Force FieldStorage to write tempfiles and never use StringIOs.

lib/galaxy/tools/actions/upload.py

@@ -20,12 +20,10 @@ class UploadToolAction( ToolAction ):
             for upload_dataset in incoming['files']:
                 f = upload_dataset['file_data']
                 if isinstance( f, FieldStorage ): 
-                    # very small files can be StringIOs
-                    if 'name' in dir( f.file ) and f.file.name != '<fdopen>':
-                        local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' )
-                        f.file.close()
-                    else:
-                        local_filename = datatypes.sniff.stream_to_file( f.file, prefix="strio_upload_file_" )[0]
+                    assert not isinstance( f.file, StringIO.StringIO )
+                    assert f.file.name != '<fdopen>'
+                    local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' )
+                    f.file.close()
                     upload_dataset['file_data'] = dict( filename = f.filename,
                                                         local_filename = local_filename )
                 if upload_dataset['url_paste'].strip() != '':

lib/galaxy/web/framework/base.py

@@ -216,11 +216,18 @@ class DefaultWebTransaction( object ):
 # tempfiles.  Necessary for externalizing the upload tool.  It's a little hacky
 # but for performance reasons it's way better to use Paste's tempfile than to
 # create a new one and copy.
-import cgi
+import cgi, tempfile
 class FieldStorage( cgi.FieldStorage ):
     def make_file(self, binary=None):
-        import tempfile
         return tempfile.NamedTemporaryFile()
+    def read_lines(self):
+    # Always make a new file
+        self.file = self.make_file()
+        self.__file = None
+        if self.outerboundary:
+            self.read_lines_to_outerboundary()
+        else:
+            self.read_lines_to_eof() 
 cgi.FieldStorage = FieldStorage
 
 class Request( webob.Request ):