8:18 p.m.
Sorry... I got it, forgot to pull first :)
leandro
-----Original Message-----
From: galaxy-dev-bounces(a)bx.psu.edu
[mailto:galaxy-dev-bounces@bx.psu.edu] On Behalf Of Hermida, Leandro
Sent: Thursday, May 21, 2009 21:56
To: Nate Coraor
Cc: galaxy-dev(a)bx.psu.edu
Subject: Re: [galaxy-dev] bug with output files_path property dataset
IDwhen Galaxy has shared histories
Hi Nate,
Thanks for fixing so fast... has this been committed to
http://www.bx.psu.edu/hg/galaxy?
Best,
Leandro
-----Original Message-----
From: Nate Coraor [mailto:nate@bx.psu.edu]
Sent: Thursday, May 21, 2009 18:46
To: Hermida, Leandro
Cc: galaxy-dev(a)bx.psu.edu
Subject: Re: [galaxy-dev] bug with output files_path property dataset ID
when Galaxy has shared histories
Leandro,
This is fixed in the latest commit.
Thanks,
--nate
Hermida, Leandro wrote:
Hello,
I've developed a few tools for Galaxy and I think I ran into a bug
that
even exists in the latest version. As you know a Galaxy server
maintains the same external dataset ID (i.e. viewable in the web URLs)
to the filesystem internal dataset ID (i.e. names in
database/files/000/) if no user in the Galaxy server has yet shared
any
histories (and their datasets). But once sharing starts the external
dataset IDs start differing from the internal dataset ID, and they are
always higher and Galaxy maintains this transparently. But this
behavior seems to be broken with the output files_path property.
If you have a tool which uses the output files_path property like this
one I have:
<command interpreter="perl">search.pl $query_list $output1
$output1.files_path</command>
On my test server I've shared one history with a single dataset. So
my
external-internal offset is 1. The above tool then produces the
following command:
perl /home/hermida/galaxy/galaxy_dist/tools/omics_data_miner/search.pl
/home/hermida/galaxy/galaxy_dist/database/files/000/dataset_28.dat
/home/hermida/galaxy/galaxy_dist/database/files/000/dataset_31.dat
/home/hermida/galaxy/galaxy_dist/database/tmp/dataset_32_files
Galaxy is not generating the correct files_path, it should end in
dataset_31_files not 32. This bug causes the tool to completely break
when you are trying to view your output in the browser and I tried to
circumvent the bug with symlinking magic but it can't fix the problem
because symlinks start stepping on existing directories once you run
the
tool more than once.
Thanks for any help on how to fix the problem,
Leandro
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