From ba968fde5cf1ec6e4b576cf062cd03560b69507d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 8 Apr 2015 22:40:08 -0400
Subject: [PATCH] Cleanup to_json caller, slightly improve exception handlers

---
 lib/galaxy/tools/__init__.py         | 40 +++++++++++++++-------------
 lib/galaxy/tools/parameters/basic.py | 10 +++----
 2 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 5679539134a..850890640ef 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2418,33 +2418,35 @@ class Tool( object, Dictifiable ):
                                 current_state = group_state
                             iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values)
                 else:
-                    # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options
+                    # identify name
+                    input_name = tool_dict.get('name')
+
+                    # create expanded input dictionary incl. repeats and dynamic_parameters
                     try:
                         tool_dict = input.to_dict(trans, other_values=other_values)
                     except Exception:
+                        log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input_name)
                         pass
 
-                    # identify name
-                    input_name = tool_dict.get('name')
-                    if input_name:
-                        # backup default value
-                        try:
-                            tool_dict['default_value'] = input.get_initial_value(trans, other_values)
-                        except Exception:
-                            # get initial value failed due to improper late validation
-                            tool_dict['default_value'] = None
-                            pass
+                    # backup default value
+                    try:
+                        tool_dict['default_value'] = input.get_initial_value(trans, other_values)
+                    except Exception:
+                        log.exception('tools::to_json() - Getting initial value failed %s.' % input_name)
+                        # get initial value failed due to improper late validation
+                        tool_dict['default_value'] = None
+                        pass
 
-                        # update input value from tool state
-                        tool_dict['value'] = state_inputs.get(input_name, None)
+                    # update input value from tool state
+                    tool_dict['value'] = state_inputs.get(input_name, None)
 
-                        # sanitize values
-                        sanitize(tool_dict, 'value')
-                        sanitize(tool_dict, 'default_value')
+                    # sanitize values
+                    sanitize(tool_dict, 'value')
+                    sanitize(tool_dict, 'default_value')
 
-                        # use default value
-                        if tool_dict['value'] is None:
-                            tool_dict['value'] = tool_dict['default_value']
+                    # use default value
+                    if tool_dict['value'] is None:
+                        tool_dict['value'] = tool_dict['default_value']
 
                 # backup final input dictionary
                 group_inputs[input_index] = tool_dict
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 07e3a2ffa6d..a075d4c72f5 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -202,7 +202,7 @@ class ToolParameter( object, Dictifiable ):
         for validator in self.validators:
             validator.validate( value, history )
 
-    def to_dict( self, trans, view='collection', value_mapper=None ):
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         """ to_dict tool parameter. This can be overridden by subclasses. """
         tool_dict = super( ToolParameter, self ).to_dict()
         #TODO: wrapping html as it causes a lot of errors on subclasses - needs histories, etc.
@@ -277,7 +277,7 @@ class TextToolParameter( ToolParameter ):
     def get_initial_value( self, trans, context, history=None ):
         return self.value
 
-    def to_dict( self, trans, view='collection', value_mapper=None ):
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         d = super(TextToolParameter, self).to_dict(trans)
         d['area'] = self.area
         d['size'] = self.size
@@ -482,7 +482,7 @@ class BooleanToolParameter( ToolParameter ):
         else:
             return self.falsevalue
 
-    def to_dict( self, trans, view='collection', value_mapper=None ):
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         d = super(BooleanToolParameter, self).to_dict(trans)
         d['value'] = self.checked
         d['truevalue'] = self.truevalue
@@ -692,7 +692,7 @@ class BaseURLToolParameter( ToolParameter ):
         # BaseURLToolParameters are ultimately "hidden" parameters
         return None
 
-    def to_dict( self, trans, view='collection', value_mapper=None ):
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         d = super( BaseURLToolParameter, self ).to_dict( trans )
         d['value'] = self.get_value( trans )
         return d
@@ -1079,7 +1079,7 @@ class GenomeBuildParameter( SelectToolParameter ):
     def get_legal_values( self, trans, other_values ):
         return set( dbkey for dbkey, _ in self._get_dbkey_names( trans=trans ) )
 
-    def to_dict( self, trans, view='collection', value_mapper=None ):
+    def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
         d = ToolParameter.to_dict( self, trans )