Make Python more idiomatic

Run `2to3-3.8 -f idioms -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>

9 files changed, 12 insertions, 16 deletions

diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 97767715..864b4e08 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -80,8 +80,7 @@ while line:
 	if kj%100000 == 0:
 		print(('checked ',kj,' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 	
 if isCont==0:
 	sys.exit(0)
@@ -148,9 +147,8 @@ for item in results:
 	
 print(Names)
 
-Names = list(map(string.lower, Names))
+Names = sorted(map(string.lower, Names))
 
-Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
 
 
 ##---- compare genelist with names ----##
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 833c3f5f..20a846a4 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -91,8 +91,7 @@ while line:
     if kj % 100000 == 0:
         print(('checked ', kj, ' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 
 if isCont == 0:
     sys.exit(0)
@@ -158,8 +157,7 @@ results = db.fetchall()
 Names = []
 for item in results:
     Names.append(item[0])
-    Names = list(map(string.lower, Names))
-    Names.sort()  # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
+    Names = sorted(map(string.lower, Names))
 
 ##---- compare genelist with names ----##
 x = y = 0
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b0119b58..06e1c551 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -254,7 +254,7 @@ class Markers(object):
         logger.debug("length of self.markers:", len(self.markers))
         logger.debug("length of p_values:", len(p_values))
 
-        if type(p_values) is list:
+        if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             # if len(self.markers) > len(p_values):
             #    self.markers = self.markers[:len(p_values)]
@@ -270,7 +270,7 @@ class Markers(object):
                     marker['lod_score'] = -math.log10(marker['p_value'])
                     # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
                     marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif type(p_values) is dict:
+        elif isinstance(p_values, dict):
             filtered_markers = []
             for marker in self.markers:
                 #logger.debug("marker[name]", marker['name'])
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ece7022c..bc03eb55 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -17,7 +17,7 @@ logger = logging.getLogger(__name__ )
 def check_resource_availability(dataset, trait_id=None):
 
     #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
+    if isinstance(dataset, str):
         return webqtlConfig.DEFAULT_PRIVILEGES
     if dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 872f22fe..874ada9d 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -332,7 +332,7 @@ class SVGelement:
                 f.write('\n'+'\t'*(level+2)+line)
             f.write('\n'+'\t'*(level+1)+']]>\n')
         if self.text:
-            if type(self.text) == type(''):  # If the text is only text
+            if isinstance(self.text, type('')):  # If the text is only text
                 f.write(_escape(str(self.text)))
             else:  # If the text is a spannedtext class
                 f.write(str(self.text))
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index f0be7a98..e58a7b87 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -175,7 +175,7 @@ class CTL(object):
         sys.stdout.flush()
 
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
-        if not type(significant) == ri.RNULLType:
+        if not isinstance(significant, ri.RNULLType):
           for x in range(len(significant[0])):
             logger.debug(significant[0][x], significant[1][x], significant[2][x])     # Debug to console
             tsS = significant[0][x].split(':')                                        # Source
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ad78ebcc..21ba7f63 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -43,7 +43,7 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+            if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait
                 if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
                 else:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c156e61b..65899ab2 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -625,7 +625,7 @@ def get_categorical_variables(this_trait, sample_list):
 
 def get_genotype_scales(genofiles):
     geno_scales = {}
-    if type(genofiles) is list:
+    if isinstance(genofiles, list):
         for the_file in genofiles:
             file_location = the_file['location']
             geno_scales[file_location] = get_scales_from_genofile(file_location)
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index cfee0079..04672b45 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -193,7 +193,7 @@ def login():
             if user_details:
                 submitted_password = params['password']
                 pwfields = user_details['password']
-                if type(pwfields) is str:
+                if isinstance(pwfields, str):
                     pwfields = json.loads(pwfields)
                 encrypted_pass_fields = encode_password(pwfields, submitted_password)
                 password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])