[BioSQL-l] Copy of script for simplified biosql Oracle

Tue Jan 18 19:36:02 EST 2005

Hi -

The main difference is that the 'official' version has lots of different 
users with different privileges and views that make the oracle schema look 
like the BioSQL schema, it's pretty much a by-the-book 
how-you-should-do-it implementation. The 'simplified' version has only one 
user and I think has no views. It is much easier for Oracle or DB novices 
to understand but may not be well suited to a production or mutli-user 
environment. In some limited testing it can be a little faster but that 
probably has more to do with your computer and how Oracle has been set up.

I'll feret around to get it and post it to the list. Richard, do you have 
a copy?

- Mark

Hilmar Lapp <hlapp at gnf.org>
Sent by: biosql-l-bounces at portal.open-bio.org
01/19/2005 03:44 AM

        To:     Andrew Wagner <awagner at nimblegen.com>
        cc:     Biosql <biosql-l at open-bio.org>, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [BioSQL-l] Copy of script for simplified biosql Oracle

Whether or not you need sysdba access depends largely on whether you 
have a DBA that would do those things you can't normally do yourself, 
or grant you permissions that by default Oracle doesn't give to every 
user.

Take a look at the BS-create-all.sql script, and make sure only those 
steps are commented in that you really want to be executed. E.g., if 
you don't care to create users or your DBA does that then leave out 
that step. Similarly for roles. There is also a part that creates 
public synonyms for views and by default Oracle doesn't grant this 
permission to a user, so if you want that you'll either need sysdba 
access or a DBA who grants the permission to you ('you' standing for 
the schema owner). However, if all you intend to use this for is 
Biojava then the views published as public synonyms (SG_%) aren't even 
going to be used and so you can do without that step. You can easily 
add that later if at some point you decide to access the schema through 
other levels as well. This holds as well for the PL/SQL API; Biojava 
will neither need nor use it.

In other words, for Biojava or Bioperl alone basically what you need is 
BS-DDL.sql and then decide on one of the two Biosql APIs. Biojava needs 
the view-based API, Bioperl needs (at this point) the synonym-based.

Let me know if you hit a problem or if you're unsure how to proceed. 
Your endeavor is a good test for the release.

                 -hilmar

On Tuesday, January 18, 2005, at 10:32  AM, Andrew Wagner wrote:

> No error or problems... I did not attempt the Original script.... just 
> reading 
> http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm
>
> "You'll need the latest version of BioJava to take advantage of the 
> full functionality of BioSQL. This can be downloaded from biojava.org. 
> You'll also need the latest Oracle BioSQL schema. Here you have a 
> choice of two options:
>
> ?              Original: by Hilmar Lapp, the original BioSQL schema 
takes full 
> advantage of Oracle's security mechanisms and produces a complex but 
> high quality schema. You'll need sysdba access to your database to 
> install it. Go to cvs.open-bio.org, select the biosql project, and 
> navigate to and download the entire biosql-schema/sql/biosql-ora 
> folder.
> ?              Simplifed: by Len Trigg, this version is simplified in 
structure 
> and sits entirely inside a single user account, requiring no sysdba 
> access to install. You'll have to ask for a copy of the script from 
> the biosql-l mailing lists."
>
> I thought Simplified was the place to start but I cna easily start 
> with the Original if that's what you reccomend.
>
> Andrew
>
>
>
> Hilmar Lapp wrote:
>
> If there is anything special about this script then I believe it 
> should be in the repository. I'm not exactly sure what 'simplified' 
> encompasses here; the biosql schema and API does sit entirely in a 
> single user account by default. The biosql standard names are not 
> exported as public synonyms by default, but first, if you're going to 
> access the database through the schema owner, this doesn't concern you 
> anyway, and second, there's a script that generates a script with 
> which to establish the synonyms for any user, and third, it is trivial 
> to modify this script such that the created synonyms are public 
> instead of private.
>
> Did you hit a specific error or problem?
>
>     -hilmar
>
> On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote:
>
>
> I  am looking for a copy of the script for simplified biosql in oracle.
>
> Thanks,
>
> Andrew
>
> *Simplifed*: by Len Trigg, this version is simplified in structure and 
> sits entirely inside a single user account, requiring no sysdba access 
> to install. You'll have to ask for a copy of the script from the 
> biosql-l <http://obda.open-bio.org/mailman/listinfo/biosql-l> mailing 
> lists.
>
> <awagner.vcf>_______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
> <awagner.vcf>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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