Refactor GitHub Actions & Add build-schema Step

.github/workflows/test_modules.yml

@@ -19,11 +19,13 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: '3.9.16'
+
     - name: Checkout code
       uses: actions/checkout@v3
       with:
         ref: ${{ github.event.pull_request.head.sha }}
         fetch-depth: 0
+
     - name: Install package and dependencies
       run: |
         pip install -r requirements.txt
@@ -44,9 +46,15 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"]
-    steps:
+        modules: 
+        - "read-lab-metadata"
+        - "read-bioinfo-metadata"
+        - "validate"
+        - "build-schema"
+    env:
+      OUTPUT_LOCATION: ${{ github.workspace }}/tests/
 
+    steps:
     - name: Set up Python 3.9.16
       uses: actions/setup-python@v3
       with:
@@ -63,17 +71,38 @@ jobs:
         pip install -r requirements.txt
         pip install .
 
-    - name: Run each module tests
+    - name: Run read-lab-metadata module
+      if: matrix.modules == 'read-lab-metadata'
+      run: |
+        relecov-tools read-lab-metadata \
+            -m tests/data/read_lab_metadata/metadata_lab_test.xlsx \
+            -s tests/data/read_lab_metadata/samples_data_test.json \
+            -o $OUTPUT_LOCATION
+
+    - name: Run validate module
+      if: matrix.modules == 'validate'
+      run: |
+        relecov-tools validate \
+            -j tests/data/map_validate/processed_metadata_lab_test.json \
+            -s relecov_tools/schema/relecov_schema.json \
+            -m tests/data/map_validate/metadata_lab_test.xlsx \
+            -o $OUTPUT_LOCATION
+
+    - name: Run build-schema module
+      if: matrix.modules == 'build-schema'
       run: |
-        if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then
-          relecov-tools read-lab-metadata -m tests/data/read_lab_metadata/metadata_lab_test.xlsx -s tests/data/read_lab_metadata/samples_data_test.json -o $OUTPUT_LOCATION
-        elif [ "${{ matrix.modules }}" == "validate" ]; then
-          relecov-tools validate -j tests/data/map_validate/processed_metadata_lab_test.json -s relecov_tools/schema/relecov_schema.json -m tests/data/map_validate/metadata_lab_test.xlsx -o $OUTPUT_LOCATION
-        fi
+        relecov-tools build-schema \
+            -i tests/data/build_schema/metadata_mapping_file.xlsx \
+            --version $SCHEMA_DEFAULT_VERSION \
+            --project $PROJECT_NAME \
+            --non-interactive \
+            -o $OUTPUT_LOCATION
       env:
-        OUTPUT_LOCATION: ${{ github.workspace }}/tests/
+        SCHEMA_DEFAULT_VERSION: "3.0.0"
+        PROJECT_NAME: "relecov"
+
     - name: Upload output file
       uses: actions/upload-artifact@v4
       with:
         name: test-output
-        path: output.txt
+        path: ${{ github.workspace }}/output.txt

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 
 # (Ad-hoc files)
 .nextflow*
+
+# CI testing stuff
+.github/*_event.json

CHANGELOG.md

@@ -18,6 +18,7 @@ Code contributions to the release:
 
 #### Added enhancements
 
+- Refactor GitHub Actions & Add build-schema Step [#417](https://github.com/BU-ISCIII/relecov-tools/pull/417)
 - Add documentation for `bioinfo_config.json` in README [#415](https://github.com/BU-ISCIII/relecov-tools/pull/415)
 - Added a more robust datatype handling in utils.py read_csv_file_return_dict() method [#379](https://github.com/BU-ISCIII/relecov-tools/pull/379)
 - Improved relecov template generator and version control [#382](https://github.com/BU-ISCIII/relecov-tools/pull/382)