[galaxy-commits] commit/galaxy-central: jgoecks: Unify Trackster tool objects with generic tool objects. This unification enhances the generic tool framework and simplifies the trackster tool framework. Also, backbone-ify Trackster tool handling.

8 Aug 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/31d2d58ebf10/
Changeset:   31d2d58ebf10
User:        jgoecks
Date:        2013-08-08 23:05:51
Summary:     Unify Trackster tool objects with generic tool objects. This unification enhances the generic tool framework and simplifies the trackster tool framework. Also, backbone-ify Trackster tool handling.
Affected #:  3 files

diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 lib/galaxy/visualization/genome/visual_analytics.py

--- a/lib/galaxy/visualization/genome/visual_analytics.py
+++ b/lib/galaxy/visualization/genome/visual_analytics.py
@@ -38,6 +38,8 @@
 
 def get_tool_def( trans, hda ):
     """ Returns definition of an interactive tool for an HDA. """
+
+    #FIXME: use tools.to_dict rather than custom code here.
     
     job = get_dataset_job( hda )
     # TODO: could use this assertion to provide more information.
@@ -71,10 +73,10 @@
             tool_params.append( param_dict )
         elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions:
             tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \
-                                  'value' : tool_param_values.get( name, None ), \
+                                  'value' : tool_param_values.get( name, '' ), \
                                   'html' : urllib.quote( input.get_html() ) } )
         
     # If tool has parameters that can be interactively modified, return tool.
     if len( tool_params ) != 0:
-        return { 'id': tool.id, 'name' : tool.name, 'params' : tool_params } 
+        return { 'id': tool.id, 'name' : tool.name, 'inputs' : tool_params } 
     return None
\ No newline at end of file

diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -41,6 +41,7 @@
         label: null,
         type: null,
         value: null,
+        html: null,
         num_samples: 5
     },
     
@@ -70,7 +71,51 @@
         }
         
         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 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))
+    }
 });
 
 /**
@@ -79,22 +124,22 @@
 var Tool = BaseModel.extend({
     // Default attributes.
     defaults: {
+        id: null,
+        name: null,
         description: null,
         target: null,
         inputs: []
     },
-    
-    relations: [
-        {
-            type: Backbone.HasMany,
-            key: 'inputs',
-            relatedModel: ToolParameter,
-            reverseRelation: {
-                key: 'tool',
-                includeInJSON: false
-            }
-        }
-    ],
+
+    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);
+        }));
+    },
     
     urlRoot: galaxy_paths.get('tool_url'),
 
@@ -209,6 +254,13 @@
 });
 
 /**
+ * Tool view.
+ */
+var ToolView = Backbone.View.extend({
+
+});
+
+/**
  * Wrap collection of tools for fast access/manipulation.
  */
 var ToolCollection = Backbone.Collection.extend({
@@ -697,6 +749,8 @@
 
 // Exports
 return {
+    ToolParameter: ToolParameter,
+    IntegerToolParameter: IntegerToolParameter,
     Tool: Tool,
     ToolSearch: ToolSearch,
     ToolPanel: ToolPanel,

diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1,7 +1,7 @@
 define( ["libs/underscore", "viz/visualization", "viz/trackster/util", 
-         "viz/trackster/slotting", "viz/trackster/painters", "mvc/data",
-         "viz/trackster/filters" ], 
-         function( _, visualization, util, slotting, painters, data, filters_mod ) {
+         "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters",
+         "mvc/data", "mvc/tools" ], 
+         function(_, visualization, util, slotting, painters, filters_mod, data, tools_mod) {
 
 var extend = _.extend;
 
@@ -1622,89 +1622,103 @@
 /**
  * Encapsulation of a tool that users can apply to tracks/datasets.
  */
-var Tool = function(track, tool_dict, tool_state_dict) {    
-    //
-    // Unpack tool information from dictionary.
-    //
-    this.track = track;
-    this.id = tool_dict.id;
-    this.name = tool_dict.name;
-    this.params = [];
-    var params_dict = tool_dict.params;
-    for (var i = 0; i < params_dict.length; i++) {
-        // FIXME: use dict for creating parameters.
-        var param_dict = params_dict[i],
-            name = param_dict.name,
-            label = param_dict.label,
-            html = unescape(param_dict.html),
-            value = param_dict.value,
-            type = param_dict.type;
-        if (type === "number") {
-            this.params.push(
-                new NumberParameter(name, label, html, 
-                                    (name in tool_state_dict ? tool_state_dict[name] : value),
-                                    param_dict.min, param_dict.max)
-                            );
+var TracksterTool = Backbone.RelationalModel.extend({
+    defaults: {
+        track: null,
+        tool: null,
+    },
+
+    relations: [
+        {
+            type: Backbone.HasOne,
+            key: 'tool',
+            relatedModel: tools_mod.Tool
         }
-        else if (type === "select") {
-            this.params.push(
-                new ToolParameter(name, label, html, 
-                                  (name in tool_state_dict ? tool_state_dict[name] : value))
-                            );
-        }
-        else {
-            console.log("WARNING: unrecognized tool parameter type:", name, type);
-        }        
-    }
-    
-    //
-    // Create div elt for tool UI.
-    //
-    this.parent_div = $("<div/>").addClass("dynamic-tool").hide();
-    // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz.
-    this.parent_div.bind("drag", function(e) {
-        e.stopPropagation();
-    }).click(function(e) {
-        e.stopPropagation();
-    }).bind("dblclick", function(e) {
-        e.stopPropagation();
-    });
-    var name_div = $("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);
-    var tool_params = this.params;
-    var tool = this;
-    $.each(this.params, function(index, param) {
-        var param_div = $("<div>").addClass("param-row").appendTo(tool.parent_div);
+    ]
+
+});
+
+/**
+ * View renders tool parameter HTML and updates parameter value as it is changed in the HTML.
+ */
+ var ToolParameterView = Backbone.View.extend({
+
+    events: {
+        'change input': 'update_value'
+    },
+
+    render: function() {
+        var param_div = this.$el.addClass("param-row"),
+            param = this.model;
+
         // Param label.
-        var label_div = $("<div>").addClass("param-label").text(param.label).appendTo(param_div);
+        var label_div = $("<div>").addClass("param-label").text(param.get('label')).appendTo(param_div);
         // Param HTML.
-        var html_div = $("<div/>").addClass("param-input").html(param.html).appendTo(param_div);
+        var html_div = $("<div/>").addClass("param-input").html(param.get('html')).appendTo(param_div);
         // Set initial value.
-        html_div.find(":input").val(param.value);
+        html_div.find(":input").val(param.get('value'));
         
         // Add to clear floating layout.
         $("<div style='clear: both;'/>").appendTo(param_div);
-    });
-    
-    // Highlight value for inputs for easy replacement.
-    this.parent_div.find("input").click(function() { $(this).select(); });
-    
-    // Add buttons for running on dataset, region.
-    var run_tool_row = $("<div>").addClass("param-row").appendTo(this.parent_div);
-    var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row);
-    var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row);
-    run_on_region_button.click( function() {
-        // Run tool to create new track.
-        tool.run_on_region();
-    });
-    run_on_dataset_button.click( function() {
-        tool.run_on_dataset();
-    });
-    
-    if ('visible' in tool_state_dict && tool_state_dict.visible) {
-        this.parent_div.show();
+    },
+
+    update_value: function(update_event) {
+        this.model.set_value($(update_event.target).val());
     }
-};
-extend(Tool.prototype, {
+ });
+
+/**
+ * View for TracksterTool.
+ */
+var TracksterToolView = Backbone.View.extend({
+
+    /**
+     * Render tool UI.
+     */
+    render: function() {
+        var self = this;
+            tool = this.model.get('tool'),
+            parent_div = this.$el.addClass("dynamic-tool").hide();
+
+        // Prevent div events from propogating to other elements.
+        parent_div.bind("drag", function(e) {
+            e.stopPropagation();
+        }).click(function(e) {
+            e.stopPropagation();
+        }).bind("dblclick", function(e) {
+            e.stopPropagation();
+        }).keydown(function(e) { e.stopPropagation(); });
+
+        // Add name, inputs.
+        var name_div = $("<div class='tool-name'>").appendTo(parent_div).text(tool.get('name'));
+        tool.get('inputs').each(function(param) {
+            var param_view = new ToolParameterView({ model: param });
+            param_view.render();
+            parent_div.append(param_view.$el);
+        });
+
+        // Highlight value for inputs for easy replacement.
+        parent_div.find("input").click(function() { $(this).select(); });
+        
+        // Add buttons for running on dataset, region.
+        var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div);
+        var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row);
+        var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row);
+        run_on_region_button.click( function() {
+            // Run tool to create new track.
+            self.run_on_region();
+        });
+        run_on_dataset_button.click( function() {
+            self.run_on_dataset();
+        });
+        
+        /*
+        if ('visible' in tool_state_dict && tool_state_dict.visible) {
+            this.parent_div.show();
+        }
+        */
+    },
+
     /**
      * Update tool parameters.
      */
@@ -1713,68 +1727,42 @@
             this.params[i].update_value();
         }
     },
+
     /**
      * Returns a dict with tool state information.
      */
     state_dict: function() {
         // Save parameter values.
-        var tool_state = {};
-        for (var i = 0; i < this.params.length; i++) {
-            tool_state[this.params[i].name] = this.params[i].value;
-        }
+        var tool_state = this.model.get('tool').get_param_values_dict();
         
         // Save visibility.
         tool_state.visible = this.parent_div.is(":visible");
         
         return tool_state;
     },
-    /** 
-     * Returns dictionary of parameter name-values.
-     */
-    get_param_values_dict: function() {
-        var param_dict = {};
-        this.parent_div.find(":input").each(function() {
-            var name = $(this).attr("name"), value = $(this).val();
-            param_dict[name] = value;
-        });
-        return param_dict;
-    },
-    /**
-     * Returns array of parameter values.
-     */
-    get_param_values: function() {
-        var param_values = [];
-        this.parent_div.find(":input").each(function() {
-            // Only include inputs with names; this excludes Run button.
-            var name = $(this).attr("name"), value = $(this).val();
-            if (name) {
-                param_values[param_values.length] = value;
-            }
-        });
-        return param_values;
-    },
+
     /**
      * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made.
      */
     run_on_dataset: function() {
-        var tool = this;
-        tool.run(
-                 // URL params.
-                 { 
-                     target_dataset_id: this.track.dataset.id,
-                     action: 'rerun',
-                     tool_id: tool.id
-                 },
-                 null,
-                 // Success callback.
-                 function(track_data) {
-                     show_modal(tool.name + " is Running", 
-                                tool.name + " is running on the complete dataset. Tool outputs are in dataset's history.", 
-                                { "Close" : hide_modal } );
-                 }
-                );
-        
+        var tool = this.model.get('tool');
+        this.run(
+            // URL params.
+            { 
+                target_dataset_id: this.model.get('track').dataset.id,
+                action: 'rerun',
+                tool_id: tool.id
+            },
+            null,
+            // Success callback.
+            function(track_data) {
+                show_modal(tool.get('name') + " is Running", 
+                            tool.get('name') + " is running on the complete dataset. Tool outputs are in dataset's history.", 
+                            { "Close" : hide_modal } );
+            }
+        );
     },
+
     /**
      * Run dataset on visible region. This creates a new track and sets the track's contents
      * to the tool's output.
@@ -1783,21 +1771,23 @@
         //
         // Create track for tool's output immediately to provide user feedback.
         //
-        var region = new visualization.GenomeRegion({
-                chrom: this.track.view.chrom,
-                start: this.track.view.low,
-                end: this.track.view.high
+        var track = this.model.get('track'),
+            tool = this.model.get('tool'),
+            region = new visualization.GenomeRegion({
+                chrom: track.view.chrom,
+                start: track.view.low,
+                end: track.view.high
             }),
             url_params = 
             { 
-                target_dataset_id: this.track.dataset.id,
+                target_dataset_id: track.dataset.id,
                 action: 'rerun',
-                tool_id: this.id,
+                tool_id: tool.id,
                 regions: [
                     region.toJSON()
                 ]
             },
-            current_track = this.track,
+            current_track = track,
             // Set name of track to include tool name, parameters, and region used.
             track_name = url_params.tool_id +
                          current_track.tool_region_and_parameters_str(region),
@@ -1838,25 +1828,25 @@
         new_track.tiles_div.text("Starting job.");
         
         // Run tool.
-        this.update_params();
         this.run(url_params, new_track,
-                 // Success callback.
-                 function(track_data) {
-                     new_track.set_dataset(new data.Dataset(track_data));
-                     new_track.tiles_div.text("Running job.");
-                     new_track.init();
-                 }
-                );
+                // Success callback.
+                function(track_data) {
+                    new_track.set_dataset(new data.Dataset(track_data));
+                    new_track.tiles_div.text("Running job.");
+                    new_track.init();
+                }
+        );
     },
+
     /**
      * Run tool using a set of URL params and a success callback.
      */
     run: function(url_params, new_track, success_callback) {
         // Run tool.
-        url_params.inputs = this.get_param_values_dict();
+        url_params.inputs = this.model.get('tool').get_inputs_dict();
         var ss_deferred = new util.ServerStateDeferred({
             ajax_settings: {
-                url: config.root + "/api/tools",
+                url: config.root + "api/tools",
                 data: JSON.stringify(url_params),
                 dataType: "json",
                 contentType: 'application/json',
@@ -1889,36 +1879,7 @@
             }            
         });
     }
-});
-
-/**
- * Tool parameters.
- */
-var ToolParameter = function(name, label, html, value) {
-    this.name = name;
-    this.label = label;
-    // Need to use jQuery for HTML so that value can be queried and updated dynamically.
-    this.html = $(html);
-    this.value = value;
-};
-
-extend(ToolParameter.prototype, {
-    update_value: function() {
-        this.value = $(this.html).val();
-    } 
-});
-
-var NumberParameter = function(name, label, html, value, min, max) {
-    ToolParameter.call(this, name, label, html, value);
-    this.min = min;
-    this.max = max;
-};
-
-extend(NumberParameter.prototype, ToolParameter.prototype, {
-    update_value: function() {
-        ToolParameter.prototype.update_value.call(this);
-        this.value = parseFloat(this.value);
-    }
+
 });
 
 /**
@@ -2819,7 +2780,12 @@
     // FIXME: prolly need function to set filters and update data_manager reference.
     this.data_manager.set('filters_manager', this.filters_manager);
     this.filters_available = false;
-    this.tool = ('tool' in obj_dict && obj_dict.tool ? new Tool(this, obj_dict.tool, obj_dict.tool_state) : null);
+    this.tool = (obj_dict.tool ? new TracksterTool({
+        'track': this, 
+        'tool': obj_dict.tool,
+        'tool_state': obj_dict.tool_state
+    }) 
+    : null);
     this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE);
     this.left_offset = 0;
     
@@ -2830,10 +2796,12 @@
         this.set_filters_manager(this.filters_manager);
         
         //
-        // Create dynamic tool div.
+        // Create dynamic tool view.
         //
-        if (this.tool) {  
-            this.dynamic_tool_div = this.tool.parent_div;
+        if (this.tool) {
+            var tool_view = new TracksterToolView({ model: this.tool });
+            tool_view.render();
+            this.dynamic_tool_div = tool_view.$el;
             this.header_div.after(this.dynamic_tool_div);
         }
     }
@@ -3427,8 +3395,9 @@
      */
     tool_region_and_parameters_str: function(region) {
         var track = this,
-            region_str = (region !== undefined ? region.toString() : "all");
-        return " - region=[" + region_str + "], parameters=[" + track.tool.get_param_values().join(", ") + "]";
+            region_str = (region !== undefined ? region.toString() : "all"),
+            param_str = _.values( track.tool.get('tool').get_inputs_dict()).join(', ');
+        return " - region=[" + region_str + "], parameters=[" + param_str + "]";
     },
 
     /**

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[galaxy-commits] commit/galaxy-central: jgoecks: Unify Trackster tool objects with generic tool objects. This unification enhances the generic tool framework and simplifies the trackster tool framework. Also, backbone-ify Trackster tool handling.

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