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