def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def variant_filters_from_request(request, db, samples_selection=None):
"""Parse a GET Request and return a list of requested filters.
A filter is a tuple (name, operation, value), corresponding to a request
of the type '?name=value'. See the REST API documentation for more information.
:rtype: FiltersCollection
"""
filters = []
filterlist = request.GET.getlist('filter', [])
if samples_selection is None:
samples_selection = samples_selection_from_request(request, db)
for f in filterlist:
m = re.match(r"(\S+?)([<>=]{1,2})(.+)", f)
if m:
k, op, v = m.groups()
filters.append((k, op, v))
else:
filters.append((f, '=', '1'))
return variant_filters_collection_factory(filters, samples_selection, db)
def variant_filters_from_request(request, db, samples_selection=None):
"""Parse a GET Request and return a list of requested filters.
A filter is a tuple (name, operation, value), corresponding to a request
of the type '?name=value'. See the REST API documentation for more information.
:rtype: FiltersCollection
"""
filters = []
filterlist = request.GET.getlist('filter', [])
if samples_selection is None:
samples_selection = samples_selection_from_request(request, db)
for f in filterlist:
m = re.match(r"(\S+?)([<>=]{1,2})(.+)", f)
if m:
k, op, v = m.groups()
filters.append((k, op, v))
else:
filters.append((f, '=', '1'))
return variant_filters_collection_factory(filters, samples_selection, db)
def variant_filters_from_request(request, db, samples_selection=None):
"""Parse a GET Request and return a list of requested filters.
A filter is a tuple (name, operation, value), corresponding to a request
of the type '?name=value'. See the REST API documentation for more information.
:rtype: FiltersCollection
"""
filters = []
filterlist = request.GET.getlist('filter', [])
if filterlist == []:
filterlist = ['genotype=none']
if samples_selection is None:
samples_selection = samples_selection_from_request(request, db)
for f in filterlist:
m = re.match(r"(\S+?)([<>=]{1,2})(.+)", f)
if m:
k, op, v = m.groups()
filters.append((k, op, v))
else:
filters.append((f, '=', '1'))
with open('/home/liaoth/Desktop/debug.info','a+') as f1:
f1.write('filters=%s ; samples=%s \n' % (str(filters),str(samples_selection)))
return variant_filters_collection_factory(filters, samples_selection, db)
def samples(request, db, user=None):
"""Return a JSON with the list of Samples."""
ss = samples_selection_from_request(request, db)
return JsonResponse(ss.expose(), safe=False)
def samples(request, db, user=None):
"""Return a JSON with the list of Samples."""
ss = samples_selection_from_request(request, db)
return JsonResponse(ss.expose(), safe=False)
def test_samples_selection_from_request(self):
"""Create a SamplesSelection from groups dessribed in URL."""
request = RequestFactory().get('', [('samples','group1=09818'),
('samples','group2=09819'), ('samples','group3=09960,09961')])
ss = samples_selection_from_request(request, db='test')
self.assertIsInstance(ss, SamplesSelection)
