Python 3: use "as" instead of comma in except clause

tools/data_source/data_source.py

@@ -88,7 +88,7 @@ def __main__():
                 page = urllib.urlopen( cur_URL )
             elif URL_method == 'post':
                 page = urllib.urlopen( cur_URL, urllib.urlencode( params ) )
-        except Exception, e:
+        except Exception as e:
             stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) )
         if max_file_size:
             file_size = int( page.info().get( 'Content-Length', 0 ) )
@@ -97,14 +97,14 @@ def __main__():
         # do sniff stream for multi_byte
         try:
             cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) )
-        except Exception, e:
+        except Exception as e:
             stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) )
 
         # here import checks that upload tool performs
         if enhanced_handling:
             try:
                 ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext=data_dict[ 'ext' ], is_multi_byte=is_multi_byte )
-            except Exception, e:
+            except Exception as e:
                 stop_err( str( e ) )
             info = dict( type='dataset',
                          dataset_id=data_dict[ 'dataset_id' ],

tools/data_source/fetch.py

@@ -20,6 +20,6 @@ try:
         if not data:
             break
         out.write(data)
-except Exception, e:
+except Exception as e:
     print 'Error getting the data -> %s' % e
 out.close()

tools/data_source/hbvar_filter.py

@@ -31,7 +31,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
 
     try:
         page = urllib.urlopen(URL)
-    except Exception, exc:
+    except Exception as exc:
         raise Exception('Problems connecting to %s (%s)' % (URL, exc) )
 
     name, data = out_data.items()[0]

tools/data_source/upload.py

@@ -96,7 +96,7 @@ def add_file( dataset, registry, json_file, output_path ):
         try:
             page = urllib.urlopen( dataset.path )  # page will be .close()ed by sniff methods
             temp_name, dataset.is_multi_byte = sniff.stream_to_file( page, prefix='url_paste', source_encoding=util.get_charset_from_http_headers( page.headers ) )
-        except Exception, e:
+        except Exception as e:
             file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file )
             return
         dataset.path = temp_name
@@ -111,7 +111,7 @@ def add_file( dataset, registry, json_file, output_path ):
         # Already set is_multi_byte above if type == 'url'
         try:
             dataset.is_multi_byte = multi_byte.is_multi_byte( codecs.open( dataset.path, 'r', 'utf-8' ).read( 100 ) )
-        except UnicodeDecodeError, e:
+        except UnicodeDecodeError as e:
             dataset.is_multi_byte = False
     # Is dataset an image?
     image = check_image( dataset.path )
@@ -364,7 +364,7 @@ def add_composite_file( dataset, json_file, output_path, files_path ):
                     if isurl:
                         try:
                             temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dp ), prefix='url_paste' )
-                        except Exception, e:
+                        except Exception as e:
                             file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file )
                             return
                         dataset.path = temp_name