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-rw-r--r--wqflask/base/GeneralObject.py4
-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/base/trait.py10
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py7
-rw-r--r--wqflask/tests/unit/base/test_data_set.py10
-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py68
-rw-r--r--wqflask/utility/svg.py24
-rw-r--r--wqflask/wqflask/api/gen_menu.py10
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py10
-rw-r--r--wqflask/wqflask/db_info.py34
-rw-r--r--wqflask/wqflask/do_search.py12
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py14
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py4
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/user_session.py4
-rw-r--r--wqflask/wqflask/views.py12
16 files changed, 116 insertions, 115 deletions
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 249195e2..ce8e60b8 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -62,5 +62,5 @@ class GeneralObject:
         return s
 
     def __eq__(self, other):
-        return (len(list(self.__dict__.keys())) ==
-                len(list(other.__dict__.keys())))
+        return (len(list(self.__dict__.keys()))
+                == len(list(other.__dict__.keys())))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8ec0aaad..5eac695e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1032,8 +1032,8 @@ class MrnaAssayDataSet(DataSet):
             else:
                 description_display = this_trait.symbol
 
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
+            if (len(description_display) > 1 and description_display != 'N/A'
+                    and len(target_string) > 1 and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 5574128d..d09cfd40 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -479,9 +479,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             else:
                 description_display = trait.symbol
 
-            if (str(description_display or "") != "" and
-                description_display != 'N/A' and
-                    str(target_string or "") != "" and target_string != 'None'):
+            if (str(description_display or "") != ""
+                and description_display != 'N/A'
+                    and str(target_string or "") != "" and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
@@ -575,6 +575,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 if str(trait.lrs or "") != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
-        raise KeyError(repr(trait.name) +
-                       ' information is not found in the database.')
+        raise KeyError(repr(trait.name)
+                       + ' information is not found in the database.')
     return trait
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index bd9c2ab4..e964c8ed 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -110,9 +110,10 @@ def write_data_matrix_file(strains, probeset_vals, filename):
 
 
 def main():
-    filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
-                "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
-                "(Oct08)_RankInv_Beta.txt")
+    filename = os.path.expanduser(
+        "~/gene/wqflask/maintenance/"
+        "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2"
+        "(Oct08)_RankInv_Beta.txt")
     dataset_name = "Eye_AXBXA_1008_RankInv"
 
     cursor = get_cursor()
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index ee5d6f06..66ad361d 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -88,8 +88,8 @@ class TestDataSetTypes(unittest.TestCase):
                  '"B139_K_1206_R": "ProbeSet", '
                  '"Test": "ProbeSet"}'))
             db_mock.db.execute.assert_called_once_with(
-                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
-                 "WHERE ProbeSetFreeze.Name = \"Test\" ")
+                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze "
+                 + "WHERE ProbeSetFreeze.Name = \"Test\" ")
             )
 
     @mock.patch('base.data_set.g')
@@ -145,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase):
                  '"Test": "Publish"}'))
 
             db_mock.db.execute.assert_called_with(
-                ("SELECT PublishFreeze.Name " +
-                 "FROM PublishFreeze, InbredSet " +
-                 "WHERE InbredSet.Name = 'Test' AND "
+                ("SELECT PublishFreeze.Name "
+                 + "FROM PublishFreeze, InbredSet "
+                 + "WHERE InbredSet.Name = 'Test' AND "
                  "PublishFreeze.InbredSetId = InbredSet.Id")
             )
 
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 57eb1650..fd0fe52e 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -105,13 +105,13 @@ class TestGenMenu(unittest.TestCase):
         for name in ["mouse", "human"]:
             db_mock.db.execute.assert_any_call(
                 ("SELECT InbredSet.Name, InbredSet.FullName, " +
-                 "IFNULL(InbredSet.Family, 'None') " +
-                 "FROM InbredSet, Species WHERE Species.Name " +
-                 "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " +
-                 "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
-                 "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " +
-                 "InbredSet.FullName) ASC, InbredSet.FullName ASC, " +
-                 "InbredSet.MenuOrderId ASC").format(name)
+                 "IFNULL(InbredSet.Family, 'None') "
+                 + "FROM InbredSet, Species WHERE Species.Name "
+                 + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+                 + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+                 + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+                 + "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+                 + "InbredSet.MenuOrderId ASC").format(name)
             )
 
     @mock.patch('wqflask.api.gen_menu.g')
@@ -172,12 +172,12 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
                          [['602', "BXDPublish", "BXD Published Phenotypes"]])
         db_mock.db.execute.assert_called_with(
-            "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
-            "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
-            "InbredSet WHERE InbredSet.Name = 'BXD' AND " +
-            "PublishFreeze.InbredSetId = InbredSet.Id AND " +
-            "InfoFiles.InfoPageName = PublishFreeze.Name " +
-            "ORDER BY PublishFreeze.CreateTime ASC"
+            "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+            + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+            + "InbredSet WHERE InbredSet.Name = 'BXD' AND "
+            + "PublishFreeze.InbredSetId = InbredSet.Id AND "
+            + "InfoFiles.InfoPageName = PublishFreeze.Name "
+            + "ORDER BY PublishFreeze.CreateTime ASC"
         )
         self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
                          [['602', "BXDPublish", "Mouse Phenome Database"]])
@@ -221,8 +221,8 @@ class TestGenMenu(unittest.TestCase):
             "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
             "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
             "GenoFreeze.InbredSetId = InbredSet.Id AND "
-            "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
-            "ORDER BY GenoFreeze.CreateTime DESC"
+            "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+            + "ORDER BY GenoFreeze.CreateTime DESC"
         )
         db_mock.db.execute.return_value.fetchone.return_value = ()
         self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
@@ -239,16 +239,16 @@ class TestGenMenu(unittest.TestCase):
             "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
         ]])
         db_mock.db.execute.assert_called_once_with(
-            "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
-            "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
-            "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
-            "Species.Name = 'Mouse' AND Species.Id = " +
-            "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
-            "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " +
-            "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
-            "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " +
-            "ProbeSetFreeze.public > 0 " +
-            "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+            "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+            + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+            + "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+            + "Species.Name = 'Mouse' AND Species.Id = "
+            + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
+            + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+            + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
+            + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+            + "ProbeSetFreeze.public > 0 "
+            + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
 
     @mock.patch('wqflask.api.gen_menu.build_datasets')
     @mock.patch('wqflask.api.gen_menu.g')
@@ -266,15 +266,15 @@ class TestGenMenu(unittest.TestCase):
                           ['H', 'H', 'Molecular Traits'],
                           ['R', 'R', 'Molecular Traits']])
         db_mock.db.execute.assert_called_once_with(
-            "SELECT DISTINCT Tissue.Name " +
-            "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
-            "Tissue, Species WHERE Species.Name = 'mouse' " +
-            "AND Species.Id = InbredSet.SpeciesId AND " +
-            "InbredSet.Name = 'random group' AND " +
-            "ProbeFreeze.TissueId = Tissue.Id AND " +
-            "ProbeFreeze.InbredSetId = InbredSet.Id AND " +
-            "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
-            "ORDER BY Tissue.Name"
+            "SELECT DISTINCT Tissue.Name "
+            + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+            + "Tissue, Species WHERE Species.Name = 'mouse' "
+            + "AND Species.Id = InbredSet.SpeciesId AND "
+            + "InbredSet.Name = 'random group' AND "
+            + "ProbeFreeze.TissueId = Tissue.Id AND "
+            + "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+            + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+            + "ORDER BY Tissue.Name"
         )
 
     @mock.patch('wqflask.api.gen_menu.build_types')
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 8d2e13ab..bc3bc833 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -229,13 +229,13 @@ class pathdata:
 
     def bezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2) +
-                         ',' + str(y2) + ' '+str(x)+','+str(y))
+        self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2)
+                         + ',' + str(y2) + ' '+str(x)+','+str(y))
 
     def relbezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2) +
-                         ',' + str(y2) + ' '+str(x)+','+str(y))
+        self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2)
+                         + ',' + str(y2) + ' '+str(x)+','+str(y))
 
     def smbezier(self, x2, y2, x, y):
         """smooth bezier with xy2 to xy absolut"""
@@ -267,13 +267,13 @@ class pathdata:
 
     def ellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot) +
-                         ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+        self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot)
+                         + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
 
     def relellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot) +
-                         ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+        self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot)
+                         + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
 
     def __repr__(self):
         return ' '.join(self.path)
@@ -319,11 +319,11 @@ class SVGelement:
         f.write('\t' * level)
         f.write('<' + self.type)
         for attkey in list(self.attributes.keys()):
-            f.write(' ' + _escape(str(attkey)) + '=' +
-                    _quoteattr(str(self.attributes[attkey])))
+            f.write(' ' + _escape(str(attkey)) + '='
+                    + _quoteattr(str(self.attributes[attkey])))
         if self.namespace:
-            f.write(' xmlns="' + _escape(str(self.namespace)) +
-                    '" xmlns:xlink="http://www.w3.org/1999/xlink"')
+            f.write(' xmlns="' + _escape(str(self.namespace))
+                    + '" xmlns:xlink="http://www.w3.org/1999/xlink"')
         if self.elements or self.text or self.cdata:
             f.write('>')
         if self.elements:
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index a64524dd..e65b36e4 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -179,11 +179,11 @@ def build_datasets(species, group, type_name):
     elif type_name == "Genotypes":
         results = g.db.execute(
             ("SELECT InfoFiles.GN_AccesionId " +
-             "FROM InfoFiles, GenoFreeze, InbredSet " +
-             "WHERE InbredSet.Name = '{}' AND " +
-             "GenoFreeze.InbredSetId = InbredSet.Id AND " +
-             "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
-             "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
+             "FROM InfoFiles, GenoFreeze, InbredSet "
+             + "WHERE InbredSet.Name = '{}' AND "
+             + "GenoFreeze.InbredSetId = InbredSet.Id AND "
+             + "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+             + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
 
         dataset_id = "None"
         if bool(results):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 8ee24246..e8b7b057 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,9 +96,9 @@ class CorrelationResults:
             self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
             self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
-            if ('loc_chr' in start_vars and
-                'min_loc_mb' in start_vars and
-                'max_loc_mb' in start_vars):
+            if ('loc_chr' in start_vars
+                and 'min_loc_mb' in start_vars
+                and 'max_loc_mb' in start_vars):
 
                 self.location_type = get_string(start_vars, 'location_type')
                 self.location_chr = get_string(start_vars, 'loc_chr')
@@ -200,8 +200,8 @@ class CorrelationResults:
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
-                if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
-                    float(self.correlation_data[trait][0]) <= self.p_range_upper):
+                if (float(self.correlation_data[trait][0]) >= self.p_range_lower
+                    and float(self.correlation_data[trait][0]) <= self.p_range_upper):
 
                     if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
                         if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 8d28fef0..938c453e 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -23,23 +23,23 @@ class InfoPage:
 
     def get_info(self, create=False):
         query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
-                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
-                      "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
-                      "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
-                      "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
-                      "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
-                      "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
-                      "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
-                      "FROM InfoFiles " +
-                      "LEFT JOIN Species USING (SpeciesId) " +
-                      "LEFT JOIN Tissue USING (TissueId) " +
-                      "LEFT JOIN InbredSet USING (InbredSetId) " +
-                      "LEFT JOIN GeneChip USING (GeneChipId) " +
-                      "LEFT JOIN AvgMethod USING (AvgMethodId) " +
-                      "LEFT JOIN Datasets USING (DatasetId) " +
-                      "LEFT JOIN Investigators USING (InvestigatorId) " +
-                      "LEFT JOIN Organizations USING (OrganizationId) " +
-                      "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, "
+                      + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, "
+                      + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, "
+                      + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, "
+                      + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, "
+                      + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, "
+                      + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics "
+                      + "FROM InfoFiles "
+                      + "LEFT JOIN Species USING (SpeciesId) "
+                      + "LEFT JOIN Tissue USING (TissueId) "
+                      + "LEFT JOIN InbredSet USING (InbredSetId) "
+                      + "LEFT JOIN GeneChip USING (GeneChipId) "
+                      + "LEFT JOIN AvgMethod USING (AvgMethodId) "
+                      + "LEFT JOIN Datasets USING (DatasetId) "
+                      + "LEFT JOIN Investigators USING (InvestigatorId) "
+                      + "LEFT JOIN Organizations USING (OrganizationId) "
+                      + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
 
         if self.gn_accession_id:
             final_query = query_base + \
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e50ff50b..48527785 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -111,8 +111,8 @@ class MrnaAssaySearch(DoSearch):
         else:
             match_clause = ""
 
-        where_clause = (match_clause +
-            """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+        where_clause = (match_clause
+            + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
                and ProbeSetXRef.ProbeSetFreezeId = %s
                         """ % (escape(str(self.dataset.id))))
 
@@ -134,8 +134,8 @@ class MrnaAssaySearch(DoSearch):
         else:
             match_clause = ""
 
-        where_clause = (match_clause +
-            """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+        where_clause = (match_clause
+            + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
                and ProbeSetXRef.ProbeSetFreezeId = %s
                         """ % (escape(str(self.dataset.id))))
 
@@ -348,8 +348,8 @@ class GenotypeSearch(DoSearch):
         from_clause = self.normalize_spaces(from_clause)
 
         if self.search_term[0] == "*":
-            query = (self.base_query +
-                    """WHERE Geno.Id = GenoXRef.GenoId
+            query = (self.base_query
+                    + """WHERE Geno.Id = GenoXRef.GenoId
                         and GenoXRef.GenoFreezeId = GenoFreeze.Id
                         and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
         else:
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index c51b7a9a..9f9591ad 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -25,8 +25,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
         trait_filename = f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno"
         gen_pheno_txt_file(samples, vals, trait_filename)
 
-        output_filename = (f"{this_dataset.group.name}_GWA_" +
-            ''.join(random.choice(string.ascii_uppercase + string.digits)
+        output_filename = (f"{this_dataset.group.name}_GWA_"
+            + ''.join(random.choice(string.ascii_uppercase + string.digits)
                     for _ in range(6))
             )
         bootstrap_filename = None
@@ -34,8 +34,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
 
         opt_list = []
         if boot_check and num_bootstrap > 0:
-            bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
-                ''.join(random.choice(string.ascii_uppercase + string.digits)
+            bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
+                + ''.join(random.choice(string.ascii_uppercase + string.digits)
                         for _ in range(6))
                 )
 
@@ -44,9 +44,9 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
             opt_list.append(
                 f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
         if num_perm > 0:
-            permu_filename = ("{this_dataset.group.name}_PERM_" +
-            ''.join(random.choice(string.ascii_uppercase +
-                string.digits) for _ in range(6))
+            permu_filename = ("{this_dataset.group.name}_PERM_"
+            + ''.join(random.choice(string.ascii_uppercase
+                + string.digits) for _ in range(6))
             )
             opt_list.append("-n " + str(num_perm))
             opt_list.append(
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6419335e..3a63c84e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,8 +57,8 @@ class SampleList:
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
-            if (self.dataset.group.name == 'AXBXA' and
-                    sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
+            if (self.dataset.group.name == 'AXBXA'
+                    and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 18cadea4..fcebbc4d 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -452,8 +452,8 @@ class ShowTrait:
 
             for sample in list(self.this_trait.data.keys()):
                 if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name):
-                    if ((self.this_trait.data[sample].name2 in primary_sample_names) and
-                            (self.this_trait.data[sample].name not in primary_sample_names)):
+                    if ((self.this_trait.data[sample].name2 in primary_sample_names)
+                            and (self.this_trait.data[sample].name not in primary_sample_names)):
                         primary_sample_names.append(
                             self.this_trait.data[sample].name)
                         primary_sample_names.remove(
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 963288b3..3e543445 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -184,8 +184,8 @@ class UserSession:
         # ZS: Get user's collections if they exist
         collections = get_user_collections(self.user_id)
         collections = [item for item in collections if item['name'] != "Your Default Collection"] + \
-            [item for item in collections if item['name'] ==
-                "Your Default Collection"]  # ZS: Ensure Default Collection is last in list
+            [item for item in collections if item['name']
+                == "Your Default Collection"]  # ZS: Ensure Default Collection is last in list
         return collections
 
     @property
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c53012a..f75209ff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -140,8 +140,8 @@ def handle_bad_request(e):
     logger.error(traceback.format_exc())
     now = datetime.datetime.utcnow()
     time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
-    formatted_lines = [request.url +
-                       " (" + time_str + ")"]+traceback.format_exc().splitlines()
+    formatted_lines = [request.url
+                       + " (" + time_str + ")"]+traceback.format_exc().splitlines()
 
     # Handle random animations
     # Use a cookie to have one animation on refresh
@@ -518,10 +518,10 @@ def export_perm_data():
         ["#N_genotypes: " + str(perm_info['n_genotypes'])],
         ["#Genotype_file: " + perm_info['genofile']],
         ["#Units_linkage: " + perm_info['units_linkage']],
-        ["#Permutation_stratified_by: " +
-            ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
-        ["#RESULTS_1: Suggestive LRS(p=0.63) = " +
-         str(np.percentile(np.array(perm_info['perm_data']), 67))],
+        ["#Permutation_stratified_by: "
+            + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
+        ["#RESULTS_1: Suggestive LRS(p=0.63) = "
+         + str(np.percentile(np.array(perm_info['perm_data']), 67))],
         ["#RESULTS_2: Significant LRS(p=0.05) = " + str(
             np.percentile(np.array(perm_info['perm_data']), 95))],
         ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-07 23:02:55 +0000