cr-connect-workflow/crc/scripts/get_zipped_files.py

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from crc import session
from crc.api.common import ApiError
from crc.models.file import FileModel, FileDataModel
from crc.scripts.script import Script
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
import os
import zipfile
class GetZippedFiles(Script):
"""This script creates a zip document from a list of file ids"""
def get_description(self):
"""Creates a zip file from a list of file_ids.
This is meant to use as an attachment to an email message"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
if 'file_ids' in kwargs.keys():
return True
return False
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 zipfile.ZipFile(zip_filename, mode='x', 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)
# Add the zipfile to the DB, and grab the file_model
with open(zip_filename, mode='rb') as handle:
file_model = FileService().add_workflow_file(workflow_id, None, task.name, zip_filename, 'application/zip', handle.read())
# Delete the temporary zipfile
os.remove(zip_filename)
# Return the file_model
return file_model
else:
raise ApiError(code='missing_file_ids',
message='You must include a list of file_ids.')