[BioSQL-l] Re: BIoJava ffor Mysql

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Tue Jan 18 19:44:09 EST 2005 

My immediate thinking is that your version of BioJava is too old. The 
BioSQL stuff is still a work in progress. Take heart that there are 
actually some people actively working on it know. I think it lay dormant 
for about a year but is now getting some stress testing.

I would suggest getting a very recent version of BioJava. Preferably from 
CVS as there have been a few bug fixes in the last few months. 
Unfotunately I'm not working with MySQL so I may not be able to help with 
specific errors caused by the MySQL helpers.

Hope this helps.

- Mark





Hilmar Lapp <hlapp at gnf.org>
01/19/2005 07:14 AM

 
        To:     Andrew Wagner <awagner at nimblegen.com>
        cc:     Len Trigg <len at reeltwo.com>, Mark Schreiber/GP/Novartis at PH, Matthew Pocock 
<matthew_pocock at yahoo.co.uk>, Biosql <biosql-l at open-bio.org>, Thomas Down 
<td2 at sanger.ac.uk>
        Subject:        Re: BIoJava ffor Mysql


I'm afraid the schema is not too old but too new ... hard to tell what 
was expected but not found if the original (root cause) exception with 
the SQL exception and the statement that caused it is not shown.

Mark/Mat/Thomas, any idea what this may be caused by?

                 -hilmar

(Andrew, please do copy the mailing list - possibly also biojava-l - 
for such questions; that way it reaches way more people who can provide 
clues and look at the problem.)

On Jan 18, 2005, at 3:06 PM, Andrew Wagner wrote:

>  A related question if you would be so kind to answer it....
>
>  Using version 1.40 of biosqldb-mysql.sql I created a MySql Database
>
> -- $Id: biosqldb-mysql.sql,v 1.40 2004/11/04 01:49:41 lapp Exp $
>
> -- conventions:
> -- <table_name>_id is primary internal id (usually autogenerated)
>
> -- Authors: Ewan Birney, Elia Stupka, Hilmar Lapp, Aaron Mackey
> --
> -- Copyright Ewan Birney. You may use, modify, and distribute this 
> code under
> -- the same terms as Perl. See the Perl Artistic License.
> --
> -- comments to biosql - biosql-l at open-bio.org
> --
> -- Migration of the MySQL schema to InnoDB by Hilmar Lapp <hlapp at 
> gmx.net>
> -- Post-Cape Town changes by Hilmar Lapp.
> -- Singapore changes by Hilmar Lapp and Aaron Mackey.
> -- post-Singapore changes by Hilmar Lapp.
> --
>
>
> I then attempted to access it with biojava-1.3.1 and even though
> the comments in version 1.40 of biosqldb-mysql.sql say it is Post-Cape 
> Town,
> I get the following exception calling:
> BioSQLSequenceDB db1 = new BioSQLSequenceDB(dbURL,
>         dbUser,
>         dbPass,
>         biodatabase,
>         createIfMissing);
>
> org.biojava.bio.BioException: This database appears to be an old 
> (pre-Cape-Town) BioSQL.  If you need to access it, try an older 
> BioJava snapshot
>         at 
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB. 
> java:100)
>         at TreeFrame.main(TreeFrame.java:87)
> Exception in thread "main"
>
>
>  Thanks,
>
>  Andrew
>
>
>  Hilmar Lapp wrote:
>
> 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>
>
> <awagner.vcf>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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