Merge github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 24 insertions, 25 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 647e58a2..db65a11f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -30,18 +30,10 @@ It needs to be run manually when database has been changed. Run it as
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import print_function, division
-
-#from flask import config
-#
-#cdict = {}
-#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
-#print("cdict is:", cdict)
-
 import sys
 
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
 
@@ -50,7 +42,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
 import MySQLdb
 
 import simplejson as json
-import urlparse
+import urllib.parse
 
 
 #import sqlalchemy as sa
@@ -63,16 +55,17 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
-                        db = parsed_uri.path[1:],
-                        host = parsed_uri.hostname,
-                        user = parsed_uri.username,
-                        passwd = parsed_uri.password)
+        db=parsed_uri.path[1:],
+        host=parsed_uri.hostname,
+        user=parsed_uri.username,
+        passwd=parsed_uri.password)
 
     print(db_conn_info)
     return db_conn_info
@@ -108,7 +101,7 @@ def get_types(groups):
     """Build types list"""
     types = {}
     #print("Groups: ", pf(groups))
-    for species, group_dict in groups.iteritems():
+    for species, group_dict in list(groups.items()):
         types[species] = {}
         for group_name, _group_full_name in group_dict:
             # make group an alias to shorten the code
@@ -127,21 +120,23 @@ def get_types(groups):
                 else:
                     if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
                         types[species].pop(group_name, None)
-                        groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
-            else: #ZS: This whole else statement might be unnecessary, need to check
+                        groups[species] = tuple(
+                            group for group in groups[species] if group[0] != group_name)
+            else:  # ZS: This whole else statement might be unnecessary, need to check
                 types_list = build_types(species, group_name)
                 if len(types_list) > 0:
                     types[species][group_name] = types_list
                 else:
                     types[species].pop(group_name, None)
-                    groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+                    groups[species] = tuple(
+                        group for group in groups[species] if group[0] != group_name)
     return types
 
 
 def phenotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from PublishFreeze
-                      where PublishFreeze.Name = '%s'""" % (group_name+"Publish"))
+                      where PublishFreeze.Name = '%s'""" % (group_name + "Publish"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -151,10 +146,11 @@ def phenotypes_exist(group_name):
     else:
         return False
 
+
 def genotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from GenoFreeze
-                      where GenoFreeze.Name = '%s'""" % (group_name+"Geno"))
+                      where GenoFreeze.Name = '%s'""" % (group_name + "Geno"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -164,6 +160,7 @@ def genotypes_exist(group_name):
     else:
         return False
 
+
 def build_types(species, group):
     """Fetches tissues
 
@@ -192,12 +189,13 @@ def build_types(species, group):
 
     return results
 
+
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
-    for species, group_dict in types.iteritems():
+    for species, group_dict in list(types.items()):
         datasets[species] = {}
-        for group, type_list in group_dict.iteritems():
+        for group, type_list in list(group_dict.items()):
             datasets[species][group] = {}
             for type_name in type_list:
                 these_datasets = build_datasets(species, group, type_name[0])
@@ -254,7 +252,7 @@ def build_datasets(species, group, type_name):
         dataset_text = "%s Genotypes" % group
         datasets.append((dataset_id, dataset_value, dataset_text))
 
-    else: # for mRNA expression/ProbeSet
+    else:  # for mRNA expression/ProbeSet
         Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
                     ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
                     Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
@@ -316,7 +314,8 @@ def _test_it():
     datasets = build_datasets("Mouse", "BXD", "Hippocampus")
     #print("build_datasets:", pf(datasets))
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
-    main()
\ No newline at end of file
+    main()