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