[BioSQL-l] BioJava/BioSQL on Oracle

[Richard HOLLAND]

I've committed some changes to biojava-live which make BioJava compatible with BioSQL when the latter is running on Oracle 9i or greater and using the official schema as per the biosql-schema CVS. This involved adding an autodetect function to detect whether Clobs were used in biosequence or not, and then creating code to work with Clobs where necessary. Two extensions to OracleDBHelper might be useful in other tasks - stringToClob() and clobToString().

I also made some changes to the Ontology part of the BioJava/BioSQL interface, which was not persisting Triples correctly. It would attempt to reference the triple by its unique ID before actually giving it one, which of course fails. This should now be fixed.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
Genome Institute of Singapore
60 Biopolis Street, #02-01 Genome, Singapore 138672
Tel: (65) 6478 8000   DID: (65) 6478 8199
Email: hollandr at gis.a-star.edu.sg
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