mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-23 21:28:32 +00:00
Put api endpoints back into api/file.py
This commit is contained in:
mike cullerton
parent
7f8ea483c9
commit
89a2650cc8
86
crc/api.yml
86
crc/api.yml
@ -793,76 +793,6 @@ paths:
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items:
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$ref: "#/components/schemas/WorkflowSpecCategory"
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# /document:
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# parameters:
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# - name: workflow_id
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# in: query
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# required: false
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# description: ID of the associated workflow
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# schema:
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# type: integer
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# - name: task_spec_name
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# in: query
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# required: false
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# description: Name of the Task Spec
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# schema:
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# type: string
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# - name: irb_doc_code
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# in: query
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# required: false
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# description: IRB Document Code. Make sure this matches a document in the irb_documents.xslx reference sheet.
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# schema:
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# type: string
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# - name: study_id
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# in: query
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# required: false
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# description: ID of the associated Study
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# schema:
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# type: integer
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# post:
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# operationId: crc.api.file_refactor.add_file
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# summary: Add a new document
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# tags:
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# - Documents
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# requestBody:
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# content:
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# multipart/form-data:
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# schema:
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# type: object
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# properties:
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# file:
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# type: string
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# format: binary
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# responses:
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# '200':
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# description: Document metadata
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# content:
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# application/json:
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# schema:
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# $ref: "#/components/schemas/File"
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# /document/{document_id}/data:
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# parameters:
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# - name: document_id
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# in: path
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# required: true
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# description: The id of the requested Document
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# schema:
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# type: integer
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# get:
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# operationId: crc.api.file_refactor.get_file_data
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# summary: Returns only the file contents
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# tags:
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# - Documents
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# responses:
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# '200':
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# description: Returns the actual file
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# content:
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# application/octet-stream:
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# schema:
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# type: string
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# format: binary
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# example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
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/file:
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parameters:
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- name: workflow_id
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@ -890,7 +820,7 @@ paths:
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schema:
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type: integer
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get:
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operationId: crc.api.file_refactor.get_files
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operationId: crc.api.file.get_files
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summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
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tags:
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- Files
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@ -905,7 +835,7 @@ paths:
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$ref: "#/components/schemas/File"
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post:
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operationId: crc.api.file_refactor.add_file
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operationId: crc.api.file.add_file
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summary: Add a new file
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tags:
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- Files
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@ -934,7 +864,7 @@ paths:
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schema:
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type: integer
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get:
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operationId: crc.api.file_refactor.get_file_info
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operationId: crc.api.file.get_file_info
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summary: Returns metadata about a file.
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tags:
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- Files
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@ -946,7 +876,7 @@ paths:
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schema:
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$ref: "#/components/schemas/File"
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put:
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operationId: crc.api.file_refactor.update_file_info
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operationId: crc.api.file.update_file_info
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summary: Updates existing file info with the given parameters.
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tags:
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- Files
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@ -963,7 +893,7 @@ paths:
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schema:
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$ref: "#/components/schemas/File"
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delete:
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operationId: crc.api.file_refactor.delete_file
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operationId: crc.api.file.delete_file
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summary: Removes an existing file.
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tags:
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- Files
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@ -991,7 +921,7 @@ paths:
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schema :
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type : integer
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get :
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operationId : crc.api.file_refactor.get_file_data_link
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operationId : crc.api.file.get_file_data_link
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summary : Returns only the file contents
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security: []
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tags :
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@ -1020,7 +950,7 @@ paths:
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schema:
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type: integer
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get:
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operationId: crc.api.file_refactor.get_file_data
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operationId: crc.api.file.get_file_data
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summary: Returns only the file contents
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tags:
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- Files
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@ -1034,7 +964,7 @@ paths:
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format: binary
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example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
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put:
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operationId: crc.api.file_refactor.update_file_data
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operationId: crc.api.file.update_file_data
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summary: Update only the file contents for a given file
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tags:
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- Files
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143
crc/api/file.py
143
crc/api/file.py
@ -7,6 +7,7 @@ from flask import send_file
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from crc import session
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from crc.api.common import ApiError
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from crc.api.user import verify_token
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from crc.models.file import File, FileSchema, FileModel, FileModelSchema
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# from crc.models.file import DocumentModel, FileSchema, File, FileModel, FileModelSchema, FileDataModel
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from crc.models.workflow import WorkflowModel
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from crc.services.document_service import DocumentService
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@ -15,14 +16,26 @@ from crc.services.user_file_service import UserFileService
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def to_file_api(file_model):
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...
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doc_dictionary = DocumentService.get_dictionary()
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return File.from_file_model(file_model, doc_dictionary)
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# file_data_model = UserFileService.get_file_data(file_model.id)
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# return File.from_models(file_model, file_data_model,
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# DocumentService.get_dictionary())
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def get_files(workflow_id=None, form_field_key=None, study_id=None):
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...
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def get_files(workflow_id=None, irb_doc_code=None, study_id=None):
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if workflow_id is None:
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raise ApiError('missing_parameter',
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'Please specify a workflow_id with an optional form_field_key')
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if study_id is not None:
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file_models = UserFileService.get_files_for_study(study_id=study_id, irb_doc_code=irb_doc_code)
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else:
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file_models = UserFileService.get_files(workflow_id=workflow_id,
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irb_doc_code=irb_doc_code)
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files = (to_file_api(model) for model in file_models)
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return FileSchema(many=True).dump(files)
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# if workflow_id is None:
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# raise ApiError('missing_parameter',
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# 'Please specify a workflow_id with an optional form_field_key')
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@ -37,8 +50,33 @@ def get_files(workflow_id=None, form_field_key=None, study_id=None):
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# return FileSchema(many=True).dump(files)
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def add_file(workflow_id=None, task_spec_name=None, form_field_key=None):
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...
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def add_file(workflow_id=None, task_spec_name=None, irb_doc_code=None):
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file = connexion.request.files['file']
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if workflow_id:
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
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if workflow is None:
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raise ApiError('invalid_workflow',
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f'Unable to find a workflow with id {workflow_id}')
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if irb_doc_code is None:
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raise ApiError('invalid_doc_code',
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'When adding a workflow related file, you must specify an irb_doc_code')
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if task_spec_name is None:
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raise ApiError('invalid_task_spec_name',
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'When adding a workflow related file, you must specify a task_spec_name')
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file_model = UserFileService.add_workflow_file(workflow_id=workflow_id,
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irb_doc_code=irb_doc_code,
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task_spec_name=task_spec_name,
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name=file.filename,
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content_type=file.content_type,
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binary_data=file.stream.read())
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# We calculate the document statuses once per request, but a script may execute more quickly
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# So force a refresh of the document status here.
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# TODO: Finish refactoring this
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# StudyService.get_documents_status(study_id=workflow.study_id, force=True)
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else:
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raise ApiError('missing_workflow_id', 'You must supply a workflow_id.')
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return FileSchema().dump(to_file_api(file_model))
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# file = connexion.request.files['file']
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# if workflow_id:
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# # TODO: should 'WorkflowModel.id == WorkflowModel.id' be 'WorkflowModel.id == workflow_id'?
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@ -66,23 +104,45 @@ def add_file(workflow_id=None, task_spec_name=None, form_field_key=None):
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def update_file_data(file_id):
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...
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# file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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# file = connexion.request.files['file']
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# if file_model is None:
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# raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist')
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# file_model = UserFileService.update_file(file_model, file.stream.read(), file.content_type)
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# return FileSchema().dump(to_file_api(file_model))
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file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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file = connexion.request.files['file']
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if file_model is None:
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raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist')
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file_model = UserFileService.update_file(file_model, file.stream.read(), file.content_type)
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return FileSchema().dump(to_file_api(file_model))
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def get_file_data_by_hash(md5_hash):
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...
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file_model = session.query(FileModel).filter(FileModel.md5_hash == md5_hash).first()
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# if document_model is not None:
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# return send_file(
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# io.BytesIO(document_model.data),
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# attachment_filename=document_model.name,
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# mimetype=document_model.content_type,
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# cache_timeout=-1 # Don't cache these files on the browser.
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# )
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# else:
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# raise ApiError('missing_file_model', f'Could not find a document_model with the hash you provided.')
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return get_file_data(file_model.id)
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# filedatamodel = session.query(FileDataModel).filter(FileDataModel.md5_hash == md5_hash).first()
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# return get_file_data(filedatamodel.file_model_id, version=filedatamodel.version)
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def get_file_data(file_id, version=None):
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...
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def get_file_data(file_id):
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file_model = session.query(FileModel).filter(FileModel.id==file_id).first()
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if file_model is not None:
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# file_data_model = UserFileService.get_file_data(file_id, version)
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# if file_data_model is not None:
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return send_file(
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io.BytesIO(file_model.data),
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attachment_filename=file_model.name,
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mimetype=file_model.content_type,
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cache_timeout=-1 # Don't cache these files on the browser.
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)
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# else:
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# raise ApiError('missing_data_model', f'The data model for file ({file_id}) does not exist')
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else:
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raise ApiError('missing_file_model', f'The file id you provided ({file_id}) does not exist')
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# file_model = session.query(FileModel).filter(FileModel.id==file_id).first()
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# if file_model is not None:
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# file_data_model = UserFileService.get_file_data(file_id, version)
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@ -99,8 +159,20 @@ def get_file_data(file_id, version=None):
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# raise ApiError('missing_file_model', f'The file id you provided ({file_id}) does not exist')
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def get_file_data_link(file_id, auth_token, version=None):
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...
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def get_file_data_link(file_id, auth_token):
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if not verify_token(auth_token):
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raise ApiError('not_authenticated', 'You need to include an authorization token in the URL with this')
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file_model = session.query(FileModel).filter(FileModel.id==file_id).first()
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if file_model is None:
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raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist')
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return send_file(
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io.BytesIO(file_model.data),
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attachment_filename=file_model.name,
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mimetype=file_model.content_type,
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cache_timeout=-1, # Don't cache these files on the browser.
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last_modified=file_model.date_created,
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as_attachment=True
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)
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# if not verify_token(auth_token):
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# raise ApiError('not_authenticated', 'You need to include an authorization token in the URL with this')
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# file_model = session.query(FileModel).filter(FileModel.id==file_id).first()
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@ -118,32 +190,29 @@ def get_file_data_link(file_id, auth_token, version=None):
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def get_file_info(file_id):
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...
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# file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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# if file_model is None:
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# raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist', status_code=404)
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# return FileSchema().dump(to_file_api(file_model))
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file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
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if file_model is None:
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raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist', status_code=404)
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return FileSchema().dump(to_file_api(file_model))
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def update_file_info(file_id, body):
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...
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# if file_id is None:
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# raise ApiError('no_such_file', 'Please provide a valid File ID.')
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#
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# file_model = session.query(FileModel).filter_by(id=file_id).first()
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#
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# if file_model is None:
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# raise ApiError('unknown_file_model', 'The file_model "' + file_id + '" is not recognized.')
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#
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# file_model = FileModelSchema().load(body, session=session)
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# session.add(file_model)
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# session.commit()
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# return FileSchema().dump(to_file_api(file_model))
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if file_id is None:
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raise ApiError('no_such_file', 'Please provide a valid File ID.')
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file_model = session.query(FileModel).filter_by(id=file_id).first()
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if file_model is None:
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raise ApiError('unknown_file_model', 'The file_model "' + file_id + '" is not recognized.')
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file_model = FileModelSchema().load(body, session=session)
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session.add(file_model)
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session.commit()
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return FileSchema().dump(to_file_api(file_model))
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def delete_file(file_id):
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...
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# UserFileService.delete_file(file_id)
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UserFileService.delete_file(file_id)
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def dmn_from_ss():
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