cr-connect-workflow/crc/api/file.py

import io
from datetime import datetime

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
from crc.models.workflow import WorkflowModel
from crc.services.document_service import DocumentService
from crc.services.study_service import StudyService
from crc.services.user_file_service import UserFileService


def to_file_api(file_model):
    file_data_model = UserFileService.get_file_data(file_model.id)
    return File.from_models(file_model, file_data_model,
                            DocumentService.get_dictionary())


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 = UserFileService.get_files_for_study(study_id=study_id, irb_doc_code=form_field_key)
    else:
        file_models = UserFileService.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 add_file(workflow_id=None, task_spec_name=None, form_field_key=None):
    file = connexion.request.files['file']
    if workflow_id:
        workflow = session.query(WorkflowModel).filter(WorkflowModel.id == WorkflowModel.id).first()
        if workflow is None:
            raise ApiError('invalid_workflow',
                           f'Unable to find a workflow with id {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 = UserFileService.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())
        # We calculate the document statuses once per request, but a script may execute more quickly
        # So force a refresh of the document status here.
        StudyService.get_documents_status(study_id=workflow.study_id, force=True)
    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', f'The file id you provided ({file_id}) does not exist')
    file_model = UserFileService.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_model = session.query(FileModel).filter(FileModel.id==file_id).first()
    if file_model is not None:
        file_data_model = UserFileService.get_file_data(file_id, version)
        if file_data_model is not None:
            return send_file(
                io.BytesIO(file_data_model.data),
                attachment_filename=file_model.name,
                mimetype=file_model.content_type,
                cache_timeout=-1  # Don't cache these files on the browser.
            )
        else:
            raise ApiError('missing_data_model', f'The data model for file ({file_id}) does not exist')
    else:
        raise ApiError('missing_file_model', f'The file id you provided ({file_id}) does not exist')


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_model = session.query(FileModel).filter(FileModel.id==file_id).first()
    file_data = UserFileService.get_file_data(file_id, version)
    if file_data is None:
        raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist')
    return send_file(
        io.BytesIO(file_data.data),
        attachment_filename=file_model.name,
        mimetype=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', f'The file id you provided ({file_id}) 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):
    UserFileService.delete_file(file_id)


def dmn_from_ss():
    file = connexion.request.files['file']
    result = UserFileService.dmn_from_spreadsheet(file)
    return send_file(
        io.BytesIO(result),
        attachment_filename='temp_dmn.dmn',
        mimetype='text/xml',
        cache_timeout=-1,  # Don't cache these files on the browser.
        last_modified=datetime.now()
    )