1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4471a94e8fbf/ changeset: 4471a94e8fbf user: dannon date: 2012-11-13 19:07:32 summary: Modules.py: Fix sa_session.add() for PJAs, remove unused imports, whitespace cleanup. affected #: 1 file
diff -r 5013377e0bf7a656ea593098f1d1b38f3d6928c6 -r 4471a94e8fbff8d8c165c58f0f76867500953b82 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -3,7 +3,6 @@ from galaxy import web from galaxy.tools.parameters import DataToolParameter, DummyDataset, RuntimeValue, check_param, visit_input_values from galaxy.tools import DefaultToolState -from galaxy.tools.parameters.grouping import Repeat, Conditional from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string from galaxy.jobs.actions.post import ActionBox @@ -13,12 +12,12 @@ log = logging.getLogger( __name__ )
class WorkflowModule( object ): - + def __init__( self, trans ): self.trans = trans - + ## ---- Creating modules from various representations --------------------- - + @classmethod def new( Class, trans, tool_id=None ): """ @@ -37,12 +36,12 @@ return Class( trans )
## ---- Saving in various forms ------------------------------------------ - + def save_to_step( self, step ): step.type = self.type - + ## ---- General attributes ----------------------------------------------- - + def get_type( self ): return self.type def get_name( self ): @@ -51,9 +50,9 @@ return None def get_tooltip( self, static_path='' ): return None - + ## ---- Configuration time ----------------------------------------------- - + def get_state( self ): return None def get_errors( self ): @@ -66,16 +65,16 @@ pass def get_config_form( self ): raise TypeError( "Abstract method" ) - + def check_and_update_state( self ): """ If the state is not in sync with the current implementation of the module, try to update. Returns a list of messages to be displayed """ pass - + ## ---- Run time --------------------------------------------------------- - + def get_runtime_inputs( self ): raise TypeError( "Abstract method" ) def get_runtime_state( self ): @@ -86,7 +85,7 @@ raise TypeError( "Abstract method" ) def update_runtime_state( self, trans, state, values ): raise TypeError( "Abstract method" ) - + def execute( self, trans, state ): raise TypeError( "Abstract method" )
@@ -112,6 +111,7 @@ if step.tool_inputs and "name" in step.tool_inputs: module.state['name'] = step.tool_inputs[ 'name' ] return module + def save_to_step( self, step ): step.type = self.type step.tool_id = None @@ -119,8 +119,10 @@
def get_data_inputs( self ): return [] + def get_data_outputs( self ): return [ dict( name='output', extensions=['input'] ) ] + def get_config_form( self ): form = web.FormBuilder( title=self.name ) \ .add_text( "name", "Name", value=self.state['name'] ) @@ -128,25 +130,29 @@ module=self, form=form ) def get_state( self, secure=True ): return to_json_string( self.state ) - + def update_state( self, incoming ): self.state['name'] = incoming.get( 'name', 'Input Dataset' ) - + def get_runtime_inputs( self, filter_set=['data'] ): label = self.state.get( "name", "Input Dataset" ) return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) ) + def get_runtime_state( self ): state = DefaultToolState() state.inputs = dict( input=None ) return state + def encode_runtime_state( self, trans, state ): fake_tool = Bunch( inputs = self.get_runtime_inputs() ) return state.encode( fake_tool, trans.app ) + def decode_runtime_state( self, trans, string ): fake_tool = Bunch( inputs = self.get_runtime_inputs() ) state = DefaultToolState() state.decode( string, fake_tool, trans.app ) return state + def update_runtime_state( self, trans, state, values ): errors = {} for name, param in self.get_runtime_inputs().iteritems(): @@ -155,14 +161,14 @@ if error: errors[ name ] = error return errors - + def execute( self, trans, state ): return None, dict( output=state.inputs['input']) - + class ToolModule( WorkflowModule ): - + type = "tool" - + def __init__( self, trans, tool_id ): self.trans = trans self.tool_id = tool_id @@ -175,11 +181,13 @@ else: self.errors = {} self.errors[ tool_id ] = 'Tool unavailable' + @classmethod def new( Class, trans, tool_id=None ): module = Class( trans, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module + @classmethod def from_dict( Class, trans, d, secure=True ): tool_id = d[ 'tool_id' ] @@ -191,6 +199,7 @@ module.post_job_actions = d.get( "post_job_actions", {} ) module.workflow_outputs = d.get( "workflow_outputs", [] ) return module + @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id @@ -215,12 +224,14 @@ module.post_job_actions = pjadict return module return None + @classmethod def __get_tool_version( cls, trans, tool_id ): # Return a ToolVersion if one exists for tool_id. return trans.sa_session.query( trans.app.model.ToolVersion ) \ .filter( trans.app.model.ToolVersion.table.c.tool_id == tool_id ) \ .first() + def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id @@ -241,24 +252,31 @@ action_arguments = v['action_arguments'] else: action_arguments = None - n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) + self.trans.sa_session.add(PostJobAction(v['action_type'], step, output_name, action_arguments)) + def get_name( self ): if self.tool: return self.tool.name return 'unavailable' + def get_tool_id( self ): return self.tool_id + def get_tool_version( self ): return self.tool.version + def get_state( self, secure=True ): return self.state.encode( self.tool, self.trans.app, secure=secure ) + def get_errors( self ): return self.errors + def get_tooltip( self, static_path='' ): if self.tool.help: return self.tool.help.render( static_path=static_path ) else: return None + def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): @@ -270,6 +288,7 @@ extensions=input.extensions ) ) visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs + def get_data_outputs( self ): data_outputs = [] data_inputs = None @@ -293,20 +312,23 @@ formats.append( format ) data_outputs.append( dict( name=name, extensions=formats ) ) return data_outputs + def get_post_job_actions( self ): return self.post_job_actions + def get_config_form( self ): self.add_dummy_datasets() - return self.trans.fill_template( "workflow/editor_tool_form.mako", + return self.trans.fill_template( "workflow/editor_tool_form.mako", tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) - def update_state( self, incoming ): + + def update_state( self, incoming ): # Build a callback that handles setting an input to be required at # runtime. We still process all other parameters the user might have # set. We also need to make sure all datasets have a dummy value # for dependencies to see - + self.post_job_actions = ActionBox.handle_incoming(incoming) - + make_runtime_key = incoming.get( 'make_runtime', None ) make_buildtime_key = incoming.get( 'make_buildtime', None ) def item_callback( trans, key, input, value, error, old_value, context ): @@ -328,8 +350,10 @@ # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None + def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) + def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name @@ -348,11 +372,12 @@ else: replacement = DummyDataset() return replacement - visit_input_values( self.tool.inputs, self.state.inputs, callback ) + visit_input_values( self.tool.inputs, self.state.inputs, callback )
class WorkflowModuleFactory( object ): def __init__( self, module_types ): self.module_types = module_types + def new( self, trans, type, tool_id=None ): """ Return module for type and (optional) tool_id intialized with @@ -360,18 +385,20 @@ """ assert type in self.module_types return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, d, **kwargs ): """ Return module initialized from the data in dictionary `d`. """ type = d['type'] assert type in self.module_types - return self.module_types[type].from_dict( trans, d, **kwargs ) + return self.module_types[type].from_dict( trans, d, **kwargs ) + def from_workflow_step( self, trans, step ): """ Return module initializd from the WorkflowStep object `step`. """ type = step.type return self.module_types[type].from_workflow_step( trans, step ) - + module_factory = WorkflowModuleFactory( dict( data_input=InputDataModule, tool=ToolModule ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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