Merge pull request #116 from djarecka/ci/new_generate_ga

new workflows to generate other formats

Author: djarecka

.github/workflows/ansr_generate_other_formats.yaml

@@ -0,0 +1,17 @@
+name: generating other formats for anatomical_structure
+
+on:
+  pull_request_target:
+    types: [opened, synchronize]
+    paths:
+      - 'linkml-schema/anatomical_structure.yaml'
+
+
+permissions:
+  contents: write
+
+jobs:
+  generate_from_reusable:
+    uses: brain-bican/models/.github/workflows/reusable-generate_other_formats.yaml@main
+    with:
+      model_name: anatomical_structure

.github/workflows/assertion_generate_other_formats.yaml

@@ -0,0 +1,17 @@
+name: generating other formats for assertion_evidence
+
+on:
+  pull_request_target:
+    types: [opened, synchronize]
+    paths:
+      - 'linkml-schema/assertion_evidence.yaml'
+
+
+permissions:
+  contents: write
+
+jobs:
+  generate_from_reusable:
+    uses: brain-bican/models/.github/workflows/reusable-generate_other_formats.yaml@main
+    with:
+      model_name: assertion_evidence

.github/workflows/generate_other_formats.yaml

@@ -0,0 +1,17 @@
+name: generating other formats for genome_annotation
+
+on:
+  pull_request_target:
+    types: [opened, synchronize]
+    paths:
+      - 'linkml-schema/genome_annotation.yaml'
+
+
+permissions:
+  contents: write
+
+jobs:
+  generate_from_reusable:
+    uses: brain-bican/models/.github/workflows/reusable-generate_other_formats.yaml@main
+    with:
+      model_name: genome_annotation

.github/workflows/genome_generate_other_formats.yaml

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+name: generating other formats for library_generation
+
+on:
+  pull_request_target:
+    types: [opened, synchronize]
+    paths:
+      - 'linkml-schema/library_generation.yaml'
+
+
+permissions:
+  contents: write
+
+jobs:
+  generate_from_reusable:
+    uses: brain-bican/models/.github/workflows/reusable-generate_other_formats.yaml@main
+    with:
+      model_name: library_generation

.github/workflows/library_generate_other_formats.yaml

@@ -0,0 +1,73 @@
+name: Reusable workflow for generating other formats
+
+on:
+  workflow_call:
+    inputs:
+      model_name:
+        description: 'A name of the model, without the .yaml extension'
+        required: true
+        type: string
+
+permissions:
+  contents: write
+
+jobs:
+  generate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install the required python packages
+        run: python -m pip install .[test]
+
+      - name: Other installations
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential git wget curl
+
+      - name: Generate other model representations
+        run: |
+          cd linkml-schema
+          name=${{ inputs.model_name }};
+          echo "Processing $name model...";
+          gen-json-schema  ${name}.yaml > ../json-schema-autogen/${name}.json;
+          # generating jsonld context and removing generation_date field to avoid constant updates
+          gen-jsonld-context ${name}.yaml > ../jsonld-context-autogen/${name}.context.jsonld;
+          sed -i "/generation_date/d" ../jsonld-context-autogen/${name}.context.jsonld;
+          gen-pydantic ${name}.yaml > ../models_py-autogen/${name}.py;
+          if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
+            echo "Fixing erdiagrams for $name";
+            python ../utils/fix_and_create_erdiagram.py;
+          else
+            gen-erdiagram ${name}.yaml > ../erdiagram-autogen/${name}.md;
+          fi
+          cd ..
+
+      - name: Adding other model representations to git
+        run: |
+          name=${{ inputs.model_name }};
+          git config --global user.name "[email protected]"
+          git config --global user.email "Github Actions"
+          git branch
+          git diff
+          git add json-schema-autogen/${name}.json
+          git add jsonld-context-autogen/${name}.context.jsonld
+          git add models_py-autogen/${name}.py
+          git add erdiagram-autogen/${name}.md
+          if ! git diff --quiet HEAD; then
+            git commit -m "generate another formats for ${name} model"
+            git pull --rebase # to avoid conflicts with different wf runs
+            git push
+          else
+            echo "No changes to commit"
+          fi