def test_default_with_samples_does_not_create_a_new_Comparison_if_one_already_exists_for_those_samples(self):
'''
Should check for a Comparison with the samples prior to creating a new one
'''
samples = [self.s]
comp_1 = Comparison.default_from_samples(samples)
comp_2 = Comparison.default_from_samples(samples)
self.assertEqual(1, Comparison.objects.all().count())
def test_get_or_create_from_clonofilters_does_not_create_a_new_comparison_if_one_already_exists_for_the_set_of_clonofilters(self):
cf_1 = ClonoFilter(sample=self.s)
cf_1.save()
cf_2 = ClonoFilter(sample=self.s)
cf_2.save()
Comparison.get_or_create_from_clonofilters([cf_1, cf_2])
Comparison.get_or_create_from_clonofilters([cf_1, cf_2])
self.assertEqual(1, Comparison.objects.all().count())
def summary_to_comparison(request, sample_id):
'''
Given a sample id, create a comparison and foward user to comparison view
'''
s = Sample.objects.get(id=sample_id)
comp = Comparison.default_from_samples([s])
return HttpResponseRedirect(reverse('cf_comparisons.views.compare_v3', args=[comp.id]))
def test_sample_compare_redirects_to_compare_view_after_post(self):
sample_ids = [sample.id for sample in Sample.objects.all()]
comparison = Comparison.default_from_samples(Sample.objects.all())
response = self.client.post(
reverse('cf_comparisons.views.sample_compare'),
{'samples': sample_ids})
self.assertRedirects(response,
reverse('cf_comparisons.views.compare', args=[comparison.id]))
def make_fake_comparison_with_2_samples():
from clonotypes.models import AminoAcid
make_fake_patient_with_2_clonotypes()
p = Patient.objects.get()
s1 = Sample.objects.get()
s2 = Sample(patient=p, draw_date='2012-12-13', cell_type='cd4+')
s2.save()
# Make sure there's an overlapping amino_acid here
aa = AminoAcid.objects.all()[0]
r = aa.recombination_set.all()[0]
c = ClonotypeFactory(
sample=s2,
recombination = r
)
Comparison.default_from_samples([s1, s2])
def sample_compare(request):
from cf_comparisons.forms import SampleCompareForm
if request.method == 'POST':
sample_compare_form = SampleCompareForm(request.POST)
if sample_compare_form.is_valid():
comparison = Comparison.default_from_samples(
sample_compare_form.cleaned_data['samples'])
return HttpResponseRedirect(reverse('cf_comparisons.views.compare', args=[comparison.id]))
sample_compare_form = SampleCompareForm()
context = {'sample_compare_form': sample_compare_form}
return render(request, 'sample_compare.html', context)
def remove_clonofilter(request):
'''
Given a comparison id and a clonofilter id from post
get or create a comparison without the specified clonofilter.
Returns updated comparison id via http response.
'''
if request.method == "POST":
comp = Comparison.objects.get(id=request.POST['comparison'])
cfs = [cf for cf in comp.clonofilters_all() if cf.id != int(request.POST['clonofilter'])]
new_comp, created = Comparison.get_or_create_from_clonofilters(cfs)
return HttpResponse(new_comp.id)
else:
return HttpResponseRedirect(reverse('cf_comparisons.views.compare_v3'))
def test_default_with_samples_populates_a_comparison_object_with_default_clonofilters(self):
'''
We should be able to create a Comparison instance given just a list of samples.
The ClonoFilters in the Comparison object should be the default ClonoFilter of
each sample.
'''
samples = [self.s]
comp = Comparison.default_from_samples(samples)
cf = ClonoFilter.objects.get()
self.assertEqual(set([cf]), set(comp.clonofilters_all()))
def compare(request, comparison_id):
'''
Compare view takes in a comparison object and generates a summary view
that compares an arbitrary number of clonofilters
'''
if request.method == 'POST':
num_forms = int(request.POST['num_forms'])
cf_forms = [ClonoFilterForm(request.POST, prefix=str(x))
for x in range(0, num_forms)]
if all([cf_form.is_valid() for cf_form in cf_forms]):
clonofilters = []
for cf_form in cf_forms:
cf, created = ClonoFilter.objects.get_or_create(
**cf_form.cleaned_data)
clonofilters.append(cf)
comparison, created = Comparison.get_or_create_from_clonofilters(clonofilters)
else:
comparison = Comparison.objects.get(id=comparison_id)
for cf_form in cf_forms:
print cf_form.errors
return HttpResponseRedirect(reverse('cf_comparisons.views.compare', args=[comparison.id]))
comparison = Comparison.objects.get(id=comparison_id)
filter_forms = comparison.filter_forms_list()
shared_amino_acids = comparison.get_shared_amino_acids_related()
samples = comparison.get_samples()
context = {
'comparison': comparison,
'samples': samples,
'shared_amino_acids': shared_amino_acids,
}
if request.is_ajax():
return render(request, 'compare_ajax.html', context)
else:
# context.update({'comparison': comparison})
return render(request, 'compare.html', context)
def test_get_or_create_from_clonofilters_returns_one_comparison_if_two_supersets_exist(self):
'''
This test replicates a bug where multiple comparisons are returned if
multiple comparisons exist which contain a subset of clonofilters. This
is most evident when creating a new comparison from a list of samples
'''
s1 = Sample.objects.all()[0]
s2 = Sample.objects.all()[1]
Comparison.default_from_samples([s1])
Comparison.default_from_samples([s1, s2])
Comparison.default_from_samples([s1])
self.assertEqual(2, Comparison.objects.all().count())
def update_clonofilters(request, comparison_id):
comparison = Comparison.objects.get(id=comparison_id)
if request.method == 'POST':
# num_forms = int(request.POST['num_forms'])
cf_forms = [ClonoFilterForm(request.POST, prefix=str(x))
for x in range(len(comparison.clonofilters_all()))]
if all([cf_form.is_valid() for cf_form in cf_forms]):
clonofilters = []
for cf_form in cf_forms:
cf, created = ClonoFilter.objects.get_or_create(
**cf_form.cleaned_data)
clonofilters.append(cf)
comparison, created = Comparison.get_or_create_from_clonofilters(clonofilters)
else:
omparison = Comparison.objects.get(id=comparison_id)
for cf_form in cf_forms:
print cf_form.errors
return HttpResponse(comparison.id, mimetype='application/json')
def add_samples_v2(request):
'''
This should be moved to cf_comparisons
Processes an ajax request.
Given an array of sampleId's, returns an array of
clonofilter forms. The clonofilter forms are then
submitted to generate a new comparison id which is
used to generate all interactive dataplots.
'''
if request.method == "POST":
sample_ids = [int(i) for i in request.POST.getlist('samples')]
samples = Sample.objects.filter(id__in=sample_ids)
# See if there is an existing sample
try:
old_comparison = Comparison.objects.get(id=request.POST['comparison'])
comparison = old_comparison.add_samples(samples)
except:
comparison = Comparison.default_from_samples(samples)
return HttpResponse(comparison.id)
else:
return HttpResponseRedirect(reverse('cf_comparisons.views.compare_v3'))
def test_get_shared_clonotypes_returns_empty_dict_if_only_one_clonofilter_is_provided(self):
cf = ClonoFilter.objects.all()[0]
comparison, created = Comparison.get_or_create_from_clonofilters([cf])
self.assertEqual({}, comparison.get_shared_clonotypes())