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()