include fix patches for genomics-workspace 2.1

.gitignore

@@ -73,6 +73,10 @@ dist/
 /blast/static/blast/css/colReorder.dataTables.css
 /blast/static/blast/css/dataTables.bootstrap.css
 /blast/static/blast/css/jquery.dataTables.css
+/blast/static/blast/css/images/ui-icons_*
+/blast/static/blast/css/images/ui-bg_g*
+/blast/static/blast/css/images/ui-bg_h*
+/blast/static/blast/css/images/ui-bg_d*
 
 /hmmer/static/hmmer/scripts/jquery.hoverIntent.js
 /hmmer/static/hmmer/scripts/jquery.validate.js

app/admin.py

@@ -30,9 +30,9 @@ def short_description(self, obj):
 
     class Media:
         css = {
-            'all': ('blast/css/organism-admin.css',)
+            'all': ('app/css/organism-admin.css',)
         }
-        js = ('blast/scripts/organism-admin.js',)
+        js = ('app/scripts/organism-admin.js',)
 
 
 admin.site.register(Organism, OrganismAdmin)

blast/static/blast/css/blast-results.css

@@ -3,13 +3,13 @@
     top: 0;
     width: 12px;
     border-width: 0;
-    background: #efefef url('images/handle.svg') no-repeat center;
+    background: #efefef;
 }
 .k-ghost-splitbar-vertical, .k-splitbar-vertical {
     left: 0;
     height: 12px;
     border-width: 0;
-    background: #efefef url('images/handle-h.svg') no-repeat center;
+    background: #efefef;
 }
 .k-splitbar:hover {
     background-color: #ddd;

blast/static/blast/css/jquery-ui-custom.css

@@ -630,7 +630,7 @@
 .ui-widget-shadow {
 	margin: -5px 0 0 -5px;
 	padding: 5px;
-	background: #000000 url("images/ui-bg_flat_10_000000_40x100.png") 50% 50% repeat-x;
+	background: #000000;
 	opacity: .2;
 	filter: Alpha(Opacity=20); /* support: IE8 */
 	border-radius: 5px;

blast/static/blast/scripts/blast-results.js

@@ -40,8 +40,6 @@ $(function () { // document ready
     //////////////////
     // Prepare Data //
     //////////////////
-    // convert arrays to objects
-    //var results_db = _.map(results_data, function (row) { return _.object(results_col_names, row); });
     var col_idx = _.object(results_col_names, _.range(results_col_names.length));
     /////////////////////////
     // Hover and Selection //
@@ -67,12 +65,6 @@ $(function () { // document ready
         }
     });
     var s = new State;
-    s.on('change:hover', function (model, value, options) {
-        //console.log('change:hover - ' + value);
-    });
-    s.on('change:selected', function (model, value, options) {
-        //console.log('change:selected - ' + value);
-    });
     //////////////////
     // BLAST Report //
     //////////////////
@@ -105,7 +97,6 @@ $(function () { // document ready
             cm_blast_report.curOp.cursorActivityHandlers = false; // don't fire event
         });
         cm_blast_report.operation(function () {
-            //$('.CodeMirror')[0].CodeMirror.scrollTo(0, 2976+551/2-42)
             var info = cm_blast_report.getScrollInfo();
             cm_blast_report.scrollTo(0, info.top + info.clientHeight / 2 - 42);
             cm_blast_report.curOp.cursorActivityHandlers = false; // don't fire event
@@ -167,17 +158,7 @@ $(function () { // document ready
             return fasta_loading[sseqid];
         }
     }
-    s.on('change:hover', function (model, value, options) {
-        //if (options.set_by == this)
-        //    return;
-        //if (value != null)
-        //    cm_fasta_viewer_load_fasta(value);
-        //else {
-        //    selected = s.get('selected')
-        //    if (selected.length > 0)
-        //        cm_fasta_viewer_load_fasta(selected[0]);
-        //}
-    }, cm_fasta_viewer);
+    s.on('change:hover', function (model, value, options) {}, cm_fasta_viewer);
     s.on('change:selected', function (model, row_indexes, options) {
         if (options.set_by == this)
             return;
@@ -218,10 +199,6 @@ $(function () { // document ready
             '<"' + toolbar_prefix + 'tl ui-corner-tr"Rifr>' +
             't' +
             '<"' + toolbar_prefix + 'bl ui-corner-br"<"btn-download btn-group dropup">T>S',
-        //dom: 'Rifrt<"btn-group dropup">S',
-        //"dom": 'T<"clear">lfrtip',
-        //deferRender: true,
-        //bJQueryUI: true,
         tableTools: {
             sRowSelect: "os",
             aButtons: [],
@@ -903,7 +880,6 @@ $(function () { // document ready
                     var r = color_scale.invertExtent(c);
                     return Math.round(r[0]);
                 });
-                //$('.score-to-color-text').text('Dynamic');
                 updateAlignmentGraph();
             } else {
                 // static
@@ -937,12 +913,6 @@ $(function () { // document ready
             .style('background', function (c) {
                 return c[0];
             })
-            /*
-    linear-gradient(60deg, rgba(30,87,153,1) 0%,rgba(0,0,0,0) 100%),
-    linear-gradient(120deg, rgba(131,179,211,1) 0%,rgba(0,0,0,0) 100%),
-    linear-gradient(60deg, rgba(0,0,0,0) 0%,rgba(136,216,144,1) 100%),
-    linear-gradient(120deg, rgba(0,0,0,0) 0%,rgba(0,109,7,1) 100%);
-             */
             .style('background', function (c) {
                 return '-moz-linear-gradient(top, ' + c[0] + ' 0%, ' + c[1] + ' 100%)';
             }) //-moz-linear-gradient(top, #1e5799 0%, #7db9e8 100%);
@@ -1042,7 +1012,6 @@ $(function () { // document ready
         var start = Math.floor(filtered_rows.indexOf(focus_row_index) / graph_page_size) * graph_page_size;
         var paged_filtered_rows = filtered_rows.toArray().slice(start, start + graph_page_size);
         // Sort data ascending by coordinate for draw order
-        //var sorted_data = _.sortBy(filtered_data, function (row) { return -row['bitscore']; });
         // Set name text
         $('#' + canvas_name + '-name').text(focus_row_data[rseqid] + ', BLAST Hits ' + (start + 1) + '-' + (start + paged_filtered_rows.length));
 

package.json

@@ -38,6 +38,7 @@
     "jquery": "^1.11.1",
     "jquery-hoverintent": "^1.9.0",
     "jquery-ui-dist": "^1.12.0",
+    "jquery-ui-themes": "^1.12.0",
     "jquery-validation": "^1.14.0",
     "jquery.dragscrollable": "^1.0.0",
     "marked": "^0.3.19",

webpack.config.js

@@ -38,6 +38,7 @@ const appScriptConfig = {
 
 const blastScripts = path.resolve(__dirname, 'blast/static/blast/scripts');
 const blastStyles = path.resolve(__dirname, 'blast/static/blast/css');
+const blastImages = path.resolve(__dirname, 'blast/static/blast/css/images');
 const blastScriptConfig = {
   entry: path.join(nodeModules, '/jquery-validation/dist/jquery.validate.js'),  // Just a fake entry, we only copy files here
   output: {
@@ -66,6 +67,25 @@ const blastScriptConfig = {
         { from: path.join(nodeModules, '/datatables.net-colreorder-dt/css/colReorder.dataTables.css'), to: blastStyles},
         { from: path.join(nodeModules, '/datatables.net-bs/css/dataTables.bootstrap.css'), to: blastStyles},
         { from: path.join(nodeModules, '/datatables.net-dt/css/jquery.dataTables.css'), to: blastStyles},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_444444_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_777620_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_cc0000_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_555555_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_777777_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-dist/images/ui-icons_ffffff_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-icons_222222_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-icons_228ef1_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-icons_ef8c08_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-icons_ffd27a_256x240.png'), to: blastImages},
+        { from: path.join(nodeModules, '/jquery-ui-themes/themes/ui-lightness/images/ui-icons_ffffff_256x240.png'), to: blastImages},
     ])
   ],
   module: {