From f4dd6a1edec17a608176c0f0eca005161345a4e8 Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Wed, 6 Nov 2024 09:32:58 -0600 Subject: [PATCH] feat: adds anatomical site to sample --- .github/pull_request_template.md | 10 +- .github/workflows/specification.yml | 49 +- CHANGELOG.md | 159 +- packages/Cargo.lock | 301 +- packages/Cargo.toml | 10 + packages/ccdi-curate/Cargo.toml | 25 + packages/ccdi-curate/src/http.rs | 89 + packages/ccdi-curate/src/main.rs | 49 + packages/ccdi-curate/src/uberon.rs | 336 + packages/ccdi-curate/src/uberon/graph.rs | 193 + packages/ccdi-models/Cargo.toml | 6 + .../field/description/harmonized/sample.rs | 19 + .../ccdi-models/src/metadata/field/unowned.rs | 9 + packages/ccdi-models/src/sample/metadata.rs | 50 +- .../src/sample/metadata/anatomical_site.rs | 130458 +++++++++++++++ .../src/sample/metadata/builder.rs | 31 + packages/ccdi-openapi/src/api.rs | 13 + packages/ccdi-server/src/filter/sample.rs | 10 + packages/ccdi-server/src/params/filter.rs | 9 + packages/ccdi-server/src/routes/file.rs | 2 +- packages/ccdi-server/src/routes/sample.rs | 2 +- packages/ccdi-server/src/routes/subject.rs | 2 +- packages/ccdi-spec/Cargo.toml | 7 + packages/ccdi-spec/src/main.rs | 42 + swagger.yml | 14572 +- 25 files changed, 146355 insertions(+), 98 deletions(-) create mode 100644 packages/ccdi-curate/Cargo.toml create mode 100644 packages/ccdi-curate/src/http.rs create mode 100644 packages/ccdi-curate/src/main.rs create mode 100644 packages/ccdi-curate/src/uberon.rs create mode 100644 packages/ccdi-curate/src/uberon/graph.rs create mode 100644 packages/ccdi-models/src/sample/metadata/anatomical_site.rs diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 19c2214..42909af 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -8,11 +8,11 @@ Before submitting this PR, please make sure: - [ ] You have added yourself or the appropriate individual as the assignee. - [ ] You have added the relevant groups/individuals to the reviewers. - [ ] Your commit messages conform to the [Conventional - Commits](https://www.conventionalcommits.org/en/v1.0.0/) standard. + Commits](https://www.conventionalcommits.org/en/v1.0.0/) standard. - [ ] You have updated the README or other documentation to account for these - changes (when appropriate). + changes (when appropriate). - [ ] You have added a line describing the change in the `CHANGELOG.md` under - `[Unreleased]`. + `[Unreleased]`.