def example_filegroup():
test_project = Project(project_id="test")
exp = test_project.add_experiment(
experiment_id="test experiment",
data_directory=f"{os.getcwd()}/test_data",
panel_definition=f"{os.getcwd()}/assets/test_panel.xlsx")
exp.add_new_sample(
sample_id="test sample",
primary_path=f"{os.getcwd()}/assets/test.FCS",
controls_path={"test_ctrl": f"{os.getcwd()}/assets/test.FCS"},
compensate=False)
yield exp.get_sample(sample_id="test sample")
test_project.delete()
def _build(dump=True):
# Initiate Gating object
if dump:
db = connect('test')
db.drop_database('test')
global_init('test')
setup_with_dummy_data()
project = Project.objects(project_id='test').get()
gate = Gating(experiment=project.load_experiment('test_experiment_dummy'),
sample_id='dummy_test')
return gate
def test_apply_all(example_experiment):
gs = create_gatingstrategy_and_load(example_experiment)
with pytest.raises(AssertionError) as err:
gs.apply_all()
assert str(err.value) == "No gates to apply"
gs = apply_some_gates(gs)
exp = Project.objects(
project_id="test").get().load_experiment("test experiment")
gs.load_data(experiment=exp, sample_id="test sample")
gs.apply_all()
assert_expected_gated_pops(gs)
with pytest.raises(AssertionError) as err:
gs.apply_all()
assert str(err.value) == "One or more of the populations generated from this gating strategy are already " \
"presented in the population tree"
def test_init_new_fcs_file(example_filegroup):
fg = example_filegroup
assert os.path.isfile(f"{os.getcwd()}/test_data/{fg.id}.hdf5")
experiment = Project.objects(
project_id="test").get().load_experiment("test experiment")
fg = experiment.get_sample("test sample")
primary_data = fg.data("primary")
ctrl_data = fg.data("test_ctrl")
assert len(fg.populations) == 1
assert fg.populations[0].population_name == "root"
assert len(fg.tree.keys()) == 1
assert list(fg.tree.keys())[0] == "root"
root = fg.populations[0]
assert root.parent == "root"
assert root.population_name == "root"
assert np.array_equal(primary_data.index.values, root.index)
assert np.array_equal(ctrl_data.index.values,
root.ctrl_index.get("test_ctrl"))
assert primary_data.shape == (30000, 7)
assert ctrl_data.shape == (30000, 7)
def test_FileGroup(self):
test_project = Project.objects(project_id='test').get()
test_exp = test_project.load_experiment('test_experiment_dummy')
# Testing data retrieval
test_grp = test_exp.pull_sample('dummy_test')
test_file = test_grp.files[0]
self.assertEqual(test_file.pull().shape, (100, 3))
self.assertEqual(test_file.pull(sample=10).shape, (10, 3))
data = test_exp.pull_sample_data('dummy_test', include_controls=True)
primary = [d for d in data if d.get('typ') == 'complete'][0]
ctrl = [d for d in data if d.get('typ') == 'control'][0]
self.assertEqual(primary.get('data').shape, (100, 3))
self.assertEqual(ctrl.get('data').shape, (100, 3))
self.assertListEqual(
ctrl.get('data').columns.tolist(),
['feature0', 'feature1', 'blobID'])
data = test_exp.pull_sample_data('dummy_test',
include_controls=True,
columns_default='channel')
primary = [d for d in data if d.get('typ') == 'complete'][0]
self.assertListEqual(
primary.get('data').columns.tolist(), ['var0', 'var1', 'var2'])
def test_delete(example_experiment, remove_associations):
gs = create_gatingstrategy_and_load(example_experiment)
gs = apply_some_gates(gs)
gs.save()
gs = GatingStrategy.objects(name="test").get()
populations = [[c.name for c in g.children] for g in gs.gates]
populations = list(set([x for sl in populations for x in sl]))
gs.delete(remove_associations=remove_associations,
delete_gates=remove_associations)
assert len(GatingStrategy.objects(name="test")) == 0
n = [0, 0]
if not remove_associations:
n = [2, 1]
for n_, gate in zip(n, [ThresholdGate, EllipseGate]):
assert len(gate.objects()) == n_
fg = (Project.objects(project_id="test").get().load_experiment(
"test experiment").get_sample("test sample"))
if remove_associations:
assert len(fg.gating_strategy) == 0
assert all([p not in fg.list_populations() for p in populations])
else:
assert len(fg.gating_strategy) == 1
assert all([p in fg.list_populations() for p in populations])
def test_add_population(example_filegroup):
fg, populations = create_populations(filegroup=example_filegroup)
fg.save()
experiment = Project.objects(
project_id="test").get().load_experiment("test experiment")
fg = experiment.get_sample("test sample")
# Check population objects
assert len(fg.populations) == 4
assert all([
x in [p.population_name for p in fg.populations]
for x in ["root", "pop1", "pop2", "pop3"]
])
# Check indexes
pop_idx = {p.population_name: p.index for p in fg.populations}
pop_ctrl_idx = {
p.population_name: p.ctrl_index.get("test_ctrl")
for p in fg.populations
}
for data_dict in [pop_idx, pop_ctrl_idx]:
for name, expected_n in zip(["root", "pop1", "pop2", "pop3"],
[30000, 24000, 12000, 6000]):
assert len(data_dict.get(name)) == expected_n
# Check cluster idx
clustered_pops = [p for p in fg.populations if p.population_name != "root"]
cluster_idx = {
p.population_name: p.clusters[0].index
for p in clustered_pops
}
for name, n in zip(["pop1", "pop2", "pop3"], [24000, 12000, 6000]):
assert len(cluster_idx.get(name)) == n * 0.25
# Check trees
assert all([x in fg.tree.keys() for x in ["root", "pop1", "pop2", "pop3"]])
assert not fg.tree.get("root").parent
assert fg.tree.get("pop1").parent == fg.tree.get("root")
assert fg.tree.get("pop2").parent == fg.tree.get("pop1")
assert fg.tree.get("pop3").parent == fg.tree.get("pop2")
def create_project():
p = Project(project_id="test")
p.save()
yield p
p.delete()
def test_Project(self):
test_panel = Panel(panel_name='test')
test_panel.save()
test_project = Project(project_id='test', owner='test')
test_project.add_experiment('test_experiment_aml', panel_name='test')
test_project.add_experiment('test_experiment_dummy', panel_name='test')
test_project.add_subject('test_subject', testing=True)
self.assertEqual(test_project.list_subjects(), ['test_subject'])
s = test_project.pull_subject('test_subject')
self.assertEqual(s.testing, True)
self.assertEqual(s.subject_id, 'test_subject')
self.assertEqual(test_project.list_fcs_experiments(), ['test_experiment_aml', 'test_experiment_dummy'])
test_project.save()
test_project.delete()
err = False
try:
Project.objects(project_id='test').get()
except DoesNotExist:
err = True
self.assertTrue(err)
def reload_file():
fg = (Project.objects(project_id="test").get().load_experiment(
"test experiment").get_sample("test sample"))
return fg