cr-connect-workflow/crc/api/file.py

134 lines
5.5 KiB
Python

import io
import connexion
from flask import send_file
from crc import session
from crc.api.common import ApiError
from crc.models.file import FileModelSchema, FileModel, FileDataModel
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
def get_files(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
if all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key]):
raise ApiError('missing_parameter',
'Please specify at least one of workflow_spec_id, study_id, '
'workflow_id, and task_id for this file in the HTTP parameters')
results = FileService.get_files(workflow_spec_id, study_id, workflow_id, task_id, form_field_key)
return FileModelSchema(many=True).dump(results)
def get_reference_files():
results = FileService.get_files(is_reference=True)
return FileModelSchema(many=True).dump(results)
def add_file(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
all_none = all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key])
missing_some = (workflow_spec_id is None) and (None in [study_id, workflow_id, task_id, form_field_key])
if all_none or missing_some:
raise ApiError('missing_parameter',
'Please specify either a workflow_spec_id or all 3 of study_id, '
'workflow_id, task_id and field_id for this file in the HTTP parameters')
if 'file' not in connexion.request.files:
raise ApiError('invalid_file',
'Expected a file named "file" in the multipart form request')
file = connexion.request.files['file']
if workflow_spec_id:
workflow_spec = session.query(WorkflowSpecModel).filter_by(id=workflow_spec_id).first()
file_model = FileService.add_workflow_spec_file(workflow_spec, file.filename, file.content_type,
file.stream.read())
else:
file_model = FileService.add_form_field_file(study_id, workflow_id, task_id, form_field_key, file.filename,
file.content_type, file.stream.read())
return FileModelSchema().dump(file_model)
def get_reference_file(name):
file_data = FileService.get_reference_file_data(name)
return send_file(
io.BytesIO(file_data.data),
attachment_filename=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1 # Don't cache these files on the browser.
)
def set_reference_file(name):
"""Uses the file service to manage reference-files. They will be used in script tasks to compute values."""
if 'file' not in connexion.request.files:
raise ApiError('invalid_file',
'Expected a file named "file" in the multipart form request', status_code=400)
file = connexion.request.files['file']
name_extension = FileService.get_extension(name)
file_extension = FileService.get_extension(file.filename)
if name_extension != file_extension:
raise ApiError('invalid_file_type',
"The file you uploaded has an extension '%s', but it should have an extension of '%s' " %
(file_extension, name_extension))
file_models = FileService.get_files(name=name, is_reference=True)
if len(file_models) == 0:
file_model = FileService.add_reference_file(name, file.content_type, file.stream.read())
else:
file_model = file_models[0]
FileService.update_file(file_models[0], file.stream.read(), file.content_type)
return FileModelSchema().dump(file_model)
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', 'The file id you provided does not exist')
file_model = FileService.update_file(file_model, file.stream.read(), file.content_type)
return FileModelSchema().dump(file_model)
def get_file_data(file_id):
file_data = FileService.get_file_data(file_id)
if file_data is None:
raise ApiError('no_such_file', 'The file id you provided does not exist')
return send_file(
io.BytesIO(file_data.data),
attachment_filename=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1, # Don't cache these files on the browser.
last_modified=file_data.last_updated
)
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', 'The file id you provided does not exist', status_code=404)
return FileModelSchema().dump(file_model)
def update_file_info(file_id, body):
if file_id is None:
raise ApiError('unknown_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 FileModelSchema().dump(file_model)
def delete_file(file_id):
session.query(FileDataModel).filter_by(file_model_id=file_id).delete()
session.query(FileModel).filter_by(id=file_id).delete()
session.commit()