[ome-devel] Fwd: OME install question

Ilya Goldberg igg at nih.gov
Wed Jun 16 16:44:33 BST 2004

Begin forwarded message:

> From: Zachary Pincus <zpincus at stanford.edu>
> Date: 16 June 2004 08:19:23 BST
> To: Jason Swedlow <j.swedlow at dundee.ac.uk>
> Subject: OME install question
> So, I got OME installed easily enough on a pretty plain-vanilla OS X 
> 10.3 system. The install seemingly went fine, but when I go to the OME 
> page, I'm redirected to 
> http://my.server.stanford.edu/perl2/serve.pl?Page=OME::Web::Home (as I 
> should be), which is a totally empty page (0 bytes), which I assume is 
> no good. Nothing in the httpd access or error logs seems amiss...
> Moreover, the shoola client dies of an uncaught "Not logged in" 
> exception when I try to connect -- and yes, it is pointed at the 
> proper server.
> Finally, running
> zpincus% perl src/perl2/OME/Tests/DatabaseTest.pl
> produces:
> OME Test Case - Database Access
> -------------------------------
> Please login to OME:
> Username? [ANYTHING -- result is the same]
> Password? [ANYTHING]
> DBI->connect(dbname=ome) failed: FATAL 1:  user "zpincus" does not 
> exist at /Library/Perl/5.8.1/OME/Database/Delegate.pm line 176

This error is caused because zpincus is not a postgres user.  In order 
to run things on the command line, the user that's logged in and 
running the unix shell must also be a postgres user (they're separate 
and independent).  The installer asks if you want a regular unix user 
to act as an OME admin user with this question:
Set up a separate admin user for OME (i.e. your account)? [y/n]
If you answer y, then it will ask you for a unix username to administer 
OME (the default is the owner of the OME distribution directory).  If 
you answer n, then the only unix user allowed to administer OME from 
the command line is the 'ome' user (or whatever user you selected when 
asked "The user which OME should be run under").
I think that this is confusing enough that the default answer to the 
"separate admin" user question should really be 'y'.
You can work around this by manually adding a postgres user like so:
 > sudo -u postgres createuser zpincus

You should probably also add zpincus to the ome unix group, but that's 
not straight forward to do on the command line in OS X (you need to use 
NetInfo).  Probably the easiest way is to run the installer again with 
the -u flag (so that it reuses your previous settings):
 > sudo perl install.pl -u
The installer will never clobber your database, so its safe to run it 
as many times as you want.

This doesn't answer why you can't log in via the web UI.  In that case, 
the user that logs in to the DB is the unix user that's used by Apache 
(www on OS X).  The installer figures out which user Apache runs under, 
and adds this user to postgres.  It also asks to confirm this during 
the installation, so if it guessed wrong, this could be the reason why 
Apache fails to log in (but see below).

> I can't really figure out if there are any logs or other places to 
> look for hints as to what the problem might be. Sorry to bother you 
> with asinine install problems, but I'm quite excited to start with OME 
> and I'm at a bit of a loss as to how to deal with this.
All error output ends up in the apache error log (on OS X and most 
other systems its /var/log/httpd/error_log).  We try to report as much 
as we can to the client (browser), but we can always do better.  If the 
installer guessed wrong about the apache user name (not likely on your 
system), then you should see a similar error in the Apache error log to 
what you saw when you tried DatabaseTest.pl on the command line.

The most likely reason that you are getting a blank page in a browser 
with OME installed on OS X 10.3 is that the mod_perl installation is 
broken.  Unfortunately, its shipped broken by Apple and you have to 
actually rebuild mod_perl manually to get it to work.  Its very easy 
(famous last words), and the relevant documentation is here:
If you did in fact rebuild and install mod_perl (without errors) and 
are still getting a blank page, then we need to do some more analysis 
of what's going on.  Feel free to contact me off-list at igg at nih.gov.


> Thanks a lot for your time,
> Zach Pincus
> Department of Biochemistry and Program in Biomedical Informatics
> Stanford University School of Medicine

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