Esempio n. 1
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    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())
Esempio n. 2
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    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())
Esempio n. 3
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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]))
Esempio n. 4
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 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]))
Esempio n. 5
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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])
Esempio n. 6
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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)
Esempio n. 7
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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'))
Esempio n. 8
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    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()))
Esempio n. 9
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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)
Esempio n. 10
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    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())
Esempio n. 11
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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')
Esempio n. 12
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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'))
Esempio n. 13
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 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())