feat!: use latest object schemas and dependency releases #293
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… fix regulatory element missing field, pin pydantic version
katiestahl
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katiestahl
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jsstevenson
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korikuzma
reviewed
Aug 7, 2024
korikuzma
reviewed
Aug 7, 2024
korikuzma
reviewed
Aug 7, 2024
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Not sure if this was caused by this PR. We can create a new issue for this. Selected `TPM3::NTRK1 Exon Junction. Then I added a linker sequence and it is doing this. Screen.Recording.2024-08-07.at.09.57.09.mov |
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This is from the same previous example |
korikuzma
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Aug 7, 2024
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Great work @katiestahl and @jsstevenson ! Minor suggestions
that's interesting, looks like a concurrency bug. @katiestahl and I can investigate further. |
korikuzma
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Aug 8, 2024
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Mentioned in standup that this is good on my end. @katiestahl have you had a chance to review this?
dangit, yeah this is because if you make any changes to the structure when the nomenclature request is still returning, it'll end up in this weird loop. I've seen it before and tried implementing a fix, but it looks like it runs deeper than my fix. we need to cancel any async requests when the structure changes. Anyway, I think it is unrelated to this PR |
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@katiestahl @jsstevenson created a new issue for this (#311). Can we merge this PR? |
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This PR is stale because it has been open 1 day(s) with no activity. Please review this PR. |
jsstevenson
approved these changes
Aug 12, 2024
korikuzma
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Aug 12, 2024
* build!: updating to vrs 2.0 models * update pydantic-to-ts2 and update models * wip: updating models, making variable casing consistent, converting descriptors * fix: utilities requests * fix: response model casing * wip: updating models * bug fixes * updating models and fixing validation * pass around formatted fusion to reduce repeated code * fixing demo data * specifying fusion type since null param gets dropped and fusor can't infer the type * fixing tests and updating data with new models, bug fixes * bug fixes for input elements * pin latest fusor * update dependencies * fix clientification of demos * fix formatting in docstrings * fix type handling of failed lookup * fix up gene lookup api * fix tx utils bug * fix bug where region and strand were incorrect in templated sequence, fix regulatory element missing field, pin pydantic version * removing console logs * fix: bug where error messages no longer displayed on summary page * fixing tests and adjusting variable casing * add reusable function for checking valid sequence locations * add reusable function for checking valid sequence locations * fixing nomenclature bugs * fixing nomenclature bugs * DOn't bother w/ semver checks (out of control of this app) and use proper fixture mode * add assertion notes * stash changes * stash * fix a few fixtures * sequence util fixes * minor rearrange * fix int/str problem * commit this * catch static files error * validation tests * fix reg element URL * remove todos * review comments --------- Co-authored-by: James Stevenson <[email protected]>
katiestahl
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Oct 2, 2024
* style: update ruff and drop black (#283) * cicd: allow missing credentials (#291) * chore: update ebextensions for downloading latest seqrepo instance (#292) * use 2024-02-20 SeqRepo instance * cicd: pin exact ruff version (#297) * refactor: address config deprecation (#299) * feat: use latest fastapi event management api (#298) * fix: update deprecated pytest async features (#300) * docs: remove docstring types and clean up formatting (#301) * fix: handle unnecessary checks for build files (#309) Does a few things @korikuzma noticed that the README description of copying build files had an incorrect path. However, this instruction is actually unnecessary (and impractical tbh). In development you'd be better off letting yarn start handle service of client files because it has hot-reloading on changes. I removed it. Rather than requiring client files to be present, catches + logs their absence if they're not there. This is better for development. Originally I added this code in the big VRS update PR but it should've been a separate issue. I would like to see us reexamine our logging initialization/setup in another issue, because it could be bad if it's not working properly. Adds some additional description of why the client service code is there + what it needs. * feat!: use latest object schemas and dependency releases (#293) * build!: updating to vrs 2.0 models * update pydantic-to-ts2 and update models * wip: updating models, making variable casing consistent, converting descriptors * fix: utilities requests * fix: response model casing * wip: updating models * bug fixes * updating models and fixing validation * pass around formatted fusion to reduce repeated code * fixing demo data * specifying fusion type since null param gets dropped and fusor can't infer the type * fixing tests and updating data with new models, bug fixes * bug fixes for input elements * pin latest fusor * update dependencies * fix clientification of demos * fix formatting in docstrings * fix type handling of failed lookup * fix up gene lookup api * fix tx utils bug * fix bug where region and strand were incorrect in templated sequence, fix regulatory element missing field, pin pydantic version * removing console logs * fix: bug where error messages no longer displayed on summary page * fixing tests and adjusting variable casing * add reusable function for checking valid sequence locations * add reusable function for checking valid sequence locations * fixing nomenclature bugs * fixing nomenclature bugs * DOn't bother w/ semver checks (out of control of this app) and use proper fixture mode * add assertion notes * stash changes * stash * fix a few fixtures * sequence util fixes * minor rearrange * fix int/str problem * commit this * catch static files error * validation tests * fix reg element URL * remove todos * review comments --------- Co-authored-by: James Stevenson <[email protected]> * cicd(fix): fix curfu path (#312) * refactor: remove unused seqrepo configuration (#308) * build(deps): bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /client (#276) Bumps [webpack-dev-middleware](https://github.com/webpack/webpack-dev-middleware) from 5.3.3 to 5.3.4. - [Release notes](https://github.com/webpack/webpack-dev-middleware/releases) - [Changelog](https://github.com/webpack/webpack-dev-middleware/blob/v5.3.4/CHANGELOG.md) - [Commits](webpack/webpack-dev-middleware@v5.3.3...v5.3.4) --- updated-dependencies: - dependency-name: webpack-dev-middleware dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * revert conftest * fix tests from merge * update requirements * remove debug code * use staging requirements.txt --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: James Stevenson <[email protected]> Co-authored-by: Kori Kuzma <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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close #272