def setUpTestData(cls):
super().setUpTestData()
cls.user = UserFactory()
cls.target_study = factory.StudyFactory()
cls.target_study.userpermission_set.create(
user=cls.user, permission_type=models.StudyPermission.WRITE
)
# IDs are hard-coded in FBA files in main/tests/files
line1 = factory.LineFactory(id=998, study=cls.target_study, name="BW1")
met1 = factory.MetaboliteFactory(id=898, type_name="D-Glucose")
met2 = factory.MetaboliteFactory(id=899, type_name="Acetate")
# optical density already defined in bootstrap
od = models.MeasurementType.objects.get(
uuid="d7510207-5beb-4d56-a54d-76afedcf14d0"
)
values = zip(cls.TIMES, cls.GLUCOSE_VALUES)
cls._build_measurements(
1000, models.Protocol.CATEGORY_HPLC, line1, met1, values
)
values = zip(cls.TIMES, cls.ACETATE_VALUES)
cls._build_measurements(
1001, models.Protocol.CATEGORY_HPLC, line1, met2, values
)
values = zip(cls.TIMES, cls.OD_VALUES)
cls._build_measurements(1002, models.Protocol.CATEGORY_OD, line1, od, values)
factory.SBMLTemplateFactory(id=666, uuid=uuid.uuid4())
def setUpTestData(cls):
super().setUpTestData()
cls.user = UserFactory()
cls.target_study = factory.StudyFactory()
cls.target_study.userpermission_set.create(
user=cls.user, permission_type=models.StudyPermission.WRITE)
# TODO: IDs are hard-coded in the *.post.*.json files
# measurement ID of Optical Density is set to 1 in bootstrap
factory.LineFactory(id=998, study=cls.target_study, name="BW1")
factory.LineFactory(id=999, study=cls.target_study, name="arcA")
factory.MetaboliteFactory(id=898, type_name="D-Glucose")
factory.MetaboliteFactory(id=899, type_name="Acetate")
def test_simple_import(self):
"""Test an import where everything is already resolved."""
line = factory.LineFactory(study=self.target_study)
protocol = factory.ProtocolFactory()
assay = factory.AssayFactory(line=line, protocol=protocol)
mtype = factory.MetaboliteFactory()
unit = factory.UnitFactory()
# no measurements exist before import
self.assertEqual(
models.Measurement.objects.filter(
study_id=self.target_study.pk).count(), 0)
self._set_permission(permission_type=models.StudyPermission.WRITE)
run = TableImport(self.target_study, self.user)
added, updated = run.import_series_data([{
"line_id":
line.id,
"assay_id":
assay.id,
"measurement_id":
mtype.id,
"comp_id":
models.Measurement.Compartment.UNKNOWN,
"units_id":
unit.id,
"metadata": {},
"data": [[0, 0]],
}])
# after the self-reported add/update are correct
self.assertEqual(added, 1)
self.assertEqual(updated, 0)
# and the counts are correct
self.assertEqual(
models.Measurement.objects.filter(
study_id=self.target_study.pk).count(), 1)
def test_resolve_broad_type_with_pubchem_existing(self):
broad = factory.CategoryFactory()
type_A = main_factory.MetaboliteFactory(pubchem_cid="9999")
tr = TypeResolver(self.user, broad)
# on_commit hook will never trigger in test
# but check that something should / should-not happen
with patch("main.models.measurement_type.transaction") as hook:
found = tr.lookup_type("CID:9999")
assert found.pk == type_A.pk
hook.on_commit.assert_not_called()
def test_resolve_metabolite_type(self):
metabolomics = factory.CategoryFactory(
type_group=models.MeasurementType.Group.METABOLITE)
type_A = main_factory.MetaboliteFactory(pubchem_cid="9999")
tr = TypeResolver(self.user, metabolomics)
# on_commit hook will never trigger in test
# but check that something should / should-not happen
with patch("main.models.measurement_type.transaction") as hook:
found = tr.lookup_type("CID:9999")
assert found.pk == type_A.pk
hook.on_commit.assert_not_called()