def get_spec_files(workflow_spec_id, include_libraries=False):
if workflow_spec_id is None:
raise ApiError(code='missing_spec_id',
message='Please specify the workflow_spec_id.')
file_models = SpecFileService.get_spec_files(
workflow_spec_id=workflow_spec_id, include_libraries=include_libraries)
files = [to_file_api(model) for model in file_models]
return FileSchema(many=True).dump(files)
def update_reference_file_info(name, body):
if name is None:
raise ApiError(code='missing_parameter',
message='Please provide a reference file name')
file_model = session.query(FileModel).filter(FileModel.name==name).first()
if file_model is None:
raise ApiError(code='no_such_file',
message=f"No reference file was found with name: {name}")
new_file_model = ReferenceFileService.update_reference_file_info(file_model, body)
return FileSchema().dump(to_file_api(new_file_model))
def get_reference_file_info(name):
"""Return metadata for a reference file"""
file_model = session.query(FileModel).\
filter_by(name=name).with_for_update().\
filter_by(archived=False).with_for_update().\
first()
if file_model is None:
# TODO: Should this be 204 or 404?
raise ApiError('no_such_file', f'The reference file name you provided ({name}) does not exist', status_code=404)
return FileSchema().dump(to_file_api(file_model))
def update_spec_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(
FileModel.id == file_id).first()
if file_model is None:
raise ApiError('unknown_file_model',
'The file_model "' + file_id + '" is not recognized.')
new_file_model = SpecFileService().update_spec_file_info(file_model, body)
return FileSchema().dump(to_file_api(new_file_model))
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
if 'file_ids' in kwargs.keys():
doc_info = StudyService().get_documents_status(study_id)
if 'filename' in kwargs.keys():
zip_filename = kwargs['filename']
else:
zip_filename = 'attachments.zip'
file_ids = kwargs['file_ids']
files = session.query(FileModel).filter(
FileModel.id.in_(file_ids)).all()
if files:
# Create a temporary zipfile with the requested files
with tempfile.NamedTemporaryFile() as temp_file:
with zipfile.ZipFile(
temp_file, mode='w',
compression=zipfile.ZIP_DEFLATED) as zfw:
for file in files:
zip_key_words = doc_info[
file.irb_doc_code]['zip_key_words']
file_name = f'{study_id} {zip_key_words} {file.name}'
file_data = session.query(FileDataModel).filter(
FileDataModel.file_model_id ==
file.id).first()
zfw.writestr(file_name, file_data.data)
with open(temp_file.name, mode='rb') as handle:
file_model = FileService().add_workflow_file(
workflow_id, None, task.get_name(), zip_filename,
'application/zip', handle.read())
# return file_model
return FileSchema().dump(to_file_api(file_model))
else:
raise ApiError(code='missing_file_ids',
message='You must include a list of file_ids.')
def add_spec_file(workflow_spec_id):
if workflow_spec_id:
file = connexion.request.files['file']
# 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 = SpecFileService.add_workflow_spec_file(workflow_spec,
file.filename,
file.content_type,
file.stream.read(),
primary=primary)
return FileSchema().dump(to_file_api(file_model))
else:
raise ApiError(code='missing_workflow_spec_id',
message="You must include a workflow_spec_id")
def update_reference_file_data(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_model = session.query(FileModel).filter(FileModel.name==name).first()
if not file_model:
raise ApiError(code='file_does_not_exist',
message=f"The reference file {name} does not exist.")
else:
ReferenceFileService().update_reference_file(file_model, file.stream.read())
return FileSchema().dump(to_file_api(file_model))
def update_spec_file_data(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')
if file_model.workflow_spec_id is None:
raise ApiError(
code='no_spec_id',
message=f'There is no workflow_spec_id for file {file_id}.')
workflow_spec_model = session.query(WorkflowSpecModel).filter(
WorkflowSpecModel.id == file_model.workflow_spec_id).first()
if workflow_spec_model is None:
raise ApiError(
code='missing_spec',
message=
f'The workflow spec for id {file_model.workflow_spec_id} does not exist.'
)
file = connexion.request.files['file']
SpecFileService().update_spec_file_data(workflow_spec_model,
file_model.name,
file.stream.read())
return FileSchema().dump(to_file_api(file_model))
def add_reference_file():
file = connexion.request.files['file']
file_model = ReferenceFileService.add_reference_file(name=file.filename,
content_type=file.content_type,
binary_data=file.stream.read())
return FileSchema().dump(to_file_api(file_model))
def get_reference_files():
"""Gets a list of all reference files"""
results = ReferenceFileService.get_reference_files()
files = (to_file_api(model) for model in results)
return FileSchema(many=True).dump(files)