order of multiple output datasets

18 Dec 2009

Hi,

(i'm using current galaxy_dist r3173:f7dee0438854)

when you have a tool in galaxy that creates multiple output datasets, the order in which you define them in the xml file is not preserved in the history.

I believe this is because galaxy collects the output objects in a dict. I made some changes (see the diff below) to use an odict() instead.

However this works only partially, the tool gets executed and the order of the output datasets is preserved, but instead of the message you normally see after executing a tool an error is raised (see below).

I don't know what went wrong and where, I particularly don't understand how the message.mako template works.


Alex 


* Error

URL: http://127.0.0.1:8080/tool_runner/index
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__
  environ, self.app)
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Beaker-1.4-py2.5.egg/beaker/middleware.py', line 152 in __call__
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__
  return self.application(environ, start_response)
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__
  return self.application(environ, start_response)
File '/Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in __call__
  body = self.call_body_method( method, trans, kwargs )
File '/Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 144 in call_body_method
  return method( trans, **kwargs )
File '/Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line 59 in index
  return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars )
File '/Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 593 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File '/Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 604 in fill_template_mako
  return template.render( **data )
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Mako-0.2.5-py2.5.egg/mako/template.py', line 133 in render
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 364 in _render
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 381 in _render_context
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 414 in _exec_template
File '/Users/alexrose/mc-galaxy/galaxy_dist/database/compiled_templates/base.mako.py', line 37 in render_body
  __M_writer(unicode(next.body()))
File '/Users/alexrose/mc-galaxy/galaxy_dist/eggs/py2.5-noplatform/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 255 in <lambda>
File '/Users/alexrose/mc-galaxy/galaxy_dist/database/compiled_templates/message.mako.py', line 45 in render_body
  __M_writer(unicode(_(message)))
File '/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/gettext.py', line 400 in ugettext
  tmsg = self._catalog.get(message, missing)
TypeError: unhashable instance


* Diff

Index: /Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/tools/__init__.py

--- a/lib/galaxy/tools/__init__.py	Wed Dec 16 17:10:05 2009 +0100
+++ b/lib/galaxy/tools/__init__.py	Fri Dec 18 16:20:53 2009 +0100
@@ -427,7 +427,7 @@
         # Parse tool help
         self.parse_help( root )
         # Description of outputs produced by an invocation of the tool
-        self.outputs = {}
+        self.outputs = odict()
         out_elem = root.find("outputs")
         if out_elem:
             for data_elem in out_elem.findall("data"):
Index: /Users/alexrose/mc-galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py	Wed Dec 16 17:10:05 2009 +0100
+++ b/lib/galaxy/tools/actions/__init__.py	Fri Dec 18 16:20:53 2009 +0100
@@ -7,6 +7,7 @@
 from galaxy.jobs import JOB_OK
 import galaxy.tools
 from types import *
+from galaxy.util.odict import odict
 
 import logging
 log = logging.getLogger( __name__ )
@@ -117,7 +118,7 @@
                     input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming )
                 else:
                     input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming )
-        out_data = {}
+        out_data = odict()
         # Collect any input datasets from the incoming parameters
         inp_data = self.collect_input_datasets( tool, incoming, trans )

    

Alexander Rose

Greg Von Kuster

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