2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bb23c38aeec/ Changeset: 9bb23c38aeec Branch: next-stable User: carlfeberhard Date: 2013-05-21 16:58:08 Summary: Fix to scatterplot to use non-dictionary hda Affected #: 1 file diff -r 0973c5acbfdac9b1de170341a19e4e57606358f8 -r 9bb23c38aeec1f26ec1c22fbcad8a098fd6ae015 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -883,48 +883,10 @@ """ Returns a page that controls and renders a scatteplot graph. """ - # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - hda_dict = hda.get_api_value() - hda_dict[ 'id' ] = dataset_id - - if( ( hda_dict[ 'metadata_column_names' ] == None ) - and ( hasattr( hda.datatype, 'column_names' ) ) ): - hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names - - # try to get the first line (assuming it's a header) - #TODO: doesn't belong here - try: - num_comment_lines = 1 - if hda_dict[ 'metadata_comment_lines' ]: - num_comment_lines = hda_dict[ 'metadata_comment_lines' ] - - infile = open( hda.file_name ) - for index, line in enumerate( infile ): - if 'comment_lines' not in hda_dict: - hda_dict[ 'comment_lines' ] = [] - hda_dict[ 'comment_lines' ].append( line ) - if index >= num_comment_lines: - break - infile.close() - - except Exception, exc: - if infile: - infile.close() - log.error( str( exc ) ) - - history_id = trans.security.encode_id( hda.history.id ) - - #TODO: add column data - # Read data. - #data_provider = ColumnDataProvider( original_dataset=hda, **kwargs ) - #data = data_provider.get_data() - - # Return plot. return trans.fill_template_mako( "visualization/scatterplot.mako", - hda=hda_dict, - historyID=history_id, - kwargs=kwargs ) + hda=hda, + query_args=kwargs ) @web.expose def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ): https://bitbucket.org/galaxy/galaxy-central/commits/137dc44f2178/ Changeset: 137dc44f2178 User: carlfeberhard Date: 2013-05-21 16:58:47 Summary: merge next-stable Affected #: 1 file diff -r 4adb47c6fe35edafaf9fcf84dfda7cd098ef1686 -r 137dc44f21782c771879af1febfe962a2ea9ae6a lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -883,48 +883,10 @@ """ Returns a page that controls and renders a scatteplot graph. """ - # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - hda_dict = hda.get_api_value() - hda_dict[ 'id' ] = dataset_id - - if( ( hda_dict[ 'metadata_column_names' ] == None ) - and ( hasattr( hda.datatype, 'column_names' ) ) ): - hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names - - # try to get the first line (assuming it's a header) - #TODO: doesn't belong here - try: - num_comment_lines = 1 - if hda_dict[ 'metadata_comment_lines' ]: - num_comment_lines = hda_dict[ 'metadata_comment_lines' ] - - infile = open( hda.file_name ) - for index, line in enumerate( infile ): - if 'comment_lines' not in hda_dict: - hda_dict[ 'comment_lines' ] = [] - hda_dict[ 'comment_lines' ].append( line ) - if index >= num_comment_lines: - break - infile.close() - - except Exception, exc: - if infile: - infile.close() - log.error( str( exc ) ) - - history_id = trans.security.encode_id( hda.history.id ) - - #TODO: add column data - # Read data. - #data_provider = ColumnDataProvider( original_dataset=hda, **kwargs ) - #data = data_provider.get_data() - - # Return plot. return trans.fill_template_mako( "visualization/scatterplot.mako", - hda=hda_dict, - historyID=history_id, - kwargs=kwargs ) + hda=hda, + query_args=kwargs ) @web.expose def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.