feat: add transcript lookup for genes

cancervariants / fusion-curation

MIT License

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feat: add transcript lookup for genes #273

Closed katiestahl closed 1 week ago

katiestahl commented 10 months ago

in this PR:

updated fusor version
updated cool-seq-tool calls to correspond with new version
updated gene-normalizer version
updated pydantic to v2
added loading spinner for fetches for Utilities tools
added api endpoint to retrieve transcripts given a gene
combined "genomic coordinates, gene" and "genomic coordinates, transcript" tools
populate Transcript field in genomic coordinate conversion tool with transcripts once a user selects a gene
updated some styling and wording to be more clear

close #224 close #222 close #272

katiestahl commented 2 months ago

@jsstevenson ruff + black are failing for files that I did not touch in this pr - I'll create a new issue to run and address those (unless you'd like me to do it in here, but I think it might make the commit history confusing)

katiestahl commented 1 month ago

going to address the comments on this once #293 is completed and merged, since that PR and this have a lot of overlap, and I think it would be most efficient to just address the merge conflicts and comments all at once

github-actions[bot] commented 3 weeks ago

This PR is stale because it has been open 3 day(s) with no activity. Please review this PR.

jsstevenson commented 3 weeks ago

sorry for delay, this is on my to-do to review this morning

jsstevenson commented 3 weeks ago

sorry for delay, this is on my to-do to review this morning

lol

github-actions[bot] commented 2 weeks ago

This PR is stale because it has been open 3 day(s) with no activity. Please review this PR.

katiestahl commented 2 weeks ago

cool-seq-tool updates are now completed, so this is back on my docket!

github-actions[bot] commented 1 week ago

This PR is stale because it has been open 3 day(s) with no activity. Please review this PR.

katiestahl commented 1 week ago

👍 looks good. I think we could consider (?) reversing the order that transcript options appear in the dropdown, although it seems like the right one tends to be preselected, which is probably enough.

added this to the issue where we'll display MANE/clinical plus transcript catergories on the dropdown!