[ome-devel] Fwd: Postgres problem

[Josiah Johnston]

For the record, this problem was a messed up installation of postgres.

-Josiah

Begin forwarded message:

> From: "McCaughey, Michael J" <michael.j.mccaughey at Vanderbilt.Edu>
> Date: August 22, 2006 10:48:34 AM EDT
> To: "Josiah Johnston" <siah at nih.gov>
> Subject: RE: [ome-devel] Postgres problem
>
> $lidir is set during the install of postgres. I apparently hosed  
> the install of 8.1.4 so that this path was not correct. I've fixed  
> this, and the installer now works.
>
> Thanks for the help!
>
> Mike
>
>
>
> Michael J. McCaughey, PhD
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
>
>
> -----Original Message-----
> From: Josiah Johnston [mailto:siah at nih.gov]
> Sent: Mon 8/21/2006 3:39 PM
> To: McCaughey, Michael J
> Subject: Re: [ome-devel] Postgres problem
>
> I screwed up the test script. Can you re-run the attached one.
> Save it to the perl2 directory you are installing from, then
>
> cd /path/to/checkout/of/OME/src/perl2/
> export PERL5LIB=.:$PERL5LIB
> sudo perl DBconnectAndCreateUserTest.pl
>
> I don't know exactly what's going on with the "$libdir/plpgsql"
> thing. Grepping led me to line 142 of OME/src/perl2/OME/Database/
> PostgresDelegate.pm
> Googling led me to discover the code there is lifted from
>         http://www.postgresql.org/docs/7.2/static/xplang-install.html
> and those instructions have been changed in version 8.1:
>         http://www.postgresql.org/docs/8.1/interactive/xplang.html
>
> If you feel slightly brave, try entering pgsql and typing the newer
> instructions from the 8.1.x manual:
>
>   CREATE FUNCTION plpgsql_call_handler() RETURNS language_handler AS
>      '$libdir/plpgsql' LANGUAGE C;
>
> CREATE FUNCTION plpgsql_validator(oid) RETURNS void AS
>      '$libdir/plpgsql' LANGUAGE C;
>
> CREATE TRUSTED PROCEDURAL LANGUAGE plpgsql
>      HANDLER plpgsql_call_handler
>      VALIDATOR plpgsql_validator;
>
> Then rerun the installer. If it's merely a question of updating the
> syntax in PostgresDelegate, then that manual step should fix your
> system.
>
> -Josiah
>
> On Aug 21, 2006, at 4:04 PM, McCaughey, Michael J wrote:
>
> > Dropped DB, copied new PostgresDelegate.pm and re-run gives me this
> > again:
> >
> > ->
> > --------------------
> >  Database Bootstrap
> > --------------------
> >
> > (All verbose information logged in /var/tmp/OME/install/
> > CoreDatabaseTablesTask.log)
> >
> > Finding DB configuration in installation environment [USING  
> DEFAULT].
> > Database connection information
> > N.B.:  The database host must already be installed and running.
> > It must already be configured for accepting the connection
> > specified here, or a superuser connection from user "postgres".
> >    Database Delegate Class: OME::Database::PostgresDelegate
> >              Database Name: ome
> >                       Host: undefined (local)
> >                       Port: undefined (default)
> > Username for DB connection: undefined (process owner)
> >
> > Are these values correct ? [y/n]:
> > Creating OME PostgreSQL SUPERUSER (ome)[SUCCESS].
> > Creating Apache PostgreSQL SUPERUSER (apache)[SUCCESS].
> > Creating Admin PostgreSQL SUPERUSER (mrmike)[SUCCESS].
> > Checking database
> > Creating PostgreSQL database ome...     [Done.]
> > Fixing OID/INTEGER compatability bug...DBD::Pg::db do failed:
> > ERROR:  could not access file "$libdir/plpgsql": No such file or
> > directory
> >
> >
> > Errors executing task: DBD::Pg::db do failed: ERROR:  could not
> > access file "$libdir/plpgsql": No such file or directory
> >
> >  at install.pl line 82
> >         main::run_tasks() called at install.pl line 266
> > # Looks like your test died before it could output anything.
> > <-
> >
> > This now looks like a problem with DBD:Pg, which I thought I had
> > cured last weekend with a reinstall.
> >
> > The log file:
> > ->
> > [mrmike at cisrdev OME]$ more /var/tmp/OME/install/
> > CoreDatabaseTablesTask.log
> > Creating OME PostgreSQL SUPERUSER (ome)
> > [mrmike at cisrdev OME]$
> > <-
> >
> > DBconnectAndCreateUserTest.pl generates:
> > ->
> > Global symbol "$self" requires explicit package name at dbtest.pl
> > line 16.
> > Global symbol "$self" requires explicit package name at dbtest.pl
> > line 22.
> > Global symbol "$superuser" requires explicit package name at
> > dbtest.pl line 39.
> > Execution of dbtest.pl aborted due to compilation errors.
> > <-
> > Removing strict gives:
> > ->
> > Could not get DB configuration enevironment
> > Maybe the installation environment did not load? at
> > DBconnectAndCreateUserTest.pl line 10
> > <-
> >
> > *sigh*
> >
> > This may be a problem with DBD::Pg again.  I'm using v1.43 from the
> > OME repository.
> > It compiles, tests, and installs fine. Postgres 8.1.4 is working
> > fine for other apps (bacula, etc.).
> >
> >
> >
> >
> > Michael J. McCaughey, PhD
> > Molecular Physiology and Biophysics
> > U9203 MRBIII
> > 6-6175
> >
> >
> >
> > -----Original Message-----
> > From: ome-devel-bounces at lists.openmicroscopy.org.uk on behalf of
> > Josiah Johnston
> > Sent: Mon 8/21/2006 1:51 PM
> > To: McCaughey, Michael J
> > Cc: ome-devel at lists.openmicroscopy.org.uk
> > Subject: Re: [ome-devel] Postgres problem
> >
> > Can you copy the attached PostgresDelegate.pm to the src/perl2/OME/
> > Database/ directory under your installation root? Then, re-run the
> > installer and resend the logs and installation info.
> >
> > After that, please run the attached perl test script,
> > "DBconnectAndCreateUserTest.pl" as sudo, and send the output of it.
> >
> > The problem is in PostgresDelegate->createUser(). I suspect it is in
> > the database connection, but I need more info to know for sure.
> >
> > Thanks,
> > Josiah
> >
> >
> >
> >
> ?
>
>