[galaxy-commits] commit/galaxy-central: 5 new changesets

13 Apr 2011

5 new changesets in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/56fc50970fc3/
changeset:   r5376:56fc50970fc3
user:        dannon
date:        2011-04-13 22:35:08
summary:     Bugfix for workflow run not reloading history, icon for document stack.
affected #:  2 files (803 bytes)

Binary file static/images/documents-stack.png has changed

--- a/templates/workflow/run_complete.mako	Wed Apr 13 16:05:34 2011 -0400
+++ b/templates/workflow/run_complete.mako	Wed Apr 13 16:35:08 2011 -0400
@@ -17,4 +17,10 @@
             %endfor
         %endfor
     </div>
-</div>
\ No newline at end of file
+</div>
+
+<script type="text/javascript">
+  if ( parent.frames && parent.frames.galaxy_history ) {
+      parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}";
+  }
+</script>


http://bitbucket.org/galaxy/galaxy-central/changeset/9a72df515de1/
changeset:   r5377:9a72df515de1
user:        dannon
date:        2011-04-13 22:46:36
summary:     Faded document stack icon.
affected #:  1 file (587 bytes)

Binary file static/images/documents-stack-faded.png has changed


http://bitbucket.org/galaxy/galaxy-central/changeset/a946c7e60d1f/
changeset:   r5378:a946c7e60d1f
user:        dannon
date:        2011-04-14 01:05:45
summary:     Merge.
affected #:  1 file (1.8 KB)

--- a/static/scripts/trackster.js	Wed Apr 13 16:46:36 2011 -0400
+++ b/static/scripts/trackster.js	Wed Apr 13 19:05:45 2011 -0400
@@ -741,7 +741,7 @@
         this.high = Math.ceil(high);
         
         // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width
-        this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / 200 ) / Math.LN10 ) );
+        this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) );
         this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )));
         
         // Overview
@@ -1016,14 +1016,16 @@
         return false;
     },
     /**
-     * Returns true iff element is in [low, high]; range is inclusive.
+     * Returns true if (a) element's value is in [low, high] (range is inclusive) 
+     * or (b) if value is non-numeric and hence unfilterable.
      */
     keep: function(element) {
         if ( !this.applies_to( element ) ) {
             // No element to filter on.
             return true;
         }
-        return (element[this.index] >= this.low && element[this.index] <= this.high);
+        var val = parseInt(element[this.index]);
+        return (isNaN(val) || (val >= this.low && val <= this.high));
     },
     /**
      * Update filter's min and max values based on element's values.
@@ -1306,11 +1308,22 @@
 });
 
 /**
- * Tiles for TiledTracks.
+ * Tiles drawn by tracks.
  */
-var Tile = function(track, canvas) {
-    this.track = track;
-    this.canvas = canvas;
+var Tile = function(index, resolution, canvas) {
+    // Wrap element in div for background
+    this.index = index;
+    this.resolution = resolution;
+    this.canvas = $("<div class='track-tile'/>").append(canvas);
+};
+
+var SummaryTreeTile = function(index, resolution, canvas, max_val) {
+    Tile.call(this, index, resolution, canvas);
+    this.max_val = max_val;
+};
+
+var FeatureTrackTile = function(index, resolution, canvas) {
+    Tile.call(this, index, resolution, canvas);
 };
 
 /**
@@ -1669,30 +1682,33 @@
             // w_scale units are pixels per base.
             w_scale = width / range,
             resolution = this.view.resolution,
-            parent_element = $("<div style='position: relative;'></div>");
+            parent_element = $("<div style='position: relative;'></div>"),
+            gen_key = function(width, w_scale, tile_index) { 
+                return width + '_' + w_scale + '_' + tile_index;
+            };
         
         if (!clear_after) { this.content_div.children().remove(); }
         this.content_div.append( parent_element );
         this.max_height = 0;
         // Index of first tile that overlaps visible region
         var tile_index = Math.floor( low / resolution / DENSITY );
-        // A set of setTimeout() ids used when drawing tiles. Each ID indicates
-        // a tile has been requested to be drawn or is being drawn.
-        var draw_tile_dict = {};
+        // A list of tiles drawn/retrieved.
+        var drawn_tiles = [];
+        var tile_count = 0
         while ( ( tile_index * DENSITY * resolution ) < high ) {
             // Check in cache
-            var key = width + '_' + w_scale + '_' + tile_index;
+            var key = gen_key(width, w_scale, tile_index);
             var cached = this.tile_cache.get(key);
             var tile_low = tile_index * DENSITY * this.view.resolution;
             var tile_high = tile_low + DENSITY * this.view.resolution;
-            // console.log(cached, this.tile_cache);
             if ( !force && cached ) {
+                drawn_tiles[drawn_tiles.length] = cached;
                 this.show_tile(cached, parent_element, tile_low, w_scale);
             } else {
-                this.delayed_draw(force, key, tile_low, tile_high, tile_index, 
-                                    resolution, parent_element, w_scale, draw_tile_dict);
+                this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles);
             }
             tile_index += 1;
+            tile_count++;
         }
                 
         //
@@ -1700,7 +1716,7 @@
         //
         var track = this;
         var intervalId = setInterval(function() {
-            if (obj_length(draw_tile_dict) === 0) {
+            if (drawn_tiles.length === tile_count) {
                 // All tiles have been drawn.
                 clearInterval(intervalId);
                 
@@ -1725,6 +1741,29 @@
                 }
                 
                 //
+                // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
+                //
+                if (track.mode == "Histogram") {
+                    // Get global max.
+                    var global_max = -1;
+                    for (var i = 0; i < drawn_tiles.length; i++) {
+                        var cur_max = drawn_tiles[i].max_val;
+                        if (cur_max > global_max) {
+                            global_max = cur_max;
+                        }
+                    }
+                    
+                    for (var i = 0; i < drawn_tiles.length; i++) {
+                        if (drawn_tiles[i].max_val !== global_max) {
+                            var tile = drawn_tiles[i];
+                            tile.canvas.remove();
+                            track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index, 
+                                               tile.resolution, parent_element, w_scale, [], { max: global_max });
+                        }
+                    }
+                }                
+                
+                //
                 // Update filter attributes, UI.
                 //
 
@@ -1755,6 +1794,19 @@
                         track.make_name_popup_menu();
                     }
                 }
+                
+                // Store initial canvas in case we need to use it for overview
+                /* This is completely broken, just saves the first tile it sees
+                   regardless of if it should be the overview
+                if (!track.initial_canvas && !window.G_vmlCanvasManager) {
+                    track.initial_canvas = $(tile_element).clone();
+                    var src_ctx = tile_element.get(0).getContext("2d");
+                    var tgt_ctx = track.initial_canvas.get(0).getContext("2d");
+                    var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
+                    tgt_ctx.putImageData(data, 0, 0);
+                    track.set_overview();
+                }
+                */                
             }
         }, 50);
              
@@ -1765,44 +1817,28 @@
             this.child_tracks[i].draw(force, clear_after);
         }
     }, 
-    delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_dict) {
-        var track = this;
-        // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
+    delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
+        var track = this,
+            tile_low = tile_index * DENSITY * resolution,
+            tile_high = tile_low + DENSITY * resolution;
+        
+        // Helper method.
         var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) {
             // DEBUG: this is still called too many times when moving slowly,
             // console.log( "draw_and_show_tile", resolution, tile_index, w_scale );
-            returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data)
-            
-            // Wrap element in div for background
-            var wrapper_element = $("<div class='track-tile'>").prepend(returned_tile);
-            tile_element = wrapper_element;
-            
-            track.tile_cache.set(key, tile_element);
-            track.show_tile(tile_element, parent_element, tile_low, w_scale);
-            
-            // TODO: this should go in a post-draw function.
-            // Store initial canvas in case we need to use it for overview
-            /* This is completely broken, just saves the first tile it sees
-               regardless of if it should be the overview
-            if (!track.initial_canvas && !window.G_vmlCanvasManager) {
-                track.initial_canvas = $(tile_element).clone();
-                var src_ctx = tile_element.get(0).getContext("2d");
-                var tgt_ctx = track.initial_canvas.get(0).getContext("2d");
-                var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
-                tgt_ctx.putImageData(data, 0, 0);
-                track.set_overview();
-            }
-            */
-            
-            delete draw_tile_dict[id];
+            var tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data);
+            track.tile_cache.set(key, tile);
+            track.show_tile(tile, parent_element, tile_low, w_scale);
+            drawn_tiles[drawn_tiles.length] = tile;
         };
+        // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
         var id = setTimeout(function() {
             if (tile_low <= track.view.high && tile_high >= track.view.low) {
                 // Show/draw tile: check cache for tile; if tile not in cache, draw it.
-                var tile_element = (force ? undefined : track.tile_cache.get(key));
-                if (tile_element) { 
-                    track.show_tile(tile_element, parent_element, tile_low, w_scale);
-                    delete draw_tile_dict[id];
+                var tile = (force ? undefined : track.tile_cache.get(key));
+                if (tile) { 
+                    track.show_tile(tile, parent_element, tile_low, w_scale);
+                    drawn_tiles[drawn_tiles.length] = tile;
                 }
                 else {
                     //
@@ -1810,6 +1846,7 @@
                     //
                     $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, 
                                                      resolution, track.data_url_extra_params)).then(function(tile_data) {
+                        extend(tile_data, more_tile_data);
                         // If sequence data needed, get that and draw. Otherwise draw.
                         if (view.reference_track && w_scale > view.canvas_manager.char_width_px) {
                             $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, 
@@ -1825,12 +1862,11 @@
                 }
             }
         }, 50);
-        draw_tile_dict[id] = true;
     }, 
     /**
      * Show track tile and perform associated actions.
      */
-    show_tile: function(tile_element, parent_element, tile_low, w_scale) {
+    show_tile: function(tile, parent_element, tile_low, w_scale) {
         // Readability.
         var track = this;
         
@@ -1844,6 +1880,7 @@
         if (this.left_offset) {
             left -= this.left_offset;
         }
+        var tile_element = tile.canvas;
         tile_element.css({ position: 'absolute', top: 0, left: left, height: '' });
 
         // Setup and show tile element.
@@ -1966,7 +2003,7 @@
                 var c_start = Math.round(c * w_scale);
                 ctx.fillText(seq[c], c_start + track.left_offset, 10);
             }
-            return canvas;
+            return new Tile(tile_index, resolution, canvas);
         }
         this.content_div.css("height", "0px");
     }
@@ -2106,7 +2143,7 @@
                                                 this.prefs, this.mode );
         painter.draw( ctx, width, height );
         
-        return canvas;
+        return new Tile(tile_length, resolution, canvas);
     } 
 });
 
@@ -2196,11 +2233,14 @@
      * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
      * is a two-item list; first item is bin start, second is bin's count.
      */
-    get_summary_tree_data: function(data, low, high, bin_size) {
-        var num_bins = Math.floor((high - low)/bin_size),
+    get_summary_tree_data: function(data, low, high, num_bins) {
+        if (num_bins > high - low) {
+            num_bins = high - low;
+        }
+        var bin_size = Math.floor((high - low)/num_bins),
             bins = [],
             max_count = 0;
-        
+            
         /*    
         // For debugging:
         for (var i = 0; i < data.length; i++)
@@ -2335,8 +2375,7 @@
             // Deal with left_offset by translating
             ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING );
             painter.draw( ctx, width, required_height );
-            // Canvas element is returned
-            return canvas;            
+            return new SummaryTreeTile(tile_index, resolution, canvas, result.max);
         }
         
         // Drawing coverage histogram. This is different from summary tree because data can feature
@@ -2359,13 +2398,15 @@
             canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
             // Paint summary tree into canvas.
             var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
+            if (result.max) {
+                binned_data.max = result.max;
+            }
             var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs);
             var ctx = canvas.getContext("2d");
             // Deal with left_offset by translating
             ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
             painter.draw(ctx, width, required_height);
-            // Canvas element is returned
-            return canvas;
+            return new SummaryTreeTile(tile_index, resolution, canvas, binned_data.max);
         }
 
         // Start dealing with row-by-row tracks
@@ -2433,7 +2474,7 @@
 
             // If there's no data, return.
             if (!result.data) {
-                return canvas;
+                return new Tile(tile_index, resolution, canvas);
             }
         }
 
@@ -2444,7 +2485,7 @@
         ctx.translate( left_offset, ERROR_PADDING );
         painter.draw( ctx, width, required_height, slots );
             
-        return canvas;
+        return new FeatureTrackTile(tile_index, resolution, canvas);
     }
 });
 
@@ -2558,7 +2599,7 @@
     this.include_label = include_label;
     this.max_rows = max_rows;
     this.measureText = measureText;
-}
+};
 
 /**
  * Slot a set of features, `this.slots` will be updated with slots by id, and
@@ -2704,7 +2745,7 @@
 // ---- Painters ----
 
 var painters_module = function(require, exports){
-
+    
 /**
  * Draw a dashed line on a canvas using filled rectangles. This function is based on:
  * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.ht...
@@ -2776,7 +2817,7 @@
     Painter.call( this, data, view_start, view_end, prefs, mode );
 }
 
-SummaryTreePainter.prototype.default_prefis = { show_counts: false };
+SummaryTreePainter.prototype.default_prefs = { show_counts: false };
 
 SummaryTreePainter.prototype.draw = function( ctx, width, height ) {
     
@@ -2790,16 +2831,15 @@
         // max rectangle is required_height.
         base_y = height;
         delta_x_px = Math.ceil(delta * w_scale);
-    
     ctx.save();
     
     for (var i = 0, len = points.length; i < len; i++) {
-        
         var x = Math.floor( (points[i][0] - view_start) * w_scale );
         var y = points[i][1];
         
         if (!y) { continue; }
-        var y_px = y / max * height;
+        var y_px = y / max * height
+        if (y !== 0 && y_px < 1) { y_px = 1; }
         
         ctx.fillStyle = "black";
         ctx.fillRect( x, base_y - y_px, delta_x_px, y_px );
@@ -2991,7 +3031,7 @@
     }
 });
 
-// Contstants specific to feature tracks moved here (HACKING, these should
+// Constants specific to feature tracks moved here (HACKING, these should
 // basically all be configuration options)
 var DENSE_TRACK_HEIGHT = 10,
     NO_DETAIL_TRACK_HEIGHT = 3,
@@ -3034,8 +3074,7 @@
         var 
             feature_uid = feature[0],
             feature_start = feature[1],
-            // -1 b/c intervals are half-open.
-            feature_end = feature[2] - 1, 
+            feature_end = feature[2], 
             feature_name = feature[3],
             f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
             f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -3134,8 +3173,7 @@
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
                     var block = feature_blocks[k],
                         block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
-                        // -1 b/c intervals are half-open.
-                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) );
+                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
 
                     // Skip drawing if block not on tile.    
                     if (block_start > block_end) { continue; }
@@ -3199,8 +3237,7 @@
         var feature = data[i],
             feature_uid = feature[0],
             feature_start = feature[1],
-            // -1 b/c intervals are half-open.
-            feature_end = feature[2] - 1,
+            feature_end = feature[2],
             feature_name = feature[3],
             // All features need a start, end, and vertical center.
             f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),


http://bitbucket.org/galaxy/galaxy-central/changeset/1c5796258fb5/
changeset:   r5379:1c5796258fb5
user:        Martijn Vermaat
date:        2011-04-14 01:04:40
summary:     Run a workflow on a selection of multiple inputs, one invocation for each.

- Makes input selections in the run workflow form support multiple
  selection.
- If multiple inputs are selected, a workflow invocation is executed for
  each selected input.
- Only of of the workflow inputs can have a multiple selection.
affected #:  6 files (3.8 KB)

--- a/lib/galaxy/tools/parameters/basic.py	Wed Apr 13 16:46:36 2011 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Thu Apr 14 01:04:40 2011 +0200
@@ -1421,6 +1421,14 @@
         else:
             return "No dataset"
 
+    def validate( self, value, history=None ):
+        for validator in self.validators:
+            if value and self.multiple and isinstance(value, list):
+                for v in value:
+                    validator.validate( v, history )
+            else:
+                validator.validate( value, history )
+
     def get_dependencies( self ):
         """
         Get the *names* of the other params this param depends on.


--- a/lib/galaxy/web/controllers/workflow.py	Wed Apr 13 16:46:36 2011 -0400
+++ b/lib/galaxy/web/controllers/workflow.py	Thu Apr 14 01:04:40 2011 +0200
@@ -1262,96 +1262,117 @@
         if kwargs:
             # If kwargs were provided, the states for each step should have
             # been POSTed
-            for step in workflow.steps:
-                step.upgrade_messages = {}
-                # Connections by input name
-                step.input_connections_by_name = \
-                    dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
-                # Extract just the arguments for this step by prefix
-                p = "%s|" % step.id
-                l = len(p)
-                step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
-                step_errors = None
-                if step.type == 'tool' or step.type is None:
-                    module = module_factory.from_workflow_step( trans, step )
-                    # Fix any missing parameters
-                    step.upgrade_messages = module.check_and_update_state()
-                    if step.upgrade_messages:
-                        has_upgrade_messages = True
-                    # Any connected input needs to have value DummyDataset (these
-                    # are not persisted so we need to do it every time)
-                    module.add_dummy_datasets( connections=step.input_connections )    
-                    # Get the tool
-                    tool = module.tool
-                    # Get the state
-                    step.state = state = module.state
-                    # Get old errors
-                    old_errors = state.inputs.pop( "__errors__", {} )
-                    # Update the state
-                    step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
-                                                     update_only=True, old_errors=old_errors )
-                else:
-                    module = step.module = module_factory.from_workflow_step( trans, step )
-                    state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
-                    step_errors = module.update_runtime_state( trans, state, step_args )
-                if step_errors:
-                    errors[step.id] = state.inputs["__errors__"] = step_errors   
-            if 'run_workflow' in kwargs and not errors:
-                new_history = None
-                if 'new_history' in kwargs:
-                    if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
-                        nh_name = kwargs['new_history_name']
+            # Get the kwarg keys for data inputs
+            input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+            # Example: prefixed='2|input'
+            # Check if one of them is a list
+            multiple_input_key = None
+            multiple_inputs = [None]
+            for input_key in input_keys:
+                if isinstance(kwargs[input_key], list):
+                    multiple_input_key = input_key
+                    multiple_inputs = kwargs[input_key]
+            # List to gather values for the template
+            invocations=[]
+            for input_number, single_input in enumerate(multiple_inputs):
+                # Example: single_input='1', single_input='2', etc...
+                # 'Fix' the kwargs, to have only the input for this iteration
+                if multiple_input_key:
+                    kwargs[multiple_input_key] = single_input
+                for step in workflow.steps:
+                    step.upgrade_messages = {}
+                    # Connections by input name
+                    step.input_connections_by_name = \
+                        dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                    # Extract just the arguments for this step by prefix
+                    p = "%s|" % step.id
+                    l = len(p)
+                    step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
+                    step_errors = None
+                    if step.type == 'tool' or step.type is None:
+                        module = module_factory.from_workflow_step( trans, step )
+                        # Fix any missing parameters
+                        step.upgrade_messages = module.check_and_update_state()
+                        if step.upgrade_messages:
+                            has_upgrade_messages = True
+                        # Any connected input needs to have value DummyDataset (these
+                        # are not persisted so we need to do it every time)
+                        module.add_dummy_datasets( connections=step.input_connections )    
+                        # Get the tool
+                        tool = module.tool
+                        # Get the state
+                        step.state = state = module.state
+                        # Get old errors
+                        old_errors = state.inputs.pop( "__errors__", {} )
+                        # Update the state
+                        step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
+                                                         update_only=True, old_errors=old_errors )
                     else:
-                        nh_name = "History from %s workflow" % workflow.name
-                    new_history = trans.app.model.History( user=trans.user, name=nh_name )
-                    trans.sa_session.add( new_history )
-                # Run each step, connecting outputs to inputs
-                workflow_invocation = model.WorkflowInvocation()
-                workflow_invocation.workflow = workflow
-                outputs = odict()
-                for i, step in enumerate( workflow.steps ):
-                    # Execute module
-                    job = None
-                    if step.type == 'tool' or step.type is None:
-                        tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
-                        input_values = step.state.inputs
-                        # Connect up
-                        def callback( input, value, prefixed_name, prefixed_label ):
-                            if isinstance( input, DataToolParameter ):
-                                if prefixed_name in step.input_connections_by_name:
-                                    conn = step.input_connections_by_name[ prefixed_name ]
-                                    return outputs[ conn.output_step.id ][ conn.output_name ]
-                        visit_input_values( tool.inputs, step.state.inputs, callback )
-                        # Execute it
-                        job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
-                        outputs[ step.id ] = out_data
-                        # Create new PJA associations with the created job, to be run on completion.
-                        # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
-                        # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-                        replacement_dict = {}
-                        for k, v in kwargs.iteritems():
-                            if k.startswith('wf_parm|'):
-                                replacement_dict[k[8:]] = v
-                        for pja in step.post_job_actions:
-                            if pja.action_type in ActionBox.immediate_actions:
-                                ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
-                            else:
-                                job.add_post_job_action(pja)
-                    else:
-                        job, out_data = step.module.execute( trans, step.state )
-                        outputs[ step.id ] = out_data
-                    # Record invocation
-                    workflow_invocation_step = model.WorkflowInvocationStep()
-                    workflow_invocation_step.workflow_invocation = workflow_invocation
-                    workflow_invocation_step.workflow_step = step
-                    workflow_invocation_step.job = job
-                # All jobs ran sucessfully, so we can save now
-                trans.sa_session.add( workflow_invocation )
-                trans.sa_session.flush()
-                return trans.fill_template( "workflow/run_complete.mako",
-                                            workflow=stored,
-                                            outputs=outputs,
-                                            new_history=new_history )
+                        # Fix this for multiple inputs
+                        module = step.module = module_factory.from_workflow_step( trans, step )
+                        state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
+                        step_errors = module.update_runtime_state( trans, state, step_args )
+                    if step_errors:
+                        errors[step.id] = state.inputs["__errors__"] = step_errors   
+                if 'run_workflow' in kwargs and not errors:
+                    new_history = None
+                    if 'new_history' in kwargs:
+                        if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
+                            nh_name = kwargs['new_history_name']
+                        else:
+                            nh_name = "History from %s workflow" % workflow.name
+                        if multiple_input_key:
+                            nh_name = '%s %d' % (nh_name, input_number + 1)
+                        new_history = trans.app.model.History( user=trans.user, name=nh_name )
+                        trans.sa_session.add( new_history )
+                    # Run each step, connecting outputs to inputs
+                    workflow_invocation = model.WorkflowInvocation()
+                    workflow_invocation.workflow = workflow
+                    outputs = odict()
+                    for i, step in enumerate( workflow.steps ):
+                        # Execute module
+                        job = None
+                        if step.type == 'tool' or step.type is None:
+                            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                            input_values = step.state.inputs
+                            # Connect up
+                            def callback( input, value, prefixed_name, prefixed_label ):
+                                if isinstance( input, DataToolParameter ):
+                                    if prefixed_name in step.input_connections_by_name:
+                                        conn = step.input_connections_by_name[ prefixed_name ]
+                                        return outputs[ conn.output_step.id ][ conn.output_name ]
+                            visit_input_values( tool.inputs, step.state.inputs, callback )
+                            # Execute it
+                            job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
+                            outputs[ step.id ] = out_data
+                            # Create new PJA associations with the created job, to be run on completion.
+                            # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
+                            # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
+                            replacement_dict = {}
+                            for k, v in kwargs.iteritems():
+                                if k.startswith('wf_parm|'):
+                                    replacement_dict[k[8:]] = v
+                            for pja in step.post_job_actions:
+                                if pja.action_type in ActionBox.immediate_actions:
+                                    ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
+                                else:
+                                    job.add_post_job_action(pja)
+                        else:
+                            job, out_data = step.module.execute( trans, step.state )
+                            outputs[ step.id ] = out_data
+                        # Record invocation
+                        workflow_invocation_step = model.WorkflowInvocationStep()
+                        workflow_invocation_step.workflow_invocation = workflow_invocation
+                        workflow_invocation_step.workflow_step = step
+                        workflow_invocation_step.job = job
+                    # All jobs ran sucessfully, so we can save now
+                    trans.sa_session.add( workflow_invocation )
+                    invocations.append({'outputs': outputs,
+                                        'new_history': new_history})
+            trans.sa_session.flush()
+            return trans.fill_template( "workflow/run_complete.mako",
+                                        workflow=stored,
+                                        invocations=invocations )
         else:
             # Prepare each step
             missing_tools = []
@@ -1816,4 +1837,4 @@
                 cleanup( prefix, input.cases[current_case].inputs, group_values )
     cleanup( "", inputs, values )
     return associations
-    
\ No newline at end of file
+    


--- a/lib/galaxy/workflow/modules.py	Wed Apr 13 16:46:36 2011 -0400
+++ b/lib/galaxy/workflow/modules.py	Thu Apr 14 01:04:40 2011 +0200
@@ -131,7 +131,7 @@
     
     def get_runtime_inputs( self, filter_set=['data'] ):
         label = self.state.get( "name", "Input Dataset" )
-        return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, type="data", format=', '.join(filter_set) ) ) )
+        return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ) ) )
     def get_runtime_state( self ):
         state = DefaultToolState()
         state.inputs = dict( input=None )


--- a/static/june_2007_style/blue/base.css	Wed Apr 13 16:46:36 2011 -0400
+++ b/static/june_2007_style/blue/base.css	Thu Apr 14 01:04:40 2011 +0200
@@ -170,3 +170,6 @@
 .editable-text{cursor:pointer;}
 .editable-text:hover{cursor:text;border:dotted #999999 1px;}
 .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;}
+.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;}
+.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;}
+.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;}


--- a/templates/workflow/run.mako	Wed Apr 13 16:46:36 2011 -0400
+++ b/templates/workflow/run.mako	Thu Apr 14 01:04:40 2011 +0200
@@ -2,7 +2,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.autocomplete" )}
+    ${h.js( "jquery.autocomplete", "jquery.tipsy" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
@@ -20,6 +20,21 @@
                     show_tool_body(title);
                 }
             }
+            function toggle_multiinput(select) {
+                if (select.attr('multiple')) {
+                    $('.multiinput').removeClass('disabled');
+                    if (select.val()) {
+                        select.val(select.val()[0]);
+                    } else {
+                        select.val($('option:last', select).val());
+                    }
+                    select.removeAttr('multiple');
+                } else {
+                    $('.multiinput').addClass('disabled');
+                    $('.multiinput', select.parent().prev()).removeClass('disabled');
+                    select.attr('multiple', 'multiple');
+                }
+            }
             $( "select[refresh_on_change='true']").change( function() {
                 $( "#tool_form" ).submit();
             });
@@ -41,6 +56,19 @@
             $("#new_history_cbx").click(function(){
                 $("#new_history_input").toggle(this.checked);
             });
+            $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) {
+                var select = $(s);
+                select.parent().prev().append(
+                    $('<span class="icon-button multiinput"></span>').click(function() {
+                        if ($(this).hasClass('disabled')) return;
+                        toggle_multiinput(select);
+                        select.focus();
+                    }).attr('original-title',
+                            'Enable/disable selection of multiple input ' +
+                            'files. Each selected file will have an ' +
+                            'instance of the workflow.').tipsy({gravity:'s'})
+                );
+            });
         });
     </script></%def>


--- a/templates/workflow/run_complete.mako	Wed Apr 13 16:46:36 2011 -0400
+++ b/templates/workflow/run_complete.mako	Thu Apr 14 01:04:40 2011 +0200
@@ -2,21 +2,25 @@
 
 <div class="donemessagelarge">
     Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue:
-    %if new_history:
-        These datasets will appear in a new history:
-        <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}">
-            '${h.to_unicode(new_history.name)}'.
-        </a>
-    %endif
-    <div style="padding-left: 10px;">
-        %for step_outputs in outputs.itervalues():
-            %for data in step_outputs.itervalues():
-                %if not new_history or data.history == new_history:
-                    <p><strong>${data.hid}</strong>: ${data.name}</p>
-                %endif
-            %endfor
-        %endfor
-    </div>
+    %for invocation in invocations:
+        <div class="workflow-invocation-complete">
+            %if invocation['new_history']:
+                <p>These datasets will appear in a new history:
+                <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(invocation['new_history'].id), use_panels=False, show_deleted=False )}">
+                    '${h.to_unicode(invocation['new_history'].name)}'.
+                </a></p>
+            %endif
+            <div style="padding-left: 10px;">
+                %for step_outputs in invocation['outputs'].itervalues():
+                    %for data in step_outputs.itervalues():
+                        %if not invocation['new_history'] or data.history == invocation['new_history']:
+                            <p><strong>${data.hid}</strong>: ${data.name}</p>
+                        %endif
+                    %endfor
+                %endfor
+            </div>
+        </div>
+    %endfor
 </div><script type="text/javascript">


http://bitbucket.org/galaxy/galaxy-central/changeset/383258d637cb/
changeset:   r5380:383258d637cb
user:        dannon
date:        2011-04-14 01:07:22
summary:     Merge.
affected #:  6 files (3.8 KB)

--- a/lib/galaxy/tools/parameters/basic.py	Wed Apr 13 19:05:45 2011 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Wed Apr 13 19:07:22 2011 -0400
@@ -1421,6 +1421,14 @@
         else:
             return "No dataset"
 
+    def validate( self, value, history=None ):
+        for validator in self.validators:
+            if value and self.multiple and isinstance(value, list):
+                for v in value:
+                    validator.validate( v, history )
+            else:
+                validator.validate( value, history )
+
     def get_dependencies( self ):
         """
         Get the *names* of the other params this param depends on.


--- a/lib/galaxy/web/controllers/workflow.py	Wed Apr 13 19:05:45 2011 -0400
+++ b/lib/galaxy/web/controllers/workflow.py	Wed Apr 13 19:07:22 2011 -0400
@@ -1262,96 +1262,117 @@
         if kwargs:
             # If kwargs were provided, the states for each step should have
             # been POSTed
-            for step in workflow.steps:
-                step.upgrade_messages = {}
-                # Connections by input name
-                step.input_connections_by_name = \
-                    dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
-                # Extract just the arguments for this step by prefix
-                p = "%s|" % step.id
-                l = len(p)
-                step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
-                step_errors = None
-                if step.type == 'tool' or step.type is None:
-                    module = module_factory.from_workflow_step( trans, step )
-                    # Fix any missing parameters
-                    step.upgrade_messages = module.check_and_update_state()
-                    if step.upgrade_messages:
-                        has_upgrade_messages = True
-                    # Any connected input needs to have value DummyDataset (these
-                    # are not persisted so we need to do it every time)
-                    module.add_dummy_datasets( connections=step.input_connections )    
-                    # Get the tool
-                    tool = module.tool
-                    # Get the state
-                    step.state = state = module.state
-                    # Get old errors
-                    old_errors = state.inputs.pop( "__errors__", {} )
-                    # Update the state
-                    step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
-                                                     update_only=True, old_errors=old_errors )
-                else:
-                    module = step.module = module_factory.from_workflow_step( trans, step )
-                    state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
-                    step_errors = module.update_runtime_state( trans, state, step_args )
-                if step_errors:
-                    errors[step.id] = state.inputs["__errors__"] = step_errors   
-            if 'run_workflow' in kwargs and not errors:
-                new_history = None
-                if 'new_history' in kwargs:
-                    if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
-                        nh_name = kwargs['new_history_name']
+            # Get the kwarg keys for data inputs
+            input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+            # Example: prefixed='2|input'
+            # Check if one of them is a list
+            multiple_input_key = None
+            multiple_inputs = [None]
+            for input_key in input_keys:
+                if isinstance(kwargs[input_key], list):
+                    multiple_input_key = input_key
+                    multiple_inputs = kwargs[input_key]
+            # List to gather values for the template
+            invocations=[]
+            for input_number, single_input in enumerate(multiple_inputs):
+                # Example: single_input='1', single_input='2', etc...
+                # 'Fix' the kwargs, to have only the input for this iteration
+                if multiple_input_key:
+                    kwargs[multiple_input_key] = single_input
+                for step in workflow.steps:
+                    step.upgrade_messages = {}
+                    # Connections by input name
+                    step.input_connections_by_name = \
+                        dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                    # Extract just the arguments for this step by prefix
+                    p = "%s|" % step.id
+                    l = len(p)
+                    step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
+                    step_errors = None
+                    if step.type == 'tool' or step.type is None:
+                        module = module_factory.from_workflow_step( trans, step )
+                        # Fix any missing parameters
+                        step.upgrade_messages = module.check_and_update_state()
+                        if step.upgrade_messages:
+                            has_upgrade_messages = True
+                        # Any connected input needs to have value DummyDataset (these
+                        # are not persisted so we need to do it every time)
+                        module.add_dummy_datasets( connections=step.input_connections )    
+                        # Get the tool
+                        tool = module.tool
+                        # Get the state
+                        step.state = state = module.state
+                        # Get old errors
+                        old_errors = state.inputs.pop( "__errors__", {} )
+                        # Update the state
+                        step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
+                                                         update_only=True, old_errors=old_errors )
                     else:
-                        nh_name = "History from %s workflow" % workflow.name
-                    new_history = trans.app.model.History( user=trans.user, name=nh_name )
-                    trans.sa_session.add( new_history )
-                # Run each step, connecting outputs to inputs
-                workflow_invocation = model.WorkflowInvocation()
-                workflow_invocation.workflow = workflow
-                outputs = odict()
-                for i, step in enumerate( workflow.steps ):
-                    # Execute module
-                    job = None
-                    if step.type == 'tool' or step.type is None:
-                        tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
-                        input_values = step.state.inputs
-                        # Connect up
-                        def callback( input, value, prefixed_name, prefixed_label ):
-                            if isinstance( input, DataToolParameter ):
-                                if prefixed_name in step.input_connections_by_name:
-                                    conn = step.input_connections_by_name[ prefixed_name ]
-                                    return outputs[ conn.output_step.id ][ conn.output_name ]
-                        visit_input_values( tool.inputs, step.state.inputs, callback )
-                        # Execute it
-                        job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
-                        outputs[ step.id ] = out_data
-                        # Create new PJA associations with the created job, to be run on completion.
-                        # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
-                        # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-                        replacement_dict = {}
-                        for k, v in kwargs.iteritems():
-                            if k.startswith('wf_parm|'):
-                                replacement_dict[k[8:]] = v
-                        for pja in step.post_job_actions:
-                            if pja.action_type in ActionBox.immediate_actions:
-                                ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
-                            else:
-                                job.add_post_job_action(pja)
-                    else:
-                        job, out_data = step.module.execute( trans, step.state )
-                        outputs[ step.id ] = out_data
-                    # Record invocation
-                    workflow_invocation_step = model.WorkflowInvocationStep()
-                    workflow_invocation_step.workflow_invocation = workflow_invocation
-                    workflow_invocation_step.workflow_step = step
-                    workflow_invocation_step.job = job
-                # All jobs ran sucessfully, so we can save now
-                trans.sa_session.add( workflow_invocation )
-                trans.sa_session.flush()
-                return trans.fill_template( "workflow/run_complete.mako",
-                                            workflow=stored,
-                                            outputs=outputs,
-                                            new_history=new_history )
+                        # Fix this for multiple inputs
+                        module = step.module = module_factory.from_workflow_step( trans, step )
+                        state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
+                        step_errors = module.update_runtime_state( trans, state, step_args )
+                    if step_errors:
+                        errors[step.id] = state.inputs["__errors__"] = step_errors   
+                if 'run_workflow' in kwargs and not errors:
+                    new_history = None
+                    if 'new_history' in kwargs:
+                        if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
+                            nh_name = kwargs['new_history_name']
+                        else:
+                            nh_name = "History from %s workflow" % workflow.name
+                        if multiple_input_key:
+                            nh_name = '%s %d' % (nh_name, input_number + 1)
+                        new_history = trans.app.model.History( user=trans.user, name=nh_name )
+                        trans.sa_session.add( new_history )
+                    # Run each step, connecting outputs to inputs
+                    workflow_invocation = model.WorkflowInvocation()
+                    workflow_invocation.workflow = workflow
+                    outputs = odict()
+                    for i, step in enumerate( workflow.steps ):
+                        # Execute module
+                        job = None
+                        if step.type == 'tool' or step.type is None:
+                            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                            input_values = step.state.inputs
+                            # Connect up
+                            def callback( input, value, prefixed_name, prefixed_label ):
+                                if isinstance( input, DataToolParameter ):
+                                    if prefixed_name in step.input_connections_by_name:
+                                        conn = step.input_connections_by_name[ prefixed_name ]
+                                        return outputs[ conn.output_step.id ][ conn.output_name ]
+                            visit_input_values( tool.inputs, step.state.inputs, callback )
+                            # Execute it
+                            job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
+                            outputs[ step.id ] = out_data
+                            # Create new PJA associations with the created job, to be run on completion.
+                            # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
+                            # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
+                            replacement_dict = {}
+                            for k, v in kwargs.iteritems():
+                                if k.startswith('wf_parm|'):
+                                    replacement_dict[k[8:]] = v
+                            for pja in step.post_job_actions:
+                                if pja.action_type in ActionBox.immediate_actions:
+                                    ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
+                                else:
+                                    job.add_post_job_action(pja)
+                        else:
+                            job, out_data = step.module.execute( trans, step.state )
+                            outputs[ step.id ] = out_data
+                        # Record invocation
+                        workflow_invocation_step = model.WorkflowInvocationStep()
+                        workflow_invocation_step.workflow_invocation = workflow_invocation
+                        workflow_invocation_step.workflow_step = step
+                        workflow_invocation_step.job = job
+                    # All jobs ran sucessfully, so we can save now
+                    trans.sa_session.add( workflow_invocation )
+                    invocations.append({'outputs': outputs,
+                                        'new_history': new_history})
+            trans.sa_session.flush()
+            return trans.fill_template( "workflow/run_complete.mako",
+                                        workflow=stored,
+                                        invocations=invocations )
         else:
             # Prepare each step
             missing_tools = []
@@ -1816,4 +1837,4 @@
                 cleanup( prefix, input.cases[current_case].inputs, group_values )
     cleanup( "", inputs, values )
     return associations
-    
\ No newline at end of file
+    


--- a/lib/galaxy/workflow/modules.py	Wed Apr 13 19:05:45 2011 -0400
+++ b/lib/galaxy/workflow/modules.py	Wed Apr 13 19:07:22 2011 -0400
@@ -131,7 +131,7 @@
     
     def get_runtime_inputs( self, filter_set=['data'] ):
         label = self.state.get( "name", "Input Dataset" )
-        return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, type="data", format=', '.join(filter_set) ) ) )
+        return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ) ) )
     def get_runtime_state( self ):
         state = DefaultToolState()
         state.inputs = dict( input=None )


--- a/static/june_2007_style/blue/base.css	Wed Apr 13 19:05:45 2011 -0400
+++ b/static/june_2007_style/blue/base.css	Wed Apr 13 19:07:22 2011 -0400
@@ -170,3 +170,6 @@
 .editable-text{cursor:pointer;}
 .editable-text:hover{cursor:text;border:dotted #999999 1px;}
 .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;}
+.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;}
+.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;}
+.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;}


--- a/templates/workflow/run.mako	Wed Apr 13 19:05:45 2011 -0400
+++ b/templates/workflow/run.mako	Wed Apr 13 19:07:22 2011 -0400
@@ -2,7 +2,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.autocomplete" )}
+    ${h.js( "jquery.autocomplete", "jquery.tipsy" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
@@ -20,6 +20,21 @@
                     show_tool_body(title);
                 }
             }
+            function toggle_multiinput(select) {
+                if (select.attr('multiple')) {
+                    $('.multiinput').removeClass('disabled');
+                    if (select.val()) {
+                        select.val(select.val()[0]);
+                    } else {
+                        select.val($('option:last', select).val());
+                    }
+                    select.removeAttr('multiple');
+                } else {
+                    $('.multiinput').addClass('disabled');
+                    $('.multiinput', select.parent().prev()).removeClass('disabled');
+                    select.attr('multiple', 'multiple');
+                }
+            }
             $( "select[refresh_on_change='true']").change( function() {
                 $( "#tool_form" ).submit();
             });
@@ -41,6 +56,19 @@
             $("#new_history_cbx").click(function(){
                 $("#new_history_input").toggle(this.checked);
             });
+            $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) {
+                var select = $(s);
+                select.parent().prev().append(
+                    $('<span class="icon-button multiinput"></span>').click(function() {
+                        if ($(this).hasClass('disabled')) return;
+                        toggle_multiinput(select);
+                        select.focus();
+                    }).attr('original-title',
+                            'Enable/disable selection of multiple input ' +
+                            'files. Each selected file will have an ' +
+                            'instance of the workflow.').tipsy({gravity:'s'})
+                );
+            });
         });
     </script></%def>


--- a/templates/workflow/run_complete.mako	Wed Apr 13 19:05:45 2011 -0400
+++ b/templates/workflow/run_complete.mako	Wed Apr 13 19:07:22 2011 -0400
@@ -2,21 +2,25 @@
 
 <div class="donemessagelarge">
     Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue:
-    %if new_history:
-        These datasets will appear in a new history:
-        <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}">
-            '${h.to_unicode(new_history.name)}'.
-        </a>
-    %endif
-    <div style="padding-left: 10px;">
-        %for step_outputs in outputs.itervalues():
-            %for data in step_outputs.itervalues():
-                %if not new_history or data.history == new_history:
-                    <p><strong>${data.hid}</strong>: ${data.name}</p>
-                %endif
-            %endfor
-        %endfor
-    </div>
+    %for invocation in invocations:
+        <div class="workflow-invocation-complete">
+            %if invocation['new_history']:
+                <p>These datasets will appear in a new history:
+                <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(invocation['new_history'].id), use_panels=False, show_deleted=False )}">
+                    '${h.to_unicode(invocation['new_history'].name)}'.
+                </a></p>
+            %endif
+            <div style="padding-left: 10px;">
+                %for step_outputs in invocation['outputs'].itervalues():
+                    %for data in step_outputs.itervalues():
+                        %if not invocation['new_history'] or data.history == invocation['new_history']:
+                            <p><strong>${data.hid}</strong>: ${data.name}</p>
+                        %endif
+                    %endfor
+                %endfor
+            </div>
+        </div>
+    %endfor
 </div><script type="text/javascript">

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

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[galaxy-commits] commit/galaxy-central: 5 new changesets

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