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

2 files changed, 26 insertions, 27 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 255bfd7f..1ec18199 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -81,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase):
     def test_gen_pheno_txt_file(self):
         """add tests for generating pheno txt file"""
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
-            gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[
-                               "x", "w", "q", "we", "R"], trait_filename="fitr.re")
+            gen_pheno_txt_file(
+                this_dataset=AttributeSetter({"name": "A"}),
+                genofile_name="", vals=[
+                    "x", "w", "q", "we", "R"])
             mock_open.assert_called_once_with(
-                '/home/user/data/gn2/fitr.re.txt', 'w')
+                '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w')
             filehandler = mock_open()
             values = ["x", "w", "q", "we", "R"]
             write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
@@ -132,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase):
 
             flat_files.assert_called_once_with('mapping')
             mock_open.assert_called_once_with(
-                'Home/Genenetwork/group_X_covariates.txt', 'w')
+                'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w')
             filehandler = mock_open()
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
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 c220a072..868b0b0b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase):
             })
         }
         self.dataset = AttributeSetter(
-            {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+            {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
 
         self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
         self.trait = AttributeSetter(
-            {"symbol": "IGFI", "chr": "X1", "mb": 123313})
+            {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
 
     def tearDown(self):
         self.dataset = AttributeSetter(
@@ -180,34 +180,36 @@ class TestRunMapping(unittest.TestCase):
 
             with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
-                                       results_path="~/results", mapping_scale="physic", score_type="-log(p)",
-                                       transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100")
+                                       results_path="~/results", mapping_method="gemma", mapping_scale="physic",
+                                       score_type="-logP", transform="qnorm",
+                                       covariates="Dataset1:Trait1,Dataset2:Trait2",
+                                       n_samples="100", vals_hash="")
 
                 write_calls = [
                     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'),
+                        'Data Set: dataset_1\n'),
+                    mock.call('Trait: Test Name\n'),
+                    mock.call('Trait Hash: \n'),
+                    mock.call('N Samples: 100\n'),
+                    mock.call('Mapping Tool: gemma\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'),
                     mock.call('Trait1 - Dataset1\n'),
                     mock.call('Trait2 - Dataset2\n'),
                     mock.call('\n'), mock.call('Name,Chr,'),
-                    mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+                    mock.call('Mb,-logP'),
                     mock.call(',Additive'), mock.call(',Dominance'),
                     mock.call('\n'), mock.call('MK1,C1,'),
-                    mock.call('12000,'), mock.call('1,'),
-                    mock.call('3'), mock.call(',VA'),
-                    mock.call(',TT'), mock.call('\n'),
-                    mock.call('MK2,C2,'), mock.call('10000,'),
-                    mock.call('15,'), mock.call('7'),
+                    mock.call('12000,'), mock.call('3'),
+                    mock.call(',VA'), mock.call(',TT'),
+                    mock.call('\n'), mock.call('MK2,C2,'),
+                    mock.call('10000,'), mock.call('7'),
                     mock.call('\n'), mock.call('MK1,C3,'),
-                    mock.call('1,'), mock.call('45,'),
-                    mock.call('7'), mock.call(',VE'),
-                    mock.call(',Tt')
-
+                    mock.call('1,'), mock.call('7'),
+                    mock.call(',VE'), mock.call(',Tt')
                 ]
                 mock_open.assert_called_once_with("~/results", "w+")
                 filehandler = mock_open()
@@ -232,25 +234,20 @@ class TestRunMapping(unittest.TestCase):
                 "c1": "c1_value",
                 "c2": "c2_value",
                 "w1": "w1_value"
-
             },
             "S2": {
                 "w1": "w2_value",
                 "w2": "w2_value"
-
             },
             "S3": {
 
                 "c1": "c1_value",
                 "c2": "c2_value"
-
             },
-
         }})
-
         results = get_perm_strata(this_trait={}, sample_list=sample_list,
                                   categorical_vars=categorical_vars, used_samples=used_samples)
-        self.assertEqual(results, [2, 1])
+        self.assertEqual(results, [1, 1])
 
     def test_get_chr_length(self):
         """test for getting chromosome length"""