I'm trying to troubleshoot why I can't retrieve output from my Galaxy cluster instance. I notice that when I click on any output, the URL is something like: http://[root galaxy address]/datasets/[some 16-character hash]/display/[file name] I'm not able to find the "datasets" directory on the local machine, and I couldn't figure anything out by searching the paster.log file and the apache access and error logs. Everytime I try to access output, it downloads a zero-byte file. The files that I want to download through Galaxy are in the correct subdirectory of /database/files/... If someone could explain to be what's going on "behind the scenes," it would help me quite a bit. I'm guessing that the absolute path is stored in a database, but beyond that I don't know any specifics. If that's the case, knowing the relevant database tables would be a huge hint. Thanks! Dan
On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C wrote:
I’m trying to troubleshoot why I can’t retrieve output from my Galaxy cluster instance. I notice that when I click on any output, the URL is something like:
http://[root galaxy address]/datasets/[some 16-character hash]/display/[file name]
I’m not able to find the “datasets” directory on the local machine, and I couldn’t figure anything out by searching the paster.log file and the apache access and error logs. Everytime I try to access output, it downloads a zero-byte file. The files that I want to download through Galaxy are in the correct subdirectory of /database/files/… If someone could explain to be what’s going on “behind the scenes,” it would help me quite a bit. I’m guessing that the absolute path is stored in a database, but beyond that I don’t know any specifics. If that’s the case, knowing the relevant database tables would be a huge hint.
Hi Dan, The hash is decoded and converted to an ID using code in lib/galaxy/web/security/__init__.py and the value of id_secret in universe_wsgi.ini. The decoded id is then passed to code in lib/galaxy/objectstore/__init__.py to assemble the path underneath galaxy-dist/database/files/ You may find galaxy-dist/scripts/helper.py in converting history dataset IDs to filesystem paths (they are also available directly in the web interface if you are an administrator or set expose_dataset_path = True in universe_wsgi.ini). --nate
Thanks!
Dan ___________________________________________________________ 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:
Thanks Nate! That's very helpful. -----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Friday, June 08, 2012 3:31 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How does Galaxy access datasets? On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C wrote:
I'm trying to troubleshoot why I can't retrieve output from my Galaxy cluster instance. I notice that when I click on any output, the URL is something like:
http://[root galaxy address]/datasets/[some 16-character hash]/display/[file name]
I'm not able to find the "datasets" directory on the local machine, and I couldn't figure anything out by searching the paster.log file and the apache access and error logs. Everytime I try to access output, it downloads a zero-byte file. The files that I want to download through Galaxy are in the correct subdirectory of /database/files/... If someone could explain to be what's going on "behind the scenes," it would help me quite a bit. I'm guessing that the absolute path is stored in a database, but beyond that I don't know any specifics. If that's the case, knowing the relevant database tables would be a huge hint.
Hi Dan, The hash is decoded and converted to an ID using code in lib/galaxy/web/security/__init__.py and the value of id_secret in universe_wsgi.ini. The decoded id is then passed to code in lib/galaxy/objectstore/__init__.py to assemble the path underneath galaxy-dist/database/files/ You may find galaxy-dist/scripts/helper.py in converting history dataset IDs to filesystem paths (they are also available directly in the web interface if you are an administrator or set expose_dataset_path = True in universe_wsgi.ini). --nate
participants (2)
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Dorset, Daniel C -
Nate Coraor