Added an "Auto-dectect" button to the Edit (metadata) Attributes form.

Cleaned up some bugs in Bed and Interval set_meta associated functions.
set_meta() will no longer be called prior to the edit form being displayed since doing this displayed attribute values that were not from the database (misleading the user).

lib/galaxy/datatypes/interval.py

@@ -234,7 +234,7 @@ class Bed( Interval ):
     
     def missing_meta( self, dataset ):
         """Checks for empty meta values"""
-        return Tabular.missing_meta(self, dataset)
+        return Interval.missing_meta(self, dataset)
     
     def init_meta( self, dataset, copy_from=None ):
         Interval.init_meta( self, dataset, copy_from=copy_from )

lib/galaxy/datatypes/tabular.py

@@ -134,8 +134,3 @@ class Tabular( data.Text ):
         m_peek = self.make_html_table( dataset.peek )
         return m_peek
 
-    def before_edit( self, dataset ):
-        data.Text.before_edit( self, dataset )
-        if self.missing_meta( dataset ):
-            self.set_meta( dataset )
-

lib/galaxy/tools/dynamic_options.py

@@ -24,8 +24,6 @@ class DynamicOptions( object ):
             while '' indicates that it is not. Currently dynamically generated select lists do not work well with optional datasets.
             """
             return None
-        # TODO: this can be eliminated after Dan's script is run.
-        #dataset.set_meta()
         return dataset
     def get_param_ref( self, trans, other_values ):
         if self.param_ref is None: return None

lib/galaxy/tools/parameters.py

@@ -610,8 +610,6 @@ class ColumnListParameter( SelectToolParameter ):
             #       while '' indicates that it is not. Currently column
             #       parameters do not work well with optional datasets
             return column_list
-        # Just to be safe... (FIXME: Is this still neccesary?)
-        #dataset.set_meta()
         # Generate options
         if not dataset.metadata.columns:
             if self.accept_default:

lib/galaxy/web/controllers/root.py

@@ -162,6 +162,7 @@ class Universe( BaseController ):
     @web.expose
     def edit(self, trans, id=None, hid=None, **kwd):
         """Returns data directly into the browser. Sets the mime-type according to the extension"""
+
         if hid is not None:
             history = trans.get_history()
             # TODO: hid handling
@@ -176,7 +177,7 @@ class Universe( BaseController ):
         p = util.Params(kwd, safe=False)
         
         if p.change:
-            """Ths user clicked the Save button on the 'Change data type' form"""
+            """The user clicked the Save button on the 'Change data type' form"""
             trans.app.datatypes_registry.change_datatype( data, p.datatype )
             trans.app.model.flush()
         elif p.save:
@@ -197,7 +198,17 @@ class Universe( BaseController ):
 
             data.datatype.after_edit( data )
             trans.app.model.flush()
-            
+            return trans.fill_template( "edit_complete.tmpl" )
+        elif p.detect:
+            """The user clicked the Auto-detect button on the 'Edit Attributes' form"""
+            for name, spec in data.datatype.metadata_spec.items():
+                # We need to be careful about the attributes we are resetting
+                if name != 'name' and name != 'info' and name != 'dbkey':
+                    if spec.get( 'default' ):
+                        setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec ))
+            data.datatype.set_meta( data )
+            data.datatype.after_edit( data )
+            trans.app.model.flush()
             return trans.fill_template( "edit_complete.tmpl" )
         elif p.convert_data:
             """The user clicked the Convert button on the 'Convert to new format' form"""

templates/edit_data.tmpl

@@ -62,6 +62,14 @@
                   <div style="clear: both"></div>
                 </div>
             #end for
+            <div style="float: left; width: 250px; margin-right: 10px;">
+                <input type="submit" name="detect" value="Auto-detect">
+            </div>
+            <div class="toolParamHelp" style="clear: both;">
+                This will inspect the dataset and attempt to correct the above column values
+                if they are not accurate.
+            </div>
+            <br/>
             <div class="form-row">
                 <input type="submit" name="save" value="Save">
             </div>
@@ -133,6 +141,6 @@
         </form>
     </div>
     </div>
-    
+
   </body>
 </html>