update linkml, linkml-runtime, bmt, tests to take advantage of newer biolink model

.github/workflows/check-dependencies.yaml

@@ -0,0 +1,52 @@
+---
+name: Check Dependencies in Pyproject.toml
+
+# Controls when the action will run.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    types: trigger-run-check-dependencies
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [ "3.9", "3.10" ]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: setup python environment
+        with:
+          python-version: ${{ matrix.python }}
+
+      # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run
+      # with the latest dependencies
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install poetry
+          rm -rf poetry.lock
+          poetry install 
+          docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0
+          docker run --detach --name kgx-neo4j-integration-test -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0
+          docker ps -a
+
+      - name: Wait
+        uses: jakejarvis/wait-action@master
+        with:
+          time: '45s'
+
+      - name: Run tests
+        run: |
+          poetry run make test

kgx/validator.py

@@ -66,7 +66,7 @@ def get_the_validator(
         Creates and manages a default singleton Validator in the module, when called
         """
         if not cls._the_validator:
-            cls.set_biolink_model("v3.1.2")
+            cls.set_biolink_model("v4.1.6")
             cls._the_validator = Validator(
                 verbose=verbose,
                 progress_monitor=progress_monitor,
@@ -232,7 +232,7 @@ def get_required_node_properties(toolkit: Optional[Toolkit] = None) -> list:
             toolkit = Validator.get_toolkit()
         node_properties = toolkit.get_all_node_properties()
         # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot.
-        node_properties.append("id")
+        # node_properties.append("id")
         required_properties = []
         for p in node_properties:
             element = toolkit.get_element(p)