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fix: projection issue for stop retained insertion (#707) #708

Merged
merged 3 commits into from
Sep 2, 2024
Merged

fix: projection issue for stop retained insertion (#707) #708

merged 3 commits into from
Sep 2, 2024

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holtgrewe
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@holtgrewe holtgrewe commented Oct 21, 2023 •
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Closes: #707

@holtgrewe holtgrewe requested a review from reece as a code owner October 21, 2023 14:49
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This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Nov 28, 2023
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github-actions bot commented Dec 5, 2023

This PR was closed because it has been stalled for 7 days with no activity.

@github-actions github-actions bot closed this Dec 5, 2023
@reece reece removed stale Issue is stale and subject to automatic closing closed-by-stale labels Dec 8, 2023
@reece reece reopened this Dec 8, 2023
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github-actions bot commented Jan 8, 2024

This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Jan 8, 2024
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This PR was closed because it has been stalled for 7 days with no activity.

@github-actions github-actions bot closed this Jan 15, 2024
@holtgrewe
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@reece ping

@reece reece reopened this Feb 19, 2024
@reece reece requested a review from a team as a code owner February 19, 2024 17:44
@reece reece added resurrected and removed stale Issue is stale and subject to automatic closing labels Feb 19, 2024
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reece commented Feb 19, 2024

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.

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This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Mar 21, 2024
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This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

Ping.

@korikuzma
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@holtgrewe thank you for your PR and sorry about the delay. It appears that your branch is out of date. Would you please pull changes from main and resolve merge conflicts? Once that's done and tests are passing, please comment to let us know.

@github-actions github-actions bot removed the stale Issue is stale and subject to automatic closing label Mar 22, 2024
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This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Apr 21, 2024
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Stay alive until I return to office please.

@theferrit32 theferrit32 removed the stale Issue is stale and subject to automatic closing label Apr 21, 2024
@jsstevenson jsstevenson added the keep alive exempt issue from staleness checks label Apr 21, 2024
@holtgrewe holtgrewe force-pushed the fix-hgvs-projection-ins-stop-retained branch from 4ae9644 to ae5fe86 Compare July 24, 2024 06:22
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holtgrewe commented Jul 24, 2024 •
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@korikuzma I found the time to update this finally. I now had to fix one new test.

As a reminder for myself, here is how I ran the test and re-created the HGVS_CACHE.

UTA_DB_URL=postgresql://anonymous:[email protected]:5432/uta/uta_20210129 HGVS_CACHE_MODE=learn pytest -vv --record-mode=rewrite -s

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korikuzma reviewed Jul 29, 2024
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The code makes sense to me. The test also matches what is in Clin Gen Allele Registry here.

@biocommons/maintainers not sure if there are any sciency things that I'm missing. Could someone review this?

src/hgvs/utils/altseq_to_hgvsp.py Outdated Show resolved Hide resolved
reece
reece approved these changes Sep 2, 2024
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@holtgrewe Thanks for this fix. I'm sorry for the embarrassingly long delay in getting in merged. :-/

@reece reece merged commit e6dbd1e into biocommons:main Sep 2, 2024
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Successfully merging this pull request may close these issues.

hgvs_c to hgvs_p projection throws IndexError for "NM_001253909.2:c.416_417insGTG"
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@holtgrewe @reece @korikuzma @theferrit32 @jsstevenson