + post: + summary: 'Create new service information' + description: 'Create a new service information resource.' + operationId: createServiceInfo + requestBody: + required: true + content: + application/json: + schema: + $ref: '#/components/schemas/Service' + responses: + 201: + description: Identifier of the created RO-Crate resource + content: + application/json: + schema: + $ref: '#/components/schemas/CreateROCResponse' + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 500: + $ref: '#/components/responses/UnexpectedError' + + get: + description: |- + Provides information about the service, this structure is based on the + standardized GA4GH service info structure. In addition, this endpoint + will also provide information about customized storage endpoints offered + by the TES server. + operationId: getServiceInfo + responses: + 200: + description: 'A successful operation to request the service information about this running service.' + content: + application/json: + schema: + $ref: '#/components/schemas/Service' + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 404: + $ref: '#/components/responses/NotFound' + 500: + $ref: '#/components/responses/UnexpectedError' + + put: + summary: 'Update existing service information' + description: 'Update an existing service information resource.' + operationId: updateServiceInfo + requestBody: + required: true + content: + application/json: + schema: + $ref: '#/components/schemas/Service' + responses: + 204: + description: No Content + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 404: + $ref: '#/components/responses/NotFound' + 500: + $ref: '#/components/responses/UnexpectedError' + + /ro-crates: + post: + summary: Create RO-Crate resource + description: Create a new RO-Crate resource. + operationId: createROC + requestBody: + required: true + content: + multipart/form-data: + schema: + x-body-name: createROCRequestBody + $ref: '#/components/schemas/CreateROCRequestBody' + responses: + 201: + description: Identifier of the created RO-Crate resource + content: + application/json: + schema: + $ref: '#/components/schemas/CreateROCResponse' + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 500: + $ref: '#/components/responses/UnexpectedError' + + get: + summary: List all RO-Crate resources + description: Retrieve a list of all RO-Crate resources stored in the database. + operationId: listROCs + responses: + 200: + description: OK + content: + application/json: + schema: + type: array + items: + $ref: '#/components/schemas/ROCrateResponse' + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 404: + $ref: '#/components/responses/NotFound' + 500: + $ref: '#/components/responses/UnexpectedError' + + /ro-crates/{roc-id}: + get: + summary: Retrieve a specific RO-Crate resource by ID + description: Retrieve a specific RO-Crate resource stored in the database. + operationId: getROC + parameters: + - name: roc-id + in: path + description: An identifier referencing an RO-Crate resource. + required: true + schema: + type: string + example: "260e7aa0-2e07-484e-9da7-ee19fdd1800d" + responses: + 200: + description: OK + content: + application/json: + schema: + $ref: '#/components/schemas/ROCrateResponse' + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 404: + $ref: '#/components/responses/NotFound' + 500: + $ref: '#/components/responses/UnexpectedError' + + put: + summary: Update an existing RO-Crate resource + description: Update an existing RO-Crate resource. + operationId: updateROC + parameters: + - name: roc-id + in: path + description: An identifier referencing an RO-Crate resource. + required: true + schema: + type: string + example: "260e7aa0-2e07-484e-9da7-ee19fdd1800d" + requestBody: + required: true + content: + multipart/form-data: + schema: + x-body-name: updateROCRequestBody + $ref: '#/components/schemas/UpdateROCRequestBody' + responses: + 204: + description: No Content + 400: + $ref: '#/components/responses/BadRequest' + 401: + $ref: '#/components/responses/Unauthorized' + 403: + $ref: '#/components/responses/Forbidden' + 404: + $ref: '#/components/responses/NotFound' + 500: + $ref: '#/components/responses/UnexpectedError' + +components: + schemas: + Service: + description: 'GA4GH service' + type: object + required: + - id + - name + - type + - organization + - version + properties: + id: + type: string + description: 'Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.' + example: 'org.ga4gh.myservice' + name: + type: string + description: 'Name of this service. Should be human readable.' + example: 'My project' + type: + $ref: '#/components/schemas/ServiceType' + description: + type: string + description: 'Description of the service. Should be human readable and provide information about the service.' + example: 'This service provides...' + organization: + type: object + description: 'Organization providing the service' + required: + - name + - url + properties: + name: + type: string + description: 'Name of the organization responsible for the service' + example: 'My organization' + url: + type: string + format: uri + description: 'URL of the website of the organization (RFC 3986 format)' + example: 'https://example.com' + contactUrl: + type: string + format: uri + description: 'URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).' + example: 'mailto:support@example.com' + documentationUrl: + type: string + format: uri + description: 'URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.' + example: 'https://docs.myservice.example.com' + createdAt: + type: string + format: date-time + description: 'Timestamp describing when the service was first deployed and available (RFC 3339 format)' + example: '2019-06-04T12:58:19Z' + updatedAt: + type: string + format: date-time + description: 'Timestamp describing when the service was last updated (RFC 3339 format)' + example: '2019-06-04T12:58:19Z' + environment: + type: string + description: 'Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.' + example: 'test' + version: + type: string + description: 'Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.' + example: '1.0.0' + + ServiceType: + description: 'Type of a GA4GH service' + type: object + required: + - group + - artifact + - version + properties: + group: + type: string + description: 'Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization''s reverse domain name).' + example: 'org.ga4gh' + artifact: + type: string + description: 'Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.' + example: 'beacon' + version: + type: string + description: 'Version of the API or specification. GA4GH specifications use semantic versioning.' + example: '1.0.0' + + CreateROCRequestBody: + type: object + properties: + rocrate: + type: string + format: binary + description: The RO-Crate file to upload. + example: rocrate.zip + description: + type: string + description: A description of the RO-Crate. + example: This is an example description of an RO-Crate. + title: + type: string + description: The title of the RO-Crate. + example: Example RO-Crate + zenodo_info: + type: object + description: Additional information for Zenodo. + example: + doi: 10.1234/example.doi + metadata: {...} + required: + - rocrate + - title + - description + + CreateROCResponse: + type: object + properties: + _id: + type: string + format: uuid + description: The unique identifier for the RO-Crate. + example: 260e7aa0-2e07-484e-9da7-ee19fdd1800d + + ROCrateResponse: + type: object + properties: + _id: + type: string + description: The unique identifier for the RO-Crate. + example: 60b6c0f9f1d2c12a5c7d6b8e + rocrate: + type: string + description: The link to the RO-Crate file in MinIO. + example: https://minio.example.com/ro-crates/rocrate.zip + created_at: + type: string + format: date-time + description: The creation date of the RO-Crate. + example: 2023-01-01T12:00:00Z + updated_at: + type: string + format: date-time + description: The last update date of the RO-Crate. + example: 2023-01-02T12:00:00Z + user_id: + type: string + format: uuid + description: The user ID extracted from the access token. + example: 260e7aa0-2e07-484e-9da7-ee19fdd1800d + title: + type: string + description: The title of the RO-Crate. + example: Example RO-Crate + description: + type: string + description: A description of the RO-Crate. + example: This is an example description of an RO-Crate. + zenodo_info: + type: object + description: Additional information for Zenodo. + example: + doi: 10.1234/example.doi + metadata: {...} + required: + - _id + - rocrate + - created_at + - updated_at + - user_id + - title + - description + + responses: + BadRequest: + description: Bad Request + content: + application/json: + schema: + type: object + properties: + code: + type: integer + format: int32 + message: + type: string + + Unauthorized: + description: Unauthorized + content: + application/json: + schema: + type: object + properties: + code: + type: integer + format: int32 + message: + type: string + + Forbidden: + description: Forbidden + content: + application/json: + schema: + type: object + properties: + code: + type: integer + format: int32 + message: + type: string + + NotFound: + description: Resource Not Found + content: + application/json: + schema: + type: object + properties: + code: + type: integer + format: int32 + message: + type: string + + UnexpectedError: + description: Unexpected Error + content: + application/json: + schema: + type: object + properties: + code: + type: integer + format: int32 + message: + type: string + + parameters: + roc-id: + name: roc-id + in: path + description: An identifier referencing an RO-Crate resource. + required: true + schema: + type: string + format: uuid + example: 260e7aa0-2e07-484e-9da7-ee19fdd1800d diff --git a/crate-db/app.py b/crate_db/app.py similarity index 71% rename from crate-db/app.py rename to crate_db/app.py index 8b16a3e..5665ca4 100644 --- a/crate-db/app.py +++ b/crate_db/app.py @@ -3,7 +3,9 @@ from pathlib import Path from connexion import FlaskApp # type: ignore -from foca import Foca # type: ignore +from foca import Foca + +from crate_db.ga4gh.service_info import ServiceInfo # type: ignore def init_app() -> FlaskApp: @@ -16,6 +18,9 @@ def init_app() -> FlaskApp: config_file=Path(__file__).resolve().parent / "config.yaml", ) app = foca.create_app() + with app.app.app_context(): + service_info = ServiceInfo() + service_info.init_service_info_from_config() return app diff --git a/crate-db/config.yaml b/crate_db/config.yaml similarity index 96% rename from crate-db/config.yaml rename to crate_db/config.yaml index d2a4977..ad7de8e 100644 --- a/crate-db/config.yaml +++ b/crate_db/config.yaml @@ -28,16 +28,15 @@ security: - public_key validation_checks: all - # Database configuration # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.DBConfig db: host: mongodb port: 27017 dbs: - ro-crate-db: + ro_crate_db: collections: - ro-crates: + ro_crates: indexes: null # API configuration @@ -45,7 +44,7 @@ db: api: specs: - path: - - api/crate-db-specs.yaml + - api/crate_db_specs.yaml add_operation_fields: x-openapi-router-controller: ga4gh.controllers.server security: diff --git a/crate_db/exceptions.py b/crate_db/exceptions.py new file mode 100644 index 0000000..0667061 --- /dev/null +++ b/crate_db/exceptions.py @@ -0,0 +1,49 @@ +"""Crate exceptions.""" + +from foca.errors.exceptions import ( + ExtraParameterProblem, + Forbidden, + Unauthorized, + OAuthProblem, + BadRequest, + InternalServerError, + NotFound, +) + +exceptions = { + Exception: { + "message": "An unexpected error occurred.", + "code": "500", + }, + BadRequest: { + "message": "The request is malformed.", + "code": "400", + }, + ExtraParameterProblem: { + "message": "The request is malformed.", + "code": "400", + }, + Unauthorized: { + "message": " The request is unauthorized.", + "code": "401", + }, + OAuthProblem: { + "message": ( + "Unauthorized! You need to be logged in to" + "perform this action." + ), + "code": 401, + }, + Forbidden: { + "message": "The requester is not authorized to perform this action.", + "code": "403", + }, + NotFound: { + "message": "The requested resource wasn't found.", + "code": "404", + }, + InternalServerError: { + "message": "An unexpected error occurred.", + "code": "500", + } +} diff --git a/crate_db/ga4gh/__init__.py b/crate_db/ga4gh/__init__.py new file mode 100644 index 0000000..f8a4833 --- /dev/null +++ b/crate_db/ga4gh/__init__.py @@ -0,0 +1 @@ +""" Contains functional module for the crate_db service""" diff --git a/crate_db/ga4gh/controllers/server.py b/crate_db/ga4gh/controllers/server.py new file mode 100644 index 0000000..2283113 --- /dev/null +++ b/crate_db/ga4gh/controllers/server.py @@ -0,0 +1,42 @@ +""" +Operations implementation for the RO-Crate API +""" + + +def createROC(ro_crate_data, ro_crate) -> dict: + print(ro_crate_data) + print(ro_crate) + return "Demo request" + + +def listROCs() -> list: + return "Demo request" + + +def getROC(ro_crate_id: str) -> dict: + print(ro_crate_id) + return "Demo request" + + +def updateROC(ro_crate_id: str) -> dict: + print(ro_crate_id) + return "Demo request" + + +def deleteROC(ro_crate_id: str) -> dict: + print(ro_crate_id) + return "Demo request" + + +def createServiceInfo(service_info) -> dict: + print(service_info) + return "Demo request" + + +def getServiceInfo() -> dict: + return "Demo request" + + +def updateServiceInfo(service_info) -> dict: + print(service_info) + return "Demo request" diff --git a/crate_db/ga4gh/service_info.py b/crate_db/ga4gh/service_info.py new file mode 100644 index 0000000..e2f15d8 --- /dev/null +++ b/crate_db/ga4gh/service_info.py @@ -0,0 +1,81 @@ +"""Controller for the `/service-info route.""" + +import logging + +from bson.objectid import ObjectId # type: ignore +from flask import current_app +from pymongo.collection import Collection # type: ignore + +from foca.errors.exceptions import NotFound + +logger = logging.getLogger(__name__) + + +class ServiceInfo: + """Class for service info server-side controller methods. + + Creates service info upon first request, if it does not exist. + + Attributes: + db_client: Database collection storing service info objects. + object_id: Database identifier for service info. + """ + + def __init__(self) -> None: + """Construct class instance.""" + self.db_client: Collection = ( + current_app.config.foca.db.dbs["ro_crates"] # type: ignore + .collections["service_info"] + .client + ) + self.object_id: str = "000000000000000000000000" + + def get_service_info(self) -> dict: + """Get latest service info from database. + + Returns: + Latest service info details. + + Raises: + NotFound: Service info was not found. + """ + service_info = self.db_client.find_one( + {"_id": ObjectId(self.object_id)}, + {"_id": False}, + ) + if service_info is None: + raise NotFound + return service_info + + def set_service_info(self, data: dict) -> None: + """Create or update service info. + + Arguments: + data: Dictionary of service info values. Cf. + """ + self.db_client.replace_one( + filter={"_id": ObjectId(self.object_id)}, + replacement=data, + upsert=True, + ) + logger.info(f"Service info set: {data}") + + def init_service_info_from_config(self) -> None: + """Initialize service info from config. + + Set service info only if it does not yet exist. + """ + service_info_conf = current_app.config.foca.serviceInfo # type: ignore + try: + service_info_db = self.get_service_info() + except NotFound: + logger.info("Initializing service info.") + self.set_service_info(data=service_info_conf) + return + if service_info_db != service_info_conf: + logger.info( + "Service info configuration changed. Updating service info." + ) + self.set_service_info(data=service_info_conf) + return + logger.debug("Service info already initialized and up to date.") diff --git a/crate_db/ga4gh/services/__init__.py b/crate_db/ga4gh/services/__init__.py new file mode 100644 index 0000000..0b92878 --- /dev/null +++ b/crate_db/ga4gh/services/__init__.py @@ -0,0 +1 @@ +""" Services to handle the crate_db API.""" diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..497717e --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1322 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "addict" +version = "2.4.0" +description = "Addict is a dictionary whose items can be set using both attribute and item syntax." +optional = false +python-versions = "*" +files = [ + {file = "addict-2.4.0-py3-none-any.whl", hash = "sha256:249bb56bbfd3cdc2a004ea0ff4c2b6ddc84d53bc2194761636eb314d5cfa5dfc"}, + {file = "addict-2.4.0.tar.gz", hash = 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The end goal is to make it easy for a user to manage any RO-Crate." +license = "Apache-2.0" +maintainers = ["Elixir Cloud AAI "] +authors = ["Elixir Cloud AAI "] +repository = "https://github.com/elixir-cloud-aai/crate-db" +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.10" +connexion = ">=2.11.2,<3" +foca = ">=0.12.1" + + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/setup.py b/setup.py deleted file mode 100644 index 92f4389..0000000 --- a/setup.py +++ /dev/null @@ -1,38 +0,0 @@ -"""Package setup.""" - -from pathlib import Path -from setuptools import setup, find_packages - -root_dir = Path(__file__).parent.resolve() - -__version__ = exec(open(root_dir / "crate-db" / "version.py").read()) - -file_name = root_dir / "README.md" -with open(file_name, "r") as _file: - long_description = _file.read() - -install_requires = [] -req = root_dir / 'requirements.txt' -with open(req, "r") as _file: - install_requires = _file.read().splitlines() - -setup( - name="foca", - version=__version__, # noqa: F821 - description=( - "Microservice for managing ROCrates" - ), - long_description=long_description, - long_description_content_type="text/markdown", - url="https://github.com/elixir-cloud-aai/crate-db", - project_urls={ - "Repository": "https://github.com/elixir-cloud-aai/crate-db", - "Tracker": "https://github.com/elixir-cloud-aai/crate-db/issues", - }, - packages=find_packages(), - setup_requires=[ - "setuptools_git==1.2", - "twine==3.8.0" - ], - install_requires=install_requires, -) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..d7090dd --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +""" Contains the tests for the crate_db service """