[Biojava-dev] BioSQL implementation

[Simon Foote]

Hi Guys,

Disregard the attached changes to one of the emails as I've made several 
more since I made that archive.  Now that the lists are back working 
again, let me know where to send the changes.  I think I've weeded out 
most of the bugs.

Regards,
Simon

Simon Foote wrote:

>Hi Thomas & Mathew,
>
>I've been following the development of the BioSQL schema and I noticed 
>in an email from Hilmar last week on the BioSQL list that a release was 
>imminent.
>
>Thus, I've been modifying the biojava code to get it working with the 
>latest schema within MySQL.  The main changes have been the following:
>
>1) Ontology_term table to term table with applicable id name changes.
>
>2) Seqfeature_location table to location table with applicable id name 
>changes
>
>3) Seqfeature_relationship table --> parent and child changes to object 
>and subject
>
>4) Changes to generate unique rank numbers within several tables as the 
>schema has unique indexes on several of them. (bioentry_qualifier_value, 
>seqfeature, etc) - some were already there but commented, others I added 
>& commented the code
>
>5) Also, changed the thrown exceptions to conform to the non-deprecated 
>constructors.
>
>6) A bunch of little things that I have commented in the code
>
>7) The only part I haven't touched is the Assembly parts as I couldn't 
>figure out how they are incorporated with the latest schema.
>
>I've been testing the various methods (addSequence, removeSequence, 
>getSequence, etc) with a bacterial genome from genbank and I think I 
>have everything working correctly.
>
>I've attached the modified files for your perusal and addition to CVS as 
>I don't have access anymore.
>
>Regards,
>Simon Foote
>  
>
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-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca