feat(testing): add testing for ontology-builder

.github/workflows/push-tests.yml

@@ -25,3 +25,29 @@ jobs:
       - uses: actions/setup-python@v5
       - name: lint checks
         uses: pre-commit/[email protected]
+
+  unit-test-ontonolgy-builder:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.11
+      - name: Python cache
+        uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install dependencies
+        run: |
+          pip install -r tools/ontology-builder/requirements.txt
+          pip install -r tools/ontology-builder/requirements-dev.txt
+      - name: Ontology Dry Run Unit Tests
+        run: |
+          cd tools/ontology-builder && make unit-tests

.pre-commit-config.yaml

@@ -34,3 +34,4 @@ repos:
       - id: mypy
         args: [--strict, --ignore-missing-imports]
         additional_dependencies: [types-PyYAML]
+        files: ^(api/python|tools/ontology-builder/src)/

Makefile

@@ -1,3 +1,2 @@
 lint:
 	pre-commit run --all-files
-

tools/ontology-builder/Makefile

@@ -0,0 +1,2 @@
+unit-tests:
+	python -m pytest tests

tools/ontology-builder/README.md

@@ -0,0 +1,4 @@
+# Run Tests
+
+1. `pip install -r requirements.txt -r requirements-dev.txt`
+2. `make unit-tests`

tools/ontology-builder/pyproject.toml

@@ -0,0 +1,4 @@
+[tool.pytest.ini_options]
+pythonpath = [
+  "src"
+]

tools/ontology-builder/requirements-dev.txt

@@ -0,0 +1 @@
+pytest

tools/ontology-builder/tests/test_all_ontology_generator.py

@@ -0,0 +1,86 @@
+import os
+import urllib.request
+from unittest.mock import MagicMock, patch
+
+import pytest
+from all_ontology_generator import _download_ontologies, _parse_ontologies
+
+
+@pytest.fixture
+def mock_ontology_info(tmpdir):
+    # Create a temporary ontology info yaml file
+    onto_info_yml = tmpdir.join("ontology_info.yml")
+    onto_info_yml.write("ontology_name:\n  source: http://example.com\n  version: v1\n  filetype: owl\n")
+    return str(onto_info_yml)
+
+
+@pytest.fixture
+def mock_raw_ontology_dir(tmpdir):
+    # Create a temporary directory for raw ontology files
+    raw_ontology_dir = tmpdir.mkdir("raw_ontology")
+    return str(raw_ontology_dir)
+
+
+@pytest.fixture
+def mock_parsed_ontology_file(tmpdir):
+    # Create a temporary gzipped json file for parsed ontology data
+    parsed_ontology_file = tmpdir.join("parsed_ontologies.json.gz")
+    return str(parsed_ontology_file)
+
+
+def test_download_ontologies(mock_ontology_info, mock_raw_ontology_dir):
+    # Mocking urllib.request.urlretrieve, urllib.request.urlopen
+    with patch("urllib.request.urlretrieve") as mock_urlretrieve, patch("urllib.request.urlopen") as mock_urlopen:
+        # Mock HTTP response
+        mock_response = MagicMock()
+        mock_response.code = 200
+        mock_urlopen.return_value = mock_response
+
+        # Call the function
+        _download_ontologies(onto_info_yml=mock_ontology_info, output_dir=mock_raw_ontology_dir)
+
+        # Assert urlretrieve is called with correct arguments
+        mock_urlretrieve.assert_called_once()
+
+
+def test_parse_ontologies(mock_raw_ontology_dir, mock_parsed_ontology_file):
+    # Mocking _load_ontology_object and _extract_ontology_term_metadata
+    with patch("all_ontology_generator._load_ontology_object") as mock_load_ontology, patch(
+        "all_ontology_generator._extract_ontology_term_metadata"
+    ) as mock_extract_metadata:
+        # Mock return values
+        mock_load_ontology.return_value = MagicMock(name="ontology_object")
+        mock_extract_metadata.return_value = {"term_id": {"label": "Term Label", "deprecated": False, "ancestors": []}}
+
+        # Call the function
+        _parse_ontologies(working_dir=mock_raw_ontology_dir, output_json_file=mock_parsed_ontology_file)
+
+        # Assert _load_ontology_object is called for each ontology file
+        assert mock_load_ontology.call_count == len(os.listdir(mock_raw_ontology_dir))
+
+        # Assert _extract_ontology_term_metadata is called for each ontology object
+        assert mock_extract_metadata.call_count == len(os.listdir(mock_raw_ontology_dir))
+
+
+def test_download_ontologies_http_error(mock_ontology_info, mock_raw_ontology_dir):
+    # Mocking urllib.request.urlopen to raise HTTPError
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_urlopen.side_effect = urllib.error.HTTPError(
+            url="http://example.com", code=404, msg="Not Found", hdrs={}, fp=None
+        )
+
+        # Assertion
+        with pytest.raises(Exception) as exc_info:
+            _download_ontologies(onto_info_yml=mock_ontology_info, output_dir=mock_raw_ontology_dir)
+        assert "returns status code 404" in str(exc_info.value)
+
+
+def test_download_ontologies_url_error(mock_ontology_info, mock_raw_ontology_dir):
+    # Mocking urllib.request.urlopen to raise URLError
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_urlopen.side_effect = urllib.error.URLError(reason="Connection refused")
+
+        # Assertion
+        with pytest.raises(Exception) as exc_info:
+            _download_ontologies(onto_info_yml=mock_ontology_info, output_dir=mock_raw_ontology_dir)
+        assert "fails due to Connection refused" in str(exc_info.value)