Fix for sniffing datatypes, sniff order is now retrieved from app.datatypes_registry rather than the default sniff_order list in the Registry class.

lib/galaxy/datatypes/sniff.py

@@ -155,7 +155,7 @@ def is_column_based(fname, sep='\t', skip=0):
                 return False
     return True
 
-def guess_ext( fname ):
+def guess_ext( fname, sniff_order=None ):
     """
     Returns an extension that can be used in the datatype factory to
     generate a data for the 'fname' file
@@ -198,9 +198,11 @@ def guess_ext( fname ):
     >>> fname = get_test_fname('alignment.lav')
     >>> guess_ext(fname)
     'lav'
-    """ 
-    datatypes_registry = registry.Registry()
-    for datatype in datatypes_registry.sniff_order:
+    """
+    if sniff_order is None:
+        datatypes_registry = registry.Registry()
+        sniff_order = datatypes_registry.sniff_order
+    for datatype in sniff_order:
         """
         Some classes may not have a sniff function, which is ok.  In fact, the
         Tabular and Text classes are 2 examples of classes that should never have

lib/galaxy/tools/actions/upload.py

@@ -150,7 +150,7 @@ class UploadToolAction( object ):
             else:
                 self.line_count = sniff.convert_newlines( temp_name )
             if file_type == 'auto':
-                ext = sniff.guess_ext( temp_name )    
+                ext = sniff.guess_ext( temp_name, sniff_order=trans.app.datatypes_registry.sniff_order )    
             else:
                 ext = file_type
             data_type = ext

tools/data_source/biomart_filter.py

@@ -11,7 +11,7 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     data_type = param_dict.get( 'type', 'txt' )
     name, data = out_data.items()[0]
     if data_type == 'txt':
-        data_type = sniff.guess_ext(data.file_name)
+        data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order )
     data = app.datatypes_registry.change_datatype(data, data_type)
     data.name = data_name
     out_data[name] = data

tools/data_source/gbrowse_filter_code.py

@@ -27,7 +27,7 @@ def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=N
     if data.state == data.states.OK:
         data.info = data.name
     if data.extension == 'txt':
-        data_type = sniff.guess_ext( data.file_name )
+        data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order )
         data = app.datatypes_registry.change_datatype( data, data_type ) 
     data.set_peek()
     data.set_size()