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ToolForm: Integrate and optimize state population for tools api

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This commit is contained in:
Aysam Guerler
2014-11-07 13:24:22 -05:00
parent 668cdc8309
commit 113f90a91b
1 changed files with 62 additions and 7 deletions
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lib/galaxy/webapps/galaxy/api/tools.py
+62 -7
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@@ -10,7 +10,7 @@ from galaxy.web.base.controller import UsesHistoryMixin
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 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix
# 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 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix
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 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix
# 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 = ''