Hello John
Thanks for taking a look, and for the explanation. It's useful to know
that it's not something intrinsically wrong with what I've been doing,
and I'll work around it for now. It's good to know that it's targeted
for a fix at some point, even if it doesn't make it into the next release.
Thanks again, best wishes
Peter
On 01/10/14 18:09, John Chilton wrote:
Sorry this has been sitting in my inbox for a while - because I wanted
to try to fix it before the next release but I don't think it is going
to happen.
Generically - it doesn't surprise me that Galaxy can handle certain
parameters changing between versions but not conditionals - they are
handled in a much more complex manner. I have updated this
(https://trello.com/c/INCluhxP) Trello card to reference this problem.
Sorry I don't have better news right now.
-John
On Tue, Sep 23, 2014 at 5:54 AM, Peter Briggs
wrote:
Dear all
One of my users has encountered a problem with extracting a workflow from a
history in our local Galaxy installation (tag latest_2014.08.11, changeset
14342:db520d154716).
The history was created with a version of a local tool which has since been
updated, and the extraction page warns that the newer version of the tool will
be used for those datasets i.e.:
Dataset was created with tool version "0.0.4", but workflow extraction will use version
"0.0.7".
However when the extraction is run it fails immediately: the user sees the "Internal
Server Error" page, and in the log I see:
=
Error - : 'platform'
URL: https://galaxy.ls.manchester.ac.uk/workflow/build_from_current_history
File
'/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
line 1220 in build_from_current_history
workflow_name=workflow_name
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line
30 in extract_workflow
steps = extract_steps( trans, history=history, job_ids=job_ids,
dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line
104 in extract_steps
tool_inputs, associations = step_inputs( trans, job )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line
271 in step_inputs
associations = __cleanup_param_values( tool.inputs, param_values )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line
330 in __cleanup_param_values
cleanup( "", inputs, values )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line
327 in cleanup
group_values = values[input.name]
KeyError: 'platform'
=
'platform' is a conditional parameter that was introduced into the tool between
the two versions. It looks like when tying to use the newer verison of the new
tool, that the new parameter is not getting picked up. Is this expected
behaviour?
(Btw I've seen a similar issue i.e. the "KeyError: 'platform' exception when I
have the two versions of this tool installed from a local toolshed, and try
switching between to the newer one from the older one.)
Any help or suggestions are greatly appreciated.
Many thanks
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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