can't find feature using identifier: rga4

pombase / pombase-chado

PomBase code for accessing Chado

MIT License

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can't find feature using identifier: rga4 #310

Closed pombase-admin closed 9 years ago

pombase-admin commented 10 years ago

This loading error makes no sense since rga4 is in the database:

error in c29f51c4cc86096d: DBIx::Class::Schema::txn_do(): can't find feature using identifier: rga4 at /home/kmr44/git/pombase-chado/lib/PomBase/Import/Canto.pm line 464

Original comment by: kimrutherford

pombase-admin commented 10 years ago

status: open --> closed-fixed

Original comment by: kimrutherford

pombase-admin commented 10 years ago

From an email: "I've tracked this down. It's happening because there is an allele with the name "rga4" and a gene with name "rga4". That should be fine but the loader is querying any feature with that name and getting two results. That is causing it to fail. It's a bug. It should be querying only for genes."

I made a ticket for that: [chado:#317]

Midori has fixed the allele name the contig file.

Original comment by: kimrutherford

pombase-admin commented 10 years ago

There are some allele names that are equivalent to gene names. I remember seeing others. Is this OK?

Original comment by: ValWood

pombase-admin commented 10 years ago

There are some allele names that are equivalent to gene names. I remember seeing others. Is this OK

It's likely to cause unnecessary warnings at the moment. Maybe we need to fix #317 sooner rather than later.

Original comment by: kimrutherford