search

pombase / canto

The PomBase community curation tool
https://curation.pombase.org
Other
18 stars 7 forks source link

Merge promoter fields on allele edit dialog #2823

Closed kimrutherford closed 4 weeks ago

kimrutherford commented 1 month ago

(I can't see an existing issue about this) - found the comment:

We decided to have just one free text field for adding a promoter.

Needs a schema change and then some Canto downtime to merge the fields in the database.

We'll remove the exogenous_promoter field in the database.

Once these changes are made:

kimrutherford commented 1 month ago

The code and schema changes are now done. Let me know if you'd like different wording for the promoter field label.

I'll update the main Canto instance with this change over the weekend - probably 2-3am one morning. It will need 15-30 minutes down time because of the schema change.

image

kimrutherford commented 1 month ago

I forgot that we also need to remove any promoters from the list of genes in the session. I'll fix that before deploying this change.

kimrutherford commented 1 month ago

Will you be putting the gene name or the systematic ID in the promoter field if it's a pombe gene?

image

kimrutherford commented 1 month ago

I forgot that we also need to remove any promoters from the list of genes in the session.

Note to self: only try to remove promoters that have no annotation.

ValWood commented 1 month ago

the gene name always so far. I don't think they will be mixed up, its quite a limited set. I guess there may be an occasion where an uncharacterized gene promoter s used, but not so far...

kimrutherford commented 1 month ago

OK, thanks. I've changed the schema upgrade code to put the gene name rather than the systematic ID in the promoter field in the database.

I forgot that we also need to remove any promoters from the list of genes in the session.

I've changed the code to do that too.

kimrutherford commented 4 weeks ago

I also need to update the japonicus Canto

kimrutherford commented 4 weeks ago

Canto has been updated now so there is only one promoter field.

I'll check the load on Sunday to make sure that all the promoter get put in the right place in Chado,

kimrutherford commented 4 weeks ago

I also need to update the japonicus Canto

I've done that, mostly so the it's uses the same code and the pombe Canto.

I'll check the load on Sunday to make sure that all the promoter get put in the right place in Chado,

All fine now. Let's open new issues if there are changes needed.