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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    Scott B. Szakonyi
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