feat!: update tx segment element with updated cool-seq-tool structure changes

cancervariants / fusion-curation

MIT License

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feat!: update tx segment element with updated cool-seq-tool structure changes #314

Closed katiestahl closed 2 weeks ago

katiestahl commented 1 month ago

update naming of functions + variables
no more strand passed into tx segment element functions
changed GenomicData -> GenomicTxSegService
updated usage of Assayed/Categorical FusionElement in accordance with recent fusor change
updated tests - a lot of these are failing from weird asyncio issues, not sure if that was pre-existing or if I have stuff set up weirdly locally. I'm still looking into this, but from testing the app, everything looks like it's functioning correctly? Other than transcript segment element with using transcript/genomic coordinates. This appears to have broken either from the last PR or was already broken. This will be resolved when I finally get to resume #273

Going to leave this in a draft for now, so I don't accidentally merge it before we have new CST and fusor releases with the changes that this PR implements

Close #272

github-actions[bot] commented 1 month ago

This PR is stale because it has been open 1 day(s) with no activity. Please review this PR.

jsstevenson commented 3 weeks ago

tests failing is a preexisting issue: https://github.com/cancervariants/fusion-curation/issues/303

katiestahl commented 3 weeks ago

tests failing is a preexisting issue: #303

oh oop, should I remove that part of this PR?

jsstevenson commented 3 weeks ago

oh oop, should I remove that part of this PR?

Oh if you've fixed stuff I think it's fine to package in. I was just saying that some of those tests were already failing so it shouldn't hold back this PR if everything else seems ok

korikuzma commented 3 weeks ago

@jarbesfeld Are you able to review this?

jarbesfeld commented 3 weeks ago

@korikuzma Yes I can review now

korikuzma commented 3 weeks ago

@jarbesfeld I'm working on deploying this to our dev environment. Do you have time to test the UI too afterwards?

jarbesfeld commented 3 weeks ago

@korikuzma Yes I can test UI as well

korikuzma commented 3 weeks ago

@katiestahl another issue that should be resolved is Transcript Segment Element needs either start or end to be valid. This is requiring start and end at the moment.

I'm also having more state issues. I fill out everything in structure, domain, reading frame, and look at summary. Once I go back to structure, I remove ending position but it still saves in the summary.

katiestahl commented 3 weeks ago

@katiestahl another issue that should be resolved is Transcript Segment Element needs either start or end to be valid. This is requiring start and end at the moment.

I'm also having more state issues. I fill out everything in structure, domain, reading frame, and look at summary. Once I go back to structure, I remove ending position but it still saves in the summary.

on it!

katiestahl commented 3 weeks ago

@katiestahl another issue that should be resolved is Transcript Segment Element needs either start or end to be valid. This is requiring start and end at the moment. I'm also having more state issues. I fill out everything in structure, domain, reading frame, and look at summary. Once I go back to structure, I remove ending position but it still saves in the summary.

on it!

so I am still trying to figure out why this is behaving like this. It looks like for the first TX Segment element, it's always invalid if it has a start (but it's fine if it has a start and end or only an end)

korikuzma commented 2 weeks ago

@katiestahl do you know why this one is failing?

https://github.com/user-attachments/assets/a027e49f-594c-4a75-9b23-dcb29367e599