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> 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> 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> 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 >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >> >> -- >> The information contained in this e-mail message or any attachment(s) may >> be confidential and/or privileged and is intended for use only by the >> individual(s) to whom this message is addressed. If you are not the >> intended recipient, any dissemination, distribution, copying, or use is >> strictly prohibited. If you receive this e-mail message in error, please >> e-mail the sender at who...@lygos.com and destroy this message and >> remove the transmission from all computer directories (including e-mail >> servers). >> >> Please consider the environment before printing this email. >> > > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
