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()
self.maxDiff = None # show full diff
# setup users
# setup super user
self.superuser = self.make_user("superuser")
self.superuser.is_staff = True
self.superuser.is_superuser = True
self.superuser.save()
# setup contributor user
self.contributor = self.make_user("contributor")
# setup owner for projects, not used in tests
owner = self.make_user("owner")
# setup cases & projects & roles
# project 1 case 1
self.project1 = ProjectFactory()
self.project1_case1, variant_set_1, _ = CaseWithVariantSetFactory.get(
"small", project=self.project1)
self.project1_case1_smallvars = SmallVariantFactory.create_batch(
1, variant_set=variant_set_1)
# project 1 case 2
self.project1_case2, variant_set_2, _ = CaseWithVariantSetFactory.get(
"small", project=self.project1)
self.project1_case2_smallvars = SmallVariantFactory.create_batch(
2, variant_set=variant_set_2)
# project 2 case 1
self.project2 = ProjectFactory()
self.project2_case1, variant_set_3, _ = CaseWithVariantSetFactory.get(
"small", project=self.project2)
self.project2_case1_smallvars = SmallVariantFactory.create_batch(
4, variant_set=variant_set_3)
# project 2 case 2
self.project2_case2, variant_set_4, _ = CaseWithVariantSetFactory.get(
"small", project=self.project2)
self.project2_case2_smallvars = SmallVariantFactory.create_batch(
8, variant_set=variant_set_4)
# init roles
role_owner = Role.objects.get_or_create(name=PROJECT_ROLE_OWNER)[0]
role_contributor = Role.objects.get_or_create(
name=PROJECT_ROLE_CONTRIBUTOR)[0]
# owner owns project1 and project2 (all projects)
self._make_assignment(self.project1, owner, role_owner)
self._make_assignment(self.project2, owner, role_owner)
# contributor gets access to project2
self._make_assignment(self.project2, self.contributor,
role_contributor)
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):
super().setUp()
self.project = ProjectFactory()
variant_sets = [None, None]
_, variant_sets[0], _ = CaseWithVariantSetFactory.get(
"small", project=self.project)
_, variant_sets[1], _ = CaseWithVariantSetFactory.get(
"small", 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):
self.data_dir = tempfile.mkdtemp()
self.small_var = SmallVariantFactory()
self.case = Case.objects.first()
write_test_files(self.data_dir, self.case.name,
[m["patient"] for m in self.case.pedigree])
self.admin = self.make_user("admin")
def setUp(self):
super().setUp()
self.case, self.variant_set, _ = CaseWithVariantSetFactory.get("small")
self.hpo_id = "HP:0000001"
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)
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, self.variant_set_above_thres, _ = CaseWithVariantSetFactory.get(
"small", project=self.project_above_thres)
self.case_below_thres, self.variant_set_below_thres, _ = CaseWithVariantSetFactory.get(
"small", project=self.project_below_thres)
self.case_below_thres.date_created = datetime.now() - timedelta(
weeks=9)
self.case_below_thres.save()
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)
def setUp(self):
self.user = self.make_user("superuser")
self.case1, self.variant_set1, _ = CaseWithVariantSetFactory.get(
"small")
self.project = CaseAwareProject.objects.get(
pk=Project.objects.first().pk)
self.case2, self.variant_set2, _ = CaseWithVariantSetFactory.get(
"small", project=self.project)
self.small_vars1 = [
SmallVariantFactory(chromosome="1", variant_set=self.variant_set1),
SmallVariantFactory(chromosome="2", variant_set=self.variant_set1),
SmallVariantFactory(chromosome="3", variant_set=self.variant_set1),
]
self.small_vars2 = [
SmallVariantFactory(
chromosome=self.small_vars1[0].chromosome,
start=self.small_vars1[0].start,
reference=self.small_vars1[0].reference,
alternative=self.small_vars1[0].alternative,
variant_set=self.variant_set2,
),
]
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 = ExportProjectCasesFileBgJob.objects.create(
project=self.bg_job.project,
bg_job=self.bg_job,
query_args=vars(
ResubmitFormDataFactory(submit="download",
names=self.project.get_members())),
file_type="xlsx",
)
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)
def setUp(self):
super().setUp()
self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
self.remote_site = Site.objects.get(role=Site.REMOTE)
ConsortiumAssignmentFactory(
consortium=self.consortium,
project=self.project,
)
self.small_variant = SmallVariantFactory(case__project=self.project)
self.beacon_allele_request = BeaconAlleleRequest(
assemblyId=self.small_variant.release,
referenceName=self.small_variant.chromosome,
start=self.small_variant.start,
referenceBases=self.small_variant.reference,
alternateBases=self.small_variant.alternative,
)
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.case, variant_set, _ = CaseWithVariantSetFactory.get("small")
small_var = SmallVariantFactory(variant_set=variant_set)
def setUp(self):
super().setUp()
variant_set = SmallVariantSetFactory()
self.case = variant_set.case
small_var = SmallVariantFactory(variant_set=variant_set)