Hi Dave,

The NoDecode flag did work for me. I added a note to the apache
configuration page of the galaxy wiki:
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

Thanks!

-Will

On Wed, May 11, 2016 at 10:23 AM, Dave Bouvier <d...@bx.psu.edu> wrote:

> Will, Scott,
>
> You should be able to use the NoDecode flag on the AllowEncodedSlashes
> option without any problems. Galaxy will have decoded the slashes
> internally by the time the request has reached the controller, and the tool
> in question will be found.
>
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
>
> On 05/11/2016 12:12 PM, Will Holtz wrote:
>
>> Hello Scott,
>>
>> Thanks for the helpful reply! Adding"AllowEncodedSlashes On" did allow
>> me to access the Data Manager tools. However, the Apache documentation
>> has the following note, "If encoded slashes are needed in path info, use
>> of NoDecode is strongly recommended as a security measure. Allowing
>> slashes to be decoded could potentially allow unsafe paths." So this
>> probably isn't a good long-term solution.
>>
>> thanks,
>> -Will
>>
>> On Wed, May 11, 2016 at 9:03 AM, Scott Szakonyi
>> <scott.b.szakony...@nd.edu <mailto:scott.b.szakony...@nd.edu>> wrote:
>>
>>     Hi Will,
>>
>>     We did manage to solve that problem by changing the Apache
>>     configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm
>>     not sure why the URL encoding changed, only that it did. See if that
>>     helps you.
>>
>>     Best,
>>
>>     Scott
>>
>>     On Tue, May 10, 2016 at 8:17 PM, Will Holtz <who...@lygos.com
>>     <mailto:who...@lygos.com>> wrote:
>>
>>         Hi Scott,
>>
>>         I've recently hit the exact same problem. Have you had any
>>         success since then with resolving this? I did some poking around
>>         and made a bit of progress, but still no solution.
>>
>>         The Data Manager page under Run Data Manager Tools contains URLs
>>         like this:
>>
>>
>> https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1
>>
>>         Loading that URL results in an attempted load of:
>>
>>
>> https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1/build
>> ?
>>
>>         Which results in a 404 error. I believe the escaping of the
>>         slashes is accidental, as the they are in the path and not in
>>         parameters. Changing the %2F to / as shown here:
>>
>>
>> https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1/build
>> ?
>>
>>         results in the URL being found and you get back a bunch of JSON
>>         about the tool. I tried looking in the Galaxy code to see if I
>>         could quickly determine where the /root controller is, but I
>>         wasn't successful. Perhaps this is now enough information that
>>         one of the developers might be able to help us.
>>
>>         -Will
>>
>>         On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi
>>         <scott.b.szakony...@nd.edu <mailto:scott.b.szakony...@nd.edu>>
>>         wrote:
>>
>>             Hello,
>>
>>             I'm having an odd problem after updating to the latest
>>             version of Galaxy. My users prepare data for analysis using
>>             data manager tools, such as
>>             "data_manager_bwa_mem_index_builder". When an attempt is
>>             made to run one of these tools, a pop up window opens
>>             stating "Tool request failed" and underneath "Uncaught
>>             error". I've pored over all the Galaxy system logs and can't
>>             find anything that might indicate what is happening. I've
>>             uninstalled and reinstalled the data manager tools,
>>             restarted both the Galaxy service and the server, to no
>>             avail. I get this same error with any installed data
>>             manager, yet all the standard tools are executing correctly
>>             and don't seem to be having any issues.
>>
>>             If anyone can offer some insight or suggestions for
>>             resolving this issue, I'd be most appreciative.
>>
>>             Best regards,
>>
>>             --
>>             Scott B. Szakonyi
>>             Research Programmer
>>
>>             *Center for Research Computing*
>>             107 Information Technology Center
>>             Notre Dame, IN 46556
>>             http://crc.nd.edu <http://crc.nd.edu/>
>>
>>             ___________________________________________________________
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>>
>>
>>
>>
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>>
>>     --
>>     Scott B. Szakonyi
>>     Research Programmer
>>
>>     *Center for Research Computing*
>>     107 Information Technology Center
>>     Notre Dame, IN 46556
>>     http://crc.nd.edu <http://crc.nd.edu/>
>>
>>
>>
>>
>> --
>> The information contained in this e-mail message or any attachment(s)
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>>
>> ___________________________________________________________
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