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feat: add transcript lookup for genes #273

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merged 45 commits into from
Sep 5, 2024
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katiestahl
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@katiestahl katiestahl commented Nov 15, 2023

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

@github-actions github-actions bot added the stale label Aug 19, 2024
@jsstevenson
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sorry for delay, this is on my to-do to review this morning

@github-actions github-actions bot removed the stale label Aug 20, 2024
@jsstevenson
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sorry for delay, this is on my to-do to review this morning

lol

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

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

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github-actions bot commented Sep 2, 2024

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

@github-actions github-actions bot added the stale label Sep 2, 2024
@korikuzma korikuzma removed the stale label Sep 3, 2024
korikuzma
korikuzma previously approved these changes Sep 5, 2024
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@jarbesfeld and I are reviewing together. It looks great!

Some suggestions to address in future issues:

  • Maybe consider having a smaller scrollable box for genes that have many transcripts
    Screenshot 2024-09-05 at 10 21 28
  • @jarbesfeld suggested labeling which transcripts are MANE select/clinical plus in the dropdown
  • Some larger transcripts get cut off
    Screenshot 2024-09-05 at 10 20 54

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👍 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.

@katiestahl
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👍 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!

@katiestahl katiestahl merged commit fcf4891 into staging Sep 5, 2024
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@korikuzma korikuzma deleted the issue-222-coord-lookup branch October 3, 2024 12:00
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4 participants