[galaxy-commits] commit/galaxy-central: jgoecks: Tools and visual analytics: (a) add tool parameter types to client-side code and automatically unpack tools; (b) update Sweepster to work with recent tool parameter enhancements; and (c) fix additional warts.

23 Aug 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/5b4c4cf9bc96/
Changeset:   5b4c4cf9bc96
User:        jgoecks
Date:        2013-08-23 22:09:22
Summary:     Tools and visual analytics: (a) add tool parameter types to client-side code and automatically unpack tools; (b) update Sweepster to work with recent tool parameter enhancements; and (c) fix additional warts.
Affected #:  6 files

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c lib/galaxy/tools/parameters/basic.py

--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -236,7 +236,7 @@
     ValueError: An integer is required
     """
 
-    dict_colletion_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' )
+    dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' )
 
     def __init__( self, tool, elem ):
         TextToolParameter.__init__( self, tool, elem )
@@ -251,12 +251,12 @@
         self.max = elem.get( 'max' )
         if self.min:
             try:
-                int( self.min )
+                self.min = int( self.min )
             except:
                 raise ValueError( "An integer is required" )
         if self.max:
             try:
-                int( self.max )
+                self.max = int( self.max )
             except:
                 raise ValueError( "An integer is required" )
         if self.min and self.max:

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -37,7 +37,7 @@
 from galaxy.datatypes.interval import ChromatinInteractions
 from galaxy.datatypes.data import Text
 
-from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation,HistoryDatasetAssociation
+from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation
 
 from galaxy.datatypes.display_applications import util as da_util
 from galaxy.datatypes.metadata import FileParameter

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -873,8 +873,8 @@
                 
         # Add tool, dataset attributes to config based on id.
         tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] )
-        viz_config[ 'tool' ] = tool.dictify( trans, for_display=True )
-        viz_config[ 'dataset' ] = dataset.dictify()
+        viz_config[ 'tool' ] = tool.dictify( trans, io_details=True )
+        viz_config[ 'dataset' ] = trans.security.encode_dict_ids( dataset.dictify() )
 
         return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config )
     

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -1,16 +1,12 @@
 /**
  * Model, view, and controller objects for Galaxy tools and tool panel.
- *
- * Models have no references to views, instead using events to indicate state 
- * changes; this is advantageous because multiple views can use the same object 
- * and models can be used without views.
  */
 
  define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/backbone/backbone-relational" ], 
          function(_, util, data) {
 
 /**
- * Mixin to enable model to track visibility.
+ * Mixin for tracking model visibility.
  */
 var VisibilityMixin = {
     hidden: false,
@@ -41,6 +37,13 @@
         html: null,
         num_samples: 5
     },
+
+    subModelTypes: {
+        'integer': 'IntegerToolParameter',
+        'float': 'FloatToolParameter',
+        'data': 'DataToolParameter',
+        'select': 'SelectToolParameter'
+    },
     
     initialize: function() {
         this.attributes.html = unescape(this.attributes.html);
@@ -49,69 +52,57 @@
     copy: function() {
         return new ToolParameter(this.toJSON());
     },
-    
+
+    set_value: function(value) {
+        this.set('value', value || '');
+    }
+});
+
+// In order to resolve subModelTypes for tool parameters, use a custom scope here rather
+// than polluting the global scope.
+var tools_scope = {};
+Backbone.Relational.store.addModelScope(tools_scope);
+
+/**
+ * A data tool parameter.
+ */
+var DataToolParameter = tools_scope.DataToolParameter = ToolParameter.extend({});
+
+/**
+ * An integer tool parameter.
+ */
+var IntegerToolParameter = tools_scope.IntegerToolParameter = ToolParameter.extend({
+    set_value: function(value) {
+        this.set('value', parseInt(value, 10));
+    },
+
     /**
      * Returns samples from a tool input.
      */
     get_samples: function() {
-        var type = this.get('type'),
-            samples = null;
-        if (type === 'number') {
-            samples = d3.scale.linear()
+        return d3.scale.linear()
                         .domain([this.get('min'), this.get('max')])
                         .ticks(this.get('num_samples'));
-        }
-        else if (type === 'select') {
-            samples = _.map(this.get('options'), function(option) {
-                return option[0];
-            });
-        }
-        
-        return samples;
-    },
-
-    set_value: function(value) {
-        this.set('value', value || '');
-    }
-},
-{
-    /**
-     * Dictionary mapping parameter type strings to parameter classes.
-     */
-    TYPE_DICT: {
-        'number': IntegerToolParameter
-    },
-
-    /**
-     * Create new parameter from a dictionary.
-     */
-    create: function(options) {
-        var param_class = ToolParameter.TYPE_DICT[options.type] || ToolParameter;
-        return new param_class(options);
     }
 });
 
-/**
- * A number tool parameter.
+var FloatToolParameter = tools_scope.FloatToolParameter = IntegerToolParameter.extend({
+    set_value: function(value) {
+        this.set('value', parseFloat(value));
+    }
+});
+
+/** 
+ * A select tool parameter.
  */
-var IntegerToolParameter = ToolParameter.extend({
-    defaults: _.extend({}, ToolParameter.prototype.defaults, {
-        min: null,
-        max: null
-    }),
-
-    initialize: function() {
-        ToolParameter.prototype.initialize.call(this);
-        if (this.attributes.min) {
-            this.attributes.min = parseInt(this.attributes.min, 10);    
-        }
-        if (this.attributes.max) {
-            this.attributes.max = parseInt(this.attributes.max, 10);
-        }
-    },
-
-    set_value: function(value) {
-        this.set('value', parseInt(value, 10))
+var SelectToolParameter = tools_scope.SelectToolParameter = ToolParameter.extend({
+    /**
+     * Returns tool options.
+     */
+    get_samples: function() {
+        return _.map(this.get('options'), function(option) {
+            return option[0];
+        });
     }
 });
 
@@ -125,21 +116,32 @@
         name: null,
         description: null,
         target: null,
-        inputs: []
+        inputs: [],
+        outputs: []
     },
 
-    initialize: function(options) {
-        // Unpack parameters manually so that different parameter types can be created.
-        this.attributes.inputs = new Backbone.Collection( _.map(options.inputs, function(param_dict) {
-            // FIXME: it is still useful to be able to save/restore tool state?
-            // Update parameter value from tool state dict.
-            //param_dict.value = tool_state_dict[ param_dict[name] ] || param_dict.value;
-            return ToolParameter.create(param_dict);
-        }));
+    relations: [
+        {
+            type: Backbone.HasMany,
+            key: 'inputs',
+            relatedModel: ToolParameter
+        }
+    ],
+
+    urlRoot: galaxy_config.root + 'api/tools',
+
+    /**
+     * Removes inputs of a particular type; this is useful because not all inputs can be handled by
+     * client and server yet.
+     */
+    remove_inputs: function(types) {
+        var tool = this,
+            incompatible_inputs = tool.get('inputs').filter( function(input) {
+                return ( types.indexOf( input.get('type') ) !== -1);
+            });
+        tool.get('inputs').remove(incompatible_inputs);
     },
     
-    urlRoot: galaxy_config.root + 'api/tools',
-
     /**
      * Returns object copy, optionally including only inputs that can be sampled.
      */
@@ -735,6 +737,7 @@
 return {
     ToolParameter: ToolParameter,
     IntegerToolParameter: IntegerToolParameter,
+    SelectToolParameter: SelectToolParameter,
     Tool: Tool,
     ToolCollection: ToolCollection,
     ToolSearch: ToolSearch,

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c static/scripts/viz/sweepster.js
--- a/static/scripts/viz/sweepster.js
+++ b/static/scripts/viz/sweepster.js
@@ -30,8 +30,6 @@
         // Set up tool parameters to work with tree.
         var self = this;
         this.get('tool').get('inputs').each(function(input) {
-            if (!input.get_samples()) { return; }
-
             // Listen for changes to input's attributes.
             input.on('change:min change:max change:num_samples', function(input) {
                 if (input.get('in_ptree')) {
@@ -270,8 +268,8 @@
         if (options.track) {
             // FIXME: find a better way to deal with needed URLs:
             var track_config = _.extend({
-                                    data_url: galaxy_paths.get('raw_data_url'),
-                                    converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
+                                    data_url: galaxy_config.root + 'dummy1',
+                                    converted_datasets_state_url: galaxy_config.root + 'dummy2'
                                 }, options.track);
             this.set('track', tracks.object_from_template(track_config, {}, null));
         }
@@ -340,8 +338,10 @@
     ],
     
     initialize: function(options) {
-        var tool_with_samplable_inputs = this.get('tool').copy(true);
+        var tool_with_samplable_inputs = this.get('tool');
         this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
+        // Remove complex parameters for now.
+        tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional' ] );
         
         this.set('parameter_tree', new ToolParameterTree({ 
             tool: tool_with_samplable_inputs,
@@ -425,7 +425,7 @@
         // Render tile placeholders.
         this.model.get('regions').each(function() {
             self.$el.append($('<td/>').addClass('tile').html(
-                $('<img/>').attr('src', galaxy_paths.get('image_path') + '/loading_large_white_bg.gif')
+                $('<img/>').attr('src', galaxy_config.root + 'images/loading_large_white_bg.gif')
             ));
         });
 
@@ -497,10 +497,10 @@
         });
 
         // Add row for parameter sweep inputs.
-        if (type === 'number') {
+        if (input instanceof tools.IntegerToolParameter) {
             sweep_inputs_row = $(_.template(this.number_input_template, this.model.toJSON()));
         }
-        else if (type === 'select') {
+        else if (input instanceof tools.SelectToolParameter) {
             var options = _.map(this.$el.find('select option'), function(option) {
                     return $(option).val();
                 }),
@@ -918,19 +918,18 @@
                 _.each(new_tracks, function(pm_track, index) {
                     setTimeout(function() {
                         // Set inputs and run tool.
-                        // console.log('running with settings', pm_track.get('settings'));
                         tool.set_input_values(pm_track.get('settings').get('values'));
                         $.when(tool.rerun(dataset, regions)).then(function(output) {
+                            // HACK: output is an HDA with track config attribute. To create a track, rearrange
+                            // track config to point to HDA.
+                            var dataset = output.first(),
+                                track_config = dataset.get('track_config');
+                            track_config.dataset = dataset;
+
                             // Create and add track for output dataset.
-                            var track_config = _.extend({
-                                    data_url: galaxy_paths.get('raw_data_url'),
-                                    converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
-                                }, output.first().get('track_config')),
-                                track_obj = tracks.object_from_template(track_config, self, null);
-
-                            // Track uses raw data.
-                            track_obj.data_manager.set('data_type', 'raw_data');
-
+                            var track_obj = tracks.object_from_template(track_config, self, null);
+                            track_obj.init_for_tool_data();
+                            
                             // Set track block colors.
                             track_obj.prefs.block_color = self.block_color;
                             track_obj.prefs.reverse_strand_color = self.reverse_strand_color;

diff -r ab74f2d8017306fb909778aafcd51b78b24e3e56 -r 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -919,7 +919,7 @@
                 { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" },
                 { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" },
                 { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" },
-                { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" },
+                { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" }
             ], 
             saved_values: obj_dict.prefs,
             onchange: function() {
@@ -1393,7 +1393,7 @@
         //
 
         // Redraw without requesting more data immediately.
-        view.request_redraw({ data_fetch: false })
+        view.request_redraw({ data_fetch: false });
 
         // Set up timeout to redraw with more data when moving stops.
         if (this.redraw_on_move_fn) {
@@ -1637,15 +1637,11 @@
     ],
 
     initialize: function(options) {
-        // HACK: remove data and group tool inputs because Trackster
-        // does not work with them right now.
-        var tool = this.get('tool'),
-            incompatible_inputs = tool.get('inputs').filter( function(input) {
-                return ( [ 'data', 'hidden_data', 'group'].indexOf( input.get('type') ) !== -1);
-            });
-        tool.get('inputs').remove(incompatible_inputs);
+        // HACK: remove some inputs because Trackster does yet not work with them.
+        this.get('tool').remove_inputs( [ 'data', 'hidden_data', 'conditional' ] );
+
+        // FIXME: need to restore tool values/visibility.
     }
-
 });
 
 /**
@@ -2320,8 +2316,12 @@
     // Attribute init.
     //
 
-    // Only create dataset if it is defined.
-    this.dataset = (obj_dict.dataset ? new data.Dataset(obj_dict.dataset) : null);
+    // Set or create dataset.
+    this.dataset = null;
+    if (obj_dict.dataset) {
+        // Dataset can be a Backbone model or a dict that can be used to create a model.
+        this.dataset = (obj_dict.dataset instanceof Backbone.Model ? obj_dict.dataset : new data.Dataset(obj_dict.dataset) );
+    }
     this.dataset_check_type = 'converted_datasets_state';
     this.data_url_extra_params = {};
     this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT);
@@ -3452,9 +3452,13 @@
         this.data_query_wait = 1000;
         this.dataset_check_type = 'state';
         
+        // FIXME: this is optional and is disabled for now because it creates
+        // additional converter jobs without a clear benefit because indexing
+        // such a small dataset provides little benefit.
         //
         // Set up one-time, post-draw to clear tool execution settings.
         //
+        /*
         this.normal_postdraw_actions = this.postdraw_actions;
         this.postdraw_actions = function(tiles, width, w_scale, clear_after) {
             var self = this;
@@ -3484,6 +3488,7 @@
             // Reset post-draw actions function.
             self.postdraw_actions = self.normal_postdraw_actions;
         };
+        */
     }
 });

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

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[galaxy-commits] commit/galaxy-central: jgoecks: Tools and visual analytics: (a) add tool parameter types to client-side code and automatically unpack tools; (b) update Sweepster to work with recent tool parameter enhancements; and (c) fix additional warts.

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