Hi Dannon,

I am in a meeting right now.  I should be done at noon.  I'll send you more 
info then.  Thank you for your assistance!

Best,
Eric


-------- Original message --------
From: Dannon Baker
Date:2014/05/22 11:08 (GMT-05:00)
To: "Paniagua, Eric"
Cc: "Galaxy ‎[galaxy-u...@bx.psu.edu]‎"
Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

Hey Eric,

Looking into this.  Can you send the exact error/trace if available?

-Dannon


On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric 
<epani...@cshl.edu<mailto:epani...@cshl.edu>> wrote:
Hi,

I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the 
process of preparing an update I have encountered some problems.  When I try to 
create a new dataset (e.g. by running a tool), I receive an error message 
indicating a syntactic problem with backend database commands.  Specifically, 
the error mentions a read-only cursor and occurs when the system is trying to 
look up the history hid number for the new dataset, a value which (as far as I 
understand it) should be an autoincrementing primary key.

My codebase is the 68a8b0397947 commit on the stable branch, plus some custom 
tool definitions, but no real modification to any core Galaxy code.  The 
database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In the target 
(production) environment, we run with 3 web server processes and 3 job runner 
processes, but I am encountering this error in a single-Galaxy-process test 
instance.  The error is reported both in the logs (with a traceback originating 
in the bowels of SQLAlchemy) and via the web interface.

I dug through the commit history and found a comit (e1bc855165bc) with the 
comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)." on 
Sep 23, 2013.  I am wondering if this means I need to upgrade my database 
backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that I need to keep 
2 parallel Galaxy instances running for an extended time period (~1 month).  
The first is the current (not updated) local Galaxy instance, and the second is 
the new (updated) Galaxy instance, which naturally implies diverging databases. 
 Does this mean I will need to maintain parallel installations of PostgreSQL 
9.1 and 9.2.x?  How would I go about setting up that configuration?

Any assistance on debugging this error would be greatly appreciated.  Our 
initial goal was to roll out this update tomorrow afternoon, but that may need 
to be delayed because of this show-stopper.  If I can provide any further 
useful information, please let me know, and I will be happy to do so.

Best,
Eric Paniagua

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___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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