def test_calculated_math(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 = 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)
res, qid1 = epidb.select_regions("test_exp1", "hg19", None, None, None,
None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
res = epidb.create_column_type_calculated("calculated_error",
"description",
"return value_of('SCORE')",
self.admin_key)
self.assertSuccess(res)
(s, req) = epidb.get_regions(
qid1, "CHROMOSOME,START,END,VALUE, calculated_error",
self.admin_key)
regions = self.get_regions_request(req)
self.assertEqual(
regions.split("\n")[0],
"chr1\t0\t10\t8.1235\tInvalid column name SCORE")
res = epidb.create_column_type_calculated(
"calculated_dummy", "description",
"return value_of('START') - value_of('END') * value_of('VALUE')",
self.admin_key)
self.assertSuccess(res)
(s, req) = epidb.get_regions(
qid1, "CHROMOSOME,START,END,VALUE, calculated_dummy",
self.admin_key)
regions = self.get_regions_request(req)
r = regions.split("\n")[0].split("\t")[4]
self.assertEqual(r, '-81.234570')
res = epidb.create_column_type_calculated(
"calculated_norm_by_length", "description",
"return math.sqrt(value_of('VALUE') / (value_of('END') - value_of('START')))",
self.admin_key)
self.assertSuccess(res)
(s, req) = epidb.get_regions(
qid1, "CHROMOSOME,START,END,VALUE, calculated_norm_by_length",
self.admin_key)
regions = self.get_regions_request(req)
r = regions.split("\n")[0].split("\t")[4]
self.assertEqual(r, '0.901302')
def test_calculated_metafield(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 = 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)
res, qid1 = epidb.select_regions("test_exp1", "hg19", None, None, None,
None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
res = epidb.create_column_type_calculated(
"calculated", "description",
"return 'EM and Name: - '.. value_of('@EPIGENETIC_MARK') .. ' - ' .. value_of('@NAME')",
self.admin_key)
self.assertSuccess(res)
(s, req) = epidb.get_regions(qid1,
"CHROMOSOME,START,END,VALUE, calculated",
self.admin_key)
self.assertSuccess(s, req)
regions = self.get_regions_request(req)
r = regions.split("\n")[0].split("\t")[4]
self.assertEqual(r, 'EM and Name: - Methylation - test_exp1')
def test_wrong_column_creation(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 = 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)
res, qid1 = epidb.select_regions("test_exp1", "hg19", None, None, None,
None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
# It is missing a ' before the EM
res = epidb.create_column_type_calculated(
"calculated", "description",
"return EM and Name: - '.. value_of('@EPIGENETIC_MARK') .. ' - ' .. value_of('@NAME')",
self.admin_key)
self.assertFailure(res)
self.assertEqual(
res[1],
'[string "function row_value()..."]:2: \'<name>\' expected near \'-\''
)
def test_wig_clone_calculated(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
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)
(s, m) = epidb.create_column_type_simple("METHYLATION_LEVEL", "",
"double", self.admin_key)
self.assertSuccess(s, m)
res = epidb.create_column_type_calculated(
"METHYLATION_LEVEL_SQRT", "Square root of the methylation level",
"return math.sqrt(value_of('VALUE'))", self.admin_key)
self.assertSuccess(res)
(s, clone_id) = epidb.clone_dataset(
_id, "New Wig File", "", "", "", "", "",
"CHROMOSOME,START,END,METHYLATION_LEVEL_SQRT", None,
self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'METHYLATION_LEVEL_SQRT' (type: calculated) is incompatible with the original column 'VALUE' (type: double)"
)
(s, clone_id) = epidb.clone_dataset(
_id, "New Wig File", "", "", "", "", "",
"CHROMOSOME,START,END,METHYLATION_LEVEL", None, self.admin_key)
self.assertSuccess(s, clone_id)
(status, wig_data) = epidb.select_regions('New Wig File', "hg19", None,
None, None, None, None, None,
None, self.admin_key)
(s, req) = epidb.get_regions(
wig_data,
"CHROMOSOME,START,END,METHYLATION_LEVEL,METHYLATION_LEVEL_SQRT",
self.admin_key)
rs = self.get_regions_request(req)
self.assertEqual(rs.split("\n")[0].split("\t")[3], "8.1235")
self.assertEqual(rs.split("\n")[0].split("\t")[4], "2.850168")
self.assertEqual(rs.split("\n")[6].split("\t")[3], "30.0000")
self.assertEqual(rs.split("\n")[6].split("\t")[4], "5.477226")