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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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Remove `nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml` and all references to it #2094

Open turbomam opened 1 week ago

turbomam commented 1 week ago

Since @mbthornton-lbl , @aclum and the Napa re-id squad have removed all legacy ids, we can now consistently use nmdc_schema/nmdc_materialized_patterns.yaml as the preferred schema file

This PR also stops the practice of generating derived schema artifacts in project/ and them moving them to nmdc_schema/. They are generated directly in nmdc_schema/ now.

Also removes CURIe-repair code from nmdc_schema/migration_recursion.py since all of our NMDC ids are valid CURIes now!

github-actions[bot] commented 1 week ago

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-2094/ on branch gh-pages at 2024-07-08 18:03 UTC

eecavanna commented 1 week ago

~Hi @turbomam, will you add a PR description (and update the PR title to reflect the contents of the branch)? I think that will make it easier for me and any other (future) reviewers to interpret the diff.~

eecavanna commented 1 week ago

My only comment is remove vs commenting out. I think IF we're going to comment things out, we should also provide a comment to justify / explain why it's commented out and not just removed.

I agree with this. One guideline I like is: Consider whether someone else (or your future self, after having context switched to/worked on a bunch of other projects) will know why something has been commented out. As a reminder, all deleted code will remain in the Git history (assuming nobody "rewrites history").

aclum commented 2 days ago

@turbomam can you resolve the poetry.lock conflicts please?

eecavanna commented 18 hours ago

My lack of review is blocking the merging of this PR. I will check with @PeopleMakeCulture (I think she had looked into whether the Runtime uses this schema still) about this and report back.

PeopleMakeCulture commented 18 hours ago

My lack of review is blocking the merging of this PR. I will check with @PeopleMakeCulture (I think she had looked into whether the Runtime uses this schema still) about this and report back.

@eecavanna Just updated runtime to remove all references to legacy_ids! https://github.com/microbiomedata/nmdc-runtime/pull/550

eecavanna commented 7 hours ago

Thanks, @PeopleMakeCulture! I will approve this PR.