Missing source IDs for TAO terms

[car...@nescent.org]

Hi Chris,

The OBO loader seems to be loading in the majority of TAO terms
without the source ids. To be specific, all of the TAO terms that are
DbXref'ed to ZFIN terms have NULL values in the source id columns, and
coincidentally for the metatype column as well. Note these are the
majority of the TAO terms. TAO terms that do not DbXref ZFIN terms
have their source ids and metatype values intact.

I traced the loading process to the DefaultOBOParser.endFileParse
(String uri) method, where the OBOSession object has its Namespace
value set. I suspect this may be what's causing the problem but I'll
keep looking until I'm sure. Can you point me to the right place from
this info? Thanks!

Cheers,

Cartik

[Chris Mungall]

Hi Cartik

I would first of all write a JUnit test that replicates this. You can
create a small obo file and add it to the test data directory. I would
first make a test that does a parse only and checks the objects, and
if that succeeds, write a second test that populates a test database.
There should be examples to use as templates in the existing test dir