[galaxy-commits] commit/galaxy-central: 3 new changesets

10 Oct 2011

3 new changesets in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/feee8fdcdaeb/
changeset:   feee8fdcdaeb
user:        John Duddy
date:        2011-08-18 23:16:03
summary:     Allow 2 new optional parameters to workflow/run controller method:
history_id: an encoded history id to use. Will not permantently switch user's
            current id
hide_fixed_params: Initially hides all workflow parameters that are not
            "Set at Runtime" and all workflow steps that only contain them.
            Intended to reduce clutter when launching "canned" workflows.

Also added configurable feature that governs how initial values are selected
from the history for workflow runtime input. When enabled, this feature
causes Galaxy to use each input only once until it has used them all. This
is for the paired-end scenario, to attempt to match inputs correctly by default.
affected #:  5 files (-1 bytes)

--- a/lib/galaxy/config.py	Thu Aug 18 14:20:48 2011 -0400
+++ b/lib/galaxy/config.py	Thu Aug 18 14:16:03 2011 -0700
@@ -46,6 +46,7 @@
         self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) )
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
+        self.enable_unique_workflow_defaults = string_as_bool ( kwargs.get ('enable_unique_workflow_defaults', False ) )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )


--- a/lib/galaxy/tools/parameters/basic.py	Thu Aug 18 14:20:48 2011 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Thu Aug 18 14:16:03 2011 -0700
@@ -75,6 +75,16 @@
         """
         return None
 
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
+        """
+        Get the starting value for the parameter, but if fetching from the history, try
+        to find a value that has not yet been used. already_used is a list of objects that
+        tools must manipulate (by adding to it) to store a memento that they can use to detect
+        if a value has already been chosen from the history. This is to support the capability to
+        choose each dataset once
+        """
+        return self.get_initial_value(trans, context);
+
     def get_required_enctype( self ):
         """
         If this parameter needs the form to have a specific encoding
@@ -1385,6 +1395,9 @@
         return field
 
     def get_initial_value( self, trans, context ):
+        return self.get_initial_value_from_history_prevent_repeats(trans, context, None);
+
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
         """
         NOTE: This is wasteful since dynamic options and dataset collection
               happens twice (here and when generating HTML). 
@@ -1397,7 +1410,7 @@
         assert history is not None, "DataToolParameter requires a history"
         if self.optional:
             return None
-        most_recent_dataset = [None]
+        most_recent_dataset = []
         filter_value = None
         if self.options:
             try:
@@ -1423,15 +1436,19 @@
                             data = converted_dataset
                     if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ):
                         continue
-                    most_recent_dataset[0] = data
+                    most_recent_dataset.append(data)
                 # Also collect children via association object
                 dataset_collector( data.children )
         dataset_collector( history.datasets )
-        most_recent_dataset = most_recent_dataset.pop()
-        if most_recent_dataset is not None:
-            return most_recent_dataset
-        else:
-            return ''
+        most_recent_dataset.reverse()
+        if already_used is not None:
+            for val in most_recent_dataset:
+                if val is not None and val not in already_used:
+                    already_used.append(val)
+                    return val
+        if len(most_recent_dataset) > 0:
+            return most_recent_dataset[0]
+        return ''
 
     def from_html( self, value, trans, other_values={} ):
         # Can't look at history in workflow mode, skip validation and such,


--- a/lib/galaxy/web/controllers/workflow.py	Thu Aug 18 14:20:48 2011 -0400
+++ b/lib/galaxy/web/controllers/workflow.py	Thu Aug 18 14:16:03 2011 -0700
@@ -1258,7 +1258,7 @@
             ##     % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) )       
         
     @web.expose
-    def run( self, trans, id, **kwargs ):
+    def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ):
         stored = self.get_stored_workflow( trans, id, check_ownership=False )
         user = trans.get_user()
         if stored.user != user:
@@ -1279,163 +1279,185 @@
         errors = {}
         has_upgrade_messages = False
         has_errors = False
-        if kwargs:
-            # If kwargs were provided, the states for each step should have
-            # been POSTed
-            # Get the kwarg keys for data inputs
-            input_keys = filter(lambda a: a.endswith('|input'), kwargs)
-            # Example: prefixed='2|input'
-            # Check if one of them is a list
-            multiple_input_key = None
-            multiple_inputs = [None]
-            for input_key in input_keys:
-                if isinstance(kwargs[input_key], list):
-                    multiple_input_key = input_key
-                    multiple_inputs = kwargs[input_key]
-            # List to gather values for the template
-            invocations=[]
-            for input_number, single_input in enumerate(multiple_inputs):
-                # Example: single_input='1', single_input='2', etc...
-                # 'Fix' the kwargs, to have only the input for this iteration
-                if multiple_input_key:
-                    kwargs[multiple_input_key] = single_input
+        saved_history = None
+        if history_id is not None:
+            saved_history = trans.get_history();
+            try:
+                decoded_history_id = trans.security.decode_id( history_id )
+                history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+                if history.user != trans.user and not trans.user_is_admin():
+                    if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                        error("History is not owned by or shared with current user")
+                trans.set_history(history)
+            except TypeError:
+                error("Malformed history id ( %s ) specified, unable to decode." % str( history_id ))
+            except:
+                error("That history does not exist.")
+        try: # use a try/finally block to restore the user's current history
+            if kwargs:
+                # If kwargs were provided, the states for each step should have
+                # been POSTed
+                # Get the kwarg keys for data inputs
+                input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+                # Example: prefixed='2|input'
+                # Check if one of them is a list
+                multiple_input_key = None
+                multiple_inputs = [None]
+                for input_key in input_keys:
+                    if isinstance(kwargs[input_key], list):
+                        multiple_input_key = input_key
+                        multiple_inputs = kwargs[input_key]
+                # List to gather values for the template
+                invocations=[]
+                for input_number, single_input in enumerate(multiple_inputs):
+                    # Example: single_input='1', single_input='2', etc...
+                    # 'Fix' the kwargs, to have only the input for this iteration
+                    if multiple_input_key:
+                        kwargs[multiple_input_key] = single_input
+                    for step in workflow.steps:
+                        step.upgrade_messages = {}
+                        # Connections by input name
+                        step.input_connections_by_name = \
+                            dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                        # Extract just the arguments for this step by prefix
+                        p = "%s|" % step.id
+                        l = len(p)
+                        step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
+                        step_errors = None
+                        if step.type == 'tool' or step.type is None:
+                            module = module_factory.from_workflow_step( trans, step )
+                            # Fix any missing parameters
+                            step.upgrade_messages = module.check_and_update_state()
+                            if step.upgrade_messages:
+                                has_upgrade_messages = True
+                            # Any connected input needs to have value DummyDataset (these
+                            # are not persisted so we need to do it every time)
+                            module.add_dummy_datasets( connections=step.input_connections )    
+                            # Get the tool
+                            tool = module.tool
+                            # Get the state
+                            step.state = state = module.state
+                            # Get old errors
+                            old_errors = state.inputs.pop( "__errors__", {} )
+                            # Update the state
+                            step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
+                                                             update_only=True, old_errors=old_errors )
+                        else:
+                            # Fix this for multiple inputs
+                            module = step.module = module_factory.from_workflow_step( trans, step )
+                            state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
+                            step_errors = module.update_runtime_state( trans, state, step_args )
+                        if step_errors:
+                            errors[step.id] = state.inputs["__errors__"] = step_errors   
+                    if 'run_workflow' in kwargs and not errors:
+                        new_history = None
+                        if 'new_history' in kwargs:
+                            if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
+                                nh_name = kwargs['new_history_name']
+                            else:
+                                nh_name = "History from %s workflow" % workflow.name
+                            if multiple_input_key:
+                                nh_name = '%s %d' % (nh_name, input_number + 1)
+                            new_history = trans.app.model.History( user=trans.user, name=nh_name )
+                            trans.sa_session.add( new_history )
+                        # Run each step, connecting outputs to inputs
+                        workflow_invocation = model.WorkflowInvocation()
+                        workflow_invocation.workflow = workflow
+                        outputs = odict()
+                        for i, step in enumerate( workflow.steps ):
+                            # Execute module
+                            job = None
+                            if step.type == 'tool' or step.type is None:
+                                tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                                input_values = step.state.inputs
+                                # Connect up
+                                def callback( input, value, prefixed_name, prefixed_label ):
+                                    if isinstance( input, DataToolParameter ):
+                                        if prefixed_name in step.input_connections_by_name:
+                                            conn = step.input_connections_by_name[ prefixed_name ]
+                                            return outputs[ conn.output_step.id ][ conn.output_name ]
+                                visit_input_values( tool.inputs, step.state.inputs, callback )
+                                # Execute it
+                                job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
+                                outputs[ step.id ] = out_data
+                                # Create new PJA associations with the created job, to be run on completion.
+                                # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
+                                # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
+                                replacement_dict = {}
+                                for k, v in kwargs.iteritems():
+                                    if k.startswith('wf_parm|'):
+                                        replacement_dict[k[8:]] = v
+                                for pja in step.post_job_actions:
+                                    if pja.action_type in ActionBox.immediate_actions:
+                                        ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
+                                    else:
+                                        job.add_post_job_action(pja)
+                            else:
+                                job, out_data = step.module.execute( trans, step.state )
+                                outputs[ step.id ] = out_data
+                            # Record invocation
+                            workflow_invocation_step = model.WorkflowInvocationStep()
+                            workflow_invocation_step.workflow_invocation = workflow_invocation
+                            workflow_invocation_step.workflow_step = step
+                            workflow_invocation_step.job = job
+                        # All jobs ran sucessfully, so we can save now
+                        trans.sa_session.add( workflow_invocation )
+                        invocations.append({'outputs': outputs,
+                                            'new_history': new_history})
+                trans.sa_session.flush()
+                return trans.fill_template( "workflow/run_complete.mako",
+                                            workflow=stored,
+                                            invocations=invocations )
+            else:
+                # Prepare each step
+                missing_tools = []
                 for step in workflow.steps:
                     step.upgrade_messages = {}
-                    # Connections by input name
-                    step.input_connections_by_name = \
-                        dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
-                    # Extract just the arguments for this step by prefix
-                    p = "%s|" % step.id
-                    l = len(p)
-                    step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
-                    step_errors = None
+                    # Contruct modules
                     if step.type == 'tool' or step.type is None:
-                        module = module_factory.from_workflow_step( trans, step )
-                        # Fix any missing parameters
-                        step.upgrade_messages = module.check_and_update_state()
+                        # Restore the tool state for the step
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        if not step.module:
+                            if step.tool_id not in missing_tools:
+                                missing_tools.append(step.tool_id)
+                            continue
+                        step.upgrade_messages = step.module.check_and_update_state()
                         if step.upgrade_messages:
                             has_upgrade_messages = True
                         # Any connected input needs to have value DummyDataset (these
                         # are not persisted so we need to do it every time)
-                        module.add_dummy_datasets( connections=step.input_connections )    
-                        # Get the tool
-                        tool = module.tool
-                        # Get the state
-                        step.state = state = module.state
-                        # Get old errors
-                        old_errors = state.inputs.pop( "__errors__", {} )
-                        # Update the state
-                        step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
-                                                         update_only=True, old_errors=old_errors )
+                        step.module.add_dummy_datasets( connections=step.input_connections )                  
+                        # Store state with the step
+                        step.state = step.module.state
+                        # Error dict
+                        if step.tool_errors:
+                            has_errors = True
+                            errors[step.id] = step.tool_errors
                     else:
-                        # Fix this for multiple inputs
-                        module = step.module = module_factory.from_workflow_step( trans, step )
-                        state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
-                        step_errors = module.update_runtime_state( trans, state, step_args )
-                    if step_errors:
-                        errors[step.id] = state.inputs["__errors__"] = step_errors   
-                if 'run_workflow' in kwargs and not errors:
-                    new_history = None
-                    if 'new_history' in kwargs:
-                        if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
-                            nh_name = kwargs['new_history_name']
-                        else:
-                            nh_name = "History from %s workflow" % workflow.name
-                        if multiple_input_key:
-                            nh_name = '%s %d' % (nh_name, input_number + 1)
-                        new_history = trans.app.model.History( user=trans.user, name=nh_name )
-                        trans.sa_session.add( new_history )
-                    # Run each step, connecting outputs to inputs
-                    workflow_invocation = model.WorkflowInvocation()
-                    workflow_invocation.workflow = workflow
-                    outputs = odict()
-                    for i, step in enumerate( workflow.steps ):
-                        # Execute module
-                        job = None
-                        if step.type == 'tool' or step.type is None:
-                            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
-                            input_values = step.state.inputs
-                            # Connect up
-                            def callback( input, value, prefixed_name, prefixed_label ):
-                                if isinstance( input, DataToolParameter ):
-                                    if prefixed_name in step.input_connections_by_name:
-                                        conn = step.input_connections_by_name[ prefixed_name ]
-                                        return outputs[ conn.output_step.id ][ conn.output_name ]
-                            visit_input_values( tool.inputs, step.state.inputs, callback )
-                            # Execute it
-                            job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
-                            outputs[ step.id ] = out_data
-                            # Create new PJA associations with the created job, to be run on completion.
-                            # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
-                            # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-                            replacement_dict = {}
-                            for k, v in kwargs.iteritems():
-                                if k.startswith('wf_parm|'):
-                                    replacement_dict[k[8:]] = v
-                            for pja in step.post_job_actions:
-                                if pja.action_type in ActionBox.immediate_actions:
-                                    ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
-                                else:
-                                    job.add_post_job_action(pja)
-                        else:
-                            job, out_data = step.module.execute( trans, step.state )
-                            outputs[ step.id ] = out_data
-                        # Record invocation
-                        workflow_invocation_step = model.WorkflowInvocationStep()
-                        workflow_invocation_step.workflow_invocation = workflow_invocation
-                        workflow_invocation_step.workflow_step = step
-                        workflow_invocation_step.job = job
-                    # All jobs ran sucessfully, so we can save now
-                    trans.sa_session.add( workflow_invocation )
-                    invocations.append({'outputs': outputs,
-                                        'new_history': new_history})
-            trans.sa_session.flush()
-            return trans.fill_template( "workflow/run_complete.mako",
-                                        workflow=stored,
-                                        invocations=invocations )
-        else:
-            # Prepare each step
-            missing_tools = []
-            for step in workflow.steps:
-                step.upgrade_messages = {}
-                # Contruct modules
-                if step.type == 'tool' or step.type is None:
-                    # Restore the tool state for the step
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    if not step.module:
-                        if step.tool_id not in missing_tools:
-                            missing_tools.append(step.tool_id)
-                        continue
-                    step.upgrade_messages = step.module.check_and_update_state()
-                    if step.upgrade_messages:
-                        has_upgrade_messages = True
-                    # Any connected input needs to have value DummyDataset (these
-                    # are not persisted so we need to do it every time)
-                    step.module.add_dummy_datasets( connections=step.input_connections )                  
-                    # Store state with the step
-                    step.state = step.module.state
-                    # Error dict
-                    if step.tool_errors:
-                        has_errors = True
-                        errors[step.id] = step.tool_errors
-                else:
-                    ## Non-tool specific stuff?
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    step.state = step.module.get_runtime_state()
-                # Connections by input name
-                step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
-            if missing_tools:
-                stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-                return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
-        # Render the form
-        stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-        return trans.fill_template(
-                    "workflow/run.mako", 
-                    steps=workflow.steps,
-                    workflow=stored,
-                    has_upgrade_messages=has_upgrade_messages,
-                    errors=errors,
-                    incoming=kwargs )
+                        ## Non-tool specific stuff?
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        step.state = step.module.get_runtime_state()
+                    # Connections by input name
+                    step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
+                if missing_tools:
+                    stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+                    return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
+            # Render the form
+            stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+            return trans.fill_template(
+                        "workflow/run.mako", 
+                        steps=workflow.steps,
+                        workflow=stored,
+                        has_upgrade_messages=has_upgrade_messages,
+                        errors=errors,
+                        incoming=kwargs,
+                        history_id=history_id,
+                        hide_fixed_params=hide_fixed_params,
+                        enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
+        finally:
+            # restore the active history
+            if saved_history is not None:
+                trans.set_history(saved_history) 
                     
     def get_item( self, trans, id ):
         return self.get_stored_workflow( trans, id ) 


--- a/templates/workflow/run.mako	Thu Aug 18 14:20:48 2011 -0400
+++ b/templates/workflow/run.mako	Thu Aug 18 14:16:03 2011 -0700
@@ -6,8 +6,12 @@
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
-                title.parent().css('border-bottom-width', '1px');
+                title.parent().show().css('border-bottom-width', '1px');
                 title.next().show('fast');
+                if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                    // show previously hidden parameters
+                    title.next().children(".form-row").show();
+                }
             }
             function hide_tool_body(title){
                 title.parent().css('border-bottom-width', '0px');
@@ -46,8 +50,15 @@
             $("div.toolFormTitle").click(function(){
                 toggle_tool_body($(this));
             });
-            // Collapse non-interactive run-workflow panels by default.
-            $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                // hide parameters that are not runtime inputs
+                $("div.form-row:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+                $("div.toolForm:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+            }
+            else {
+                // Collapse non-interactive run-workflow panels by default.
+                $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            }
             $("#show_all_tool_body").click(function(){
                 $("div.toolFormTitle").each(function(){
                     show_tool_body($(this));
@@ -163,6 +174,8 @@
 import colorsys
 import random
 
+used_accumulator = []
+
 wf_parms = {}
 for step in steps:
     for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
@@ -178,7 +191,7 @@
         hue += hue_offset
 %>
 
-<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None )">
+<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
   %if other_values is None:
       <% other_values = values %>
   %endif
@@ -196,7 +209,7 @@
             <div class="repeat-group-item"><% index = repeat_values[i]['__index__'] %><div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
-            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values )}
+            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values, already_used )}
             ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div></div>
           %endfor
@@ -207,15 +220,15 @@
       <% current_case = group_values['__current_case__'] %><% new_prefix = prefix + input.name + "|" %><% group_errors = errors.get( input.name, {} ) %>
-      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step )}
-      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values )}
+      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step, already_used )}
+      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used )}
     %else:
-      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step )}
+      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used )}
     %endif
   %endfor
 </%def>
 
-<%def name="row_for_param( param, value, other_values, error_dict, prefix, step )">
+<%def name="row_for_param( param, value, other_values, error_dict, prefix, step, already_used )">
     ## -- ${param.name} -- ${step.state.inputs} --
     %if error_dict.has_key( param.name ):
         <% cls = "form-row form-row-error" %>
@@ -235,7 +248,9 @@
                     ## FIXME: Initialize in the controller
                     <%
                     if value is None:
-                        value = other_values[ param.name ] = param.get_initial_value( t, other_values )
+                        value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                        if not enable_unique_defaults:
+                            del already_used[:]
                     %>
                     ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                     <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" />
@@ -250,7 +265,11 @@
                 ## controller should go through the inputs on the first
                 ## load, fill in initial values where needed, and mark
                 ## all that are runtime modifiable in some way.
-                <% value = other_values[ param.name ] = param.get_initial_value( t, other_values ) %>
+                <%
+                    value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                    if not enable_unique_defaults:
+                        del already_used[:]
+                %>
                 ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                 <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" />
             %else:
@@ -342,7 +361,6 @@
     });
     </script>
 %endif
-
 %for i, step in enumerate( steps ):
     %if step.type == 'tool' or step.type is None:
       <% tool = app.toolbox.tools_by_id[step.tool_id] %>
@@ -355,36 +373,36 @@
               % endif
           </div><div class="toolFormBody">
-            ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step )}
-            % if step.post_job_actions:
-                <hr/>
-                <div class='form-row'>
-                % if len(step.post_job_actions) > 1:
-                    <label>Actions:</label>
-                % else:
-                    <label>Action:</label>
+                ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
+                % if step.post_job_actions:
+                    <hr/>
+                    <div class='form-row'>
+                    % if len(step.post_job_actions) > 1:
+                        <label>Actions:</label>
+                    % else:
+                        <label>Action:</label>
+                    % endif
+                    <%
+                    pja_ss_all = []
+                    for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
+                        for rematch in re.findall('\$\{.+?\}', pja_ss):
+                            pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
+                        pja_ss_all.append(pja_ss)
+                    %>
+                    ${'<br/>'.join(pja_ss_all)}
+                    </div>
                 % endif
-                <%
-                pja_ss_all = []
-                for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
-                    for rematch in re.findall('\$\{.+?\}', pja_ss):
-                        pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
-                    pja_ss_all.append(pja_ss)
-                %>
-                ${'<br/>'.join(pja_ss_all)}
-                </div>
-            % endif
+              </div></div>
-      </div>
-    %else:
-    <% module = step.module %>
-      <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
-      <div class="toolForm">
-          <div class="toolFormTitle">
-              <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
-              % if step.annotations:
-                <div class="step-annotation">${step.annotations[0].annotation}</div>
-              % endif
+        %else:
+        <% module = step.module %>
+          <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
+          <div class="toolForm">
+              <div class="toolFormTitle">
+                  <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
+                  % if step.annotations:
+                    <div class="step-annotation">${step.annotations[0].annotation}</div>
+                  % endif
           </div><div class="toolFormBody"><%
@@ -397,7 +415,7 @@
               if not type_filter:
                   type_filter = ['data']
               %>
-              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step )}
+              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
           </div></div>
     %endif
@@ -411,10 +429,12 @@
     %endfor
     </ul>
 %else:
+    %if history_id is None:
 <p id='new_history_p'><input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label><span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span></p>
+    %endif
 <input type="submit" name="run_workflow" value="Run workflow" /></form>
 %endif


--- a/universe_wsgi.ini.sample	Thu Aug 18 14:20:48 2011 -0400
+++ b/universe_wsgi.ini.sample	Thu Aug 18 14:16:03 2011 -0700
@@ -444,6 +444,14 @@
 # large servers.
 #enable_tool_tags = False
 
+# Enable a feature when running workflows. When enabled, default datasets
+# are selected for "Set at Runtime" inputs from the history such that the
+# same input will not be selected twice, unless there are more inputs than
+# compatible datasets in the history.
+# When False, the most recently added compatible item in the history will
+# be used for each "Set at Runtime" input, independent of others in the Workflow
+#enable_unique_workflow_defaults = False
+
 # Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
 # configure an FTP server (we've used ProFTPd since it can use Galaxy's
 # database for authentication) and set the following two options.
@@ -459,6 +467,15 @@
 # Enable enforcement of quotas.  Quotas can be set from the Admin interface.
 #enable_quotas = False
 
+# Enable a feature when running workflows. When enabled, default datasets
+# are selected for "Set at Runtime" inputs from the history such that the
+# same input will not be selected twice, unless there are more inputs than
+# compatible datasets in the history.
+# When False, the most recently added compatible item in the history will
+# be used for each "Set at Runtime" input, independent of others in the Workflow
+#enable_unique_workflow_defaults = False
+
+
 # -- Job Execution
 
 # If running multiple Galaxy processes, one can be designated as the job


http://bitbucket.org/galaxy/galaxy-central/changeset/b58453168699/
changeset:   b58453168699
user:        John Duddy
date:        2011-08-18 23:38:26
summary:     Removed duplicate section (merge error)
affected #:  1 file (-1 bytes)

--- a/universe_wsgi.ini.sample	Thu Aug 18 14:16:03 2011 -0700
+++ b/universe_wsgi.ini.sample	Thu Aug 18 14:38:26 2011 -0700
@@ -444,14 +444,6 @@
 # large servers.
 #enable_tool_tags = False
 
-# Enable a feature when running workflows. When enabled, default datasets
-# are selected for "Set at Runtime" inputs from the history such that the
-# same input will not be selected twice, unless there are more inputs than
-# compatible datasets in the history.
-# When False, the most recently added compatible item in the history will
-# be used for each "Set at Runtime" input, independent of others in the Workflow
-#enable_unique_workflow_defaults = False
-
 # Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
 # configure an FTP server (we've used ProFTPd since it can use Galaxy's
 # database for authentication) and set the following two options.


http://bitbucket.org/galaxy/galaxy-central/changeset/553cdfbd3ad7/
changeset:   553cdfbd3ad7
user:        dannon
date:        2011-10-10 15:39:20
summary:     Workflow unique default inputs:  Merge in from John Duddy.
affected #:  5 files (-1 bytes)

--- a/lib/galaxy/config.py	Fri Oct 07 15:24:27 2011 -0400
+++ b/lib/galaxy/config.py	Mon Oct 10 09:39:20 2011 -0400
@@ -47,6 +47,7 @@
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
         self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' )
+        self.enable_unique_workflow_defaults = string_as_bool ( kwargs.get ('enable_unique_workflow_defaults', False ) )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )


--- a/lib/galaxy/tools/parameters/basic.py	Fri Oct 07 15:24:27 2011 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Mon Oct 10 09:39:20 2011 -0400
@@ -75,6 +75,16 @@
         """
         return None
 
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
+        """
+        Get the starting value for the parameter, but if fetching from the history, try
+        to find a value that has not yet been used. already_used is a list of objects that
+        tools must manipulate (by adding to it) to store a memento that they can use to detect
+        if a value has already been chosen from the history. This is to support the capability to
+        choose each dataset once
+        """
+        return self.get_initial_value(trans, context);
+
     def get_required_enctype( self ):
         """
         If this parameter needs the form to have a specific encoding
@@ -1389,6 +1399,9 @@
         return field
 
     def get_initial_value( self, trans, context ):
+        return self.get_initial_value_from_history_prevent_repeats(trans, context, None);
+
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
         """
         NOTE: This is wasteful since dynamic options and dataset collection
               happens twice (here and when generating HTML). 
@@ -1401,7 +1414,7 @@
         assert history is not None, "DataToolParameter requires a history"
         if self.optional:
             return None
-        most_recent_dataset = [None]
+        most_recent_dataset = []
         filter_value = None
         if self.options:
             try:
@@ -1427,15 +1440,19 @@
                             data = converted_dataset
                     if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ):
                         continue
-                    most_recent_dataset[0] = data
+                    most_recent_dataset.append(data)
                 # Also collect children via association object
                 dataset_collector( data.children )
         dataset_collector( history.datasets )
-        most_recent_dataset = most_recent_dataset.pop()
-        if most_recent_dataset is not None:
-            return most_recent_dataset
-        else:
-            return ''
+        most_recent_dataset.reverse()
+        if already_used is not None:
+            for val in most_recent_dataset:
+                if val is not None and val not in already_used:
+                    already_used.append(val)
+                    return val
+        if len(most_recent_dataset) > 0:
+            return most_recent_dataset[0]
+        return ''
 
     def from_html( self, value, trans, other_values={} ):
         # Can't look at history in workflow mode, skip validation and such,


--- a/lib/galaxy/web/controllers/workflow.py	Fri Oct 07 15:24:27 2011 -0400
+++ b/lib/galaxy/web/controllers/workflow.py	Mon Oct 10 09:39:20 2011 -0400
@@ -1258,7 +1258,7 @@
             ##     % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) )       
         
     @web.expose
-    def run( self, trans, id, **kwargs ):
+    def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ):
         stored = self.get_stored_workflow( trans, id, check_ownership=False )
         user = trans.get_user()
         if stored.user != user:
@@ -1279,163 +1279,185 @@
         errors = {}
         has_upgrade_messages = False
         has_errors = False
-        if kwargs:
-            # If kwargs were provided, the states for each step should have
-            # been POSTed
-            # Get the kwarg keys for data inputs
-            input_keys = filter(lambda a: a.endswith('|input'), kwargs)
-            # Example: prefixed='2|input'
-            # Check if one of them is a list
-            multiple_input_key = None
-            multiple_inputs = [None]
-            for input_key in input_keys:
-                if isinstance(kwargs[input_key], list):
-                    multiple_input_key = input_key
-                    multiple_inputs = kwargs[input_key]
-            # List to gather values for the template
-            invocations=[]
-            for input_number, single_input in enumerate(multiple_inputs):
-                # Example: single_input='1', single_input='2', etc...
-                # 'Fix' the kwargs, to have only the input for this iteration
-                if multiple_input_key:
-                    kwargs[multiple_input_key] = single_input
+        saved_history = None
+        if history_id is not None:
+            saved_history = trans.get_history();
+            try:
+                decoded_history_id = trans.security.decode_id( history_id )
+                history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+                if history.user != trans.user and not trans.user_is_admin():
+                    if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                        error("History is not owned by or shared with current user")
+                trans.set_history(history)
+            except TypeError:
+                error("Malformed history id ( %s ) specified, unable to decode." % str( history_id ))
+            except:
+                error("That history does not exist.")
+        try: # use a try/finally block to restore the user's current history
+            if kwargs:
+                # If kwargs were provided, the states for each step should have
+                # been POSTed
+                # Get the kwarg keys for data inputs
+                input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+                # Example: prefixed='2|input'
+                # Check if one of them is a list
+                multiple_input_key = None
+                multiple_inputs = [None]
+                for input_key in input_keys:
+                    if isinstance(kwargs[input_key], list):
+                        multiple_input_key = input_key
+                        multiple_inputs = kwargs[input_key]
+                # List to gather values for the template
+                invocations=[]
+                for input_number, single_input in enumerate(multiple_inputs):
+                    # Example: single_input='1', single_input='2', etc...
+                    # 'Fix' the kwargs, to have only the input for this iteration
+                    if multiple_input_key:
+                        kwargs[multiple_input_key] = single_input
+                    for step in workflow.steps:
+                        step.upgrade_messages = {}
+                        # Connections by input name
+                        step.input_connections_by_name = \
+                            dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                        # Extract just the arguments for this step by prefix
+                        p = "%s|" % step.id
+                        l = len(p)
+                        step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
+                        step_errors = None
+                        if step.type == 'tool' or step.type is None:
+                            module = module_factory.from_workflow_step( trans, step )
+                            # Fix any missing parameters
+                            step.upgrade_messages = module.check_and_update_state()
+                            if step.upgrade_messages:
+                                has_upgrade_messages = True
+                            # Any connected input needs to have value DummyDataset (these
+                            # are not persisted so we need to do it every time)
+                            module.add_dummy_datasets( connections=step.input_connections )    
+                            # Get the tool
+                            tool = module.tool
+                            # Get the state
+                            step.state = state = module.state
+                            # Get old errors
+                            old_errors = state.inputs.pop( "__errors__", {} )
+                            # Update the state
+                            step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
+                                                             update_only=True, old_errors=old_errors )
+                        else:
+                            # Fix this for multiple inputs
+                            module = step.module = module_factory.from_workflow_step( trans, step )
+                            state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
+                            step_errors = module.update_runtime_state( trans, state, step_args )
+                        if step_errors:
+                            errors[step.id] = state.inputs["__errors__"] = step_errors   
+                    if 'run_workflow' in kwargs and not errors:
+                        new_history = None
+                        if 'new_history' in kwargs:
+                            if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
+                                nh_name = kwargs['new_history_name']
+                            else:
+                                nh_name = "History from %s workflow" % workflow.name
+                            if multiple_input_key:
+                                nh_name = '%s %d' % (nh_name, input_number + 1)
+                            new_history = trans.app.model.History( user=trans.user, name=nh_name )
+                            trans.sa_session.add( new_history )
+                        # Run each step, connecting outputs to inputs
+                        workflow_invocation = model.WorkflowInvocation()
+                        workflow_invocation.workflow = workflow
+                        outputs = odict()
+                        for i, step in enumerate( workflow.steps ):
+                            # Execute module
+                            job = None
+                            if step.type == 'tool' or step.type is None:
+                                tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                                input_values = step.state.inputs
+                                # Connect up
+                                def callback( input, value, prefixed_name, prefixed_label ):
+                                    if isinstance( input, DataToolParameter ):
+                                        if prefixed_name in step.input_connections_by_name:
+                                            conn = step.input_connections_by_name[ prefixed_name ]
+                                            return outputs[ conn.output_step.id ][ conn.output_name ]
+                                visit_input_values( tool.inputs, step.state.inputs, callback )
+                                # Execute it
+                                job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
+                                outputs[ step.id ] = out_data
+                                # Create new PJA associations with the created job, to be run on completion.
+                                # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
+                                # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
+                                replacement_dict = {}
+                                for k, v in kwargs.iteritems():
+                                    if k.startswith('wf_parm|'):
+                                        replacement_dict[k[8:]] = v
+                                for pja in step.post_job_actions:
+                                    if pja.action_type in ActionBox.immediate_actions:
+                                        ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
+                                    else:
+                                        job.add_post_job_action(pja)
+                            else:
+                                job, out_data = step.module.execute( trans, step.state )
+                                outputs[ step.id ] = out_data
+                            # Record invocation
+                            workflow_invocation_step = model.WorkflowInvocationStep()
+                            workflow_invocation_step.workflow_invocation = workflow_invocation
+                            workflow_invocation_step.workflow_step = step
+                            workflow_invocation_step.job = job
+                        # All jobs ran sucessfully, so we can save now
+                        trans.sa_session.add( workflow_invocation )
+                        invocations.append({'outputs': outputs,
+                                            'new_history': new_history})
+                trans.sa_session.flush()
+                return trans.fill_template( "workflow/run_complete.mako",
+                                            workflow=stored,
+                                            invocations=invocations )
+            else:
+                # Prepare each step
+                missing_tools = []
                 for step in workflow.steps:
                     step.upgrade_messages = {}
-                    # Connections by input name
-                    step.input_connections_by_name = \
-                        dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
-                    # Extract just the arguments for this step by prefix
-                    p = "%s|" % step.id
-                    l = len(p)
-                    step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
-                    step_errors = None
+                    # Contruct modules
                     if step.type == 'tool' or step.type is None:
-                        module = module_factory.from_workflow_step( trans, step )
-                        # Fix any missing parameters
-                        step.upgrade_messages = module.check_and_update_state()
+                        # Restore the tool state for the step
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        if not step.module:
+                            if step.tool_id not in missing_tools:
+                                missing_tools.append(step.tool_id)
+                            continue
+                        step.upgrade_messages = step.module.check_and_update_state()
                         if step.upgrade_messages:
                             has_upgrade_messages = True
                         # Any connected input needs to have value DummyDataset (these
                         # are not persisted so we need to do it every time)
-                        module.add_dummy_datasets( connections=step.input_connections )    
-                        # Get the tool
-                        tool = module.tool
-                        # Get the state
-                        step.state = state = module.state
-                        # Get old errors
-                        old_errors = state.inputs.pop( "__errors__", {} )
-                        # Update the state
-                        step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
-                                                         update_only=True, old_errors=old_errors )
+                        step.module.add_dummy_datasets( connections=step.input_connections )                  
+                        # Store state with the step
+                        step.state = step.module.state
+                        # Error dict
+                        if step.tool_errors:
+                            has_errors = True
+                            errors[step.id] = step.tool_errors
                     else:
-                        # Fix this for multiple inputs
-                        module = step.module = module_factory.from_workflow_step( trans, step )
-                        state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
-                        step_errors = module.update_runtime_state( trans, state, step_args )
-                    if step_errors:
-                        errors[step.id] = state.inputs["__errors__"] = step_errors   
-                if 'run_workflow' in kwargs and not errors:
-                    new_history = None
-                    if 'new_history' in kwargs:
-                        if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
-                            nh_name = kwargs['new_history_name']
-                        else:
-                            nh_name = "History from %s workflow" % workflow.name
-                        if multiple_input_key:
-                            nh_name = '%s %d' % (nh_name, input_number + 1)
-                        new_history = trans.app.model.History( user=trans.user, name=nh_name )
-                        trans.sa_session.add( new_history )
-                    # Run each step, connecting outputs to inputs
-                    workflow_invocation = model.WorkflowInvocation()
-                    workflow_invocation.workflow = workflow
-                    outputs = odict()
-                    for i, step in enumerate( workflow.steps ):
-                        # Execute module
-                        job = None
-                        if step.type == 'tool' or step.type is None:
-                            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
-                            input_values = step.state.inputs
-                            # Connect up
-                            def callback( input, value, prefixed_name, prefixed_label ):
-                                if isinstance( input, DataToolParameter ):
-                                    if prefixed_name in step.input_connections_by_name:
-                                        conn = step.input_connections_by_name[ prefixed_name ]
-                                        return outputs[ conn.output_step.id ][ conn.output_name ]
-                            visit_input_values( tool.inputs, step.state.inputs, callback )
-                            # Execute it
-                            job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
-                            outputs[ step.id ] = out_data
-                            # Create new PJA associations with the created job, to be run on completion.
-                            # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
-                            # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-                            replacement_dict = {}
-                            for k, v in kwargs.iteritems():
-                                if k.startswith('wf_parm|'):
-                                    replacement_dict[k[8:]] = v
-                            for pja in step.post_job_actions:
-                                if pja.action_type in ActionBox.immediate_actions:
-                                    ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
-                                else:
-                                    job.add_post_job_action(pja)
-                        else:
-                            job, out_data = step.module.execute( trans, step.state )
-                            outputs[ step.id ] = out_data
-                        # Record invocation
-                        workflow_invocation_step = model.WorkflowInvocationStep()
-                        workflow_invocation_step.workflow_invocation = workflow_invocation
-                        workflow_invocation_step.workflow_step = step
-                        workflow_invocation_step.job = job
-                    # All jobs ran sucessfully, so we can save now
-                    trans.sa_session.add( workflow_invocation )
-                    invocations.append({'outputs': outputs,
-                                        'new_history': new_history})
-            trans.sa_session.flush()
-            return trans.fill_template( "workflow/run_complete.mako",
-                                        workflow=stored,
-                                        invocations=invocations )
-        else:
-            # Prepare each step
-            missing_tools = []
-            for step in workflow.steps:
-                step.upgrade_messages = {}
-                # Contruct modules
-                if step.type == 'tool' or step.type is None:
-                    # Restore the tool state for the step
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    if not step.module:
-                        if step.tool_id not in missing_tools:
-                            missing_tools.append(step.tool_id)
-                        continue
-                    step.upgrade_messages = step.module.check_and_update_state()
-                    if step.upgrade_messages:
-                        has_upgrade_messages = True
-                    # Any connected input needs to have value DummyDataset (these
-                    # are not persisted so we need to do it every time)
-                    step.module.add_dummy_datasets( connections=step.input_connections )                  
-                    # Store state with the step
-                    step.state = step.module.state
-                    # Error dict
-                    if step.tool_errors:
-                        has_errors = True
-                        errors[step.id] = step.tool_errors
-                else:
-                    ## Non-tool specific stuff?
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    step.state = step.module.get_runtime_state()
-                # Connections by input name
-                step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
-            if missing_tools:
-                stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-                return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
-        # Render the form
-        stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-        return trans.fill_template(
-                    "workflow/run.mako", 
-                    steps=workflow.steps,
-                    workflow=stored,
-                    has_upgrade_messages=has_upgrade_messages,
-                    errors=errors,
-                    incoming=kwargs )
+                        ## Non-tool specific stuff?
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        step.state = step.module.get_runtime_state()
+                    # Connections by input name
+                    step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
+                if missing_tools:
+                    stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+                    return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
+            # Render the form
+            stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+            return trans.fill_template(
+                        "workflow/run.mako", 
+                        steps=workflow.steps,
+                        workflow=stored,
+                        has_upgrade_messages=has_upgrade_messages,
+                        errors=errors,
+                        incoming=kwargs,
+                        history_id=history_id,
+                        hide_fixed_params=hide_fixed_params,
+                        enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
+        finally:
+            # restore the active history
+            if saved_history is not None:
+                trans.set_history(saved_history) 
                     
     def get_item( self, trans, id ):
         return self.get_stored_workflow( trans, id ) 


--- a/templates/workflow/run.mako	Fri Oct 07 15:24:27 2011 -0400
+++ b/templates/workflow/run.mako	Mon Oct 10 09:39:20 2011 -0400
@@ -6,8 +6,12 @@
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
-                title.parent().css('border-bottom-width', '1px');
+                title.parent().show().css('border-bottom-width', '1px');
                 title.next().show('fast');
+                if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                    // show previously hidden parameters
+                    title.next().children(".form-row").show();
+                }
             }
             function hide_tool_body(title){
                 title.parent().css('border-bottom-width', '0px');
@@ -46,8 +50,15 @@
             $("div.toolFormTitle").click(function(){
                 toggle_tool_body($(this));
             });
-            // Collapse non-interactive run-workflow panels by default.
-            $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                // hide parameters that are not runtime inputs
+                $("div.form-row:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+                $("div.toolForm:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+            }
+            else {
+                // Collapse non-interactive run-workflow panels by default.
+                $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            }
             $("#show_all_tool_body").click(function(){
                 $("div.toolFormTitle").each(function(){
                     show_tool_body($(this));
@@ -163,6 +174,8 @@
 import colorsys
 import random
 
+used_accumulator = []
+
 wf_parms = {}
 for step in steps:
     for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
@@ -178,7 +191,7 @@
         hue += hue_offset
 %>
 
-<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None )">
+<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
   %if other_values is None:
       <% other_values = values %>
   %endif
@@ -196,7 +209,7 @@
             <div class="repeat-group-item"><% index = repeat_values[i]['__index__'] %><div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
-            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values )}
+            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values, already_used )}
             ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div></div>
           %endfor
@@ -207,15 +220,15 @@
       <% current_case = group_values['__current_case__'] %><% new_prefix = prefix + input.name + "|" %><% group_errors = errors.get( input.name, {} ) %>
-      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step )}
-      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values )}
+      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step, already_used )}
+      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used )}
     %else:
-      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step )}
+      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used )}
     %endif
   %endfor
 </%def>
 
-<%def name="row_for_param( param, value, other_values, error_dict, prefix, step )">
+<%def name="row_for_param( param, value, other_values, error_dict, prefix, step, already_used )">
     ## -- ${param.name} -- ${step.state.inputs} --
     %if error_dict.has_key( param.name ):
         <% cls = "form-row form-row-error" %>
@@ -235,7 +248,9 @@
                     ## FIXME: Initialize in the controller
                     <%
                     if value is None:
-                        value = other_values[ param.name ] = param.get_initial_value( t, other_values )
+                        value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                        if not enable_unique_defaults:
+                            del already_used[:]
                     %>
                     ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                     <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" />
@@ -250,7 +265,11 @@
                 ## controller should go through the inputs on the first
                 ## load, fill in initial values where needed, and mark
                 ## all that are runtime modifiable in some way.
-                <% value = other_values[ param.name ] = param.get_initial_value( t, other_values ) %>
+                <%
+                    value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                    if not enable_unique_defaults:
+                        del already_used[:]
+                %>
                 ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                 <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" />
             %else:
@@ -342,7 +361,6 @@
     });
     </script>
 %endif
-
 %for i, step in enumerate( steps ):
     %if step.type == 'tool' or step.type is None:
       <% tool = app.toolbox.tools_by_id[step.tool_id] %>
@@ -355,36 +373,36 @@
               % endif
           </div><div class="toolFormBody">
-            ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step )}
-            % if step.post_job_actions:
-                <hr/>
-                <div class='form-row'>
-                % if len(step.post_job_actions) > 1:
-                    <label>Actions:</label>
-                % else:
-                    <label>Action:</label>
+                ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
+                % if step.post_job_actions:
+                    <hr/>
+                    <div class='form-row'>
+                    % if len(step.post_job_actions) > 1:
+                        <label>Actions:</label>
+                    % else:
+                        <label>Action:</label>
+                    % endif
+                    <%
+                    pja_ss_all = []
+                    for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
+                        for rematch in re.findall('\$\{.+?\}', pja_ss):
+                            pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
+                        pja_ss_all.append(pja_ss)
+                    %>
+                    ${'<br/>'.join(pja_ss_all)}
+                    </div>
                 % endif
-                <%
-                pja_ss_all = []
-                for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
-                    for rematch in re.findall('\$\{.+?\}', pja_ss):
-                        pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
-                    pja_ss_all.append(pja_ss)
-                %>
-                ${'<br/>'.join(pja_ss_all)}
-                </div>
-            % endif
+              </div></div>
-      </div>
-    %else:
-    <% module = step.module %>
-      <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
-      <div class="toolForm">
-          <div class="toolFormTitle">
-              <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
-              % if step.annotations:
-                <div class="step-annotation">${step.annotations[0].annotation}</div>
-              % endif
+        %else:
+        <% module = step.module %>
+          <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
+          <div class="toolForm">
+              <div class="toolFormTitle">
+                  <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
+                  % if step.annotations:
+                    <div class="step-annotation">${step.annotations[0].annotation}</div>
+                  % endif
           </div><div class="toolFormBody"><%
@@ -397,7 +415,7 @@
               if not type_filter:
                   type_filter = ['data']
               %>
-              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step )}
+              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
           </div></div>
     %endif
@@ -411,10 +429,12 @@
     %endfor
     </ul>
 %else:
+    %if history_id is None:
 <p id='new_history_p'><input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label><span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span></p>
+    %endif
 <input type="submit" name="run_workflow" value="Run workflow" /></form>
 %endif


--- a/universe_wsgi.ini.sample	Fri Oct 07 15:24:27 2011 -0400
+++ b/universe_wsgi.ini.sample	Mon Oct 10 09:39:20 2011 -0400
@@ -461,6 +461,15 @@
 # Enable enforcement of quotas.  Quotas can be set from the Admin interface.
 #enable_quotas = False
 
+# Enable a feature when running workflows. When enabled, default datasets
+# are selected for "Set at Runtime" inputs from the history such that the
+# same input will not be selected twice, unless there are more inputs than
+# compatible datasets in the history.
+# When False, the most recently added compatible item in the history will
+# be used for each "Set at Runtime" input, independent of others in the Workflow
+#enable_unique_workflow_defaults = False
+
+
 # -- Job Execution
 
 # If running multiple Galaxy processes, one can be designated as the job

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 3 new changesets

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