Tool form section tag

client/galaxy/scripts/mvc/form/form-data.js

@@ -96,9 +96,9 @@ return Backbone.Model.extend({
                                 convert(job_input_id, head[input.id + '-section-' + selectedCase]);
                             }
                             break;
-                        // handle custom sub sections
+                        // handle sections
                         case 'section':
-                            convert('', node);
+                            convert(job_input_id, node);
                             break;
                         default:
                             // get field
@@ -191,6 +191,9 @@ return Backbone.Model.extend({
                             search (index, node.cases[selectedCase].inputs);
                         }
                         break;
+                    case 'section':
+                        search (index, node.inputs);
+                        break;
                     default:
                         var input_id = self.map_dict[index];
                         if (input_id) {

client/galaxy/scripts/mvc/form/form-section.js

@@ -286,7 +286,7 @@ define(['utils/utils',
             });
 
             // show sub section if requested
-            if (input_def.expand) {
+            if (input_def.expanded) {
                 portlet.$header.trigger('click');
             }
 

client/galaxy/scripts/mvc/form/form-view.js

@@ -200,6 +200,13 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                 inputs : this.options.inputs
             });
 
+            // switch to classic tool form mako if the form definition is incompatible
+            if (this.incompatible) {
+                this.$el.hide();
+                $('#tool-form-classic').show();
+                return;
+            }
+
             // create portlet
             this.portlet = new Portlet.View({
                 icon        : 'fa-wrench',

lib/galaxy/tools/__init__.py

@@ -40,7 +40,7 @@
                                            DataToolParameter, DataCollectionToolParameter, HiddenToolParameter, LibraryDatasetToolParameter,
                                            SelectToolParameter, ToolParameter, UnvalidatedValue,
                                            IntegerToolParameter, FloatToolParameter)
-from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, UploadDataset
+from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.output import ToolOutputActionGroup
 from galaxy.tools.parameters.validation import LateValidationError
@@ -972,6 +972,15 @@ def parse_input_elem( self, page_source, enctypes, context=None ):
                         case.inputs = odict()
                         group.cases.append( case )
                 rval[group.name] = group
+            elif input_type == "section":
+                group = Section()
+                group.name = input_source.get( "name" )
+                group.title = input_source.get( "title" )
+                group.help = input_source.get( "help", None )
+                group.expanded = input_source.get_bool( "expanded", False )
+                page_source = input_source.parse_nested_inputs_source()
+                group.inputs = self.parse_input_elem( page_source, enctypes, context )
+                rval[group.name] = group
             elif input_type == "upload_dataset":
                 elem = input_source.elem()
                 group = UploadDataset()
@@ -1505,6 +1514,20 @@ def populate_state( self, trans, inputs, state, incoming, history=None, source="
                     group_state['__current_case__'] = current_case
                     # Store the value of the test element
                     group_state[ input.test_param.name ] = value
+            elif isinstance( input, Section ):
+                group_state = state[input.name]
+                group_prefix = "%s|" % ( key )
+                self.fill_in_new_state( trans, input.inputs, group_state, context, history=history )
+                group_errors = self.populate_state( trans,
+                                                    input.inputs,
+                                                    group_state,
+                                                    incoming,
+                                                    history,
+                                                    source,
+                                                    prefix=group_prefix,
+                                                    context=context )
+                if group_errors:
+                    errors[ input.name ] = group_errors
             elif isinstance( input, UploadDataset ):
                 group_state = state[input.name]
                 group_errors = []
@@ -1714,6 +1737,22 @@ def update_state( self, trans, inputs, state, incoming, source='html', prefix=""
                 group_state['__current_case__'] = current_case
                 # Store the value of the test element
                 group_state[ input.test_param.name ] = value
+            elif isinstance( input, Section ):
+                group_state = state[input.name]
+                group_old_errors = old_errors.get( input.name, {} )
+                group_prefix = "%s|" % ( key )
+                group_errors = self.update_state( trans,
+                                                  input.inputs,
+                                                  group_state,
+                                                  incoming,
+                                                  prefix=group_prefix,
+                                                  context=context,
+                                                  source=source,
+                                                  update_only=update_only,
+                                                  old_errors=group_old_errors,
+                                                  item_callback=item_callback )
+                if group_errors:
+                    errors[ input.name ] = group_errors
             elif isinstance( input, UploadDataset ):
                 group_state = state[input.name]
                 group_errors = []
@@ -2383,6 +2422,10 @@ def populate_state(trans, inputs, state, errors, incoming, prefix="", context=No
                             errors[test_param_key] = 'The selected case is unavailable/invalid.'
                             pass
                     group_state[input.test_param.name] = value
+                elif input.type == 'section':
+                    group_state = state[input.name]
+                    group_prefix = "%s|" % ( key )
+                    populate_state(trans, input.inputs, group_state, errors, incoming, prefix=group_prefix, context=context)
                 else:
                     default_value = incoming.get(key, state.get(input.name, None))
                     value, error = check_state(trans, input, default_value, context)
@@ -2417,6 +2460,8 @@ def iterate(group_inputs, inputs, state_inputs, other_values=None):
                             if i == group_state.get('__current_case__', None):
                                 current_state = group_state
                             iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values)
+                elif input.type == 'section':
+                    iterate( tool_dict['inputs'], input.inputs, group_state, other_values )
                 else:
                     # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options
                     try:

lib/galaxy/tools/evaluation.py

@@ -22,7 +22,7 @@
     LibraryDatasetToolParameter,
     SelectToolParameter,
 )
-from galaxy.tools.parameters.grouping import Conditional, Repeat
+from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
 from galaxy.jobs.datasets import dataset_path_rewrites
 
 import logging
@@ -143,6 +143,9 @@ def do_walk( inputs, input_values ):
                     values = input_values[ input.name ]
                     current = values["__current_case__"]
                     do_walk( input.cases[current].inputs, values )
+                elif isinstance( input, Section ):
+                    values = input_values[ input.name ]
+                    do_walk( input.inputs, values )
                 else:
                     func( input_values, input )
 

lib/galaxy/tools/parameters/__init__.py

@@ -33,6 +33,11 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
             label_prefix = label_prefix
             new_name_prefix = name_prefix + input.name + "|"
             visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix )
+        elif isinstance( input, Section ):
+            values = input_values[ input.name ]
+            label_prefix = label_prefix
+            new_name_prefix = name_prefix + input.name + "|"
+            visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix )
         else:
             new_value = callback( input,
                                   input_values[input.name],
@@ -124,6 +129,10 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="", to_
             new_name_prefix = name_prefix + input.name + "|"
             incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ]
             params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix, to_html=to_html )
+        elif isinstance( input, Section ):
+            values = input_values[ input.name ]
+            new_name_prefix = name_prefix + input.name + "|"
+            params_to_incoming( incoming, input.inputs, values, app, new_name_prefix, to_html=to_html )
         else:
             value = input_values.get( input.name )
             if to_html:

lib/galaxy/tools/parameters/grouping.py

@@ -129,6 +129,55 @@ def input_to_dict( input ):
         repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() )
         return repeat_dict
 
+class Section( Group ):
+
+    dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'expanded')
+
+    type = "section"
+    def __init__( self ):
+        Group.__init__( self )
+        self.title = None
+        self.inputs = None
+        self.help = None
+        self.expanded = False
+    @property
+    def title_plural( self ):
+        return inflector.pluralize( self.title )
+    def label( self ):
+        return "Section (%s)" % self.title
+    def value_to_basic( self, value, app ):
+        rval = {}
+        for input in self.inputs.itervalues():
+            rval[ input.name ] = input.value_to_basic( value[input.name], app )
+        return rval
+    def value_from_basic( self, value, app, ignore_errors=False ):
+        rval = {}
+        try:
+            for input in self.inputs.itervalues():
+                if not ignore_errors or input.name in value:
+                    rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors )
+        except Exception, e:
+            if not ignore_errors:
+                raise e
+        return rval
+    def visit_inputs( self, prefix, value, callback ):
+        for input in self.inputs.itervalues():
+            if isinstance( input, ToolParameter ):
+                callback( prefix, input, value[input.name], parent = value )
+            else:
+                input.visit_inputs( prefix, value[input.name], callback )
+    def get_initial_value( self, trans, context, history=None ):
+        rval = {}
+        child_context = ExpressionContext( rval, context )
+        for child_input in self.inputs.itervalues():
+            rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history )
+        return rval
+    def to_dict( self, trans, view='collection', value_mapper=None ):
+        section_dict = super( Section, self ).to_dict( trans, view=view, value_mapper=value_mapper )
+        def input_to_dict( input ):
+            return input.to_dict( trans, view=view, value_mapper=value_mapper )
+        section_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() )
+        return section_dict
 
 class UploadDataset( Group ):
     type = "upload_dataset"

lib/galaxy/tools/parameters/wrapped.py

@@ -8,6 +8,7 @@
 from galaxy.tools.parameters.grouping import (
     Repeat,
     Conditional,
+    Section
 )
 PARAMS_UNWRAPPED = object()
 
@@ -44,6 +45,9 @@ def wrap_values( self, inputs, input_values, skip_missing_values=False ):
                 values = input_values[ input.name ]
                 current = values[ "__current_case__" ]
                 self.wrap_values( input.cases[current].inputs, values, skip_missing_values=skip_missing_values )
+            elif isinstance( input, Section ):
+                values = input_values[ input.name ]
+                self.wrap_values( input.inputs, values, skip_missing_values=skip_missing_values )
             elif isinstance( input, DataToolParameter ) and input.multiple:
                 input_values[ input.name ] = \
                     galaxy.tools.DatasetListWrapper( input_values[ input.name ],

lib/galaxy/tools/parser/xml.py

@@ -422,6 +422,13 @@ def __expand_input_elems( root_elem, prefix="" ):
         __pull_up_params( root_elem, cond_elem )
         root_elem.remove( cond_elem )
 
+    section_elems = root_elem.findall( 'section' )
+    for section_elem in section_elems:
+        new_prefix = __prefix_join( prefix, section_elem.get( "name" ) )
+        __expand_input_elems( section_elem, new_prefix )
+        __pull_up_params( root_elem, section_elem )
+        root_elem.remove( section_elem )
+
 
 def __append_prefix_to_params( elem, prefix ):
     for param_elem in elem.findall( 'param' ):

lib/galaxy/tools/test.py

@@ -166,7 +166,12 @@ def __process_raw_inputs( self, tool_inputs, raw_inputs, parent_context=None ):
                         # an infinite loop - hence the "case_value is not None"
                         # check.
                         expanded_inputs[ case_context.for_state() ] = expanded_case_value
-
+            elif isinstance( value, galaxy.tools.parameters.grouping.Section ):
+                context = ParamContext( name=value.name, parent_context=parent_context )
+                for r_name, r_value in value.inputs.iteritems():
+                    expanded_input = self.__process_raw_inputs( { context.for_state(): r_value }, raw_inputs, parent_context=context )
+                    if expanded_input:
+                        expanded_inputs.update( expanded_input )
             elif isinstance( value, galaxy.tools.parameters.grouping.Repeat ):
                 repeat_index = 0
                 while True: