I think your tool has an XML error in it (the in_graph_filename param
is not being closed) - I imagine this would prevent Galaxy from
displaying the tool - cannot say if it is the only error though:
<param format="graphml" name="in_graph_filename" type="data"
label="Protein interaction graph"
</inputs>
-John
On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden <p...@sanbi.ac.za> wrote:
> 1. Yes, its definitely a delete (checked the box).
>
> 2. The tool, once added, creates:
>
> a. the correct directory structure in shed_tools/
> b. an entry in the tool_shed_repository table that *appears* to be correct
> c. an entry in shed_tool_conf.xml with the annotation of the Graph
> section (where it was originally located before being deleted
> d. *no entry* in integrated_tool_panel.xml
>
> 3. When the tool is deleted:
>
> a. the shed_tools/ directory is cleaned out except for the top level
> directory (graph_report) of the tool
> b. the entry in the tool_shed_repository table remains
> c. the entry in shed_tool_conf.xml remains
> d. there is still no integrated_tool_panel.xml
>
> In terms of the database, tool_version_association references
> tool_version which references tool_shed_repository, so you need to
> delete entries all along that chain to remove an entry from
> tool_shed_repository.
>
> The tool and its type dependency are attached.
>
> On 12/08/2014 16:43, John Chilton wrote:
>> Hey Peter,
>>
>> When you are deleting and reinstalling the tool - can you confirm for
>> me that you are definitely deleting the tool and not just deactivating
>> it?
>>
>> I don't know where to hack around from there - I think repositories
>> are tracked in the database (tool_shed_repository) table, in
>> shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory,
>> tool_dependencies directory. It would be interesting to know which of
>> these still have references to the tool after you delete it.
>>
>> I am also interested in the underlying bug - are you running multiple
>> Galaxy processes? Can you send me the tool that produced this error?
>>
>> -John
>>
>> On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <p...@sanbi.ac.za> wrote:
>>> Hi there
>>>
>>> I updated a tool of mine recently, committed to the local toolshed, did
>>> the update from within the Admin panel and then got this error:
>>>
>>> Error - <type 'exceptions.AttributeError'>: 'Tool' object has no
>>> attribute 'citations'
>>>
>>>
>>> A restart of Galaxy seemed to fix the problem, but since then the tool
>>> could not be found - it is not in any of the Tool categories. Deleting
>>> and re-installing the tool does not fix this problem - and on
>>> installation time I never get asked what group to add it to. It seems as
>>> if it is somehow "stuck" in an incorrect state.
>>>
>>> Any ideas where to go poking? Presumably there is somewhere in the
>>> database to go poking to "reset" things.
>>>
>>> Thanks,
>>> Peter
>>> P.S. this is with the latest Galaxy from galaxy-central.
>>>
>>>
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