gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] instance v's schemas

[pjm <pj...@sa...>]

Jonathan,

we have always had a serate instance for testing and development in production
software - quite handy when some dodgy SQL brings the server to its knees. The
only thing in the code that changes is the connection to the DB itself, nothing
else. Does Oracle run on just the one machine?

We have scripts to dump data (all or a subset) from the live DB into the test
one so we have working real data.

As for getting the schema into our instance, I am attempting to write a script
that will run as each user to create the nessacery tables and log what happened.
I have also come accross 2 buglets;

the *-indexes.sql just contain line returns or white space, not actual code.

I added this line to core-tableinfo.sql;
        alter session set NLS_DATE_FORMAT='YYYY-MM-DD HH24:MI:SS';
Oracle 8 & 9 have a default date field of 'DD--MON-RR' I believe.


Paul.

Re: [Gusdev-gusdev] DBA stuff

[<cra...@SN...>]

Hi Paul-

Thanks to Martin for creating that script; it occurred to me sometime yesterday
that you'd have to create the users first, but it slipped my mind before I got
a chance to do something about it.  It should definitely be added to CVS, although 
we'll probably want to do substitutions similar to those you've applied to the
CREATE TABLE script i.e., substituting &1 for 'temp_01' and &2 for 'users'.  It's
also possible that people will want to choose different passwords for the various
users.  Finally, something we haven't really considered yet is how we would set up
two distinct copies of "GUS 3.0" on the same Oracle instance.  In other words, what
naming convention should be adopted to 1. tell it apart from other copies of GUS 
3.0-compliant databases and 2. make it clear which Oracle users/schemas (core, 
corever, sres, etc.)  are part of the same [GUS 3.0 not Oracle] instance.

For example, here are a couple of possibilities:

1. A GUS 3.0 "development" database used to test new features:
    core-dev
    corever-dev
    sres-dev
    etc.

2. On second thoughts it's probably better to use a common prefix for sorting
   purposes:
     dev-core
     dev-corever
     dev-sres
     etc.

It makes things a little more verbose but otherwise I don't see how we're going to
be able to maintain different GUS 3.0 instances in the same Oracle instance (which
I'm assuming is something we'll want to try at some point, if only to create an
empty test copy of the latest schema before checking it into CVS.)  I *believe* that
the Perl object layer should take the name of the "core" database as an argument,
and it should be able to figure out the names of the remaining dbs by looking at
core.tableinfo.  What does everyone else think about this?

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115

[Gusdev-gusdev] DBA stuff

[pjm <pj...@sa...>]

Deborah,

our head DBA, Martin Widlake, has written a script (see below) that may need to
go into CVS. It created the six users for the six schemas. Also this quote from
Martin;

"I checked the view creation scripts and it looks like that for each view the
owner is stated but the owner of the table it is on is not. However, in every
case the table belongs to the same schema and no other schema will have that
table in it, so is should work fine."

Might be worth specifying the schemas?

I am about to run the table creation scripts and will let you know how I get on.
I have changed USER3 to be &1 so it can fit in with our stuff easily.

Paul.

-- cre_gus_new_users.sql
-- create the users needed for GUS30
-- Needs to be run from a suer which has create user system priv
-- (Run from a user with DBA role!)
--
drop user core cascade;
drop user corever cascade;
drop user dots cascade;
drop user dotsver cascade;
drop user sres cascade;
drop user sresver cascade;
--
set echo on
spool cre_gus_new_users.lst
create user core identified by core
temporary tablespace temp_01
default tablespace users
/
grant connect to core;
grant resource to core;
--
create user corever identified by corever
temporary tablespace temp_01
default tablespace users
/
grant connect to corever;
grant resource to corever;
--
create user dots identified by dots
temporary tablespace temp_01
default tablespace users
/
grant connect to dots;
grant resource to dots;
--
create user dotsver identified by dotsver
temporary tablespace temp_01
default tablespace users
/
grant connect to dotsver;
grant resource to dotsver;
--
create user sres identified by sres
temporary tablespace temp_01
default tablespace users
/
grant connect to sres;
grant resource to sres;
--
create user sresver identified by sresver
temporary tablespace temp_01
default tablespace users
/
grant connect to sresver;
grant resource to sresver;
spool off
set echo off
--

Re: [Gusdev-gusdev] create table statements in CVS

[<cra...@SN...>]

Pjm wrote:
> 
> Steve,
> 
> just done a checkout on the module scratch and some of the files have zero
> length in the GUS30Schema directory. Is this correct?
> 
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 core-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 corever-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 dots-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 dotsver-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sres-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sres-views.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sresver-sequences.sql
> -rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sresver-views.sql
> 
> Paul.
> 

Paul-

This is definitely *not* correct; Debbie is looking into what went wrong here
and we'll let you know as soon as it's sorted out.

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115

Re: [Gusdev-gusdev] create table statements in CVS

[Pjm <pj...@sa...>]

Steve,

just done a checkout on the module scratch and some of the files have zero 
length in the GUS30Schema directory. Is this correct?

-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 core-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 corever-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 dots-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 dotsver-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sres-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sres-views.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sresver-sequences.sql
-rw-rw-r--   1 pjm      system         0 Jun 25 20:05 sresver-views.sql

Paul.

steve fischer wrote:
> folks-
> 
> we have generated the create table statements from our installed gus 3.0
> 
> they are in the sourceforge cvs under scratch/GUS30Schema
> 
> steve
> 
> 
> 
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[Gusdev-gusdev] create table statements in CVS

[steve f. <st...@SN...>]

folks-

we have generated the create table statements from our installed gus 3.0

they are in the sourceforge cvs under scratch/GUS30Schema

steve

[Gusdev-gusdev] CVS

[Pjm <pj...@sa...>]

Hi all,

I have just spoken to James Cuff, our sys admin in charge of external CVS. He 
will have a read/write cvs repository setup by Monday for us to try out. If you 
are still keen I will need to pass on your desired user names to him so he can 
set them up on the machine in question (kaka I think). Please email them to me.

This machine lives outside of the firwall and gets backed-up regularly (plans 
for 10 times a day to disk for quick recovery). It has its own password file. 
When your accounts are created I will phone you to say what the passwords are 
and then you can ssh in to run passwd. Port 22 (?) is the only one open - this 
is for ssh. The machine runs only the services needed for CVS and mySQL and is 
monitored automatically. Your shell would be minimal. The machine is locked down 
as hard as the sys admins know how.

In theory someone could gain access as one of us and alter the CVS repository in 
some subtle way and everything would still work. Ensembl have majordomo group 
setup so if anyone commits a change the group gets emailed. You can opt in/out 
of the group.

I think thats it... any comments?

Paul.

[Gusdev-gusdev] please confirm your membership

[steve f. <st...@SN...>]

hey folks-

i've added you to the gusdev mailing list.

please send me mail confirming that you have received this mail, so i 
know i didn't introduce any typos...

st...@pc...

thanks,
steve