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refactor: C4GH and storage changes #265

Merged
merged 6 commits into from
Sep 19, 2024
Merged

refactor: C4GH and storage changes #265

merged 6 commits into from
Sep 19, 2024

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mmalenic
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Changes

  • Add some traits to htsget-storage:
    • StorageMiddleware controls pre-processing and post-processing requests to the storage layer, which is used in C4GHStorage to decrypt/encrypt data.
    • StorageClone allows cloning a Box<dyn StorageTrait + Send + Sync + 'static>.
    • Remove requirement for Arc<Mutex<..>> inside C4GHStorage.
    • Split the storage traits and storage types into different files.
  • Add tests for C4GHStorage.
  • Rename c4gh-experimental to experimental.

@mmalenic mmalenic self-assigned this Sep 19, 2024
@mmalenic mmalenic added the refactor changes related to code refactoring label Sep 19, 2024
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mmalenic commented Sep 19, 2024

Update

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🚀

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Update

* Bump dependencies, ~should fix~ [lexical-core has multiple soundness issues](/umccr/htsget-rs/security/dependabot/21) was fixed upstream only a few days ago so not published yet: [zaeleus/noodles@185574c](https://github.com/zaeleus/noodles/commit/185574c9263192078b273af162707961c60ecbf0)

Gotcha, probably worth holding to noodles release before merging this PR then? Two birds one shot?

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mmalenic commented Sep 19, 2024

Gotcha, probably worth holding to noodles release before merging this PR then? Two birds one shot?

Nah, I'd like to get this merged so I can move on to the next PRs. It will be easy enough to fix in a different PR when it gets released. This could be a stand-alone dependency bump PR, or as part of a PR including features.

@mmalenic mmalenic added this pull request to the merge queue Sep 19, 2024
Merged via the queue into main with commit c653daa Sep 19, 2024
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@brainstorm brainstorm deleted the feat/c4gh-misc branch September 19, 2024 07:00
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