Single mutant phenotypes can be modified even if involved in GI

[manulera]

Hello @kimrutherford @ValWood

I noticed that single mutant phenotypes can be changed using the "Edit" button, even if they are involved in a genetic interaction. The genetic interaction is then updated and linked to the new phenotypes when you refresh the page.

This was good for me, as I was just updating to a more specific term, but this is different from the behaviour on the double mutant, where you cannot edit unless you remove the genetic interactions first (see image).

I think it's better to be able to edit those with GIs, even the double mutant. A dialogue confirmation saying "This phenotype annotation is involved is in a GI, are you sure you want to edit it?" prior to the editing window would be enough, I think.

[manulera]

Actually, I think being able to edit the single mutant phentoypes might be causing an error, because in this session: https://curation.pombase.org/pombe/curs/0fa0811aad33bde1

I can add a single mutant phenotype that no longer exists as part of a genetic interaction:

To reproduce, you can select pom1-as1(aaT778G)[WT level] shk1-as2(aaM460A)[WT level], and try to add a Phenotypic Enhancement GI linked to a shk1-as2(aaM460A) phenotype.

[ValWood]

@kimrutherford Is this one still current?
I thought you couldn't edit phenotypes that are part of genetic interactions?

[kimrutherford]

@kimrutherford Is this one still current?

Yep, I haven't fixed this yet.

I thought you couldn't edit phenotypes that are part of genetic interactions?

The phenotype and extension can be edited.

I've just noticed that there is a bug if you try to change the genotype of an annotation that's part of a genotype interaction:

[kimrutherford]

Decision: grey out / disable the edit button on the single allele genotype annotation

[kimrutherford]

For now, I've fixed this problem by disabling edit and delete for genotypes that are part of genotype-genotype interactions.

The fix is in the queue behind #2544 so the change will be visible on Monday. I'll leave the issue open until then.

[kimrutherford]

Val from pombase/pombase-chado#986 (comment):

We found that we could not edit any annotation for an existing allele in *any *
annotation where the allele was used in a genetic interaction, even if that annotation was not used in the interaction.

e.g.

Let me know if you want to discuss.

CC @PCarme

[kimrutherford]

We found that we could not edit any annotation for an existing allele in *any * annotation

Sorry about that! It should be fixed now.

[kimrutherford]

I think this can be closed now. The problems were fixed in:

• cant edit annotations #2815