# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg <dan@bx.psu.edu> # Date 1288640846 14400 # Node ID 1efe19f6f3d1a75bda9c198633dd8102d3063410 # Parent 2c934a168af968dc84300412220c2f2cb74bf676 Fixes for rerun action to recurse grouping options when checking unvalidated values and cloned HDAs. Better selection of corresponding HDAs from cloned histories, when multiple copies exist. --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -123,16 +123,6 @@ class ToolRunner( BaseController ): params_objects = job.get_param_values( trans.app ) except: raise Exception( "Failed to get paramemeters for dataset id %d " % data.id ) - # Unpack unvalidated values to strings, they'll be validated when the - # form is submitted (this happens when re-running a job that was - # initially run by a workflow) - validated_params = {} - for name, value in params_objects.items(): - if isinstance( value, UnvalidatedValue ): - validated_params [ str(name) ] = str(value) - else: - validated_params [ str(name) ] = value - params_objects = validated_params # Need to remap dataset parameters. Job parameters point to original # dataset used; parameter should be the analygous dataset in the # current history. @@ -141,12 +131,22 @@ class ToolRunner( BaseController ): for hda in history.datasets: source_hda = hda.copied_from_history_dataset_association while source_hda:#should this check library datasets as well? - hda_source_dict[ source_hda ] = hda + #FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories, + #but is still less than perfect when eg individual datasets are copied between histories + if source_hda not in hda_source_dict or source_hda.hid == hda.hid: + hda_source_dict[ source_hda ] = hda source_hda = source_hda.copied_from_history_dataset_association - for name, value in validated_params.items(): - if isinstance( value, trans.app.model.HistoryDatasetAssociation ): - if value not in history.datasets: - validated_params[ name ] = hda_source_dict[ value ] + # Unpack unvalidated values to strings, they'll be validated when the + # form is submitted (this happens when re-running a job that was + # initially run by a workflow) + #This needs to be done recursively through grouping parameters + def rerun_callback( input, value, prefixed_name, prefixed_label ): + if isinstance( value, UnvalidatedValue ): + return str( value ) + if isinstance( input, DataToolParameter ): + if value not in history.datasets and value in hda_source_dict: + return hda_source_dict[ value ] + visit_input_values( tool.inputs, params_objects, rerun_callback ) # Create a fake tool_state for the tool, with the parameters values state = tool.new_state( trans ) state.inputs = params_objects