def setUp(self): super().setUp() self.project = ProjectFactory() variant_sets = SmallVariantSetFactory.create_batch( 2, case__project=self.project) SmallVariantFactory(variant_set=variant_sets[0]) SmallVariantFactory(variant_set=variant_sets[1]) for variant_set in variant_sets: update_variant_counts(variant_set.case)
def setUp(self): super().setUp() user = self.make_user("superuser") self.bgjob = ProjectCasesFilterBgJobFactory(user=user) variant_sets = SmallVariantSetFactory.create_batch( 2, case__project=self.bgjob.project) SmallVariantFactory.create_batch(3, variant_set=variant_sets[0]) SmallVariantFactory.create_batch(3, variant_set=variant_sets[1]) self.bgjob.projectcasessmallvariantquery.query_settings.update( vars(FormDataFactory(names=self.bgjob.project.get_members())))
def setUp(self): self.user = self.make_user("superuser") self.variant_set_active_above_thres = SmallVariantSetFactory(state="active") self.variant_set_active_above_thres.date_created = datetime.now() - timedelta(hours=1) self.variant_set_active_above_thres.save() self.variant_set_inactive_above_thres = SmallVariantSetFactory(state="importing") self.variant_set_inactive_above_thres.date_created = datetime.now() - timedelta(hours=2) self.variant_set_inactive_above_thres.save() self.variant_set_active_below_thres = SmallVariantSetFactory(state="active") self.variant_set_active_below_thres.date_created = datetime.now() - timedelta(hours=13) self.variant_set_active_below_thres.save() self.variant_set_inactive_below_thres = SmallVariantSetFactory(state="importing") self.variant_set_inactive_below_thres.date_created = datetime.now() - timedelta(hours=14) self.variant_set_inactive_below_thres.save()
def setUp(self): self.user = self.make_user("superuser") variant_set = SmallVariantSetFactory() self.bg_job = BackgroundJob.objects.create( name="job name", project=Project.objects.first(), job_type="variants.export_file_bg_job", user=self.user, ) self.export_job = ExportFileBgJob.objects.create( project=self.bg_job.project, bg_job=self.bg_job, case=variant_set.case, query_args={"some": "args"}, file_type="xlsx", )
def setUp(self): super().setUp() self.variant_set = SmallVariantSetFactory() self.hponame = HpoNameFactory(hpo_id="HP:0000001") self.hpos = [ HpoFactory( database_id="OMIM:000001", hpo_id="HP:0000002", name="Disease 1;;Alternative Description", ), HpoFactory( database_id="OMIM:000001", hpo_id="HP:0000003", name="Disease 1;;Alternative Description", ), ] self.maxDiff = None
def setUp(self): self.user = self.make_user("superuser") self.variant_set = SmallVariantSetFactory() self.small_vars = SmallVariantFactory.create_batch(3, variant_set=self.variant_set) self.case = self.variant_set.case self.bg_job = BackgroundJob.objects.create( name="job name", project=Project.objects.first(), job_type="variants.export_file_bg_job", user=self.user, ) self.export_job = ExportFileBgJob.objects.create( project=self.bg_job.project, bg_job=self.bg_job, case=self.case, query_args={"export_flags": True, "export_comments": True}, file_type="xlsx", )
def setUp(self): super().setUp() self.variant_set = SmallVariantSetFactory() self.hpo_id = "HP:0000001" self.case = self.variant_set.case self.user = self.make_user("superuser") self.small_vars = [ SmallVariantFactory(chromosome="1", refseq_gene_id="1234", variant_set=self.variant_set), SmallVariantFactory(chromosome="1", refseq_gene_id="2234", variant_set=self.variant_set), SmallVariantFactory(chromosome="1", refseq_gene_id="2234", variant_set=self.variant_set, in_clinvar=True), ] self.bgjob = FilterBgJobFactory(case=self.case, user=self.user)
class TestCleanupVariantSets(TestCase): def setUp(self): self.user = self.make_user("superuser") self.variant_set_active_above_thres = SmallVariantSetFactory(state="active") self.variant_set_active_above_thres.date_created = datetime.now() - timedelta(hours=1) self.variant_set_active_above_thres.save() self.variant_set_inactive_above_thres = SmallVariantSetFactory(state="importing") self.variant_set_inactive_above_thres.date_created = datetime.now() - timedelta(hours=2) self.variant_set_inactive_above_thres.save() self.variant_set_active_below_thres = SmallVariantSetFactory(state="active") self.variant_set_active_below_thres.date_created = datetime.now() - timedelta(hours=13) self.variant_set_active_below_thres.save() self.variant_set_inactive_below_thres = SmallVariantSetFactory(state="importing") self.variant_set_inactive_below_thres.date_created = datetime.now() - timedelta(hours=14) self.variant_set_inactive_below_thres.save() def test_cleanup_variant_sets(self): self.assertEqual(SmallVariantSet.objects.all().count(), 4) cleanup_variant_sets() variant_sets = SmallVariantSet.objects.all().order_by("-date_created") self.assertEqual(variant_sets.count(), 3) self.assertEqual(variant_sets[0].id, self.variant_set_active_above_thres.id) self.assertEqual(variant_sets[1].id, self.variant_set_inactive_above_thres.id) self.assertEqual(variant_sets[2].id, self.variant_set_active_below_thres.id)
def setUp(self): super().setUp() variant_set = SmallVariantSetFactory() self.case = variant_set.case small_var = SmallVariantFactory(variant_set=variant_set)
def setUp(self): super().setUp() variant_set = SmallVariantSetFactory() self.case = variant_set.case SampleVariantStatisticsFactory(variant_set=variant_set, sample_name=variant_set.case.index)