GH action: Finished setting up GH action to run subset pipeline and t…

…ests

- Updated the GH action workflow that does build & tests:
  - download inputs
  - download robot.jar
- Add: Docs
- Bug fix: Tests: Corrected the robot.jar command

.github/workflows/main.yaml

@@ -19,20 +19,51 @@ jobs:
       matrix:
         python-version: ["3.11"]
     steps:
-      # Setup
+      # Common setup
       - name: Check out repository
         uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install Poetry
+      - name: Install package manager
         uses: snok/[email protected]
-      - name: Install dependencies & project
+      - name: Install Python dependencies
         run: poetry install --no-interaction
-      # Build
-      - name: Run test suite
-        run: poetry run comploinc --fast-run build
-      # Test
-      - name: Run test suite
-        run: poetry run python -m unittest discover
+      # Download additional non-Python dependencies
+      - name: Download additional dependencies
+        run: wget https://github.com/ontodev/robot/releases/latest/download/robot.jar
+      # Download and extract build sources
+      - name: Download inputs / sources
+        run: |
+          echo "${{ secrets.DL_LINK_ID }}" > env
+          cat env
+          ls -las env
+          echo "${{ secrets.DL_LINK }}" > env
+          cat env
+          ls -las env
+          echo ${{ secrets.DL_LINK_ID }} > env
+          cat env
+          ls -las env
+          echo ${{ secrets.DL_LINK }} > env
+          cat env
+          ls -las env
+#          echo 'https://drive.google.com/uc?export=download&id="{{ secrets.DL_LINK_ID }}' -o confirmation.html
+#          echo "https://drive.usercontent.google.com/download?id="{{ secrets.DL_LINK_ID }}&export=download&confirm=t" -o build-sources.zip
+#          echo 'https://drive.google.com/uc?export=download&id="${{ secrets.DL_LINK_ID }}"' -o confirmation.html
+#          echo "https://drive.usercontent.google.com/download?id="${{ secrets.DL_LINK_ID }}"&export=download&confirm=t" -o build-sources.zip
+#          echo 'https://drive.google.com/uc?export=download&id="{{ secrets.DL_LINK }}' -o confirmation.html
+#          echo "https://drive.usercontent.google.com/download?id="{{ secrets.DL_LINK }}&export=download&confirm=t" -o build-sources.zip
+#          echo 'https://drive.google.com/uc?export=download&id="${{ secrets.DL_LINK }}"' -o confirmation.html
+#          echo "https://drive.usercontent.google.com/download?id="${{ secrets.DL_LINK }}"&export=download&confirm=t" -o build-sources.zip
+#        run: |
+#          curl -L -c cookies.txt 'https://drive.google.com/uc?export=download&id="${{ secrets.DL_LINK_ID }}"' -o confirmation.html
+#          curl -L -b cookies.txt "https://drive.usercontent.google.com/download?id="${{ secrets.DL_LINK_ID }}"&export=download&confirm=t" -o build-sources.zip
+#          unzip build-sources.zip
+#          rm build-sources.zip cookies.txt confirmation.html
+#      # Build
+#      - name: Build
+#        run: poetry run comploinc --fast-run build
+#      # Test
+#      - name: Run test suite
+#        run: poetry run python -m unittest discover

README.md

@@ -75,15 +75,26 @@ See: `comploinc_config.yaml`
 
 If following the setup exactly, this configuration will not need to be modified.
 
-## Tests
+## Developer docs
 <details><summary>Details</summary>
 
-### Tests: prerequisites
+### Tests
+#### Tests: prerequisites
 1. [`robot`](https://robot.obolibrary.org/)
 2. Files in `output/build-default/fast-run/`
   - Can populate via `comploinc --fast-run build default`
 
-### Tests: Running
+#### Tests: Running
 `python -m unittest discover`
 
+### Standard operating procedures (SOPs)
+#### Setting up new/updated inputs/sources
+1. Create a new `YYYY-MM-DD_comploinc-build-sources.zip` in the [Google Drive folder](
+https://drive.google.com/drive/folders/1Ae5NX959S_CV60nbf9N_37Ao-wJzM0fh). Ensure it has the correct structure (folder 
+names and files at the right paths).
+2. Make the link public: In the Google Drive folder, right-click the file, select "Share", and click "Share."  At the 
+bottom, under "General Access", click the left dropdown and select "Anyone with the link."  Click "Copy link".
+3. Update `DL_LINK_ID` in GitHub: Go to the [page](https://github.com/loinc/comp-loinc/settings/secrets/actions/DL_LINK_ID) 
+for updating it. Paste the link from the previous step into the box, and click "Update secret."
+
 </details>

test/utils.py

@@ -12,7 +12,7 @@
 except ModuleNotFoundError:
     from config import ROBOT_JAR_PATH, TEST_IN_DIR, TEST_OUT_DIR, TEST_SPARQL_QEURY_DIR
 
-robot_cmd_options = ['robot', ROBOT_JAR_PATH]
+robot_cmd_options = ['robot', f'java -jar {ROBOT_JAR_PATH}']
 
 
 def _get_paths(onto_filename: str, sparql_filename: str) -> tuple[str, str, str]: