Merge pull request #80 from djarecka/autogen_testing_branch

updates to the automatic generation GA workflows
brain-bican · Nov 5, 2024 · a4c4ad9 · a4c4ad9
2 parents c30dd97 + 6570f47
commit a4c4ad9
Show file tree

Hide file tree

Showing 16 changed files with 35 additions and 7,521 deletions.
diff --git a/.github/workflows/generate_other_formats.yaml b/.github/workflows/generate_other_formats.yaml
@@ -40,7 +40,7 @@ jobs:
         run: |
           cd linkml-schema
           for file in *.yaml; do
-            if [ "$file" != "bican_biolink.yaml" ]; then
+            if [[ "$file" != *bican* && "$file" != *core* ]];; then
               name=`basename ${file} .yaml`;
               echo "Processing $name file..";
               gen-json-schema  ${file} > ../json-schema-autogen/${name}.json;

diff --git a/.github/workflows/test_other_formats.yaml b/.github/workflows/test_other_formats.yaml
@@ -6,6 +6,9 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: write
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -25,25 +28,43 @@ jobs:
       - name: Other installations
         run: |
           sudo apt-get update
-          sudo apt-get install -y build-essential git wget curl
+          sudo apt-get install -y build-essential git wget curl colordiff
 
       - name: Generate other model representations
         run: |
           cd linkml-schema
+          mkdir tests_artifacts
+          mkdir tests_artifacts/json-schema-autogen
+          mkdir tests_artifacts/jsonld-context-autogen
+          mkdir tests_artifacts/models_py-autogen
+          mkdir tests_artifacts/erdiagram-autogen
           for file in *.yaml; do
-            if [ "$file" != "bican_biolink.yaml" ]; then
+            if [[ "$file" != *bican* && "$file" != *core* ]]; then
               name=`basename ${file} .yaml`;
               echo "Processing $name file..";
-              # generating json schema
-              gen-json-schema  ${file};
-              # generating jsonld context
-              gen-jsonld-context ${file};
-              # generating pydantic schema
-              gen-pydantic ${file};
-              if [ ${name} != "library_generation" ] && [ ${name} != "genome_annotation" ]; then
-                gen-erdiagram ${file};
+              gen-json-schema  ${file} > tests_artifacts/json-schema-autogen/${name}.json;
+              echo "Diff in json schema for $name file (comparing to the current version)"
+              colordiff ../json-schema-autogen/${name}.json tests_artifacts/json-schema-autogen/${name}.json || true
+              # generating jsonld context and removing generation_date field to avoid constant updates
+              gen-jsonld-context ${file} > tests_artifacts/jsonld-context-autogen/${name}.context.jsonld;
+              sed -i "/generation_date/d" tests_artifacts/jsonld-context-autogen/${name}.context.jsonld;
+              echo "Diff in jsonld context for $name file (comparing to the current version)"
+              colordiff ../jsonld-context-autogen/${name}.context.jsonld tests_artifacts/jsonld-context-autogen/${name}.context.jsonld || true
+              gen-pydantic ${file} > tests_artifacts/models_py-autogen/${name}.py;
+              echo "Diff in pydantic model for $name file (comparing to the current version)"
+              colordiff ../models_py-autogen/${name}.py tests_artifacts/models_py-autogen/${name}.py || true
+              if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
+                echo "Creating and Fixing diagrams for $name";
+                python ../utils/fix_and_create_erdiagram.py
+              else
+                gen-erdiagram ${file} > tests_artifacts/erdiagram-autogen/${name}.md;
               fi
             fi
           done
-          cd ..
+          ls -l tests_artifacts/json-schema-autogen
 
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifacts
+          path: linkml-schema/tests_artifacts/*
diff --git a/erdiagram-autogen/anatomical_structure_core.md b/erdiagram-autogen/anatomical_structure_core.md
diff --git a/erdiagram-autogen/bican_core.md b/erdiagram-autogen/bican_core.md
diff --git a/erdiagram-autogen/bican_prov.md b/erdiagram-autogen/bican_prov.md
diff --git a/json-schema-autogen/anatomical_structure_core.json b/json-schema-autogen/anatomical_structure_core.json