Remove former populate_state

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

@@ -7,7 +7,7 @@ define(['utils/utils',
         'mvc/ui/ui-select-library',
         'mvc/ui/ui-select-ftp',
         'mvc/ui/ui-color-picker'],
-    function(Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker) {
+    function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker ) {
 
     // create form view
     return Backbone.Model.extend({
@@ -31,50 +31,30 @@ define(['utils/utils',
             'ftpfile'           : '_fieldFtp'
         },
 
-        // initialize
-        initialize: function(app, options) {
+        initialize: function( app, options ) {
             this.app = app;
         },
 
         /** Returns an input field for a given field type
         */
-        create: function(input_def) {
-            // add regular/default value if missing
-            if (input_def.value === undefined) {
-                input_def.value = null;
-            }
-            if (input_def.default_value === undefined) {
-                input_def.default_value = input_def.value;
-            }
-
-            // create field wrapper
-            var field = null;
-            var fieldClass = this.types[input_def.type];
-            if (fieldClass && typeof(this[fieldClass]) === 'function') {
-                field = this[fieldClass].call(this, input_def);
-            }
-
-            // match unavailable field types
-            if (!field) {
+        create: function( input_def ) {
+            var fieldClass = this.types[ input_def.type ];
+            var field = typeof( this[ fieldClass ] ) === 'function' ? this[ fieldClass ].call( this, input_def ) : null;
+            if ( !field ) {
                 this.app.incompatible = true;
-                if (input_def.options) {
-                    field = this._fieldSelect(input_def);
-                } else {
-                    field = this._fieldText(input_def);
-                }
+                field = input_def.options ? this._fieldSelect( input_def ) : this._fieldText( input_def );
                 Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');
             }
-
-            // set initial field value
-            input_def.value !== undefined && ( field.value( input_def.value ) );
+            input_def.value === undefined && ( input_def.value = null );
+            field.value( input_def.value );
             return field;
         },
 
         /** Data input field
         */
-        _fieldData: function(input_def) {
+        _fieldData: function( input_def ) {
             var self = this;
-            return new SelectContent.View(this.app, {
+            return new SelectContent.View( this.app, {
                 id          : 'field-' + input_def.id,
                 extensions  : input_def.extensions,
                 optional    : input_def.optional,
@@ -82,37 +62,33 @@ define(['utils/utils',
                 type        : input_def.type,
                 data        : input_def.options,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Select/Checkbox/Radio options field
         */
-        _fieldSelect: function (input_def) {
+        _fieldSelect: function ( input_def ) {
             // show text field e.g. in workflow editor
             if( input_def.is_workflow ) {
                 return this._fieldText( input_def );
             }
 
             // customize properties
-            if (input_def.type == 'data_column') {
+            if ( input_def.type == 'data_column' ) {
                 input_def.error_text = 'Missing columns in referenced dataset.'
             }
 
             // configure options fields
             var options = [];
-            for (var i in input_def.options) {
-                var option = input_def.options[i];
-                options.push({
-                    label: option[0],
-                    value: option[1]
-                });
-            }
+            _.each( input_def.options, function( option ) {
+                options.push( { label: option[ 0 ], value: option[ 1 ] } );
+            });
 
             // identify display type
             var SelectClass = Ui.Select;
-            switch (input_def.display) {
+            switch ( input_def.display ) {
                 case 'checkboxes':
                     SelectClass = Ui.Checkbox;
                     break;
@@ -127,19 +103,18 @@ define(['utils/utils',
                 id          : 'field-' + input_def.id,
                 data        : options,
                 error_text  : input_def.error_text || 'No options available',
-                optional    : input_def.optional && input_def.default_value === null,
                 multiple    : input_def.multiple,
                 optional    : input_def.optional,
                 searchable  : input_def.searchable,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Drill down options field
         */
-        _fieldDrilldown: function (input_def) {
+        _fieldDrilldown: function ( input_def ) {
             // show text field e.g. in workflow editor
             if( input_def.is_workflow ) {
                 return this._fieldText( input_def );
@@ -152,25 +127,25 @@ define(['utils/utils',
                 data        : input_def.options,
                 display     : input_def.display,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Text input field
         */
-        _fieldText: function(input_def) {
+        _fieldText: function( input_def ) {
             // field replaces e.g. a select field
-            if (input_def.options) {
+            if ( input_def.options ) {
                 input_def.area = input_def.multiple;
-                if (!Utils.validate(input_def.value)) {
+                if ( !Utils.validate( input_def.value ) ) {
                     input_def.value = null;
                 } else {
-                    if ($.isArray(input_def.value)) {
+                    if ( $.isArray( input_def.value ) ) {
                         var str_value = '';
-                        for (var i in input_def.value) {
-                            str_value += String(input_def.value[i]);
-                            if (!input_def.multiple) {
+                        for ( var i in input_def.value ) {
+                            str_value += String( input_def.value[ i ] );
+                            if ( !input_def.multiple ) {
                                 break;
                             }
                             str_value += '\n';
@@ -192,7 +167,7 @@ define(['utils/utils',
 
         /** Slider field
         */
-        _fieldSlider: function(input_def) {
+        _fieldSlider: function( input_def ) {
             var self = this;
             return new Ui.Slider.View({
                 id          : 'field-' + input_def.id,
@@ -201,14 +176,14 @@ define(['utils/utils',
                 min         : input_def.min,
                 max         : input_def.max,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Hidden field
         */
-        _fieldHidden: function(input_def) {
+        _fieldHidden: function( input_def ) {
             return new Ui.Hidden({
                 id          : 'field-' + input_def.id,
                 info        : input_def.info
@@ -217,54 +192,54 @@ define(['utils/utils',
 
         /** Boolean field
         */
-        _fieldBoolean: function(input_def) {
+        _fieldBoolean: function( input_def ) {
             var self = this;
             return new Ui.RadioButton.View({
                 id          : 'field-' + input_def.id,
                 data        : [ { label : 'Yes', value : 'true'  },
                                 { label : 'No',  value : 'false' }],
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Color picker field
         */
-        _fieldColor: function(input_def) {
+        _fieldColor: function( input_def ) {
             var self = this;
             return new ColorPicker({
                 id          : 'field-' + input_def.id,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** Library dataset field
         */
-        _fieldLibrary: function(input_def) {
+        _fieldLibrary: function( input_def ) {
             var self = this;
             return new SelectLibrary.View({
                 id          : 'field-' + input_def.id,
                 optional    : input_def.optional,
                 multiple    : input_def.multiple,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         },
 
         /** FTP file field
         */
-        _fieldFtp: function(input_def) {
+        _fieldFtp: function( input_def ) {
             var self = this;
             return new SelectFtp.View({
                 id          : 'field-' + input_def.id,
                 optional    : input_def.optional,
                 multiple    : input_def.multiple,
                 onchange    : function() {
-                    self.app.trigger('change');
+                    self.app.trigger( 'change' );
                 }
             });
         }

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

@@ -231,7 +231,6 @@ define(['utils/utils',
                 name                : input_def.name,
                 label               : input_def.label || input_def.name,
                 value               : input_def.value,
-                default_value       : input_def.default_value,
                 text_value          : input_def.text_value || input_def.value,
                 collapsible_value   : input_def.collapsible_value,
                 collapsible_preview : input_def.collapsible_preview,

client/galaxy/scripts/utils/utils.js

@@ -48,15 +48,12 @@ function sanitize(content) {
  * usually used for selectable options
  * @param{String}   value - Value or list to be validated
  */
-function validate (value) {
-    if (!(value instanceof Array)) {
-        value = [value];
+function validate ( value ) {
+    if ( !( value instanceof Array ) ) {
+        value = [ value ];
     }
-    if (value.length === 0) {
-        return false;
-    }
-    for (var i in value) {
-        if (['__null__', '__undefined__', null, undefined].indexOf(value[i]) > -1) {
+    for( var i in value ) {
+        if ( [ '__null__', '__undefined__', null, undefined ].indexOf( value[ i ] ) > -1 ) {
             return false;
         }
     }

lib/galaxy/tools/__init__.py

@@ -1108,7 +1108,7 @@ class Tool( object, Dictifiable ):
             else:
                 input.visit_inputs( "", value[input.name], callback )
 
-    def handle_input( self, trans, incoming, history=None, source='html' ):
+    def handle_input( self, trans, incoming, history=None ):
         """
         Process incoming parameters for this tool from the dict `incoming`,
         update the tool state (or create if none existed), and either return
@@ -1135,32 +1135,31 @@ class Tool( object, Dictifiable ):
         if rerun_remap_job_id and len( expanded_incomings ) > 1:
             raise exceptions.MessageException( 'Failure executing tool (cannot create multiple jobs when remapping existing job).' )
 
+        # Process incoming data
         validation_timer = ExecutionTimer()
         all_errors = []
         all_params = []
-        validate_input = self.get_hook( 'validate_input' )
         for expanded_incoming in expanded_incomings:
-            expanded_state = self.new_state( request_context )
-            # Process incoming data
+            params = {}
+            errors = {}
             if not self.check_values:
                 # If `self.check_values` is false we don't do any checking or
                 # processing on input  This is used to pass raw values
                 # through to/from external sites.
-                errors = {}
-                params = expanded_incoming
+                state_inputs = expanded_incoming
             else:
                 # Update state for all inputs on the current page taking new
                 # values from `incoming`.
-                errors = self.populate_state( request_context, self.inputs, expanded_state.inputs, expanded_incoming, source=source )
+                self._populate_state( request_context, self.inputs, expanded_incoming, params, errors )
+
                 # If the tool provides a `validate_input` hook, call it.
+                validate_input = self.get_hook( 'validate_input' )
                 if validate_input:
-                    validate_input( trans, errors, expanded_state.inputs, self.inputs )
-                params = expanded_state.inputs
+                    validate_input( request_context, errors, params, self.inputs )
             all_errors.append( errors )
             all_params.append( params )
-        log.debug("Validated and populated state for tool request %s" % validation_timer)
-        # If there were errors, we stay on the same page and display
-        # error messages
+        log.debug( 'Validated and populated state for tool request %s' % validation_timer )
+        # If there were errors, we stay on the same page and display them
         if any( all_errors ):
             raise exceptions.MessageException( err_data=all_errors[ 0 ] )
         else:
@@ -1175,6 +1174,7 @@ class Tool( object, Dictifiable ):
             else:
                 raise exceptions.MessageException( execution_tracker.execution_errors[ 0 ] )
 
+
     def handle_single_execution( self, trans, rerun_remap_job_id, params, history, mapping_over_collection, execution_cache=None ):
         """
         Return a pair with whether execution is successful as well as either
@@ -1199,6 +1199,7 @@ class Tool( object, Dictifiable ):
                 message = 'Failure executing tool (invalid data returned from tool execution)'
             return False, message
 
+
     def find_fieldstorage( self, x ):
         if isinstance( x, FieldStorage ):
             raise InterruptedUpload( None )
@@ -1207,145 +1208,6 @@ class Tool( object, Dictifiable ):
         elif isinstance(x, list):
             [ self.find_fieldstorage( y ) for y in x ]
 
-    def populate_state( self, trans, inputs, state, incoming, source="html", prefix="", context=None ):
-        errors = dict()
-        # Push this level onto the context stack
-        context = ExpressionContext( state, context )
-        for input in inputs.itervalues():
-            key = prefix + input.name
-            if isinstance( input, Repeat ):
-                group_state = state[input.name]
-                # Create list of empty errors for each previously existing state
-                group_errors = [ ]
-                any_group_errors = False
-                rep_index = 0
-                del group_state[:]  # Clear prepopulated defaults if repeat.min set.
-                while True:
-                    rep_name = "%s_%d" % ( key, rep_index )
-                    if not any( [ incoming_key.startswith(rep_name) for incoming_key in incoming.keys() ] ):
-                        break
-                    if rep_index < input.max:
-                        new_state = {}
-                        new_state['__index__'] = rep_index
-                        self.fill_in_new_state( trans, input.inputs, new_state, context )
-                        group_state.append( new_state )
-                        group_errors.append( {} )
-                        rep_errors = self.populate_state( trans,
-                                                          input.inputs,
-                                                          new_state,
-                                                          incoming,
-                                                          source,
-                                                          prefix=rep_name + "|",
-                                                          context=context )
-                        if rep_errors:
-                            any_group_errors = True
-                            group_errors[rep_index].update( rep_errors )
-
-                    else:
-                        group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max }
-                        any_group_errors = True
-                    rep_index += 1
-                if any_group_errors:
-                    errors[ input.name ] = group_errors
-            elif isinstance( input, Conditional ):
-                group_state = state[input.name]
-                group_prefix = "%s|" % ( key )
-                # Deal with the 'test' element and see if its value changed
-                if input.value_ref and not input.value_ref_in_group:
-                    # We are referencing an existent parameter, which is not
-                    # part of this group
-                    test_param_key = prefix + input.test_param.name
-                else:
-                    test_param_key = group_prefix + input.test_param.name
-                # Get value of test param and determine current case
-                value, test_param_error = check_param_from_incoming( trans,
-                                                                     group_state,
-                                                                     input.test_param,
-                                                                     incoming,
-                                                                     test_param_key,
-                                                                     context,
-                                                                     source )
-
-                if test_param_error:
-                    errors[ input.name ] = [ test_param_error ]
-                    # Store the value of the test element
-                    group_state[ input.test_param.name ] = value
-                else:
-                    current_case = input.get_current_case( value, trans )
-                    # Current case has changed, throw away old state
-                    group_state = state[input.name] = {}
-                    # TODO: we should try to preserve values if we can
-                    self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context )
-                    group_errors = self.populate_state( trans,
-                                                        input.cases[current_case].inputs,
-                                                        group_state,
-                                                        incoming,
-                                                        source,
-                                                        prefix=group_prefix,
-                                                        context=context)
-                    if group_errors:
-                        errors[ input.name ] = group_errors
-                    # Store the current case in a special value
-                    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 )
-                group_errors = self.populate_state( trans,
-                                                    input.inputs,
-                                                    group_state,
-                                                    incoming,
-                                                    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 = []
-                any_group_errors = False
-                d_type = input.get_datatype( trans, context )
-                writable_files = d_type.writable_files
-                # remove extra files
-                while len( group_state ) > len( writable_files ):
-                    del group_state[-1]
-
-                # Add new fileupload as needed
-                while len( writable_files ) > len( group_state ):
-                    new_state = {}
-                    new_state['__index__'] = len( group_state )
-                    self.fill_in_new_state( trans, input.inputs, new_state, context )
-                    group_state.append( new_state )
-                    if any_group_errors:
-                        group_errors.append( {} )
-
-                # Update state
-                for i, rep_state in enumerate( group_state ):
-                    rep_index = rep_state['__index__']
-                    rep_prefix = "%s_%d|" % ( key, rep_index )
-                    rep_errors = self.populate_state( trans,
-                                                      input.inputs,
-                                                      rep_state,
-                                                      incoming,
-                                                      source,
-                                                      prefix=rep_prefix,
-                                                      context=context)
-                    if rep_errors:
-                        any_group_errors = True
-                        group_errors.append( rep_errors )
-                    else:
-                        group_errors.append( {} )
-                # Were there *any* errors for any repetition?
-                if any_group_errors:
-                    errors[input.name] = group_errors
-            else:
-                value, error = check_param_from_incoming( trans, state, input, incoming, key, context, source )
-                if error:
-                    errors[ input.name ] = error
-                state[ input.name ] = value
-        return errors
 
     def update_state( self, trans, inputs, state, incoming, source='html', prefix="", context=None,
                       update_only=False, old_errors={}, item_callback=None ):
@@ -1663,7 +1525,7 @@ class Tool( object, Dictifiable ):
                     if input.min:
                         messages[ input.name ] = []
                         for i in range( input.min ):
-                            rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
+                            rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 )
                             rep_dict = dict()
                             messages[ input.name ].append( rep_dict )
                             self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, update_values=update_values )
@@ -1677,13 +1539,13 @@ class Tool( object, Dictifiable ):
             else:
                 if isinstance( input, Repeat ):
                     for i, d in enumerate( values[ input.name ] ):
-                        rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
+                        rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 )
                         self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix, update_values=update_values )
                 elif isinstance( input, Conditional ):
                     group_values = values[ input.name ]
                     use_initial_value = False
                     if '__current_case__' in group_values:
-                        if int( group_values['__current_case__'] ) >= len( input.cases ):
+                        if int( group_values[ '__current_case__' ] ) >= len( input.cases ):
                             use_initial_value = True
                     else:
                         use_initial_value = True
@@ -1691,11 +1553,11 @@ class Tool( object, Dictifiable ):
                         # No test param invalidates the whole conditional
                         values[ input.name ] = group_values = input.get_initial_value( trans, context )
                         messages[ input.test_param.name ] = "No value found for '%s%s', using default" % ( prefix, input.test_param.label )
-                        current_case = group_values['__current_case__']
+                        current_case = group_values[ '__current_case__' ]
                         for child_input in input.cases[current_case].inputs.itervalues():
                             messages[ child_input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, child_input.label )
                     else:
-                        current = group_values["__current_case__"]
+                        current = group_values[ '__current_case__' ]
                         self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, update_values=update_values )
                 elif isinstance( input, Section ):
                     messages[ input.name ] = {}
@@ -1710,14 +1572,14 @@ class Tool( object, Dictifiable ):
                         else:
                             # skip check if is workflow parameters
                             ck_param = True
-                            search = input.type in ["text"]
+                            search = input.type in [ 'text' ]
                             if trans.workflow_building_mode and contains_workflow_parameter( values[ input.name ], search=search ):
                                 ck_param = False
                             # this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input
                             if ck_param:
                                 input.value_from_basic( input.value_to_basic( value, self.app ), self.app, ignore_errors=False )
                     except:
-                        log.info("Parameter validation failed.", exc_info=True)
+                        log.info( "Parameter validation failed.", exc_info=True )
                         messages[ input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, input.label )
                         if update_values:
                             values[ input.name ] = input.get_initial_value( trans, context )
@@ -2018,7 +1880,7 @@ class Tool( object, Dictifiable ):
 
         # If an admin user, expose the path to the actual tool config XML file.
         if trans.user_is_admin():
-            tool_dict['config_file'] = os.path.abspath(self.config_file)
+            tool_dict[ 'config_file' ] = os.path.abspath( self.config_file )
 
         # Add link details.
         if link_details:
@@ -2042,11 +1904,11 @@ class Tool( object, Dictifiable ):
 
         return tool_dict
 
-    def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
+    def to_json( self, trans, kwd={}, job=None, workflow_mode=False ):
         """
         Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
         """
-        history_id = kwd.get('history_id', None)
+        history_id = kwd.get( 'history_id', None )
         history = None
         try:
             if history_id is not None:
@@ -2070,7 +1932,7 @@ class Tool( object, Dictifiable ):
                 self._map_source_to_history( request_context, self.inputs, job_params )
                 tool_message = self._compare_tool_version( job )
                 params_to_incoming( kwd, self.inputs, job_params, self.app )
-            except Exception, e:
+            except Exception as e:
                 raise exceptions.MessageException( str( e ) )
 
         # create parameter object
@@ -2116,7 +1978,7 @@ class Tool( object, Dictifiable ):
                 return None
 
         # ensures that input dictionary is jsonifiable
-        def sanitize(dict, key='value'):
+        def sanitize( dict, key='value' ):
             # get current value
             value = dict[key] if key in dict else None
 
@@ -2138,142 +2000,52 @@ class Tool( object, Dictifiable ):
             # update and return
             dict[key] = value
 
-        # check the current state of a value and update it if necessary
-        def check_state( input, value, context ):
-            error = 'State validation failed.'
-            if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ):
-                return [ None, None ]
-            elif isinstance( value, galaxy.tools.parameters.basic.RuntimeValue ):
-                return [ { '__class__' : 'RuntimeValue' }, None ]
-            elif isinstance( value, dict ):
-                if value.get( '__class__' ) == 'RuntimeValue':
-                    return [ value, None ]
-            try:
-                value, error = check_param( request_context, input, value, context, boolean_fix=True )
-            except Exception, err:
-                log.error( 'Checking parameter %s failed. %s', input.name, str( err ) )
-                pass
-            return [ value, error ]
-
-        # populates state with incoming url parameters
-        def populate_state( inputs, state, errors, incoming, prefix="", context=None ):
-            context = ExpressionContext(state, context)
-            for input in inputs.itervalues():
-                state[input.name] = input.get_initial_value( request_context, context )
-                key = prefix + input.name
-                if input.type == 'repeat':
-                    group_state = state[input.name]
-                    rep_index = 0
-                    del group_state[:]
-                    while True:
-                        rep_name = "%s_%d" % (key, rep_index)
-                        if not any([incoming_key.startswith(rep_name) for incoming_key in incoming.keys()]) and rep_index >= input.min:
-                            break
-                        if rep_index < input.max:
-                            new_state = {}
-                            new_state['__index__'] = rep_index
-                            group_state.append(new_state)
-                            populate_state( input.inputs, new_state, errors, incoming, prefix=rep_name + "|", context=context )
-                        rep_index += 1
-                elif input.type == 'conditional':
-                    group_state = state[input.name]
-                    group_prefix = "%s|" % ( key )
-                    test_param_key = group_prefix + input.test_param.name
-                    default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None))
-                    value, error = check_state( input.test_param, default_value, context )
-                    if error:
-                        errors[test_param_key] = error
-                    else:
-                        try:
-                            current_case = input.get_current_case( value, request_context )
-                            group_state = state[input.name] = {}
-                            populate_state( input.cases[current_case].inputs, group_state, errors, incoming, prefix=group_prefix, context=context )
-                            group_state['__current_case__'] = current_case
-                        except Exception:
-                            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( 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( input, default_value, context )
-                    if error:
-                        errors[key] = error
-                    state[input.name] = value
-
-        # builds tool model including all attributes
-        def iterate( group_inputs, inputs, state_inputs, other_values=None ):
+        # populates model from state
+        def populate_model( inputs, state_inputs, group_inputs, other_values=None ):
             other_values = ExpressionContext( state_inputs, other_values )
             for input_index, input in enumerate( inputs.itervalues() ):
                 tool_dict = None
-                group_state = state_inputs.get(input.name, {})
+                group_state = state_inputs.get( input.name, {} )
                 if input.type == 'repeat':
                     tool_dict = input.to_dict( request_context )
-                    group_cache = tool_dict['cache'] = {}
+                    group_cache = tool_dict[ 'cache' ] = {}
                     for i in range( len( group_state ) ):
-                        group_cache[i] = {}
-                        iterate( group_cache[i], input.inputs, group_state[i], other_values )
+                        group_cache[ i ] = {}
+                        populate_model( input.inputs, group_state[ i ], group_cache[ i ], other_values )
                 elif input.type == 'conditional':
                     tool_dict = input.to_dict( request_context )
                     if 'test_param' in tool_dict:
-                        test_param = tool_dict['test_param']
-                        test_param['default_value'] = jsonify( input.test_param.get_initial_value( request_context, other_values ) )
-                        test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value']))
-                        test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], self.app)
-                        for i in range(len( tool_dict['cases'] ) ):
+                        test_param = tool_dict[ 'test_param' ]
+                        test_param[ 'value' ] = jsonify( group_state.get( test_param[ 'name' ], input.test_param.get_initial_value( request_context, other_values ) ) )
+                        test_param[ 'text_value' ] = input.test_param.value_to_display_text( test_param[ 'value' ], self.app )
+                        for i in range( len( tool_dict['cases'] ) ):
                             current_state = {}
-                            if i == group_state.get('__current_case__', None):
+                            if i == group_state.get( '__current_case__' ):
                                 current_state = group_state
-                            iterate( tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values )
+                            populate_model( input.cases[ i ].inputs, current_state, tool_dict[ 'cases' ][ i ][ 'inputs' ], other_values )
                 elif input.type == 'section':
                     tool_dict = input.to_dict( request_context )
-                    iterate( tool_dict['inputs'], input.inputs, group_state, other_values )
+                    populate_model( tool_dict[ 'inputs' ], input.inputs, group_state, other_values )
                 else:
-                    # expand input dictionary, resolve dynamic parameters
-                    try:
-                        tool_dict = input.to_dict( request_context, other_values=other_values )
-                    except Exception:
-                        tool_dict = input.to_dict( request_context )
-                        log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input.name)
-                        pass
-
-                    # backup default value
-                    try:
-                        tool_dict['default_value'] = input.get_initial_value( request_context, other_values )
-                    except Exception:
-                        tool_dict['default_value'] = None
-                        log.exception('tools::to_json() - Getting initial value failed %s.' % input.name)
-                        pass
-
-                    # update input value from tool state
-                    tool_dict['value'] = state_inputs.get(input.name, tool_dict['default_value'])
-
-                    # add text value
+                    tool_dict = input.to_dict( request_context, other_values=other_values )
+                    tool_dict[ 'value' ] = state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) )
                     tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], self.app )
+                    sanitize( tool_dict, 'value' )
+                group_inputs[ input_index ] = tool_dict
 
-                    # sanitize values
-                    sanitize(tool_dict, 'value')
-                    sanitize(tool_dict, 'default_value')
-
-                # backup final input dictionary
-                group_inputs[input_index] = tool_dict
-
-        # sanatization for the final tool state
-        def sanitize_state(state):
+        # sanatizes tool state
+        def sanitize_state( state ):
             keys = None
-            if isinstance(state, dict):
+            if isinstance( state, dict ):
                 keys = state
-            elif isinstance(state, list):
-                keys = range( len(state) )
+            elif isinstance( state, list ):
+                keys = range( len( state ) )
             if keys:
                 for k in keys:
-                    if isinstance(state[k], dict) or isinstance(state[k], list):
-                        sanitize_state(state[k])
+                    if isinstance( state[ k ], dict ) or isinstance( state[ k ], list ):
+                        sanitize_state( state[ k ] )
                     else:
-                        state[k] = jsonify(state[k])
+                        state[ k ] = jsonify( state[ k ] )
 
         # expand incoming parameters (parameters might trigger multiple tool executions,
         # here we select the first execution only in order to resolve dynamic parameters)
@@ -2284,75 +2056,110 @@ class Tool( object, Dictifiable ):
         if self.input_translator:
             self.input_translator.translate( params )
 
-        # initialize and populate tool state
+        # create tool state
         state_inputs = {}
         state_errors = {}
-        populate_state( self.inputs, state_inputs, state_errors, params.__dict__ )
+        self._populate_state( request_context, self.inputs, params.__dict__, state_inputs, state_errors )
 
-        # create basic tool model
+        # create tool model
         tool_model = self.to_dict( request_context )
-        tool_model['inputs'] = {}
-
-        # build tool model and tool state
-        iterate( tool_model['inputs'], self.inputs, state_inputs, '' )
+        tool_model[ 'inputs' ] = {}
+        populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] )
 
         # sanitize tool state
-        sanitize_state(state_inputs)
+        sanitize_state( state_inputs )
 
-        # load tool help
+        # create tool help
         tool_help = ''
         if self.help:
-            tool_help = self.help
-            tool_help = tool_help.render( static_path=url_for( '/static' ), host_url=url_for('/', qualified=True) )
+            tool_help = self.help.render( static_path=url_for( '/static' ), host_url=url_for( '/', qualified=True ) )
             if type( tool_help ) is not unicode:
-                tool_help = unicode( tool_help, 'utf-8')
+                tool_help = unicode( tool_help, 'utf-8' )
 
-        # check if citations exist
-        tool_citations = False
-        if self.citations:
-            tool_citations = True
-
-        # get tool versions
+        # create tool versions
         tool_versions = []
-        tools = self.app.toolbox.get_loaded_tools_by_lineage(self.id)
+        tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id )
         for t in tools:
             if t.version not in tool_versions:
-                tool_versions.append(t.version)
+                tool_versions.append( t.version )
 
-        # add information with underlying requirements and their versions
-        tool_requirements = []
-        if self.requirements:
-            for requirement in self.requirements:
-                tool_requirements.append({
-                    'name'      : requirement.name,
-                    'version'   : requirement.version
-                })
-
-        # add toolshed url
-        sharable_url = None
-        if self.tool_shed_repository:
-            sharable_url = self.tool_shed_repository.get_sharable_url( self.app )
-
-        # add additional properties
+        # update tool model
         tool_model.update({
             'id'            : self.id,
             'help'          : tool_help,
-            'citations'     : tool_citations,
+            'citations'     : bool( self.citations ),
             'biostar_url'   : self.app.config.biostar_url,
-            'sharable_url'  : sharable_url,
+            'sharable_url'  : self.tool_shed_repository.get_sharable_url( self.app ) if self.tool_shed_repository else None,
             'message'       : tool_message,
             'versions'      : tool_versions,
-            'requirements'  : tool_requirements,
+            'requirements'  : [ { 'name' : r.name, 'version' : r.version } for r in self.requirements ],
             'errors'        : state_errors,
             'state_inputs'  : state_inputs,
             'job_id'        : trans.security.encode_id( job.id ) if job else None,
             'job_remap'     : self._get_job_remap( job ),
             'history_id'    : trans.security.encode_id( history.id )
         })
-
-        # return enriched tool model
         return tool_model
 
+    # populates state from incoming parameters
+    def _populate_state( self, request_context, inputs, incoming, state, errors, prefix='', context=None ):
+        context = ExpressionContext( state, context )
+        for input in inputs.itervalues():
+            state[ input.name ] = input.get_initial_value( request_context, context )
+            key = prefix + input.name
+            group_state = state[ input.name ]
+            group_prefix = '%s|' % ( key )
+            if input.type == 'repeat':
+                rep_index = 0
+                del group_state[:]
+                while True:
+                    rep_prefix = '%s_%d' % ( key, rep_index )
+                    if not any( [ incoming_key.startswith( rep_prefix ) for incoming_key in incoming.keys() ] ) and rep_index >= input.min:
+                        break
+                    if rep_index < input.max:
+                        new_state = { '__index__' : rep_index }
+                        group_state.append( new_state )
+                        self._populate_state( request_context, input.inputs, incoming, new_state, errors, prefix=rep_prefix + '|', context=context )
+                    rep_index += 1
+            elif input.type == 'conditional':
+                test_param_key = group_prefix + input.test_param.name
+                test_param_value = incoming.get( test_param_key, group_state.get( input.test_param.name ) )
+                value, error = check_param( request_context, input.test_param, test_param_value, context )
+                if error:
+                    errors[ test_param_key ] = error
+                else:
+                    try:
+                        current_case = input.get_current_case( value, request_context )
+                        group_state = state[ input.name ] = {}
+                        self._populate_state( request_context, input.cases[ current_case ].inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
+                        group_state[ '__current_case__' ] = current_case
+                    except Exception:
+                        errors[ test_param_key ] = 'The selected case is unavailable/invalid.'
+                        pass
+                group_state[ input.test_param.name ] = value
+            elif input.type == 'section':
+                self._populate_state( request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
+            elif input.type == 'upload_dataset':
+                d_type = input.get_datatype( request_context, context=context )
+                writable_files = d_type.writable_files
+                while len( group_state ) > len( writable_files ):
+                    del group_state[ -1 ]
+                while len( writable_files ) > len( group_state ):
+                    new_state = { '__index__' : len( group_state ) }
+                    for upload_item in input.inputs.itervalues():
+                        new_state[ upload_item.name ] = upload_item.get_initial_value( request_context, context )
+                    group_state.append( new_state )
+                for i, rep_state in enumerate( group_state ):
+                    rep_index = rep_state[ '__index__' ]
+                    rep_prefix = '%s_%d|' % ( key, rep_index )
+                    self._populate_state( request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context )
+            else:
+                param_value = incoming.get( key, state.get( input.name ) )
+                value, error = check_param( request_context, input, param_value, context )
+                if error:
+                    errors[ key ] = error
+                state[ input.name ] = value
+
     def _get_job_remap( self, job):
         if job:
             if job.state == job.states.ERROR:
@@ -2373,28 +2180,28 @@ class Tool( object, Dictifiable ):
         # Create index for hdas.
         hda_source_dict = {}
         for hda in history.datasets:
-            key = '%s_%s' % (hda.hid, hda.dataset.id)
+            key = '%s_%s' % ( hda.hid, hda.dataset.id )
             hda_source_dict[ hda.dataset.id ] = hda_source_dict[ key ] = hda
 
         # Ditto for dataset collections.
         hdca_source_dict = {}
         for hdca in history.dataset_collections:
-            key = '%s_%s' % (hdca.hid, hdca.collection.id)
+            key = '%s_%s' % ( hdca.hid, hdca.collection.id )
             hdca_source_dict[ hdca.collection.id ] = hdca_source_dict[ key ] = hdca
 
         # Map dataset or collection to current history
-        def map_to_history(value):
+        def map_to_history( value ):
             id = None
             source = None
-            if isinstance(value, self.app.model.HistoryDatasetAssociation):
+            if isinstance( value, self.app.model.HistoryDatasetAssociation ):
                 id = value.dataset.id
                 source = hda_source_dict
-            elif isinstance(value, self.app.model.HistoryDatasetCollectionAssociation):
+            elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ):
                 id = value.collection.id
                 source = hdca_source_dict
             else:
                 return None
-            key = '%s_%s' % (value.hid, id)
+            key = '%s_%s' % ( value.hid, id )
             if key in source:
                 return source[ key ]
             elif id in source:
@@ -2442,16 +2249,15 @@ class Tool( object, Dictifiable ):
                         else:
                             message += 'You can re-run the job with this tool version, which is a different version of the original tool.'
                 else:
-                    new_tool_shed_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + '/%s/' % tool.tool_shed_repository.changeset_revision
-                    old_tool_shed = tool_id.split( "/repos/" )[0]
-                    old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, old_tool_shed )
-                    old_tool_shed_url = old_tool_shed_url + "/view/%s/%s/" % (tool.repository_owner, tool.repository_name)
-                    message = 'This job was run with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, version "%s", which is not available.  ' % (old_tool_shed_url, tool_id, tool_version)
+                    new_tool_shed_url = '%s/%s/' % ( tool.tool_shed_repository.get_sharable_url( tool.app ), tool.tool_shed_repository.changeset_revision )
+                    old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_id.split( '/repos/' )[ 0 ] )
+                    old_tool_shed_url = '%s/view/%s/%s/' % ( old_tool_shed_url, tool.repository_owner, tool.repository_name )
+                    message = 'This job was run with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, version "%s", which is not available.  ' % ( old_tool_shed_url, tool_id, tool_version )
                     if len( tools ) > 1:
-                        message += 'You can re-run the job with the selected <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a> or choose another derivation of the tool.' % (new_tool_shed_url, self.id)
+                        message += 'You can re-run the job with the selected <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a> or choose another derivation of the tool.' % ( new_tool_shed_url, self.id )
                     else:
-                        message += 'You can re-run the job with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, which is a derivation of the original tool.' % (new_tool_shed_url, self.id)
-        except Exception, e:
+                        message += 'You can re-run the job with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, which is a derivation of the original tool.' % ( new_tool_shed_url, self.id )
+        except Exception as e:
             raise exceptions.MessageException( str( e ) )
         return message
 
@@ -2787,18 +2593,6 @@ def json_fix( val ):
         return val
 
 
-def check_param_from_incoming( trans, state, input, incoming, key, context, source ):
-    """
-    Unlike "update" state, this preserves default if no incoming value found.
-    This lets API user specify just a subset of params and allow defaults to be
-    used when available.
-    """
-    default_input_value = state.get( input.name, None )
-    incoming_value = get_incoming_value( incoming, key, default_input_value )
-    value, error = check_param( trans, input, incoming_value, context, source=source )
-    return value, error
-
-
 def get_incoming_value( incoming, key, default ):
     """
     Fetch value from incoming dict directly or check special nginx upload

lib/galaxy/tools/parameters/__init__.py

@@ -19,47 +19,43 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
     and a display label.
 
     If the callback returns a value, it will be replace the old value.
-
-    FIXME: There is redundancy between this and the visit_inputs methods of
-           Repeat and Group. This tracks labels and those do not. It would
-           be nice to unify all the places that recursively visit inputs.
     """
     context = ExpressionContext( input_values, context )
     for input in inputs.itervalues():
         if isinstance( input, Repeat ) or isinstance( input, UploadDataset ):
             for i, d in enumerate( input_values[ input.name ] ):
                 index = d['__index__']
-                new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index )
-                new_label_prefix = label_prefix + "%s %d > " % ( input.title, i + 1 )
+                new_name_prefix = name_prefix + '%s_%d|' % ( input.name, index )
+                new_label_prefix = label_prefix + '%s %d > ' % ( input.title, i + 1 )
                 visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         elif isinstance( input, Conditional ):
             values = input_values[ input.name ]
-            current = values["__current_case__"]
-            new_name_prefix = name_prefix + input.name + "|"
+            current = values[ '__current_case__' ]
+            new_name_prefix = name_prefix + input.name + '|'
             visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         elif isinstance( input, Section ):
             values = input_values[ input.name ]
-            new_name_prefix = name_prefix + input.name + "|"
+            new_name_prefix = name_prefix + input.name + '|'
             visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         else:
             args = {
                 'input'             : input,
                 'value'             : input_values.get( input.name ),
-                'prefixed_name'     : "%s%s" % ( name_prefix, input.name ),
-                'prefixed_label'    : "%s%s" % ( label_prefix, input.label )
+                'prefixed_name'     : '%s%s' % ( name_prefix, input.name ),
+                'prefixed_label'    : '%s%s' % ( label_prefix, input.label )
             }
             if details:
                 args[ 'context' ] = context
             new_value = callback( **args )
             if no_replacement_value is REPLACE_ON_TRUTHY:
-                replace = bool(new_value)
+                replace = bool( new_value )
             else:
                 replace = new_value != no_replacement_value
             if replace:
-                input_values[input.name] = new_value
+                input_values[ input.name ] = new_value
 
 
-def check_param( trans, param, incoming_value, param_values, source='html', boolean_fix=False ):
+def check_param( trans, param, incoming_value, param_values ):
     """
     Check the value of a single parameter `param`. The value in
     `incoming_value` is converted from its HTML encoding and validated.
@@ -70,20 +66,16 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
     value = incoming_value
     error = None
     try:
-        # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code
-        if boolean_fix and param.type == 'boolean' and isinstance( value, basestring ):
-            return [ string_as_bool( value ), None ]
-        if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
-            # Convert value from HTML representation
-            if source == 'html':
-                value = param.from_html( value, trans, param_values )
-            else:
-                value = param.from_json( value, trans, param_values )
-            # Then do any further validation on the value
-            param.validate( value, trans )
-        elif value is None and isinstance( param, SelectToolParameter ):
-            # An empty select list or column list
-            param.validate( value, trans )
+        if trans.workflow_building_mode:
+            if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ):
+                return [ None, None ]
+            if isinstance( value, galaxy.tools.parameters.basic.RuntimeValue ):
+                return [ { '__class__' : 'RuntimeValue' }, None ]
+            if isinstance( value, dict ):
+                if value.get( '__class__' ) == 'RuntimeValue':
+                    return [ value, None ]
+        value = param.from_html( value, trans, param_values )
+        param.validate( value, trans )
     except ValueError, e:
         error = str( e )
     return value, error
@@ -116,7 +108,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ):
     for key, value in param_values.iteritems():
         value = json_fix( loads( value ) )
         if key in params:
-            value = params[key].value_from_basic( value, app, ignore_errors )
+            value = params[ key ].value_from_basic( value, app, ignore_errors )
         rval[ key ] = value
     return rval
 
@@ -131,18 +123,18 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ):
     for input in inputs.itervalues():
         if isinstance( input, Repeat ) or isinstance( input, UploadDataset ):
             for d in input_values[ input.name ]:
-                index = d['__index__']
-                new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index )
+                index = d[ '__index__' ]
+                new_name_prefix = name_prefix + '%s_%d|' % ( input.name, index )
                 params_to_incoming( incoming, input.inputs, d, app, new_name_prefix )
         elif isinstance( input, Conditional ):
             values = input_values[ input.name ]
-            current = values["__current_case__"]
-            new_name_prefix = name_prefix + input.name + "|"
+            current = values[ '__current_case__' ]
+            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 )
         elif isinstance( input, Section ):
             values = input_values[ input.name ]
-            new_name_prefix = name_prefix + input.name + "|"
+            new_name_prefix = name_prefix + input.name + '|'
             params_to_incoming( incoming, input.inputs, values, app, new_name_prefix )
         else:
             value = input_values.get( input.name )

lib/galaxy/tools/parameters/basic.py

@@ -111,9 +111,6 @@ class ToolParameter( object, Dictifiable ):
         """
         return value
 
-    def from_json( self, value, trans=None, other_values={} ):
-        return self.from_html( value, trans, other_values )
-
     def get_initial_value( self, trans, other_values ):
         """
         Return the starting value of the parameter
@@ -481,9 +478,6 @@ class BooleanToolParameter( ToolParameter ):
         return form_builder.CheckboxField( self.name, checked, refresh_on_change=self.refresh_on_change )
 
     def from_html( self, value, trans=None, other_values={} ):
-        return form_builder.CheckboxField.is_checked( value )
-
-    def from_json( self, value, trans=None, other_values={} ):
         return string_as_bool( value )
 
     def to_python( self, value, app ):

lib/galaxy/webapps/galaxy/api/tools.py

@@ -255,7 +255,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
         # TODO: handle dbkeys
         params = util.Params( inputs, sanitize=False )
         incoming = params.__dict__
-        vars = tool.handle_input( trans, incoming, history=target_history, source='json' )
+        vars = tool.handle_input( trans, incoming, history=target_history )
 
         # TODO: check for errors and ensure that output dataset(s) are available.
         output_datasets = vars.get( 'out_data', [] )

lib/galaxy/workflow/modules.py

@@ -163,7 +163,7 @@ class WorkflowModule( object ):
         """
         raise TypeError( "Abstract method" )
 
-    def compute_runtime_state( self, trans, step_updates=None, source="html" ):
+    def compute_runtime_state( self, trans, step_updates=None ):
         """ Determine the runtime state (potentially different from self.state
         which describes configuration state). This (again unlike self.state) is
         currently always a `DefaultToolState` object.
@@ -278,7 +278,7 @@ class SimpleWorkflowModule( WorkflowModule ):
                 errors[ name ] = error
         return errors
 
-    def compute_runtime_state( self, trans, step_updates=None, source="html" ):
+    def compute_runtime_state( self, trans, step_updates=None ):
         if step_updates and "tool_state" in step_updates:
             # Fix this for multiple inputs
             state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) )
@@ -441,7 +441,7 @@ class SubWorkflowModule( WorkflowModule ):
                 errors[ name ] = error
         return errors
 
-    def compute_runtime_state( self, trans, step_updates=None, source="html" ):
+    def compute_runtime_state( self, trans, step_updates=None ):
         state = self.get_runtime_state()
         step_errors = {}
         return state, step_errors
@@ -1084,7 +1084,7 @@ class ToolModule( WorkflowModule ):
         inputs = self.state.inputs
         return self.tool.check_and_update_param_values( inputs, self.trans, workflow_building_mode=True )
 
-    def compute_runtime_state( self, trans, step_updates=None, source="html" ):
+    def compute_runtime_state( self, trans, step_updates=None ):
         # Warning: This method destructively modifies existing step state.
         step_errors = None
         state = self.state
@@ -1097,7 +1097,7 @@ class ToolModule( WorkflowModule ):
             # Update the state
             self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {})
             step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates,
-                                             update_only=True, old_errors=old_errors, source=source )
+                                             update_only=True, old_errors=old_errors )
             step_metadata_runtime_state = self.__step_meta_runtime_state()
             if step_metadata_runtime_state:
                 state.inputs[ RUNTIME_STEP_META_STATE_KEY ] = step_metadata_runtime_state
@@ -1385,7 +1385,7 @@ class WorkflowModuleInjector(object):
         self.trans = trans
         self.allow_tool_state_corrections = allow_tool_state_corrections
 
-    def inject( self, step, step_args=None, source="html" ):
+    def inject( self, step, step_args=None ):
         """ Pre-condition: `step` is an ORM object coming from the database, if
         supplied `step_args` is the representation of the inputs for that step
         supplied via web form.
@@ -1421,7 +1421,7 @@ class WorkflowModuleInjector(object):
         # are not persisted so we need to do it every time)
         module.add_dummy_datasets( connections=step.input_connections )
 
-        state, step_errors = module.compute_runtime_state( trans, step_args, source=source )
+        state, step_errors = module.compute_runtime_state( trans, step_args )
 
         step.state = state
 
@@ -1440,7 +1440,7 @@ def populate_module_and_state( trans, workflow, param_map, allow_tool_state_corr
         module_injector = WorkflowModuleInjector( trans, allow_tool_state_corrections )
     for step in workflow.steps:
         step_args = param_map.get( step.id, {} )
-        step_errors = module_injector.inject( step, step_args=step_args, source="json" )
+        step_errors = module_injector.inject( step, step_args=step_args )
         if step.type == 'tool' or step.type is None:
             if step_errors:
                 message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors

static/maps/mvc/form/form-parameters.js.map

@@ -1 +1 @@
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static/maps/mvc/form/form-section.js.map

@@ -1 +1 @@
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static/maps/utils/utils.js.map

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static/scripts/mvc/form/form-parameters.js

@@ -1,2 +1,2 @@
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+define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){var b=this.types[a.type],c="function"==typeof this[b]?this[b].call(this,a):null;return c||(this.app.incompatible=!0,c=a.options?this._fieldSelect(a):this._fieldText(a),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+a.type+").")),void 0===a.value&&(a.value=null),c.value(a.value),c},_fieldData:function(a){var b=this;return new c.View(this.app,{id:"field-"+a.id,extensions:a.extensions,optional:a.optional,multiple:a.multiple,type:a.type,data:a.options,onchange:function(){b.app.trigger("change")}})},_fieldSelect:function(a){if(a.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];_.each(a.options,function(a){c.push({label:a[0],value:a[1]})});var d=b.Select;switch(a.display){case"checkboxes":d=b.Checkbox;break;case"radio":d=b.Radio}var e=this;return new d.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){e.app.trigger("change")}})},_fieldDrilldown:function(a){if(a.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value=null;var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(a){c.onchange?c.onchange(a):f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,is_workflow:a.is_workflow,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map

static/scripts/mvc/form/form-section.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.options.sustain_conditionals&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title||"Repeat",title_new:a.title||"",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min),a.default);j++)b(i>j?a.cache[j]:a.inputs);this.app.options.sustain_repeats&&g.hideOptions();var k=new f(this.app,{label:a.title||a.name,help:a.help,field:g});this.table.add(k.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-form-info").html(a.help)),g.setOperation("button_visible",function(){g.collapsed?g.expand():g.collapse()}),g.on("expanded",function(){f.setIcon("fa-eye")}),g.on("collapsed",function(){f.setIcon("fa-eye-slash")}),this.app.on("expand",function(a){g.$("#"+a).length>0&&g.expand()}),a.expanded&&g.expand(),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{name:a.name,label:a.label||a.name,value:a.value,default_value:a.default_value,text_value:a.text_value||a.value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.options.sustain_conditionals&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title||"Repeat",title_new:a.title||"",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min),a.default);j++)b(i>j?a.cache[j]:a.inputs);this.app.options.sustain_repeats&&g.hideOptions();var k=new f(this.app,{label:a.title||a.name,help:a.help,field:g});this.table.add(k.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-form-info").html(a.help)),g.setOperation("button_visible",function(){g.collapsed?g.expand():g.collapse()}),g.on("expanded",function(){f.setIcon("fa-eye")}),g.on("collapsed",function(){f.setIcon("fa-eye-slash")}),this.app.on("expand",function(a){g.$("#"+a).length>0&&g.expand()}),a.expanded&&g.expand(),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{name:a.name,label:a.label||a.name,value:a.value,text_value:a.text_value||a.value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
 //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map

static/scripts/utils/utils.js

@@ -1,2 +1,2 @@
-define([],function(){function a(a){return'<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>'}function b(a,c){for(var d in a){var e=a[d];if(_.isObject(e)){var f=c(e);f&&(a[d]=f),b(e,c)}}}function c(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function d(a){return $("<div/>").text(a).html()}function e(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function f(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function g(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):h({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function h(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?($.isEmptyObject(b.data)||(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url+=$.param(b.data,!0)),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)}).always(function(){a.complete&&a.complete()})}function i(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function j(a){$('link[href^="'+a+'"]').length||$('<link href="'+Galaxy.root+a+'" rel="stylesheet">').appendTo("head")}function k(a,b){return a?_.defaults(a,b):b}function l(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function m(a,b,c){c=void 0!==c?c:1;var d="";if(a>=s)a/=s,d="TB";else if(a>=r)a/=r,d="GB";else if(a>=q)a/=q,d="MB";else if(a>=p)a/=p,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:l(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function n(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function o(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}var p=1024,q=p*p,r=q*p,s=r*p;return{cssLoadFile:j,cssGetAttribute:i,get:g,merge:k,iframe:a,bytesToString:m,uid:n,time:o,request:h,sanitize:d,textify:f,validate:e,deepeach:b,isJSON:c}});
+define([],function(){function a(a){return'<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>'}function b(a,c){for(var d in a){var e=a[d];if(_.isObject(e)){var f=c(e);f&&(a[d]=f),b(e,c)}}}function c(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function d(a){return $("<div/>").text(a).html()}function e(a){a instanceof Array||(a=[a]);for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function f(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function g(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):h({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function h(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?($.isEmptyObject(b.data)||(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url+=$.param(b.data,!0)),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)}).always(function(){a.complete&&a.complete()})}function i(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function j(a){$('link[href^="'+a+'"]').length||$('<link href="'+Galaxy.root+a+'" rel="stylesheet">').appendTo("head")}function k(a,b){return a?_.defaults(a,b):b}function l(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function m(a,b,c){c=void 0!==c?c:1;var d="";if(a>=s)a/=s,d="TB";else if(a>=r)a/=r,d="GB";else if(a>=q)a/=q,d="MB";else if(a>=p)a/=p,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:l(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function n(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function o(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}var p=1024,q=p*p,r=q*p,s=r*p;return{cssLoadFile:j,cssGetAttribute:i,get:g,merge:k,iframe:a,bytesToString:m,uid:n,time:o,request:h,sanitize:d,textify:f,validate:e,deepeach:b,isJSON:c}});
 //# sourceMappingURL=../../maps/utils/utils.js.map

test/qunit/tests/masthead_tests.js

@@ -110,7 +110,6 @@ define([ "test-app", "layout/masthead"
         ok( $menu.css( 'display', 'none' ), 'Menu manually hidden' );
         tab.set( 'show_menu', true );
         ok( $menu.css( 'display', 'block' ), 'Menu manually shown, again' );
-
         var tab = this.masthead.collection.findWhere( { id: 'enable-scratchbook' } );
         var $tab = $( '#enable-scratchbook' ).find( '.dropdown' );
         ok( tab && $tab.length == 1, 'Found tab to enable scratchbook' );