added ga.py and lg.py before merging upstream changes

.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_yaml_model.yaml

@@ -1,7 +1,13 @@
 # Generates linkml yaml schema from metadata in googlesheets using schemasheets
 name: generating yaml file
 
-on: workflow_dispatch
+on:
+  workflow_dispatch:
+    inputs:
+      model:
+        description: 'model name'
+        required: true
+        type: string
 
 jobs:
   generate_libgen_yaml:
@@ -26,11 +32,27 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y build-essential git wget curl
 
+      # Check if download-dir exists; if not, create it
+      - name: Check if download-dir exists
+        run: |
+          if [ ! -d "linkml-schema/source_${{ inputs.model }}/gsheet_output" ]; then
+            echo "Directory does not exist. Making directory"
+            mkdir -p linkml-schema/source_${{ inputs.model }}/gsheet_output
+          fi
+      
+      # Check if gsheet.yaml exists
+      - name: Check if gsheet.yaml exists
+        run: |
+          if [ ! -f "linkml-schema/source_${{ inputs.model }}/gsheet.yaml" ]; then
+            echo "gsheet.yaml does not exist. Exiting"
+            exit 1
+          fi
+
       # Generate yaml model
       - name: Generate yaml model
         run: |
           cd linkml-schema
-          bkbit schema2model -o library_generation.yaml --gsheet --gsheet-download-dir source_library_generation/gsheet_output  source_library_generation/gsheet.yaml  --no-inlined
+          bkbit schema2model -o ${{ inputs.model }}.yaml --gsheet --gsheet-download-dir source_${{ inputs.model }}/gsheet_output  source_${{ inputs.model }}/gsheet.yaml  --no-inlined
           cd ..
 
       # Generate unique branch name 
@@ -45,8 +67,8 @@ jobs:
         uses: peter-evans/create-pull-request@v4
         with:
           token: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
-          commit-message: "Generate new version of the linkml model"
+          commit-message: "Generate new version of the linkml model for ${{ inputs.model }}"
           branch: ${{ env.BRANCH_NAME }}
-          title: "Auto PR: yaml generated from google spreadsheets using schemasheets"
-          body: "This PR adds a autogenerated yaml file."
+          title: "Auto PR: ${{ inputs.model }}.yaml generated from google spreadsheets using schemasheets"
+          body: "This PR adds a autogenerated ${{ inputs.model }}.yaml file."
           base: main

.github/workflows/genome_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/library_generate_other_formats.yaml

@@ -0,0 +1,17 @@
+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/reusable-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=${{ inputs.model_name }};
+          git config --global user.name "action@github.com"
+          git config --global user.email "Github Actions"
+          git branch
+          git diff
+          git add json-schema-autogen/${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

.github/workflows/reusable-generate_other_formats_new.yaml

@@ -0,0 +1,94 @@
+name: Reusable workflow for generating other formats
+
+on:
+  workflow_call:
+    inputs:
+      model_name:
+        description: 'A name of the model(s), without the .yaml extension. Models should be separated by a comma.'
+        required: true
+        type: string
+      linkml_version:
+        description: 'linkml version to test (optional, by default it uses one from the pyproject.toml)'
+        required: false
+        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: Updating linkml if requested
+        if: ${{ inputs.linkml_version != null }}
+        run: |
+          pip install linkml==${{ inputs.linkml_version }}
+          echo "linkml version: ${{ inputs.linkml_version }} has been installed"
+
+      - name: Other installations
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential git wget curl
+
+      - name: Generate other model representations
+        run: |
+          cd linkml-schema
+          models_list="${{ inputs.model_name }}"
+          echo " "
+          echo "Model list: $models_list"
+          for name in $(echo "$models_list" | tr ',' '\n'); do
+            echo "Processing $name model...";
+            linkml generate json-schema ${name}.yaml > ../json-schema-autogen/${name}.json;
+            echo "json-schema generated";
+            # generating jsonld context and removing generation_date field to avoid constant updates
+            linkml generate jsonld-context ${name}.yaml > ../jsonld-context-autogen/${name}.context.jsonld;
+            sed -i "/generation_date/d" ../jsonld-context-autogen/${name}.context.jsonld;
+            echo "jsonld-context generated";
+            linkml generate pydantic ${name}.yaml > ../models_py-autogen/${name}.py;
+            echo "pydantic model generated";
+            if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
+              echo "Fixing erdiagrams for $name";
+              python ../utils/fix_and_create_erdiagram.py;
+            else
+              linkml generate erdiagram ${name}.yaml > ../erdiagram-autogen/${name}.md;
+            fi
+            echo "erdiagram generated";
+          done
+          cd ..
+
+      - name: Adding other model representations to git
+        run: |
+          git config --global user.name "action@github.com"
+          git config --global user.email "Github Actions"
+          git branch
+          models_list="${{ inputs.model_name }}"
+          echo "Model list: $models_list"
+          for name in $(echo "$models_list" | tr ',' '\n'); do
+            echo "Processing: $name"
+            git add json-schema-autogen/${name}.json
+            git add jsonld-context-autogen/${name}.context.jsonld
+            git add models_py-autogen/${name}.py
+            git add erdiagram-autogen/${name}.md
+          done
+          if ! git diff --quiet HEAD; then
+            git commit -m "generate another formats for ${models_list} model(s)"
+            git pull --rebase # to avoid conflicts with different wf runs
+            git push
+          else
+            echo "No changes to commit"
+          fi

.github/workflows/software_update_generate_other_formats.yaml

@@ -0,0 +1,19 @@
+name: testing a linkml version, generating other formats for multiple models
+
+on:
+  workflow_dispatch:
+    inputs:
+      linkml_version:
+        description: 'linkml version to test'
+        required: true
+        type: string
+
+permissions:
+  contents: write
+
+jobs:
+  generate_from_reusable:
+    uses: brain-bican/models/.github/workflows/reusable-generate_other_formats_new.yaml@main
+    with:
+      model_name: genome_annotation,library_generation,anatomical_structure,assertion_evidence
+      linkml_version: ${{ github.event.inputs.linkml_version }}