pombase-admin
commented
10 years ago The qualifier used in the other annotations is col17=... and that's what the code is looking for too.
It's a good thing you spotted that though and the loading code was doing the wrong thing. It should have been storing the "column 17" value as a Chado property with the name "gene_product_form_id" - which is what the GAF export code expects. Instead it was storing with prop name "col17" so it wasn't been exported.
If fixed the code to handle "col17" or "column_17" and it now uses the correct property name.
I'll close this after testing the load.
Original comment by: kimrutherford
error in ff16db44d9ab6882: DBIx::Class::Schema::txn_do(): unhandled type: column_17 at /home/kmr44/git/pombase-chado/lib/PomBase/Import/Canto.pm line 445
this one looks ok, so i can't figure out how to fix.
There are 2 column 17 extensions
column_17=PR:000037081 and column_17=PR:000037081,annotation_extension=happens_during(GO:0051329)
I'm pretty sure I have used this syntax too in other sessions, ans this is the only one that throws ans error?
v
Original comment by: ValWood