From c1fe8aac0a646b2bed0b3dbfbf0cd75b595f1690 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 23 Mar 2016 13:29:38 -0400
Subject: [PATCH] Fix inconsistency in update state handling for tool modules

---
 lib/galaxy/tools/__init__.py   |  8 +-------
 lib/galaxy/workflow/modules.py | 11 +++--------
 2 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c9175afa763..30c40c4611b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1661,12 +1661,6 @@ class Tool( object, Dictifiable ):
         tool_model[ 'inputs' ] = {}
         populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] )
 
-        # sanitize tool state
-        def value_to_basic( input, value, parent, **kwargs ):
-            parent[ input.name ] = input.value_to_basic( value, self.app )
-
-        visit_input_values( self.inputs, state_inputs, value_to_basic )
-
         # create tool help
         tool_help = ''
         if self.help:
@@ -1692,7 +1686,7 @@ class Tool( object, Dictifiable ):
             'versions'      : tool_versions,
             'requirements'  : [ { 'name' : r.name, 'version' : r.version } for r in self.requirements ],
             'errors'        : state_errors,
-            'state_inputs'  : state_inputs,
+            'state_inputs'  : params_to_strings( self.inputs, state_inputs, self.app ),
             'job_id'        : trans.security.encode_id( job.id ) if job else None,
             'job_remap'     : self._get_job_remap( job ),
             'history_id'    : trans.security.encode_id( history.id ),
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 356625e0f5a..d60be2364ae 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1,7 +1,6 @@
 """
 Modules used in building workflows
 """
-import copy
 import logging
 from json import dumps, loads
 from xml.etree.ElementTree import Element
@@ -965,11 +964,8 @@ class ToolModule( WorkflowModule ):
                         input_dicts.append( { "name": name, "description": "runtime parameter for tool %s" % self.get_name() } )
         return input_dicts
 
-    def get_post_job_actions( self, incoming=None):
-        if incoming is None:
-            return self.post_job_actions
-        else:
-            return ActionBox.handle_incoming(incoming)
+    def get_post_job_actions( self, incoming ):
+        return ActionBox.handle_incoming( incoming )
 
     def get_config_form( self ):
         self.add_dummy_datasets()
@@ -977,8 +973,7 @@ class ToolModule( WorkflowModule ):
                                          tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) )
 
     def update_state( self, incoming ):
-        self.label = incoming.get( 'label' )
-        self.state.inputs = copy.deepcopy( incoming )
+        self.recover_state( incoming )
 
     def check_and_update_state( self ):
         inputs = self.state.inputs