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.comwrote:
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/X/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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