def test_bug_do_not_reuse_existing_query(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
data = "chr1\t100\t110\t1\nchr1\t200\t400\t0\nchr1\t400\t500\t1\nchr1\t200\t400\t0\n"
format = "CHROMOSOME,START,END,SCORE"
(res, a_1) = epidb.add_experiment(
"test", "hg19", "H3K4me3", sample_id, "tech1", "ENCODE",
"wgEncodeBroadHistoneH1hescH3k27me3StdPk.bed from ENCODE", data,
format, None, self.admin_key)
self.assertSuccess(res, a_1)
(s, q0) = epidb.select_regions("test", "hg19", None, None, None, None,
"chr1", None, None, self.admin_key)
(s, q1) = epidb.query_experiment_type(q0, "peaks", self.admin_key)
(s, q00) = epidb.select_regions("test", "hg19", None, None, None, None,
"chr1", None, None, self.admin_key)
(s, q11) = epidb.query_experiment_type(q0, "peaks", self.admin_key)
self.assertEqual(q0, q00)
self.assertEqual(q1, q11)
def test_select_only_signal(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
files = ["reference_example"]
for filename in files:
wig_data = helpers.load_bedgraph(filename)
res = epidb.add_experiment(filename, "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
wig_data, "bedgraph", None,
self.admin_key)
self.assertSuccess(res)
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
(s, q) = epidb.select_regions("", "hg19", None, None, None, None, None,
None, None, self.admin_key)
(s, req) = epidb.count_regions(q, self.admin_key)
self.assertSuccess(s, req)
count = self.count_request(req)
## Total amount of regions
self.assertEqual(30, count)
(s, q) = epidb.select_regions("", "hg19", None, None, None, None, None,
None, None, self.admin_key)
(s, new_query_peaks) = epidb.query_experiment_type(
q, "peaks", self.admin_key)
self.assertSuccess(s, new_query_peaks)
(s, req) = epidb.count_regions(new_query_peaks, self.admin_key)
count = self.count_request(req)
## Only peaks
self.assertEqual(21, count)
(s, new_query_signal) = epidb.query_experiment_type(
q, "signal", self.admin_key)
self.assertSuccess(s, new_query_signal)
(s, req) = epidb.count_regions(new_query_signal, self.admin_key)
count = self.count_request(req)
## Only signal
self.assertEqual(9, count)
(s, new_peaks_new_query_signal) = epidb.query_experiment_type(
new_query_signal, "peaks", self.admin_key)
self.assertSuccess(s, new_peaks_new_query_signal)
(s, req) = epidb.count_regions(new_peaks_new_query_signal,
self.admin_key)
count = self.count_request(req)
## Only peaks again, but deriving from an signal query
self.assertEqual(21, count)
(s, req2) = epidb.count_regions(new_peaks_new_query_signal,
self.admin_key)
count = self.count_request(req2)
## Only peaks again, but deriving from an signal query
self.assertEqual(21, count)
self.assertEqual(req, req2)
