feat: upload assets on release (#56)

## Reason for Change

- #4 
- #7 
- create a first release of the asset data

## Changes

- add GHA to upload release assets when ontology assets are updated
- updated ontology builder to get ontology_info.yml from the
./ontology-assets directory.
- update ontology buidl to save all_ontology.json.gz to
./ontology-assets directory

## Testing steps

- generated releases using a test branch a verified the assets were
uploaded.

.github/workflows/release.yml

@@ -18,3 +18,44 @@ jobs:
         with:
           manifest-file: ".release-please-manifest.json"
           config-file: "release-please-config.json"
+          target-branch: main
+    outputs:
+      release_created: ${{ steps.release.outputs.ontology-assets--release_created }}
+      upload_url: ${{ steps.release.outputs.ontology-assets--upload_url }}
+
+  add-release-artifacts:
+    runs-on: [ubuntu-latest]
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created == 'true' }}
+    strategy:
+      matrix:
+        include:
+          - file_name: "ontology_info.yml"
+            content_type: "application/yml"
+          - file_name: "all_ontology.json.gz"
+            content_type: "application/zip"
+          - file_name: "cell_class_list.json"
+            content_type: "application/json"
+          - file_name: "cell_subclass_list.json"
+            content_type: "application/json"
+          - file_name: "organ_list.json"
+            content_type: "application/json"
+          - file_name: "tissue_general_list.json"
+            content_type: "application/json"
+          - file_name: "system_list.json"
+            content_type: "application/json"
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v2
+        with:
+          ref: main
+          fetch-depth: 1
+      - name: Upload release asset
+        uses: actions/upload-release-asset@v1
+        with:
+          upload_url: ${{ needs.release-please.outputs.upload_url }}
+          asset_path: "ontology-assets/${{ matrix.file_name }}"
+          asset_name: ${{ matrix.file_name }}
+          asset_content_type: ${{ matrix.content_type }}
+        env:
+          GITHUB_TOKEN: ${{ github.token }}

ontology-assets/ontology_info.yml

@@ -0,0 +1,36 @@
+CL:
+  version: v2024-01-04
+  source: https://github.com/obophenotype/cell-ontology/releases/download
+  filetype: owl
+EFO:
+  version: v3.62.0
+  source: https://github.com/EBISPOT/efo/releases/download
+  filetype: owl
+HANCESTRO:
+  version: 3.0
+  source: https://github.com/EBISPOT/hancestro/raw/
+  filetype: owl
+HsapDv:
+  version: 11
+  source: http://aber-owl.net/media/ontologies/HSAPDV/
+  filetype: owl
+MONDO:
+  version: v2024-01-03
+  source: https://github.com/monarch-initiative/mondo/releases/download/
+  filetype: owl
+MmusDv:
+  version: 9
+  source: http://aber-owl.net/media/ontologies/MMUSDV/
+  filetype: owl
+NCBITaxon:
+  version: v2023-06-20
+  source: https://github.com/obophenotype/ncbitaxon/releases/download/
+  filetype: owl.gz
+UBERON:
+  version: v2024-01-18
+  source: https://github.com/obophenotype/uberon/releases/download/
+  filetype: owl
+PATO:
+  version: v2023-05-18
+  source: https://github.com/pato-ontology/pato/raw/
+  filetype: owl

tools/ontology-builder/src/env.py

@@ -1,12 +1,9 @@
 import os
 
 PACKAGE_ROOT = os.path.dirname(os.path.realpath(__file__))
-ROOT_DIR = os.path.dirname(os.path.dirname(os.path.dirname(PACKAGE_ROOT)))
-FIXTURES_ROOT = os.path.join(ROOT_DIR, "api/python/src/cellxgene_ontology_guide/artifacts")
-ONTOLOGY_REF_DIR = os.path.join(PACKAGE_ROOT, "ontology-references")
-RAW_ONTOLOGY_DIR = os.path.join(ONTOLOGY_REF_DIR, "raw-files")
-ONTO_INFO_YAML = os.path.join(FIXTURES_ROOT, "ontology_info.yml")
-PARSED_ONTOLOGIES_FILE = os.path.join(FIXTURES_ROOT, "all_ontology.json.gz")
+RAW_ONTOLOGY_DIR = os.path.join(PACKAGE_ROOT, "raw-files")
 PROJECT_ROOT_DIR = os.path.realpath(__file__).rsplit("/", maxsplit=4)[0]
+ONTO_INFO_YAML = os.path.join(PROJECT_ROOT_DIR, "ontology_info.yml")
+PARSED_ONTOLOGIES_FILE = os.path.join(PROJECT_ROOT_DIR, "all_ontology.json.gz")
 SCHEMA_DIR = os.path.join(PROJECT_ROOT_DIR, "artifact-schemas")
 ONTOLOGY_ASSETS_DIR = os.path.join(PROJECT_ROOT_DIR, "ontology-assets")