Merge pull request #96 from djarecka/enh/bican_biolink_update

adding script and GA to edit bican_biolink

Author: djarecka

.github/workflows/bican_biolink_edit.yaml

@@ -0,0 +1,50 @@
+name: generating other formats
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'linkml-schema/bican_biolink.yaml'
+
+permissions:
+  contents: write
+
+
+jobs:
+  generate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v3
+
+      - 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: Editing the bican biolink yaml file
+        run: |
+          cd linkml-schema
+          python ../utils/bican_biolink_edit.py bican_biolink.yaml
+          cd ..
+
+      - name: Adding edited file to git
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          if ! git diff linkml-schema/bican_biolink.yaml --quiet; then
+            git add linkml-schema/bican_biolink.yaml
+            git commit -m "Updating the bican biolink yaml file for the bican specific case"
+            git push
+          else
+            echo "No changes to commit"
+          fi

.github/workflows/generate_other_formats.yaml

@@ -7,7 +7,7 @@ on:
     paths:
       - 'linkml-schema/**'
   workflow_run:
-    workflows: [ generating yaml file ]
+    workflows: [ "generating yaml file", "bican_biolink_edit" ]
     types:
       - completed
 

utils/bican_biolink_edit.py

@@ -0,0 +1,28 @@
+# Functions to edit the biolink model after running the general trimmer from bkbit
+# Edits are specific to our needs in bican and are not generalizable.
+# Earlier the issues were "fixed" by adding "slot_usage", but it might be easier to add it to the bican_biolink directly.
+import sys
+import yaml
+from pathlib import Path
+
+def bican_biolink_edit(schema_yaml: str) -> None:
+    """
+    Edit the biolink model to fit the bican needs
+
+    :param schema: SchemaView object
+    """
+    # Change the category slot to have a curie range and a pattern for bican categories
+    schema_yaml_path = Path(schema_yaml)
+    with schema_yaml_path.open("r") as f:
+        schema_dict = yaml.safe_load(f)
+    schema_dict["slots"]["category"]["range"] = "curie"
+    schema_dict["slots"]["category"]["pattern"] = r"^bican:[A-Z][A-Za-z]+$"
+    schema_dict["slots"]["category"]["description"] = schema_dict["slots"]["category"]["description"] + ". NOTE: The category slot was modified to have a curie range and a pattern for bican categories."
+
+    with schema_yaml_path.open("w") as f:
+        f.write(yaml.dump(schema_dict, sort_keys=False))
+
+
+if __name__ == '__main__':
+    bican_biolink_yaml_path = sys.argv[1]
+    bican_biolink_edit(bican_biolink_yaml_path)