[galaxy-commits] commit/galaxy-central: 2 new changesets

17 Sep 2012

2 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/67c3ec05a121/
changeset:   67c3ec05a121
user:        james_taylor
date:        2012-09-17 22:14:52
summary:     trackster: misc fixes and reorganization
affected #:  3 files

diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 static/scripts/base.js

--- a/static/scripts/base.js
+++ b/static/scripts/base.js
@@ -1,15 +1,15 @@
-define( "libs/backbone", function( backbone ) {
+define( ["libs/backbone/backbone"], function( Backbone ) {
 
 	var Base = function() {
 		if( this.initialize ) {
 			this.initialize.apply(this, arguments);
 		}
 	};
-	Base.extend = backbone.Backbone.Model.extend;
+	Base.extend = Backbone.Model.extend;
 
 	return {
 		Base: Base,
-		Backbone: backbone.Backbone
+		Backbone: Backbone
 	};
 
 });
\ No newline at end of file


diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 static/scripts/viz/trackster_ui.js
--- a/static/scripts/viz/trackster_ui.js
+++ b/static/scripts/viz/trackster_ui.js
@@ -1,4 +1,4 @@
-define( ["libs/underscore","viz/trackster/slotting", "viz/trackster/painters","viz/trackster/tracks"], function( _, slotting, painters, tracks ) {
+define( ["base","libs/underscore","viz/trackster/slotting", "viz/trackster/painters","viz/trackster/tracks"], function( base, _, slotting, painters, tracks ) {
 
 /************************************************************************
  * Functions used for creating and managing the Trackster user interface.
@@ -6,139 +6,191 @@
 
 var object_from_template = tracks.object_from_template;
 
-/**
- * Add bookmark.
- */
-var add_bookmark = function(position, annotation, editable) {
-    // Create HTML.
-    var bookmarks_container = $("#bookmarks-container"),
-        new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container);
+var TracksterUI = base.Base.extend({
 
-    var position_div = $("<div/>").addClass("position").appendTo(new_bookmark),
-        position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() {
-            view.go_to(position);
-            return false;
-        }),
-        annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark);
+    initialize: function( baseURL ) {
+        this.baseURL = baseURL;
+    },
 
-    // If editable, enable bookmark deletion and annotation editing.
-    if (editable) {
-        var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){
-                // Remove bookmark.
-                new_bookmark.slideUp("fast");
-                new_bookmark.remove();
-                view.has_changes = true;
+    /**
+     * Use a popup to select a dataset of create bookmarks from
+     */
+    add_bookmarks: function() {
+        var baseURL = this.baseURL;
+        show_modal( "Select dataset for new bookmarks", "progress" );
+        $.ajax({
+            url: this.baseURL + "/visualization/list_histories",
+            data: { "f-dbkey": view.dbkey },
+            error: function() { alert( "Grid failed" ); },
+            success: function(table_html) {
+                show_modal(
+                    "Select dataset for new bookmarks",
+                    table_html, {
+                        "Cancel": function() {
+                            hide_modal();
+                        },
+                        "Insert": function() {
+                            // Just use the first selected
+                            $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){
+                                var data, id = $(this).val();
+                                    if ($(this).attr("name") === "id") {
+                                        data = { hda_id: id };
+                                    } else {
+                                        data = { ldda_id: id};
+                                    }
+
+                                    $.ajax({
+                                        url: this.baseURL + "/visualization/bookmarks_from_dataset",
+                                        data: data,
+                                        dataType: "json",
+                                    }).then( function(data) {
+                                        for( i = 0; i < data.data.length; i++ ) {
+                                            var row = data.data[i];
+                                            add_bookmark( row[0], row[1] );
+                                        }
+                                    });
+                            });
+                            hide_modal();
+                        }
+                    }
+                );
+            }
+        });
+    },
+
+    /**
+     * Add bookmark.
+     */
+    add_bookmark: function(position, annotation, editable) {
+        // Create HTML.
+        var bookmarks_container = $("#bookmarks-container"),
+            new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container);
+
+        var position_div = $("<div/>").addClass("position").appendTo(new_bookmark),
+            position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() {
+                view.go_to(position);
                 return false;
             }),
-            delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container);
-        annotation_div.make_text_editable({
-            num_rows: 3,
-            use_textarea: true,
-            help_text: "Edit bookmark note"
-        }).addClass("annotation");
+            annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark);
+
+        // If editable, enable bookmark deletion and annotation editing.
+        if (editable) {
+            var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){
+                    // Remove bookmark.
+                    new_bookmark.slideUp("fast");
+                    new_bookmark.remove();
+                    view.has_changes = true;
+                    return false;
+                }),
+                delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container);
+            annotation_div.make_text_editable({
+                num_rows: 3,
+                use_textarea: true,
+                help_text: "Edit bookmark note"
+            }).addClass("annotation");
+        }
+
+        view.has_changes = true;
+        return new_bookmark;
+    },
+
+    /**
+     * Create a complete Trackster visualization. Returns view.
+     */
+    create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
+        
+        // Create view.
+        view = new tracks.View(view_config);
+        view.editor = true;
+        $.when( view.load_chroms_deferred ).then(function() {
+            // Viewport config.
+            if (viewport_config) {
+                var 
+                    chrom = viewport_config.chrom,
+                    start = viewport_config.start,
+                    end = viewport_config.end,
+                    overview_drawable_name = viewport_config.overview;
+            
+                if (chrom && (start !== undefined) && end) {
+                    view.change_chrom(chrom, start, end);
+                }
+            }
+            
+            // Add drawables to view.
+            if (drawables_config) {
+                // FIXME: can from_dict() be used to create view and add drawables?
+                var drawable_config,
+                    drawable_type,
+                    drawable;
+                for (var i = 0; i < drawables_config.length; i++) {
+                    view.add_drawable( object_from_template( drawables_config[i], view, view ) );
+                }
+            }
+            
+            // Need to update intro div after drawables have been added.
+            view.update_intro_div();
+            
+            // Set overview.
+            var overview_drawable;
+            for (var i = 0; i < view.drawables.length; i++) {
+                if (view.drawables[i].name === overview_drawable_name) {
+                    view.set_overview(view.drawables[i]);
+                    break;
+                }
+            }
+            
+            // Load bookmarks.
+            if (bookmarks_config) {
+                var bookmark;
+                for (var i = 0; i < bookmarks_config.length; i++) {
+                    bookmark = bookmarks_config[i];
+                    add_bookmark(bookmark['position'], bookmark['annotation'], editable);
+                }
+            }
+
+            // View has no changes as of yet.
+            view.has_changes = false;
+        });
+        
+        return view;
+    },
+
+    /**
+     * Set up keyboard navigation for a visualization.
+     */
+     init_keyboard_nav: function(view) {
+        // Keyboard navigation. Scroll ~7% of height when scrolling up/down.
+        $(document).keydown(function(e) {
+            // Do not navigate if arrow keys used in input element.
+            if ($(e.srcElement).is(':input')) {
+                return;
+            }
+            
+            // Key codes: left == 37, up == 38, right == 39, down == 40
+            switch(e.which) {
+                case 37:
+                    view.move_fraction(0.25);
+                    break
+                case 38:
+                    var change = Math.round(view.viewport_container.height()/15.0);
+                    view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20);
+                    break;
+                case 39:
+                    view.move_fraction(-0.25);
+                    break;
+                case 40:
+                    var change = Math.round(view.viewport_container.height()/15.0);
+                    view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20);
+                    break;
+            }
+        });
     }
 
-    view.has_changes = true;
-    return new_bookmark;
-};
-
-/**
- * Create a complete Trackster visualization. Returns view.
- */
-var create_visualization = function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
-    
-    // Create view.
-    view = new tracks.View(view_config);
-    view.editor = true;
-    $.when( view.load_chroms_deferred ).then(function() {
-        // Viewport config.
-        if (viewport_config) {
-            var 
-                chrom = viewport_config.chrom,
-                start = viewport_config.start,
-                end = viewport_config.end,
-                overview_drawable_name = viewport_config.overview;
-        
-            if (chrom && (start !== undefined) && end) {
-                view.change_chrom(chrom, start, end);
-            }
-        }
-        
-        // Add drawables to view.
-        if (drawables_config) {
-            // FIXME: can from_dict() be used to create view and add drawables?
-            var drawable_config,
-                drawable_type,
-                drawable;
-            for (var i = 0; i < drawables_config.length; i++) {
-                view.add_drawable( object_from_template( drawables_config[i], view, view ) );
-            }
-        }
-        
-        // Need to update intro div after drawables have been added.
-        view.update_intro_div();
-        
-        // Set overview.
-        var overview_drawable;
-        for (var i = 0; i < view.drawables.length; i++) {
-            if (view.drawables[i].name === overview_drawable_name) {
-                view.set_overview(view.drawables[i]);
-                break;
-            }
-        }
-        
-        // Load bookmarks.
-        if (bookmarks_config) {
-            var bookmark;
-            for (var i = 0; i < bookmarks_config.length; i++) {
-                bookmark = bookmarks_config[i];
-                add_bookmark(bookmark['position'], bookmark['annotation'], editable);
-            }
-        }
-
-        // View has no changes as of yet.
-        view.has_changes = false;
-    });
-    
-    return view;
-};
-
-/**
- * Set up keyboard navigation for a visualization.
- */
- var init_keyboard_nav = function(view) {
-    // Keyboard navigation. Scroll ~7% of height when scrolling up/down.
-    $(document).keydown(function(e) {
-        // Do not navigate if arrow keys used in input element.
-        if ($(e.srcElement).is(':input')) {
-            return;
-        }
-        
-        // Key codes: left == 37, up == 38, right == 39, down == 40
-        switch(e.which) {
-            case 37:
-                view.move_fraction(0.25);
-                break
-            case 38:
-                var change = Math.round(view.viewport_container.height()/15.0);
-                view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20);
-                break;
-            case 39:
-                view.move_fraction(-0.25);
-                break;
-            case 40:
-                var change = Math.round(view.viewport_container.height()/15.0);
-                view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20);
-                break;
-        }
-    });
-};
+});
 
 return {
-    add_bookmark: add_bookmark,
     object_from_template: object_from_template,
-    create_visualization: create_visualization,
-    init_keyboard_nav: init_keyboard_nav
+    TracksterUI: TracksterUI
 };
 
 });


diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 templates/tracks/browser.mako
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -31,12 +31,11 @@
     require.config({ 
         baseUrl: "${h.url_for('/static/scripts') }",
         shim: {
-            "libs/underscore": { exports: "_" }
+            "libs/underscore": { exports: "_" },
+            "libs/backbone/backbone": { exports: "Backbone" }
         }
     });
-    require( ["viz/trackster_ui","viz/trackster/util","viz/trackster/tracks"], function( trackster_ui, util, tracks ) {
-
-    var add_bookmark = trackster_ui.add_bookmark
+    require( ["base", "viz/trackster_ui","viz/trackster/util","viz/trackster/tracks"], function( base, trackster_ui, util, tracks ) {
 
     //
     // Place URLs here so that url_for can be used to generate them.
@@ -48,8 +47,9 @@
     ${render_trackster_js_vars()}
 
     var view,
-        browser_router;
-        
+        browser_router,
+        ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" );
+
     /**
      * Set up router.
      */
@@ -58,51 +58,7 @@
         Backbone.history.start();   
     };
     
-    /**
-     * Use a popup grid to bookmarks from a dataset.
-     */
-    var add_bookmarks = function() {
-        show_modal( "Select dataset for new bookmarks", "progress" );
-        $.ajax({
-            url: "${h.url_for( controller='visualization', action='list_histories' )}",
-            data: { "f-dbkey": view.dbkey },
-            error: function() { alert( "Grid failed" ); },
-            success: function(table_html) {
-                show_modal(
-                    "Select dataset for new bookmarks",
-                    table_html, {
-                        "Cancel": function() {
-                            hide_modal();
-                        },
-                        "Insert": function() {
-                            // Just use the first selected
-                            $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){
-                                var data, id = $(this).val();
-                                    if ($(this).attr("name") === "id") {
-                                        data = { hda_id: id };
-                                    } else {
-                                        data = { ldda_id: id};
-                                    }
 
-                                    $.ajax({
-                                        url: "${h.url_for( action='bookmarks_from_dataset' )}",
-                                        data: data,
-                                        dataType: "json",
-                                    }).then( function(data) {
-                                        for( i = 0; i < data.data.length; i++ ) {
-                                            var row = data.data[i];
-                                            add_bookmark( row[0], row[1] );
-                                        }
-                                    });
-                            });
-                            hide_modal();
-                        }
-                    }
-                );
-            }
-        });
-    };
-    
     var browser_router;
     $(function() {
         // Create and initialize menu.
@@ -192,7 +148,7 @@
         $("#right-border").click(function() { view.resize_window(); });
         
         %if config:
-            view = trackster_ui.create_visualization( {
+            view = ui.create_visualization( {
                                             container: $("#browser-container"), 
                                             name: "${config.get('title') | h}",
                                             vis_id: "${config.get('vis_id')}", 
@@ -262,7 +218,7 @@
                 // Add new bookmark.
                 var position = view.chrom + ":" + view.low + "-" + view.high,
                     annotation = "Bookmark description";
-                return add_bookmark(position, annotation, true);
+                return ui.add_bookmark(position, annotation, true);
             });
 
             // make_popupmenu( $("#bookmarks-more-button"), {
@@ -271,7 +227,7 @@
             //     }
             // });
 
-            trackster_ui.init_keyboard_nav(view);
+            ui.init_keyboard_nav(view);
         };
         
     });



https://bitbucket.org/galaxy/galaxy-central/changeset/6c0bb542d2e0/
changeset:   6c0bb542d2e0
user:        james_taylor
date:        2012-09-17 22:15:09
summary:     pack scripts
affected #:  2 files

diff -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d static/scripts/packed/base.js
--- a/static/scripts/packed/base.js
+++ b/static/scripts/packed/base.js
@@ -1,1 +1,1 @@
-define("libs/backbone",function(b){var a=function(){if(this.initialize){this.initialize.apply(this,arguments)}};a.extend=b.Backbone.Model.extend;return{Base:a,Backbone:b.Backbone}});
\ No newline at end of file
+define(["libs/backbone/backbone"],function(b){var a=function(){if(this.initialize){this.initialize.apply(this,arguments)}};a.extend=b.Model.extend;return{Base:a,Backbone:b}});
\ No newline at end of file


diff -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d static/scripts/packed/viz/trackster_ui.js
--- a/static/scripts/packed/viz/trackster_ui.js
+++ b/static/scripts/packed/viz/trackster_ui.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(d,h,g,c){var a=c.object_from_template;var f=function(m,k,i){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(i){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q};var b=function(l,i,k,m,j){view=new c.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(i){var v=i.chrom,n=i.start,s=i.end,p=i.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];f(u.position,u.annotation,j)}}view.has_changes=false});return view};var e=function(i){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:i.move_fraction(0.25);break;case 38:var k=Math.round(i.viewport_container.height()/15);i.viewport_container.scrollTop(i.viewport_container.scrollTop()-20);break;case 39:i.move_fraction(-0.25);break;case 40:var k=Math.round(i.viewport_container.height()/15);i.viewport_container.scrollTop(i.viewport_container.scrollTop()+20);break}})};return{add_bookmark:f,object_from_template:a,create_visualization:b,init_keyboard_nav:e}});
\ No newline at end of file
+define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json",}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}});
\ No newline at end of file

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

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[galaxy-commits] commit/galaxy-central: 2 new changesets

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