1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/acb2548443ae/ Changeset: acb2548443ae Branch: stable User: jmchilton Date: 2014-11-26 17:42:00+00:00 Summary: Fix boolean parameter handling at workflow runtime.
Broken with 011c8b2118be778eaf1ba952730ff876d6447ba9.
Note to self - update pause module when merging into next-stable. Affected #: 1 file
diff -r c50a228167b0a1a4541f46bb19b8d67c9010248d -r acb2548443ae42d39ef200d035ccc0481d6b930c lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -147,7 +147,7 @@ """ raise TypeError( "Abstract method" )
- def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. @@ -258,7 +258,7 @@ errors[ name ] = error return errors
- def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): if step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -598,7 +598,7 @@ def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True )
- def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -609,7 +609,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors, source="json" ) + update_only=True, old_errors=old_errors, source=source ) return state, step_errors
def execute( self, trans, progress, invocation, step ): @@ -784,7 +784,7 @@ def __init__( self, trans ): self.trans = trans
- def inject( self, step, step_args=None ): + def inject( self, step, step_args=None, source="html" ): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. @@ -827,7 +827,7 @@ # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections )
- state, step_errors = module.compute_runtime_state( trans, step_args ) + state, step_errors = module.compute_runtime_state( trans, step_args, source=source ) step.state = state
return step_errors @@ -840,7 +840,7 @@ module_injector = WorkflowModuleInjector( trans ) for step in workflow.steps: step_args = param_map.get( step.id, {} ) - step_errors = module_injector.inject( step, step_args=step_args ) + step_errors = module_injector.inject( step, step_args=step_args, source="json" ) if step.type == 'tool' or step.type is None: if step_errors: message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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