Hi Rico,
Can you provide the specific GET request URL with which you encountered this
problem? There are very few GET requests when installing repositories from the
tool shed - the only one I can locate without a lot of digging is the
following, which I don't think is causing the problem.
# Get the information necessary to install each repository.
url = suc.url_join( tool_shed_url,
'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s'
% \
( repository_ids, changeset_revisions ) )
Thanks,
Greg Von Kuster
On Sep 13, 2013, at 10:59 AM, Richard Burhans <r...@bx.psu.edu> wrote:
> Folks,
>
> After checking a little closer last night, I have one clarification.
> The Tool Shed does use POSTs as well as GETs, but even when it's
> POSTing, the encoded dictionaries (encoded_repo_info_dicts) are part
> of the query string. The encoded_repo_info_dicts should probably
> become part of the POSTed data.
>
> -rico
>
> On Sep 12, 2013, at 3:55 PM, Richard Burhans wrote:
>
>> When installing Galaxy Tool Shed repositories into a local Galaxy
>> instance, tool shed dependecies are exchanged as an encoded python
>> dictionary via the HTTP GET method.
>>
>> If a tool shed repository contains enough dependencies, the length
>> of this encoded dictionary can become extremely long. In my case,
>> it became long enough for my Apache server to choke on it:
>>
>> [Wed Sep 11 15:34:53 2013] [error] [client XXX.XXX.XXX.XXX] request failed:
>> URI too long (longer than 8190)
>>
>> The HTTP standard does not place a limit on the length of a URI,
>> but the de facto limit is 2000 characters. See the following
>> stackoverflow answer:
>>
>> http://stackoverflow.com/a/417184
>>
>> I would recommend either:
>> 1) communicating toolshed dependencies via an HTTP POST
>> 2) redesigning tool shed <-> instance communications
>>
>> As a stopgap measure, I've modified lib/tool_shed/util/encoding_util.py
>> to use a more compact encoding scheme. I'm attaching a copy in
>> case someone else runs into the same problem.
>>
>> -rico<encoding_util.py>
>
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