Hello Anna,

Yeah - this is readily reproducible. I will work on this problem today
- sorry about that.

-John


On Thu, Dec 18, 2014 at 8:55 AM, Anna Terry <iseegl...@googlemail.com> wrote:
> Deleting the newer 0.3 version of Bowtie fixes the problem with version 0.2.
>
> On 18 December 2014 at 13:29, Anna Terry <iseegl...@googlemail.com> wrote:
>>
>> Hi again,
>> I have just updated Picard, and am getting a similar error with some tools
>> from that repository when I switch to older version from tool page.
>> I also noticed that some tools from the Picard repo appear as multiple
>> entries for different in the tool panel rather than selecting the different
>> versions from the drop down.
>> These errors are all on tools with version dropdowns, however I don't get
>> these errors on all of the version dropdowns, for instance I can switch to
>> an older version of fastqc no problem.
>> So are the new versions of tools breaking old versions, or is there a
>> problem with the tool panel?
>>
>> Any help appreciated!!
>>
>>
>> SamToFastq:
>> URL: http://....../tool_runner/index
>> File
>> '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>> line 364 in respond
>>   app_iter = self.application(environ, detect_start_response)
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>> line 107 in __call__
>>   return self.app( environ, start_response )
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
>> in handle_request
>>   body = method( trans, **kwargs )
>> File
>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>> line 90 in index
>>   template, vars = tool.handle_input( trans, params.__dict__ )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
>> handle_input
>>   errors, params = self.__check_param_values( trans, expanded_incoming,
>> expanded_state, old_errors, process_state, history=history, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
>> __check_param_values
>>   errors = self.update_state( trans, inputs, state.inputs, incoming,
>> old_errors=old_errors or {}, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
>> update_state
>>   group_state = state[input.name]
>> KeyError: 'single_paired_end_type'
>>
>>
>> ReorderSam:
>> URL: http://....../tool_runner/index
>> File
>> '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>> line 364 in respond
>>   app_iter = self.application(environ, detect_start_response)
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>> line 107 in __call__
>>   return self.app( environ, start_response )
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
>> in handle_request
>>   body = method( trans, **kwargs )
>> File
>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>> line 90 in index
>>   template, vars = tool.handle_input( trans, params.__dict__ )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
>> handle_input
>>   errors, params = self.__check_param_values( trans, expanded_incoming,
>> expanded_state, old_errors, process_state, history=history, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
>> __check_param_values
>>   errors = self.update_state( trans, inputs, state.inputs, incoming,
>> old_errors=old_errors or {}, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
>> update_state
>>   group_state = state[input.name]
>> KeyError: 'source'
>>
>> FastqToSam:
>> URL: http://...../tool_runner/index
>> File
>> '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>> line 364 in respond
>>   app_iter = self.application(environ, detect_start_response)
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>> line 107 in __call__
>>   return self.app( environ, start_response )
>> File
>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
>> in handle_request
>>   body = method( trans, **kwargs )
>> File
>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>> line 90 in index
>>   template, vars = tool.handle_input( trans, params.__dict__ )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
>> handle_input
>>   errors, params = self.__check_param_values( trans, expanded_incoming,
>> expanded_state, old_errors, process_state, history=history, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
>> __check_param_values
>>   errors = self.update_state( trans, inputs, state.inputs, incoming,
>> old_errors=old_errors or {}, source=source )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
>> update_state
>>   group_state = state[input.name]
>> KeyError: 'param_type'
>>
>>
>>
>>
>> On 18 December 2014 at 01:12, Anna Terry <iseegl...@googlemail.com> wrote:
>>>
>>> Hi,
>>> I am getting an error page when I try to open the bowtie2 tool page
>>> (after selecting older version 0.2 a54de7e658f7 from drop down on version
>>> 0.3 c1ec08cb34f9 page).
>>>
>>> URL: http://....../tool_runner/index
>>> File
>>> '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>>> line 364 in respond
>>>   app_iter = self.application(environ, detect_start_response)
>>> File
>>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>>> line 107 in __call__
>>>   return self.app( environ, start_response )
>>> File
>>> '/home/galaxy/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/galaxy-dist/lib/galaxy/web/framework/base.py', line
>>> 132 in __call__
>>>   return self.handle_request( environ, start_response )
>>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>>> 190 in handle_request
>>>   body = method( trans, **kwargs )
>>> File
>>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>>> line 90 in index
>>>   template, vars = tool.handle_input( trans, params.__dict__ )
>>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136
>>> in handle_input
>>>   errors, params = self.__check_param_values( trans, expanded_incoming,
>>> expanded_state, old_errors, process_state, history=history, source=source )
>>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251
>>> in __check_param_values
>>>   errors = self.update_state( trans, inputs, state.inputs, incoming,
>>> old_errors=old_errors or {}, source=source )
>>> File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514
>>> in update_state
>>>   group_state = state[input.name]
>>> KeyError: 'params'
>>>
>>> I can't see anything that gives me a clue where to investigate further,
>>> hopefully someone here knows?
>>> I have tried updating to latest changeset, and have restarted a few
>>> times, but still the same error.
>>>
>>> Thanks in advance for help
>>> Anna
>>>
>
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