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authorBonfaceKilz2021-04-30 12:45:59 +0300
committerBonfaceKilz2021-04-30 13:45:15 +0300
commit03b6bcee689c1910bd850c6109cc37adc509cf5a (patch)
tree2ca686d7f1b6649bfbd593607aa406eff8efbfb7 /wqflask/tests/unit
parent6be1111fd76a2c47de7a20cc18bb9f4d8d2d4ffa (diff)
downloadgenenetwork2-03b6bcee689c1910bd850c6109cc37adc509cf5a.tar.gz
autopep8: Fix E501
Diffstat (limited to 'wqflask/tests/unit')
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py3
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py15
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py6
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py3
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py3
-rw-r--r--wqflask/tests/unit/wqflask/test_server_side.py9
6 files changed, 26 insertions, 13 deletions
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 219a6a29..f4869c45 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -39,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase):
cgi="/testing/",
enctype='multipart/form-data',
name="formName",
- submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
+ submit=HtmlGenWrapper.create_input_tag(
+ type_='hidden', name='Default_Name')
)
test_image = HtmlGenWrapper.create_image_tag(
src="test.png",
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index f194c6c9..5cbaf0e0 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -70,7 +70,8 @@ class TestGemmaMapping(unittest.TestCase):
], vals=[], covariates="", use_loco=True)
self.assertEqual(mock_os.system.call_count, 2)
mock_gen_pheno_txt.assert_called_once()
- mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True)
+ mock_parse_loco.assert_called_once_with(
+ dataset, "GP1_GWA_RRRRRR", True)
mock_os.path.isfile.assert_called_once_with(
('/home/user/imgfile_output.assoc.txt'))
self.assertEqual(mock_flat_files.call_count, 4)
@@ -102,7 +103,8 @@ class TestGemmaMapping(unittest.TestCase):
create_trait_side_effect = []
for i in range(4):
- create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'}))
+ create_dataset_side_effect.append(
+ AttributeSetter({"name": f'name_{i}'}))
create_trait_side_effect.append(
AttributeSetter({"data": [f'data_{i}']}))
@@ -160,9 +162,12 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
expected_results = [
- {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
- {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
- {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
+ 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
+ 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
+ 'additive': 11.6, 'lod_score': 0.1549019599857432},
{'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 5cc8fd0f..c762982b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -13,10 +13,12 @@ class TestQtlReaperMapping(unittest.TestCase):
samples = ["S1", "S2", "S3", "S4","S5"]
trait_filename = "trait_file"
with mock.patch("builtins.open", mock.mock_open())as mock_open:
- gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename)
+ gen_pheno_txt_file(samples=samples, vals=vals,
+ trait_filename=trait_filename)
mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
filehandler = mock_open()
- write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
+ write_calls = [mock.call('Trait\t'), mock.call(
+ 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 6267ce9a..6996c275 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -20,7 +20,8 @@ class TestRqtlMapping(unittest.TestCase):
def test_get_trait_data(self, mock_logger, mock_db):
"""test for getting trait data_type return True"""
query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
- mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
+ mock_db.db.execute.return_value.fetchone.return_value = [
+ """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
results = get_trait_data_type("traid_id")
mock_db.db.execute.assert_called_with(query_value)
self.assertEqual(results, "fer434f")
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index a29d8cfb..78cd3be9 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -187,7 +187,8 @@ class TestRunMapping(unittest.TestCase):
mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
mock.call('Population: Human GP1_\n'), mock.call(
'Data Set: dataser_1\n'),
- mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'),
+ mock.call('N Samples: 100\n'), mock.call(
+ 'Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
'Location: X1 @ 123313 Mb\n'),
mock.call('Cofactors (dataset - trait):\n'),
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 4f91d8ca..69977146 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -22,10 +22,13 @@ class TestServerSideTableTests(unittest.TestCase):
{'first': 'c', 'second': 1, 'third': 'ss'},
]
headers = ['first', 'second', 'third']
- request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+ request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1',
+ 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
- test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+ test_page = ServerSideTable(
+ rows_count, table_rows, headers, request_args).get_page()
self.assertEqual(test_page['sEcho'], '1')
self.assertEqual(test_page['iTotalRecords'], 'nan')
self.assertEqual(test_page['iTotalDisplayRecords'], '3')
- self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
+ self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {
+ 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])