[BioSQL-l] Copy of script for simplified biosql Oracle
Richard HOLLAND
hollandr at gis.a-star.edu.sg
Tue Jan 18 20:09:30 EST 2005
Mark's right about the differences between the versions. You should only use the single-user script if you are going to be keeping your dataset fairly small and really don't have DBA access to be able to set up the full version.
The single-user script written by Len Trigg is not in the BioSQL repository. Hilmar, where should I put it? The copy I have here works just fine, but I had to make one or two changes to the original version. Andrew I will email the script directly to you as you can't send attachments to this mailing list.
cheers,
Richard
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at group.novartis.com
> [mailto:mark.schreiber at group.novartis.com]
> Sent: Wednesday, January 19, 2005 8:36 AM
> To: Hilmar Lapp
> Cc: Andrew Wagner; Biosql;
> biosql-l-bounces at portal.open-bio.org; Richard HOLLAND
> Subject: Re: [BioSQL-l] Copy of script for simplified biosql Oracle
>
>
> 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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