bws

BWS is a Django app to run web-services for BOADICEA. It use the Django REST framework to provide the Web APIs.

Quick start

1. Installation:

   pip install -e git+https://[email protected]/CCGE-BOADICEA/bws.git#egg=bws
   

This will install the bws app and the dependencies.

2. Locate the installation directory (e.g. with pip show bws). Update the bws.settings.py. In particular change the FORTRAN_HOME parameter to set the directory location for the cancer risk models. Depending on the file structure it may be necessary to also change the HOME location in BC_MODEL and OC_MODEL in this file. These and the EXE parameters define the location of the executables for the mutation probability and risk calculation:

FORTRAN_HOME = "/usr/src/"
....

#
# BREAST CANCER MODEL
BC_MODEL = {
    'NAME': 'BC',
    'HOME': os.path.join(FORTRAN_HOME, 'boadicea'),
    'EXE': 'boadicea.exe',
....

3. If you need to start a Django project:

   django-admin startproject [project_name]
   

4. Add "rest_framework", "rest_framework.authtoken" and "bws" to your INSTALLED_APPS in settings.py:

   INSTALLED_APPS = (
       ...
       'rest_framework',
       'rest_framework.authtoken',
       'bws',
   )
   

5. Import the bws settings in settings.py:

   from bws.settings import *
   

6. Add web-service endpoints to the `urls.py:

   from bws import rest_api
   from rest_framework.authtoken.views import ObtainAuthToken
   ....
   
   url_rest_patterns = [
       path('boadicea/', rest_api.BwsView.as_view(), name='bws'),    # breast cancer risk model
       path('ovarian/', rest_api.OwsView.as_view(), name='ows'),     # ovarian cancer risk model
       path('auth-token/', ObtainAuthToken.as_view()),
   ]
   urlpatterns.extend(url_rest_patterns)
   

7. Run tests:

   python manage.py test bws.tests.test_bws \
                         bws.tests.test_ows.OwsTests \
                         bws.tests.test_throttling \
                         bws.tests.tests_pedigree_validation
   

The run_webservice.py script can be used to submit requests to the BWS web-service. It takes a username and pedigree file and will prompt for the password and run the risk calculation via the web-service:

${PATH_TO_BWS}/bws/scripts/run_webservice.py --help
${PATH_TO_BWS}/bws/scripts/run_webservice.py --url ${URL} -u ${USER} \
                                             -p ${PATH_TO_BWS}/bws/tests/data/pedigree_data.txt

License

This software is distributed under the GPL either version 3 or later license.

Publication

pedigreejs: a web-based graphical pedigree editor. Carver T, et al. Bioinformatics, Volume 34, Issue 6, 15 March 2018.