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_insert_local_file(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
# adding two experiments with the same data should work
(res, _id) = epidb.add_experiment(
"test_exp1", "hg19", "Methylation", sample_id, "tech1", "ENCODE",
"desc1", "", "wig",
{"__local_file__": "../tests/data/wig/scores1.wig"},
self.admin_key)
self.assertSuccess(res, _id)
res = epidb.add_experiment("test_exp1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1", "",
"wig",
{"__local_file__": "inexistent_file.wig"},
self.admin_key)
self.assertFailure(res)
res, experiments = epidb.list_experiments("hg19", "signal", None,
"K562", None, None, None,
self.admin_key)
self.assertSuccess(res, experiments)
self.assertEqual(len(experiments), 1)
res, qid1 = epidb.select_regions("test_exp1", "hg19", None, None, None,
None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
(s, req1) = epidb.get_regions(qid1, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, req1)
data1 = self.get_regions_request(req1)
res, qid1 = epidb.select_regions(_id, None, None, None, None, None,
None, None, None, self.admin_key)
self.assertSuccess(res, qid1)
(s, req2) = epidb.get_regions(qid1, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, req2)
data2 = self.get_regions_request(req2)
self.assertEqual(data1, data2)
def test_experiment_sets(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
epidb.list_experiments
(s, ees) = epidb.list_experiments("", "", "", "", "", "", "",
self.admin_key)
(s, names) = epidb.extract_names(ees)
print names
print
(s, es1) = epidb.create_experiments_set("Test 1", "set test one", True,
names, self.admin_key)
print s
print es1
(s, info_es1) = epidb.info(es1, self.admin_key)
print info_es1
