From a3d694de70a58cfc553a6e2fff4df37ce4870a55 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 8 May 2015 09:30:04 -0400
Subject: [PATCH] Fixes for BaseURLToolParameter. Data source tools will now
 work again. Restores consistency to various ways that one might get the
 parameter value.

---
 lib/galaxy/tools/__init__.py         |  8 +++++---
 lib/galaxy/tools/parameters/basic.py | 15 +++++++++++++++
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c131a42f349..88af8170c98 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1890,10 +1890,12 @@ class Tool( object, Dictifiable ):
         """
         args = dict()
         for key, param in self.inputs.iteritems():
-            if isinstance( param, HiddenToolParameter ):
+            # BaseURLToolParameter is now a subclass of HiddenToolParameter, so
+            # we must check if param is a BaseURLToolParameter first
+            if isinstance( param, BaseURLToolParameter ):
+                args[key] = param.get_initial_value( trans, None )
+            elif isinstance( param, HiddenToolParameter ):
                 args[key] = model.User.expand_user_properties( trans.user, param.value )
-            elif isinstance( param, BaseURLToolParameter ):
-                args[key] = param.get_value( trans )
             else:
                 raise Exception( "Unexpected parameter type" )
         return args
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 03cbcc31dcb..adbd85890ee 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -652,6 +652,7 @@ class HiddenToolParameter( ToolParameter ):
     def get_label( self ):
         return None
 
+
 class ColorToolParameter( ToolParameter ):
     """
     Parameter that stores a color.
@@ -682,9 +683,23 @@ class BaseURLToolParameter( HiddenToolParameter ):
         super( BaseURLToolParameter, self ).__init__( tool, input_source )
         self.value = input_source.get( 'value', '' )
 
+    def get_initial_value( self, trans, context, history=None ):
+        return self._get_value()
+
+    def get_html_field( self, trans=None, value=None, other_values={} ):
+        return form_builder.HiddenField( self.name, self._get_value() )
+
     def from_html( self, value=None, trans=None, context={} ):
+        return self._get_value()
+
+    def _get_value( self ):
         return url_for( self.value, qualified=True )
 
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
+        d = super( BaseURLToolParameter, self ).to_dict( trans )
+        d[ 'value' ] = self._get_value()
+        return d
+
 
 DEFAULT_VALUE_MAP = lambda x: x