import io from typing import List import connexion 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 FileSchema, FileModel, File, FileModelSchema, FileDataModel, FileType from crc.models.workflow import WorkflowSpecModel from crc.services.document_service import DocumentService from crc.services.file_service import FileService def to_file_api(file_model): """Converts a FileModel object to something we can return via the api""" return File.from_models(file_model, FileService.get_file_data(file_model.id), DocumentService.get_dictionary()) def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None,study_id=None): if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key,study_id]): raise ApiError('missing_parameter', 'Please specify either a workflow_spec_id or a ' 'workflow_id with an optional form_field_key') if study_id is not None: file_models = FileService.get_files_for_study(study_id=study_id, irb_doc_code=form_field_key) else: file_models = FileService.get_files(workflow_spec_id=workflow_spec_id, workflow_id=workflow_id, irb_doc_code=form_field_key) files = (to_file_api(model) for model in file_models) return FileSchema(many=True).dump(files) def get_reference_files(): results = FileService.get_files(is_reference=True) files = (to_file_api(model) for model in results) return FileSchema(many=True).dump(files) def add_file(workflow_spec_id=None, workflow_id=None, form_field_key=None): file = connexion.request.files['file'] if workflow_id: if form_field_key is None: raise ApiError('invalid_workflow_file', 'When adding a workflow related file, you must specify a form_field_key') file_model = FileService.add_workflow_file(workflow_id=workflow_id, irb_doc_code=form_field_key, name=file.filename, content_type=file.content_type, binary_data=file.stream.read()) elif workflow_spec_id: # check if we have a primary already have_primary = FileModel.query.filter(FileModel.workflow_spec_id==workflow_spec_id, FileModel.type==FileType.bpmn, FileModel.primary==True).all() # set this to primary if we don't already have one if not have_primary: primary = True else: primary = False 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(), primary=primary) else: raise ApiError("invalid_file", "You must supply either a workflow spec id or a workflow_id and form_field_key.") return FileSchema().dump(to_file_api(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 FileSchema().dump(to_file_api(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 FileSchema().dump(to_file_api(file_model)) def get_file_data_by_hash(md5_hash): 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): file_data = FileService.get_file_data(file_id, version) 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.date_created ) def get_file_data_link(file_id, auth_token, version=None): if not verify_token(auth_token): raise ApiError('not_authenticated', 'You need to include an authorization token in the URL with this') file_data = FileService.get_file_data(file_id, version) 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.date_created, as_attachment = True ) 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 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)) def delete_file(file_id): FileService.delete_file(file_id)