autopep8: Fix W504

9 files changed, 52 insertions, 52 deletions

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(