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

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)