details: http://www.bx.psu.edu/hg/galaxy/rev/531be9ea2486 changeset: 1602:531be9ea2486 user: Greg Von Kuster greg@bx.psu.edu date: Tue Nov 04 11:56:09 2008 -0500 description: Upload tool will now create a job record, no job queued though.

1 file(s) affected in this change:

lib/galaxy/tools/actions/upload.py

diffs (120 lines):

diff -r 52e504c91cbc -r 531be9ea2486 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Nov 04 09:27:49 2008 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Nov 04 11:56:09 2008 -0500 @@ -25,7 +25,19 @@ space_to_tab = True temp_name = "" data_list = [] - + # Create the job object + job = trans.app.model.Job() + job.session_id = trans.get_galaxy_session().id + job.history_id = trans.history.id + job.tool_id = tool.id + try: + # For backward compatibility, some tools may not have versions yet. + job.tool_version = tool.version + except: + job.tool_version = "1.0.0" + job.flush() + log.debug( 'tool %s created job id %d' % ( tool.id, job.id ) ) + trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) if 'local_filename' in dir( data_file ): # Use the existing file try: @@ -34,7 +46,7 @@ file_name = file_name.split( '/' )[-1] 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: - return self.upload_empty( trans, "Error:", str( e ) ) + return self.upload_empty( trans, job, "Error:", str( e ) ) elif 'filename' in dir( data_file ): try: file_name = data_file.filename @@ -43,7 +55,7 @@ temp_name = sniff.stream_to_file( data_file.file ) data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, "Error:", str( e ) ) + 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: url_paste = url_paste.replace( '\r', '' ).split( '\n' ) @@ -54,7 +66,7 @@ temp_name = sniff.stream_to_file( urllib.urlopen( line ) ) 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: - return self.upload_empty( trans, "Error:", str( e ) ) + return self.upload_empty( trans, job, "Error:", str( e ) ) else: is_valid = False for line in url_paste: @@ -67,26 +79,40 @@ temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ) ) 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: - return self.upload_empty( trans, "Error:", str( e ) ) + return self.upload_empty( trans, job, "Error:", str( e ) ) else: - return self.upload_empty( trans, "No data error:", "you pasted no data." ) + return self.upload_empty( trans, job, "No data error:", "you pasted no data." ) if self.empty: - return self.upload_empty( trans, "Empty file error:", "you attempted to upload an empty file." ) + return self.upload_empty( trans, job, "Empty file error:", "you attempted to upload an empty file." ) elif len( data_list ) < 1: - return self.upload_empty( trans, "No data error:", "either you pasted no data, the url you specified is invalid, or you have not specified a file." ) - return dict( output=data_list[0] ) + return self.upload_empty( trans, job, "No data error:", "either you pasted no data, the url you specified is invalid, or you have not specified a file." ) + hda = data_list[0] + job.state = trans.app.model.Job.states.OK + file_size_str = nice_size( hda.dataset.file_size ) + job.info = "Uploaded file '%s', size: %s" % ( file_name, file_size_str ) + job.flush() + log.debug( 'tool %s job id %d ended ok, file: %s, size: %s' % ( tool.id, job.id, file_name, file_size_str ) ) + trans.log_event( 'job id %d ended ok, file: %s, size: %s' % ( job.id, file_name, file_size_str ), tool_id=tool.id ) + return dict( output=hda )

- def upload_empty(self, trans, err_code, err_msg): + def upload_empty(self, trans, job, err_code, err_msg): data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) data.name = err_code data.extension = "txt" data.dbkey = "?" data.info = err_msg data.file_size = 0 + data.state = data.states.EMPTY data.flush() - data.state = data.states.EMPTY trans.history.add_dataset( data ) trans.app.model.flush() + # Indicate job failure by setting state and message + job.state = trans.app.model.Job.states.ERROR + job.info = err_msg + # If the failure is due to a Galaxy framework exception, save the traceback + job.flush() + log.debug( 'tool %s job id %d ended with errors' % ( job.tool_id, job.id ) ) + trans.log_event( 'job id %d ended with errors' % job.id, tool_id=job.tool_id ) return dict( output=data )

def add_file( self, trans, temp_name, file_name, file_type, dbkey, info=None, space_to_tab=False ): @@ -275,5 +301,20 @@ temp.close() return False

+def nice_size( size ): + """Returns a readably formatted string with the size""" + words = [ 'bytes', 'Kb', 'Mb', 'Gb' ] + try: + size = float( size ) + except: + return '??? bytes' + for ind, word in enumerate( words ): + step = 1024 ** ( ind + 1 ) + if step > size: + size = size / float( 1024 ** ind ) + out = "%.1f %s" % ( size, word ) + return out + return '??? bytes' + class BadFileException( Exception ): pass