def setUp(self):
super().setUp()
self.submissionset = SubmissionSetFactory(project=self.project)
self.submission = SubmissionFactory(submission_set=self.submissionset)
self.case = CaseFactory(project=self.project)
create_families_and_individuals(self.project)
self.individual = Individual.objects.filter(
family__project=self.project).order_by("-date_created")[0]
class TestClearOldKioskCases(TestCase):
def setUp(self):
self.user = self.make_user("kiosk_user")
self.category = ProjectFactory(
title=settings.KIOSK_CAT, type=SODAR_CONSTANTS["PROJECT_TYPE_CATEGORY"]
)
self.project_above_thres = ProjectFactory(
title=settings.KIOSK_PROJ_PREFIX + str(uuid.uuid4()), parent=self.category
)
self.project_below_thres = ProjectFactory(
title=settings.KIOSK_PROJ_PREFIX + str(uuid.uuid4()), parent=self.category
)
self.case_above_thres = CaseFactory(project=self.project_above_thres)
self.case_below_thres = CaseFactory(project=self.project_below_thres)
self.case_below_thres.date_created = datetime.now() - timedelta(weeks=9)
self.case_below_thres.save()
self.variant_set_above_thres = SmallVariantSetFactory(case=self.case_above_thres)
self.variant_set_below_thres = SmallVariantSetFactory(case=self.case_below_thres)
self.small_vars_above_thres = SmallVariantFactory.create_batch(
3, variant_set=self.variant_set_above_thres
)
self.small_vars_below_thres = SmallVariantFactory.create_batch(
3, variant_set=self.variant_set_below_thres
)
@patch("django.conf.settings.KIOSK_MODE", True)
def test_clear_old_kiosk_cases(self):
self.assertEqual(Project.objects.filter(parent=self.category).count(), 2)
self.assertEqual(Case.objects.all().count(), 2)
self.assertEqual(SmallVariant.objects.all().count(), 6)
clear_old_kiosk_cases()
projects = Project.objects.filter(parent=self.category)
cases = Case.objects.all().order_by("-date_created")
self.assertEqual(projects.count(), 1)
self.assertEqual(cases.count(), 1)
self.assertEqual(SmallVariant.objects.all().count(), 3)
self.assertEqual(projects[0].id, self.project_above_thres.id)
self.assertEqual(cases[0].id, self.case_above_thres.id)
def setUp(self):
super().setUp()
self.case = CaseFactory(project=self.project)
self.submissionset = SubmissionSetFactory(project=self.project)
self.organisation = OrganisationFactory()
self.submittingorg = SubmittingOrgFactory(
organisation=self.organisation, submission_set=self.submissionset)
self.submission = SubmissionFactory(submission_set=self.submissionset)
self.individual = Individual.objects.get_or_create_in_project(
project=self.project,
case=self.case,
name=self.case.pedigree[0]["patient"])
self.submission_individual = SubmissionIndividualFactory(
submission=self.submission, individual=self.individual)
def setUp(self):
self.user = self.make_user("kiosk_user")
self.category = ProjectFactory(
title=settings.KIOSK_CAT, type=SODAR_CONSTANTS["PROJECT_TYPE_CATEGORY"]
)
self.project_above_thres = ProjectFactory(
title=settings.KIOSK_PROJ_PREFIX + str(uuid.uuid4()), parent=self.category
)
self.project_below_thres = ProjectFactory(
title=settings.KIOSK_PROJ_PREFIX + str(uuid.uuid4()), parent=self.category
)
self.case_above_thres = CaseFactory(project=self.project_above_thres)
self.case_below_thres = CaseFactory(project=self.project_below_thres)
self.case_below_thres.date_created = datetime.now() - timedelta(weeks=9)
self.case_below_thres.save()
self.variant_set_above_thres = SmallVariantSetFactory(case=self.case_above_thres)
self.variant_set_below_thres = SmallVariantSetFactory(case=self.case_below_thres)
self.small_vars_above_thres = SmallVariantFactory.create_batch(
3, variant_set=self.variant_set_above_thres
)
self.small_vars_below_thres = SmallVariantFactory.create_batch(
3, variant_set=self.variant_set_below_thres
)
class TestFamily(TestCase):
"""Basic tests for the ``Family`` model and manager."""
def testCreate(self):
self.assertEquals(Family.objects.count(), 0)
FamilyFactory()
self.assertEquals(Family.objects.count(), 1)
def testGetOrCreateInProjectByCaseName(self):
case = CaseFactory()
self.assertEquals(Family.objects.count(), 0)
family = Family.objects.get_or_create_in_project(project=case.project,
case_name=case.name)
self.assertEquals(Family.objects.count(), 1)
self.assertEquals(family.case.id, case.id)
def setUp(self):
super().setUp()
self.case = CaseFactory(project=self.project)
self.small_variant = SmallVariantFactory(case_id=self.case.id)
kwargs = {
key: getattr(self.small_variant, key)
for key in ("release", "chromosome", "start", "end", "bin",
"reference", "alternative")
}
self.comment = SmallVariantCommentFactory(user=self.superuser,
case=self.case,
**kwargs)
self.flags = SmallVariantFlagsFactory(case=self.case, **kwargs)
self.rating = AcmgCriteriaRatingFactory(user=self.superuser,
case=self.case,
**kwargs)
class TestIndividual(TestCase):
"""Basic tests for the ``Individual`` model and manager."""
def testCreate(self):
self.assertEquals(Family.objects.count(), 0)
self.assertEquals(Individual.objects.count(), 0)
IndividualFactory()
self.assertEquals(Family.objects.count(), 1)
self.assertEquals(Individual.objects.count(), 1)
def testGetOrCreateInProjectByCaseName(self):
case = CaseFactory()
self.assertEquals(Family.objects.count(), 0)
indiv = Individual.objects.get_or_create_in_project(
project=case.project,
name=case.pedigree[0]["patient"],
case_name=case.name)
self.assertEquals(Family.objects.count(), 1)
self.assertEquals(indiv.family.case.id, case.id)
self.assertEquals(Family.objects.count(), 0)
FamilyFactory()
self.assertEquals(Family.objects.count(), 1)
def testGetOrCreateInProjectByCaseName(self):
case = CaseFactory()
self.assertEquals(Family.objects.count(), 0)
family = Family.objects.get_or_create_in_project(project=case.project,
case_name=case.name)
self.assertEquals(Family.objects.count(), 1)
self.assertEquals(family.case.id, case.id)
def testGetOrCreateInProjectByCaseNameFails(self):
case = CaseFactory()
self.assertEquals(Family.objects.count(), 0)
with self.assertRaises(Case.DoesNotExist):
Family.objects.get_or_create_in_project(project=case.project,
case_name=case.name + "_")
self.assertEquals(Family.objects.count(), 0)
def testGetOrCreateInProjectByCase(self):
case = CaseFactory()
self.assertEquals(Family.objects.count(), 0)
family = Family.objects.get_or_create_in_project(project=case.project,
case=case)
def setUp(self):
super().setUp()
self.case = CaseFactory(project=self.project)
def setUp(self):
self.data_dir = tempfile.mkdtemp()
self.case = CaseFactory()
self.admin = self.make_user("admin")
write_test_files(self.data_dir, self.case.name,
[m["patient"] for m in self.case.pedigree])