Scatterplot: use named data provider, fix encoding of ids; pack scripts

lib/galaxy/datatypes/tabular.py

@@ -328,7 +328,6 @@ class Tabular( data.Text ):
         """
         Returns a list of visualizations for datatype.
         """
-
         # Can visualize tabular data as scatterplot if there are 2+ numerical
         # columns.
         num_numerical_cols = 0

lib/galaxy/visualization/data_providers/basic.py

@@ -67,11 +67,14 @@ class ColumnDataProvider( BaseDataProvider ):
         # allow throttling
         self.max_lines_returned = max_lines_returned
         
-    def get_data( self, columns, start_val=0, max_vals=None, skip_comments=True, **kwargs ):
+    def get_data( self, columns=None, start_val=0, max_vals=None, skip_comments=True, **kwargs ):
         """
         Returns data from specified columns in dataset. Format is list of lists 
         where each list is a line of data.
         """
+        if not columns:
+            raise TypeError( 'parameter required: columns' )
+
         #TODO: validate kwargs
         try:
             max_vals = int( max_vals )
@@ -88,11 +91,10 @@ class ColumnDataProvider( BaseDataProvider ):
         # skip comment lines (if any/avail)
         # pre: should have original_dataset and
         if( skip_comments
-        and start_val == 0
-        and self.original_dataset.metadata.comment_lines ):
-            start_val = int( self.original_dataset.metadata.comment_lines ) + 1
+        and self.original_dataset.metadata.comment_lines
+        and start_val < self.original_dataset.metadata.comment_lines ):
+            start_val = int( self.original_dataset.metadata.comment_lines )
         
-        #TODO bail if columns None, not parsable, not within meta.columns
         # columns is an array of ints for now (should handle column names later)
         columns = from_json_string( columns )
         for column in columns:

static/scripts/mvc/visualizations/scatterplotControlForm.js

@@ -562,6 +562,7 @@ var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({
         
         var params = {
             data_type   : 'raw_data',
+            provider    : 'column',
             columns     : '[' + columns + ']'
         };
         this.log( '\t data settings (url params):', params );

static/scripts/viz/scatterplot.js

@@ -138,16 +138,16 @@ function TwoVarScatterplot( config ){
         bottom = bottom || 0;
         left = left || 0;
         this.svg
-            .attr( "width",  this.config.width +  ( this.config.marginRight  + right ) + 
-                                                  ( this.config.marginLeft   + left ) )
-            .attr( "height", this.config.height + ( this.config.marginTop    + top ) +
-                                                  ( this.config.marginBottom + bottom ) )
+            .attr( "width",  this.config.width  + ( this.config.marginRight  + right )
+                                                + ( this.config.marginLeft   + left ) )
+            .attr( "height", this.config.height + ( this.config.marginTop    + top )
+                                                + ( this.config.marginBottom + bottom ) )
             // initial is hidden - show it
             .style( 'display', 'block' );
             
         // move content group away from margins
         //TODO: allow top, right axis
-        this.content = this.svg.select( "g.content" )       
+        this.content = this.svg.select( "g.content" )
             .attr( "transform", this.translateStr( this.config.marginLeft + left, this.config.marginTop + top ) );
     };
     
@@ -260,7 +260,7 @@ function TwoVarScatterplot( config ){
             .attr( 'text-anchor', 'middle' )
             .attr( 'transform', this.rotateStr( -90, this.config.yAxisLabelBumpX, this.config.height / 2 ) )
             .text( this.config.yLabel );
-        //this.log( 'yAxisLabel:', this.yAxisLabel ); 
+        //this.log( 'yAxisLabel:', this.yAxisLabel );
     };
     
     // ........................................................ grid lines
@@ -284,7 +284,7 @@ function TwoVarScatterplot( config ){
             
         // remove unneeded (less ticks)
         this.vGridLines.exit().remove();
-        //this.log( 'vGridLines:', this.vGridLines ); 
+        //this.log( 'vGridLines:', this.vGridLines );
 
         // HORIZONTAL
         this.hGridLines = this.content.selectAll( 'line.h-grid-line' )

templates/webapps/galaxy/visualization/scatterplot.mako

@@ -222,8 +222,7 @@ ${h.js(
 <script type="text/javascript">
 $(function(){
 
-    var hda             = ${h.to_json_string( hda.get_api_value() )},
-        historyID       = '${trans.security.encode_id( hda.history.id )}',
+    var hda             = ${h.to_json_string( trans.security.encode_dict_ids( hda.get_api_value() ) )},
         querySettings   = ${h.to_json_string( query_args )},
         chartConfig     = _.extend( querySettings, {
             containerSelector : '#chart',