[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(56): proxy: HTTP: canonicalising URL //localhost:8080/datasets/b23533e4ff1bb7ec/display/

[Wed Jan 18 09:31:06 2012] [error] [client 172.26.14.93] (20023)The given path was above the root path: xsendfile: unable to find file: /panfs/galaxy_data/database/files/000/dataset_118.dat, referer: http://galaxy-dev.haib.org/galaxy/history

[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(1836): proxy: end body send

So it seems that there is some issue with the xsendfile module, or with apache serving up the dataset files, because '/panfs/galaxy_data/database/files/000/dataset_118.dat' is present. The only thing that I recall changing recently was to move the /panfs/galaxy_data/database/ directory from the local file system to an nfs share with the exact same path (mounted on /panfs). I'm not sure how that would make a difference though. I'm still looking into the xsendfile error lead though.

-Josh

On Tue, Jan 17, 2012 at 11:08 AM, Josh Nielsen <jnielsen@hudsonalpha.com> wrote:

Also, I just uploaded a 1.3GB FASTQ file and the small preview box in the history pane shows the first few lines, and when I click on the eye it actually displays in the window with the message "This dataset is large and only the first megabyte is shown below. Show all | Save" and it shows the first megabyte with no problems, but if I click 'Show all' or 'Save' I get the message "The requested URL /galaxy/datasets/2faba7054d92b2df/display/ was not found on this server" from apache. So I'm having a specific problem with displaying the whole dataset according to the URL it is trying to load.

-Josh

---------- Forwarded message ----------
From: Josh Nielsen <jnielsen@hudsonalpha.com>
Date: Tue, Jan 17, 2012 at 10:22 AM
Subject: Issues displaying/downloading datasets
To: galaxy-dev@lists.bx.psu.edu

Hello all,

I recently have been having problems viewing/displaying datasets (with the eye icon) as well as downloading datasets in Galaxy which I have uploaded, although I can actually point to those datasets as input to other tools and they show up on the drop down menus and it runs perfectly. Every time that I click on the eye icon for a dataset in my history pane I get an apache error which displays in the window that says it cannot find /galaxy/datasets/XXXXX/display/?preview=True. I see a corresponding entry like this in paster.log (for example):

[17/Jan/2012:09:53:03 -0500] "GET /galaxy/datasets/92b83968e0b52980/display/?preview=True HTTP/1.1" 200 - "http://galaxy-dev.haib.org/galaxy/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101 Firefox/8.0.1"

For downloads I get the same error except that the requested URL is: GET /galaxy/datasets/92b83968e0b52980/display?to_ext=txt

The alphanumeric code is of course different for each dataset but I am puzzled at how to even debug this because I cannot find anywhere on the file system or under the galaxy-dist directory any path that is named "datasets" and has a "display" subfolder (so I assume it is an internal url/path notation). I looked at the python code some and all I got was a headache. I see that it uses a fetch url method to grab a specific url for each dataset but I'm not sure what it is actually looking for on the file system, or if the url is just an alias to something else. I thought to check in the MySQL database but didn't see any corresponding values that matched "datasets" or the alphanumeric code (which I still can't tell where it is getting that from). Everything else in Galaxy works fine except for this. Could anyone please point me in the right direction about how to debug this? It would be much appreciated!

Thanks,
Josh