Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/pass_sample_vals_as_json

1 files changed, 14 insertions, 37 deletions

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 b8c13ab4..fe2569b8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -5,7 +5,6 @@ from unittest import mock
 from wqflask.marker_regression.gemma_mapping import run_gemma
 from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
 from wqflask.marker_regression.gemma_mapping import gen_covariates_file
-from wqflask.marker_regression.gemma_mapping import parse_gemma_output
 from wqflask.marker_regression.gemma_mapping import parse_loco_output
 
 
@@ -69,11 +68,9 @@ class TestGemmaMapping(unittest.TestCase):
         mock_parse_loco.return_value = []
         results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
         ], vals=[], covariates="", use_loco=True)
-        system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'),
-                        mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')]
-        mock_os.system.assert_has_calls(system_calls)
+        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")
+        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)
@@ -138,31 +135,6 @@ class TestGemmaMapping(unittest.TestCase):
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/")
-    def test_parse_gemma_output(self):
-        """add test for generating gemma output with obj returned"""
-        file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7
-X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
-125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67
-"""
-        with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open:
-            results = parse_gemma_output(genofile_name="gema_file")
-            expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812},
-                        {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}]
-            mock_open.assert_called_once_with(
-                "/home/user/img/gema_file_output.assoc.txt")
-            self.assertEqual(results, expected)
-
-    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
-    def test_parse_gemma_output_with_empty_return(self):
-        """add tests for parse gemma output where nothing returned"""
-        output_file_results = """chr\t today"""
-        with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open:
-            results = parse_gemma_output(genofile_name="gema_file")
-            self.assertEqual(results, [])
-
     @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
     @mock.patch("wqflask.marker_regression.gemma_mapping.os")
     @mock.patch("wqflask.marker_regression.gemma_mapping.json")
@@ -172,21 +144,26 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
             "files": [["file_name", "user", "~/file1"],
                       ["file_name", "user", "~/file2"]]
         }
-        return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7"""
-        return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5"""
+        return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
+Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
+X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
+
+        return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4"""
         mock_os.path.isfile.return_value = True
         file_to_write = """{"files":["file_1","file_2"]}"""
         with mock.patch("builtins.open") as mock_open:
 
             handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open(
-                read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value)
+                read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value)
             mock_open.side_effect = handles
             results = parse_loco_output(
                 this_dataset={}, gwa_output_filename=".xw/")
-            expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {
-                'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}]
+            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': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
 
             self.assertEqual(expected_results, results)