Merge branch 'testing' into feature/add_resizeable_columns

4 files changed, 40 insertions, 42 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 4003d68f..58a44b2a 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(
@@ -112,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase):
         create_trait.side_effect = create_trait_side_effect
 
         group = MockGroup({"name": "group_X", "samplelist": samplelist})
-        this_dataset = AttributeSetter({"group": group})
+        this_dataset = AttributeSetter({"group": group, "name": "A"})
         flat_files.return_value = "Home/Genenetwork"
 
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -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"""
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 290c4a14..80094057 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -104,7 +104,7 @@ class RunMapping:
         if "results_path" in start_vars:
             self.mapping_results_path = start_vars['results_path']
         else:
-            mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_")
+            mapping_results_filename = "_".join([self.dataset.group.name, self.mapping_method, self.vals_hash]).replace("/", "_")
             self.mapping_results_path = "{}{}.csv".format(
                 webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
@@ -405,8 +405,8 @@ class RunMapping:
                 total_markers = len(self.qtl_results)
 
                 with Bench("Exporting Results"):
-                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results,
-                                           self.mapping_results_path, self.mapping_scale, self.score_type,
+                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+                                           self.mapping_method, self.mapping_scale, self.score_type,
                                            self.transform, self.covariates, self.n_samples, self.vals_hash)
 
                 with Bench("Trimming Markers for Figure"):
@@ -525,7 +525,11 @@ class RunMapping:
         return trimmed_genotype_data
 
 
-def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
+def export_mapping_results(dataset, trait, markers, results_path, mapping_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
+    if mapping_scale == "physic":
+        scale_string = "Mb"
+    else:
+        scale_string = "cM"
     with open(results_path, "w+") as output_file:
         output_file.write(
             "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
@@ -535,6 +539,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("Trait: " + trait.display_name + "\n")
         output_file.write("Trait Hash: " + vals_hash + "\n")
         output_file.write("N Samples: " + str(n_samples) + "\n")
+        output_file.write("Mapping Tool: " + str(mapping_method) + "\n")
         if len(transform) > 0:
             transform_text = "Transform - "
             if transform == "qnorm":
@@ -564,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("Name,Chr,")
         if score_type.lower() == "-logP":
             score_type = "-logP"
-        if 'Mb' in markers[0]:
-            output_file.write("Mb," + score_type)
-        if 'cM' in markers[0]:
-            output_file.write("Cm," + score_type)
+        output_file.write(scale_string + "," + score_type)
         if "additive" in list(markers[0].keys()):
             output_file.write(",Additive")
         if "dominance" in list(markers[0].keys()):
@@ -575,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("\n")
         for i, marker in enumerate(markers):
             output_file.write(marker['name'] + "," + str(marker['chr']) + ",")
-            if 'Mb' in marker:
-                output_file.write(str(marker['Mb']) + ",")
-            if 'cM' in marker:
-                output_file.write(str(marker['cM']) + ",")
-            if "lod_score" in marker.keys():
+            output_file.write(str(marker[scale_string]) + ",")
+            if score_type == "-logP":
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 897f79ff..96ef7a04 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -191,6 +191,7 @@ function loadDataTable(first_run=false, table_id, table_data){
       $(row).addClass("value_se");
       if (data.outlier) {
         $(row).addClass("outlier");
+        $(row).attr("style", "background-color: orange;");
       }
       $('td', row).eq(1).addClass("column_name-Index")
       $('td', row).eq(2).addClass("column_name-Sample")
@@ -262,7 +263,6 @@ function loadDataTable(first_run=false, table_id, table_data){
     } );
   } ).draw();
 
-
   if (first_run){
     $('#' + table_type.toLowerCase() + '_container').css("width", String($('#' + table_id).width() + 17) + "px");
   }