def test_add_with_out_of_bound_region(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg18_out_of_bounds")
_format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
res = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, _format, None, self.admin_key)
self.assertFailure(res)
res = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, _format,
{"__trim_to_chromosome_size__": True},
self.admin_key)
self.assertSuccess(res)
res, q_exp = epidb.select_regions("test_exp1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
res, req = epidb.get_regions(q_exp, _format, self.admin_key)
data = self.get_regions_request(req)
regions_data_okay = helpers.load_bed("hg18_out_of_bounds_okay")
self.assertEqual(data, regions_data_okay)
def test_category_fail(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
format = ",".join([
"CHROMOSOME",
"START",
"END",
"NAME",
"SCORE",
"STRAND_X",
"SIGNAL_VALUE",
"P_VALUE",
"Q_VALUE",
"PEAK"
])
res = epidb.create_column_type_category("STRAND_X", "strand of the region", ["X", "-"], self.admin_key)
self.assertSuccess(res)
regions_data = helpers.load_bed("hg19_chr1_1")
res, msg = epidb.add_experiment("test_exp_fail2", "hg19", "Methylation", sample_id, "tech1", "ENCODE",
"desc1", regions_data, format, None, self.admin_key)
self.assertFailure(res, msg)
self.assertTrue("STRAND_X" in msg)
def test_remove_technique(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
(res, add_technique_id) = epidb.add_technique(
"Hypster Technique", "I knew this technique before everybody else",
{}, self.admin_key)
self.assertSuccess(res, add_technique_id)
# adding two experiments with the same data should work
res, eid = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "Hypster Technique",
"ENCODE", "desc1", regions_data,
format, None, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(add_technique_id, self.admin_key)
self.assertFailure(res)
res = epidb.remove(eid, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(add_technique_id, self.admin_key)
self.assertSuccess(res)
def test_remove_epigenetic_mark(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
(res, epigenetic_mark_id) = epidb.add_epigenetic_mark(
"H3K666ac3", "acetil metal \,,,/",
{"category": "heavy histone metal"}, self.admin_key)
self.assertSuccess(res, epigenetic_mark_id)
# adding two experiments with the same data should work
res, eid = epidb.add_experiment("test_exp1", "hg19", "H3K666ac3",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None,
self.admin_key)
self.assertSuccess(res)
res = epidb.remove(epigenetic_mark_id, self.admin_key)
self.assertFailure(res)
res = epidb.remove(eid, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(epigenetic_mark_id, self.admin_key)
self.assertSuccess(res)
def test_remove_project(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
res, projects = epidb.list_projects(self.admin_key)
# adding two experiments with the same data should work
res, eid = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", projects[0][1],
"desc1", regions_data, format, None,
self.admin_key)
self.assertSuccess(res, eid)
res = epidb.remove(projects[0][0], self.admin_key)
self.assertFailure(res)
res = epidb.remove(eid, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(projects[0][0], self.admin_key)
self.assertSuccess(res)
def test_double_experiment_same_user_fail(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
uid, user_key = self.insert_user(epidb, "test_user")
s, tmp_user = epidb.modify_user_admin(uid, "permission_level",
"INCLUDE_EXPERIMENTS",
self.admin_key)
self.assertSuccess(s)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
# adding the same experiments with different users should work
exp = ("test_exp1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "desc1", regions_data, format, None)
res = epidb.add_experiment(*(exp + (self.admin_key, )))
self.assertSuccess(res)
res = epidb.add_experiment(*(exp + (user_key, )))
self.assertFailure(res)
self.assertEqual(
res[1],
"102001:The experiment name 'test_exp1' is already being used.")
def test_add_with_invalid_epigenetic_mark(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
res = epidb.add_experiment("test_exp1", "hg19", "No Epigenetic ",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None, self.admin_key)
self.assertFailure(res)
def test_experiments_pass(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
# adding two experiments with the same data should work
res = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None, self.admin_key)
self.assertSuccess(res)
res = epidb.add_experiment("test_exp2", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None, self.admin_key)
self.assertSuccess(res)
res, experiments = epidb.list_experiments("hg19", "peaks", None,
"NO_BIOSOURCE", None, None,
None, self.admin_key)
self.assertSuccess(res, experiments)
self.assertEqual(len(experiments), 0)
res, experiments = epidb.list_experiments(None, None, None, None, None,
None, None, self.admin_key)
self.assertSuccess(res, experiments)
self.assertEqual(len(experiments), 2)
res, experiments = epidb.list_experiments("hg19", "peaks", None,
"K562", None, None, None,
self.admin_key)
self.assertSuccess(res, experiments)
self.assertEqual(len(experiments), 2)
experiments_names = [x[1] for x in experiments]
self.assertTrue("test_exp1" in experiments_names)
self.assertTrue("test_exp2" in experiments_names)
s, ids = epidb.name_to_id(['test_exp1'], 'experiments', self.admin_key)
self.assertEqual(ids, [['e1', 'test_exp1']])
s, ids = epidb.name_to_id(['test_exp1', 'test_exp2'], 'experiments',
self.admin_key)
self.assertEqual([['e1', 'test_exp1'], ['e2', 'test_exp2']], ids)
s, ids = epidb.name_to_id('test_exp1', 'experiments', self.admin_key)
self.assertEqual([['e1', 'test_exp1']], ids)
def test_double_experiment_fail(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
# adding the same experiment with the same user should fail
exp = ("test_exp1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "desc1", regions_data, format, None)
res = epidb.add_experiment(*(exp + (self.admin_key, )))
self.assertSuccess(res)
res = epidb.add_experiment(*(exp + (self.admin_key, )))
self.assertFailure(res)
def test_experiments_preview(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
# adding two experiments with the same data should work
res = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None, self.admin_key)
self.assertSuccess(res)
status, preview = epidb.preview_experiment('test_exp1', self.admin_key)
self.assertEqual(
preview,
'CHROMOSOME\tSTART\tEND\tNAME\tSCORE\tSTRAND\tSIGNAL_VALUE\tP_VALUE\tQ_VALUE\tPEAK\nchr1\t713240\t713390\t.\t0.0000\t+\t21.0000\t69.6000\t-1.0000\t-1\nchr1\t713520\t713670\t.\t0.0000\t-\t21.0000\t22.4866\t-1.0000\t-1\nchr1\t713900\t714050\t.\t0.0000\t+\t59.0000\t71.2352\t-1.0000\t-1\nchr1\t714160\t714310\t.\t0.0000\t+\t22.0000\t101.8740\t-1.0000\t-1\nchr1\t714540\t714690\t.\t0.0000\t+\t77.0000\t105.3120\t-1.0000\t-1'
)
def test_list_recent(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
res, eid1 = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None,
self.admin_key)
self.assertSuccess(res, eid1)
# get some distance in insertion times
time.sleep(5)
res, eid2 = epidb.add_experiment("test_exp2", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None,
self.admin_key)
self.assertEqual(res, "okay")
time.sleep(3)
ago = 1.0 / 24 / 60 / 60 * 5
res, experiments = epidb.list_recent_experiments(
ago, "hg19", None, None, None, None, self.admin_key)
self.assertSuccess(res, experiments)
experiments_names = [x[1] for x in experiments]
self.assertTrue("test_exp1" not in experiments_names)
self.assertTrue("test_exp2" in experiments_names)
res, experiments = epidb.list_recent_experiments(
1.0, "hg19", None, None, None, None, self.admin_key)
self.assertSuccess(res, experiments)
experiments_names = [x[1] for x in experiments]
self.assertTrue("test_exp1" in experiments_names)
self.assertTrue("test_exp2" in experiments_names)
def test_experiment_metadata(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
res, eid1 = epidb.add_experiment("test_exp1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "desc1", regions_data, format, {"source": "ncbi"}, self.admin_key)
self.assertSuccess(res, eid1)
res, eid2 = epidb.add_experiment("test_exp2", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "desc1", regions_data, format, {"source":"encode"}, self.admin_key)
self.assertSuccess(res, eid2)
res, ids = epidb.search("ncbi", "Experiments", self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], eid1)
# Should be the first because the "encode" name appears twice (project and extra metadata)
res, ids = epidb.search("encode", "experiments", self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], eid2)
