1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/04644e64c498/ Changeset: 04644e64c498 User: guerler Date: 2014-11-07 18:24:22+00:00 Summary: ToolForm: Integrate and optimize state population for tools api Affected #: 1 file
diff -r 1a465f5f15ec782c01926056c125fc4769d7fc06 -r 04644e64c498ca4eacbfa1c6df26cb546705b96c lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -10,7 +10,7 @@ from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import dumps from galaxy.visualization.data_providers.genome import * -from galaxy.tools.parameters import params_to_incoming +from galaxy.tools.parameters import params_to_incoming, check_param from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.meta import expand_meta_parameters from galaxy.managers.collections_util import dictify_dataset_collection_instance @@ -574,7 +574,62 @@ # update and return dict['value'] = value return dict - + + # populate state + def initialize_state(trans, inputs, state, context=None): + context = ExpressionContext(state, context) + for input in inputs.itervalues(): + state[input.name] = input.get_initial_value(trans, context) + def populate_state(trans, inputs, state, incoming, prefix="", context=None ): + errors = dict() + context = ExpressionContext(state, context) + for input in inputs.itervalues(): + key = prefix + input.name + if input.type == 'repeat': + group_state = state[input.name] + group_errors = [] + rep_index = 0 + del group_state[:] + while True: + rep_name = "%s_%d" % (key, rep_index) + if not any([incoming_key.startswith(rep_name) for incoming_key in incoming.keys()]): + break + if rep_index < input.max: + new_state = {} + new_state['__index__'] = rep_index + initialize_state(trans, input.inputs, new_state, context) + group_state.append(new_state) + group_errors.append({}) + rep_errors = populate_state(trans, input.inputs, new_state, incoming, prefix=rep_name + "|", context=context) + if rep_errors: + group_errors[rep_index].update( rep_errors ) + else: + group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max } + rep_index += 1 + elif input.type == 'conditional': + group_state = state[input.name] + group_prefix = "%s|" % ( key ) + test_param_key = group_prefix + input.test_param.name + default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None)) + value, test_param_error = check_param( trans, input.test_param, default_value, context) + if test_param_error: + errors[input.name] = [test_param_error] + else: + current_case = input.get_current_case(value, trans) + group_state = state[input.name] = {} + initialize_state(trans, input.cases[current_case].inputs, group_state, context) + group_errors = populate_state( trans, input.cases[current_case].inputs, group_state, incoming, prefix=group_prefix, context=context) + if group_errors: + errors[input.name] = group_errors + group_state['__current_case__'] = current_case + group_state[ input.test_param.name ] = value + else: + value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) + if error: + errors[input.name] = error + state[input.name] = value + return errors + # build model def iterate(group_inputs, inputs, tool_state, errors, other_values=None): other_values = ExpressionContext( tool_state, other_values ) @@ -593,7 +648,6 @@ group_errors = errors[input.name][i] if input.name in errors else dict() iterate( group_cache[i], input.inputs, group_state[i], group_errors, other_values ) elif input.type == 'conditional': - # TODO: loop over all cases try: test_param = group_inputs[input_index]['test_param'] test_param['value'] = convert(group_state[test_param['name']]) @@ -622,17 +676,18 @@ # do param translation here, used by datasource tools if tool.input_translator: tool.input_translator.translate( params ) - + # create tool state - state = tool.new_state(trans, all_pages=True) - errors = tool.populate_state( trans, tool.inputs, state.inputs, params.__dict__ ) + state_inputs = {} + initialize_state(trans, tool.inputs, state_inputs) + errors = populate_state(trans, tool.inputs, state_inputs, params.__dict__)
# create basic tool model tool_model = tool.to_dict(trans) tool_model['inputs'] = {}
# build tool model - iterate(tool_model['inputs'], tool.inputs, state.inputs, errors, '') + iterate(tool_model['inputs'], tool.inputs, state_inputs, errors, '')
# load tool help tool_help = ''
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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