[GeneX-dev] Re: DBI->PostgreSQL permission issue

[<ja...@op...>]

> Hi, we're interested in giving GeneX a try, so we've installed the
> software on our linux cluster.  

Hi, we're interested in making sure that GeneX works ;-)

> But we've run into a small snag that I've decided to ask for your
> help on.  It's likely a trivial problem (probably not even a bug!)
> but it's holding things up a bit.  In case other users might hit
> this problem I thought I'd pass it by you.

Thanks! To reach a wider audience, you can use the 'genex-dev' list
(to which I've Cc:ed this reply). That way more people are both likely
to see and reply.

> This documentation describes how connect behaves given different
> combinations of arguments, and reminded me that PostgreSQL
> authenticates users and allows connections according to the file:
> 
>   /var/lib/pgsql/data/pg_hba.conf
> 
> For our installation, this file looks like:
> 
> # By default, allow anything over UNIX domain sockets and localhost.
> local   all                                     trust
> host    all     127.0.0.1       255.255.255.255 trust
> host    all     131.215.34.21   255.255.255.255 crypt
> host    all     131.215.34.24   255.255.255.255 crypt
> host    all     131.215.34.25   255.255.255.255 crypt
> host    all     131.215.34.38   255.255.255.255 crypt
> host    all     131.215.34.70   255.255.255.255 crypt

This is most likely the culprit. Even though this *ought* to work, I'm
sure that every installation we've run uses Unix sockets and *not*
tcp/ip sockets to communicate with the DB. So I bet there is some
authentication issue that we had not considered.

Can you reconfigure GeneX to *not* use tcp/ip to connect with the DB,
and give that a try. 

Re-run install-all.pl and it should automatically detect the existence
of your previous configuration file and ask you whether you want to
run in 'automatic' mode or 'prompting' mode. You want 'prompting' (so
that you can change some of the config params).

The one you want to change is prefixed by '*** GeneX DB Host
Configuration ***'. Instead of entering the true hostname, use
'localhost'. 

The rest should be the same.

NOTE: this will only work if your http server is running on the same
machine as your postmaster daemon.

> P.S. I'm working with Barbara Wold's group at Caltech, assisting
> with data analysis & management; (some of us are at JPL, but most of
> the group is at Caltech, which runs JPL).  A few other groups at
> Caltech and USC looking to us for microarray database solutions as
> well, which is why we're looking at community projects
> vs. home-grown solutions.  Probably lots of the analyses we do could
> be connected up or added to GeneX, though Caltech likes to keep
> rights.  I see how you've handled connections to other licensed
> software, which could probably work for Caltech as well.  So if we
> get GeneX going and generate sufficient interest, we'll have more to
> discuss.

Interesting. I was an undergrad at Caltech in the '80s. Barbara
started there at about the same time. I remember her as an ambitious
and somewhat stressed-out researcher going for tenure. She was a fun
instructor, and I was glad to hear she had gotten tenure.

I'm looking for a good excuse to get to SoCal again to visit some Tech
friends. Do you think there would be any interest in having me come
and give a GeneX talk? It would be related to my MGED talk -- although
I promise not to go so badly overtime :-(

I could even work together with your group and help get things set up
if need be.

Cheers,
jas.