def add_samples(self, samples):
'''
Given an array of sample ids, add them to the current comparison
and then return a new comparison
'''
cfs = list(self.clonofilters_all())
new_cfs = [ClonoFilter.default_from_sample(sample)
for sample in samples]
comparison, created = Comparison.get_or_create_from_clonofilters(
cfs+new_cfs)
return comparison
def default_from_samples(samples):
'''
In the case where samples are known, but no clonofilter has yet been defined,
take in a list of samples, generate the default clonofilter, populate
the Comparison object and save the object.
'''
# Get a list of default clonofilters for the samples
default_clonofilters = [ClonoFilter.default_from_sample(sample)
for sample in samples]
comparison, created = Comparison.get_or_create_from_clonofilters(
default_clonofilters)
return comparison
def summary(request, sample_id):
''' summary takes in a request and a sample id and
displays an array of summary images and statistics.
It can also take a clonofilter via POST or GET
'''
s = Sample.objects.get(id=sample_id)
if request.method == 'POST': # Handling changes to filter form via POST
cf_form = ClonoFilterForm(request.POST)
if cf_form.is_valid():
# This code does not create a new clonofilter object if one
# with the same form parameters has already been generated
cf, created = ClonoFilter.objects.get_or_create(
**cf_form.cleaned_data)
url = "%s?clonofilter=%s" % (
reverse('samples.views.summary', args=[cf.sample.id]), cf.id)
else:
url = reverse('samples.views.summary', args=[s.id])
return HttpResponseRedirect(url)
else: # Handling requests via GET
# Sets up the form to reflect the clonofilter supplied by GET
if 'clonofilter' in request.GET:
cf_id = request.GET['clonofilter']
try:
cf = ClonoFilter.objects.get(id=cf_id)
f = ClonoFilterForm(
initial=ClonoFilter.objects.filter(id=cf_id).values()[0])
except:
return HttpResponseRedirect(reverse('samples.views.summary', args=[s.id]))
# If there is no clonofilter specified, just return the default
# clonofilter with no values
else:
f = ClonoFilterForm(initial={'sample': s.id})
cf = ClonoFilter.default_from_sample(s)
context = {'sample': s,
'filter_form': f,
'clonofilter': cf,
}
return render(request, 'summary.html', context)
def test_default_from_sample_creates_a_default_clonofilter_if_one_does_not_exist(self):
ClonoFilter.objects.all().delete()
cf = ClonoFilter.default_from_sample(self.s)
self.assertEqual(cf, ClonoFilter.objects.get())
def test_default_from_sample_does_not_create_a_default_if_one_exists(self):
ClonoFilter.objects.all().delete()
ClonoFilter.default_from_sample(self.s)
ClonoFilter.default_from_sample(self.s)
self.assertEqual(1, ClonoFilter.objects.all().count())
