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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Attachment: capsule_with_dependencies_graphex.sanbi.ac.za_colon_9009_graph_report_pvanheus_81283dded1d9.tar.gz
Description: application/gzip

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