details: http://www.bx.psu.edu/hg/galaxy/rev/19d18731ce19 changeset: 1716:19d18731ce19 user: Greg Von Kuster greg@bx.psu.edu date: Thu Jan 22 11:22:39 2009 -0500 description: Fixes in the upload tool for removing temporary files.

1 file(s) affected in this change:

lib/galaxy/tools/actions/upload.py

diffs (81 lines):

diff -r 5c293dbf0726 -r 19d18731ce19 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Jan 22 08:50:52 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Thu Jan 22 11:22:39 2009 -0500 @@ -13,7 +13,11 @@ def __init__( self ): self.empty = False self.line_count = None - + def remove_tempfile( self, filename ): + try: + os.unlink( filename ) + except: + log.exception( 'failure removing temporary file: %s' % filename ) def execute( self, tool, trans, incoming={}, set_output_hid = True ): data_file = incoming['file_data'] file_type = incoming['file_type'] @@ -48,6 +52,7 @@ data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) ) + self.remove_tempfile( data_file.local_filename ) return self.upload_empty( trans, job, "Error:", str( e ) ) elif 'filename' in dir( data_file ): file_name = data_file.filename @@ -57,16 +62,13 @@ temp_name = sniff.stream_to_file( data_file.file, prefix='upload' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) if url_paste not in [ None, "" ]: if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0: @@ -78,16 +80,13 @@ temp_name = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, line, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) else: is_valid = False @@ -101,16 +100,13 @@ temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) ) except Exception, e: log.excception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) else: return self.upload_empty( trans, job, "No data error:", "you pasted no data." )