def add_file(workflow_id=None, task_spec_name=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'
)
if task_spec_name is None:
raise ApiError(
'invalid_workflow_file',
'When adding a workflow related file, you must specify a task_spec_name'
)
file_model = FileService.add_workflow_file(
workflow_id=workflow_id,
irb_doc_code=form_field_key,
task_spec_name=task_spec_name,
name=file.filename,
content_type=file.content_type,
binary_data=file.stream.read())
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 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_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))
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 get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None):
if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key]):
raise ApiError('missing_parameter',
'Please specify either a workflow_spec_id or a '
'workflow_id with an optional form_field_key')
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 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 get_files(workflow_id=None, form_field_key=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 = FileService.get_files_for_study(
study_id=study_id, irb_doc_code=form_field_key)
else:
file_models = FileService.get_files(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 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 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_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 get_documents_status(study_id):
"""Returns a list of documents related to the study, and any file information
that is available.."""
# Get PB required docs, if Protocol Builder Service is enabled.
if ProtocolBuilderService.is_enabled() and study_id is not None:
try:
pb_docs = ProtocolBuilderService.get_required_docs(
study_id=study_id)
except requests.exceptions.ConnectionError as ce:
app.logger.error(
f'Failed to connect to the Protocol Builder - {str(ce)}',
exc_info=True)
pb_docs = []
else:
pb_docs = []
# Loop through all known document types, get the counts for those files,
# and use pb_docs to mark those as required.
doc_dictionary = DocumentService.get_dictionary()
documents = {}
for code, doc in doc_dictionary.items():
doc['required'] = False
if ProtocolBuilderService.is_enabled() and doc['id'] != '':
pb_data = next(
(item for item in pb_docs['AUXDOCS']
if int(item['SS_AUXILIARY_DOC_TYPE_ID']) == int(doc['id'])
), None)
if pb_data:
doc['required'] = True
doc['study_id'] = study_id
doc['code'] = code
# Make a display name out of categories
name_list = []
for cat_key in ['category1', 'category2', 'category3']:
if doc[cat_key] not in ['', 'NULL', None]:
name_list.append(doc[cat_key])
doc['display_name'] = ' / '.join(name_list)
# For each file, get associated workflow status
doc_files = FileService.get_files_for_study(study_id=study_id,
irb_doc_code=code)
doc['count'] = len(doc_files)
doc['files'] = []
for file_model in doc_files:
file = File.from_models(
file_model, FileService.get_file_data(file_model.id), [])
file_data = FileSchema().dump(file)
del file_data['document']
doc['files'].append(Box(file_data))
# update the document status to match the status of the workflow it is in.
if 'status' not in doc or doc['status'] is None:
status = session.query(WorkflowModel.status).filter_by(
id=file.workflow_id).scalar()
doc['status'] = status.value
documents[code] = doc
return Box(documents)
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)
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():
results = FileService.get_files(is_reference=True)
files = (to_file_api(model) for model in results)
return FileSchema(many=True).dump(files)