[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.

18 Sep 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/32091cc60876/
changeset:   32091cc60876
user:        jgoecks
date:        2012-09-18 17:40:57
summary:     Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.
affected #:  5 files

diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/data.py

--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -545,6 +545,15 @@
             raise Exception('Result %s from %s' % (result, cmd))
     merge = staticmethod(merge)
 
+    def get_visualizations( self ):
+        """
+        Returns a list of visualizations for datatype.
+        """
+
+        if hasattr( self, 'get_track_type' ):
+            return [ 'trackster', 'circster' ]
+        return []
+
 class Text( Data ):
     file_ext = 'txt'
     line_class = 'line'


diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -301,6 +301,12 @@
     def as_ucsc_display_file( self, dataset, **kwd ):
         return open( dataset.file_name )
 
+    def get_visualizations( self ):
+        """
+        Returns a list of visualizations for datatype.
+        """
+        return super( Tabular, self ).get_visualizations() + [ 'scatterplot' ]
+
 class Taxonomy( Tabular ):
     def __init__(self, **kwd):
         """Initialize taxonomy datatype"""


diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -708,9 +708,12 @@
         
         # Get new dataset if specified.
         new_dataset = kwargs.get("dataset_id", None)
+        '''
+        FIXME:
         if new_dataset is not None:
             if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]:
                 new_dataset = None # Already in browser, so don't add
+        '''
         return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset )
 
     @web.json


diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history.mako
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -116,6 +116,95 @@
     });
 };
 
+// Create trackster action function.
+function create_trackster_action_fn(vis_url, dataset_params, dbkey) {
+    return function() {
+        var params = {};
+        if (dbkey) { params['dbkey'] = dbkey; }
+        $.ajax({
+            url: vis_url + '/list_tracks?f-' + $.param(params),
+            dataType: "html",
+            error: function() { alert( "Could not add this dataset to browser." ); },
+            success: function(table_html) {
+                var parent = window.parent;
+                
+                parent.show_modal("View Data in a New or Saved Visualization", "", {
+                    "Cancel": function() {
+                        parent.hide_modal();
+                    },
+                    "View in saved visualization": function() {
+                        // Show new modal with saved visualizations.
+                        parent.show_modal("Add Data to Saved Visualization", table_html, {
+                            "Cancel": function() {
+                                parent.hide_modal();
+                            },
+                            "Add to visualization": function() {
+                                $(parent.document).find('input[name=id]:checked').each(function() {
+                                    var vis_id = $(this).val();
+                                    dataset_params['id'] = vis_id
+                                    parent.location = vis_url + "/trackster?" + $.param(dataset_params);
+                                });
+                            }, 
+                        });
+                    },
+                    "View in new visualization": function() {
+                        parent.location = vis_url + "/trackster?" + $.param(dataset_params);
+                    }
+                });
+            }
+        });
+        return false;
+    };
+};
+
+/**
+ * Create popup menu for visualization icon.
+ */
+function init_viz_icon(icon) {
+    var icon = $(icon),
+        vis_url = icon.attr('href'),
+        dataset_id = icon.attr('dataset_id'),
+        visualizations = icon.attr('visualizations').split(','),
+        dbkey = icon.attr('dbkey'),
+        popup_menu_dict = {},
+
+        // Create visualization action.
+        create_viz_action = function(visualization) {
+            var action;
+            if (visualization === 'trackster') {
+                action = create_trackster_action_fn(vis_url, params, dbkey);
+            }
+            else {
+                action = function() {
+                    window.parent.location = vis_url + '/' + visualization + '?' + 
+                                             $.param(params);
+                };
+            }
+            return action;
+        },
+        params = {dataset_id: dataset_id};
+
+    // Add dbkey to params if it exists.
+    if (dbkey) { params['dbkey'] = dbkey; }
+
+    // Populate menu dict with visualizations.
+    _.each(visualizations, function(visualization) {
+        popup_menu_dict[
+            visualization.charAt(0).toUpperCase() + visualization.slice(1)
+                        ] = create_viz_action(visualization);
+    });
+
+    // Set up action or menu.
+    if (visualizations.length === 1) {
+        // No need for popup menu because there's a single visualization.
+        icon.click(create_viz_action(visualizations[0]));
+    }
+    else {
+        make_popupmenu(icon, popup_menu_dict);
+    }
+};
+
+
 // Update the message for async operations
 function render_message(message, status) {
     $("div#message-container").html( "<div class=\"" + status + "message\">" + message + "</div><br/>" );
@@ -258,96 +347,6 @@
         
     });
     
-    // Trackster links
-    function init_trackster_links() {
-        // Add to trackster browser functionality
-        $(".trackster-add").live("click", function() {
-            var dataset = this,
-                dataset_jquery = $(this);
-            $.ajax({
-                url: dataset_jquery.attr("data-url"),
-                dataType: "html",
-                error: function() { alert( "Could not add this dataset to browser." ); },
-                success: function(table_html) {
-                    var parent = window.parent;
-                    
-                    parent.show_modal("View Data in a New or Saved Visualization", "", {
-                        "Cancel": function() {
-                            parent.hide_modal();
-                        },
-                        "View in saved visualization": function() {
-                            // Show new modal with saved visualizations.
-                            parent.show_modal("Add Data to Saved Visualization", table_html, {
-                                "Cancel": function() {
-                                    parent.hide_modal();
-                                },
-                                "Add to visualization": function() {
-                                    $(parent.document).find('input[name=id]:checked').each(function() {
-                                        var vis_id = $(this).val();
-                                        parent.location = dataset_jquery.attr("action-url") + "&id=" + vis_id;
-                                    });
-                                }, 
-                            });
-                        },
-                        "View in new visualization": function() {
-                            parent.location = dataset_jquery.attr("new-url");
-                        }
-                    });
-                }
-            });
-        });
-    }
-    
-    /**
-     * Create popup menu for visualization icon.
-     */
-    function init_viz_icon(icon) {
-        var icon_link = $(icon);
-        make_popupmenu( icon_link , {
-            "${_("Trackster")}": function() {
-                $.ajax({
-                    url: icon_link.attr("data-url"),
-                    dataType: "html",
-                    error: function() { alert( "Could not add this dataset to browser." ); },
-                    success: function(table_html) {
-                        var parent = window.parent;
-
-                        parent.show_modal("View Data in a New or Saved Visualization", "", {
-                            "Cancel": function() {
-                                parent.hide_modal();
-                            },
-                            "View in saved visualization": function() {
-                                // Show new modal with saved visualizations.
-                                parent.hide_modal();
-                                parent.show_modal("Add Data to Saved Visualization", table_html, {
-                                    "Cancel": function() {
-                                        parent.hide_modal();
-                                    },
-                                    "Add to visualization": function() {
-                                        $(parent.document).find('input[name=id]:checked').each(function() {
-                                            var vis_id = $(this).val();
-                                            parent.location = icon_link.attr("action-url") + "&id=" + vis_id;
-                                        });
-                                    }, 
-                                });
-                            },
-                            "View in new visualization": function() {
-                                parent.location = icon_link.attr("new-url");
-                            }
-                        });
-                    }
-                });
-            },
-            //"${_("Scatterplot")}": function() {
-            //    var data_id = icon_link.parents(".historyItemContainer").attr("id").split("-")[1];
-            //    parent.galaxy_main.location =
-            //        "${h.url_for( controller='visualization', action='scatterplot', col1=9, col2=13 )}"
-            //        + "&dataset_id=" + data_id;
-            //}
-        } );
-        return icon;        
-    };
-    
     _.each( $(".visualize-icon"), function(icon) {
         init_viz_icon(icon);
     });
@@ -472,6 +471,9 @@
                 init_history_items( $("div.historyItemWrapper"), "noinit" );
                 tag_handling(container);
                 annotation_handling(container);
+                var viz_icon = container.find(".visualize-icon")[0];
+                if (viz_icon) { init_viz_icon(viz_icon); }
+                
                 // If new state is terminal, stop tracking
                 if (TERMINAL_STATES.indexOf(val.state) !== -1) {
                     if ( val.force_history_refresh ){


diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -226,17 +226,24 @@
                     
                     %if for_editing:
                         <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
-                        %if data.ext in app.datatypes_registry.get_available_tracks():
-                            <%
-                            if data.dbkey != '?':
-                                data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=data.dbkey )
-                                data_url = data_url.replace( 'dbkey', 'f-dbkey' )
-                            else:
-                                data_url = h.url_for( controller='visualization', action='list_tracks' )
-                            %>
-                            <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip visualize-icon"
-                                action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}"
-                                new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize"></a>
+                        ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed
+                        ## information--URL base, dataset id, dbkey, visualizations--in anchor.
+                        <% 
+                            visualizations = data.datatype.get_visualizations() 
+                            ## HACK: if there are visualizations, only provide trackster for now since others
+                            ## are not ready.
+                            if visualizations:
+                                visualizations = [ 'trackster' ]
+                        %>
+                        %if visualizations:
+                            <a href="${h.url_for( controller='visualization' )}" 
+                               class="icon-button chart_curve tooltip visualize-icon"
+                               title="Visualize"
+                               dataset_id="${dataset_id}"
+                               %if data.dbkey != '?':
+                                   dbkey="${data.dbkey}" 
+                               %endif
+                               visualizations="${','.join(visualizations)}"></a>
                         %endif
                         <%
                             isPhylogenyData = isinstance(data.datatype,  (Phyloxml, Nexus, Newick))

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

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[galaxy-commits] commit/galaxy-central: jgoecks: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.

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