I seem to be getting somewhere by monitoring the /var/log/httpd/error_log
file (I don't know why I didn't think of that before). For each dataset I
click I am seeing a corresponding message like this:

*[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 <jniel...@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 <jniel...@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
>
>
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