BWS is a Django app to run web-services for BOADICEA.
Installation:
pip install -e git+https://git@github.com/CCGE-BOADICEA/bws.git#egg=bws
Update the
bws.settings.py
. In particular change theFORTRAN_HOME
parameter to set the directory location for the cancer risk models. Depending on the file structure it may be necessary to also change theHOME
location inBC_MODEL
andOC_MODEL
in this file. These and thePROBS_EXE
andRISKS_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'), 'PROBS_EXE': 'boadicea_probs.exe', 'RISKS_EXE': 'boadicea_risks.exe', ....
If you do not have access to the vcf2prs module, then comment out the related imports in the
bws.settings.py
:#import vcf2prs #from vcf2prs import SnpFile, Vcf2PrsError
and change the get_alpha function to return as follows:
def get_alpha(ref_file): ''' Get PRS alpha from a reference file header. ''' return # moduledir = os.path.dirname(os.path.abspath(vcf2prs.__file__)) # ref_file = os.path.join(moduledir, "PRS_files", ref_file) # try: # snp_file = open(ref_file, 'r') # alpha = SnpFile.extractAlpha(snp_file.__next__()) # except (IOError, UnicodeDecodeError, StopIteration): # raise Vcf2PrsError('Error: Unable to open the file "{0}".'.format(ref_file)) # finally: # snp_file.close() # return alpha
If you need to start a Django project:
django-admin startproject [project_name]
Add "rest_framework", "rest_framework.authtoken" and "bws" to your
INSTALLED_APPS
insettings.py
:INSTALLED_APPS = ( ... 'rest_framework', 'rest_framework.authtoken', 'bws', )
Import the bws settings in
settings.py
:from bws.settings import *
Add web-service endpoints to the
`urls.py
:from bws import rest_api from rest_framework.authtoken.views import ObtainAuthToken from django.conf.urls import include, url .... url_rest_patterns = [ url(r'^boadicea/', rest_api.BwsView.as_view(), name='bws'), # breast cancer risk model url(r'^ovarian/', rest_api.OwsView.as_view(), name='ows'), # ovarian cancer risk model url(r'^auth-token/', ObtainAuthToken.as_view()), ] urlpatterns.extend(url_rest_patterns)
Run tests:
python manage.py test bws.tests.test_bws \ bws.tests.test_ows.OwsTests \ bws.tests.test_throttling \ bws.tests.tests_pedigree_validation
Note: To set-up the BWS web-services to use the polygenic risk score (PRS) and cancer risk factor components (i.e. used with BOADICEA v5 or higher) requires extra Django Permissions to be granted.
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
This software is distributed under the GPL either version 3 or later license.
pedigreejs: a web-based graphical pedigree editor. Carver T, et al. Bioinformatics, Volume 34, Issue 6, 15 March 2018.