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] (20023)The given
path was above the root path: xsendfile: unable to find file:
/panfs/galaxy_data/database/files/000/dataset_118.dat, referer:
*[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(1836): proxy: end body

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.


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
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:


Reply via email to