Add unit tests and enable CI pipeline

.github/workflows/ci.yml

@@ -1,42 +1,34 @@
-# name: CI Pipeline
-# on:
-#   workflow_dispatch:
-#   # push:
-#   #   branches:
-#   #     - main
-
-# jobs:
-#   lint-and-test:
-#     runs-on: ubuntu-latest
-
-#     steps:
-#       - name: Checkout code
-#         uses: actions/checkout@v4
-
-#       - name: Install uv
-#         uses: astral-sh/setup-uv@v5
-
-#       - name: Set up Python
-#         uses: actions/setup-python@v5
-#         with:
-#           python-version-file: .python-version
-
-#       - name: Install dependencies
-#         run: |
-#           uv sync --all-groups
-
-#       - name: Linting Check
-#         run: |
-#           uv run ruff check . --show-fixes
-
-#       - name: Auto-format with Ruff
-#         run: |
-#           uv run ruff check . --fix --exit-non-zero-on-fix
-
-#       - name: Type check with mypy
-#         run: uv run mypy
-
-#       - name: Run tests
-#         env:
-#           AWS_REGION: ${{ secrets.AWS_REGION }}
-#         run: uv run pytest
+name: CI Pipeline
+on:
+  push:
+    branches: [main, feature/*]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint-and-test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: .python-version
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Linting Check
+        run: uv run ruff check . --show-fixes
+
+      - name: Type check with mypy
+        run: uv run mypy
+
+      - name: Run tests
+        run: uv run pytest --tb=short

pyproject.toml

@@ -45,6 +45,7 @@ lint = [
     "ruff>=0.14.0",
 ]
 test = [
+    "httpx>=0.28.1",
     "pytest>=8.4.2",
     "pytest-asyncio>=1.2.0",
 ]

tests/unit/test_additional_domain_models.py

@@ -0,0 +1,81 @@
+"""Unit tests for additional domain models."""
+
+from biomedical_graphrag.domain.citation import CitationNetwork
+from biomedical_graphrag.domain.dataset import (
+    GeneDataset,
+    GeneMetadata,
+    PaperDataset,
+    PaperMetadata,
+)
+from biomedical_graphrag.domain.gene import GeneRecord
+
+
+class TestGeneRecord:
+    def test_default_creation(self) -> None:
+        gene = GeneRecord()
+        assert gene.gene_id == ""
+        assert gene.name == ""
+        assert gene.linked_pmids == []
+
+    def test_full_creation(self) -> None:
+        gene = GeneRecord(
+            gene_id="672",
+            name="BRCA1",
+            description="BRCA1 DNA repair associated",
+            chromosome="17",
+            map_location="17q21.31",
+            organism="Homo sapiens",
+            aliases="BRCA1/BRCA2-containing complex",
+            linked_pmids=["12345", "67890"],
+        )
+        assert gene.gene_id == "672"
+        assert gene.name == "BRCA1"
+        assert len(gene.linked_pmids) == 2
+
+
+class TestCitationNetwork:
+    def test_default_creation(self) -> None:
+        citation = CitationNetwork()
+        assert citation.pmid == ""
+        assert citation.cited_by == []
+        assert citation.references == []
+
+    def test_with_data(self) -> None:
+        citation = CitationNetwork(
+            pmid="12345",
+            cited_by=["11111", "22222"],
+            references=["33333"],
+        )
+        assert len(citation.cited_by) == 2
+        assert len(citation.references) == 1
+
+
+class TestDatasetModels:
+    def test_paper_metadata_defaults(self) -> None:
+        meta = PaperMetadata()
+        assert meta.total_papers == 0
+        assert meta.collection_date == ""
+
+    def test_paper_dataset_defaults(self) -> None:
+        ds = PaperDataset()
+        assert ds.papers == []
+        assert ds.citation_network == {}
+
+    def test_gene_metadata_defaults(self) -> None:
+        meta = GeneMetadata()
+        assert meta.total_genes == 0
+        assert meta.genes_with_pubmed_links == 0
+
+    def test_gene_dataset_defaults(self) -> None:
+        ds = GeneDataset()
+        assert ds.genes == []
+
+    def test_gene_dataset_with_data(self) -> None:
+        gene = GeneRecord(gene_id="672", name="BRCA1")
+        ds = GeneDataset(
+            metadata=GeneMetadata(total_genes=1, genes_with_pubmed_links=1),
+            genes=[gene],
+        )
+        assert ds.metadata.total_genes == 1
+        assert len(ds.genes) == 1
+        assert ds.genes[0].name == "BRCA1"

tests/unit/test_api_server.py

@@ -0,0 +1,79 @@
+"""Unit tests for FastAPI server endpoints."""
+
+import pytest
+from fastapi.testclient import TestClient
+
+from biomedical_graphrag.api.server import (
+    HealthResponse,
+    SearchRequest,
+    SearchResponse,
+    TraceStep,
+    app,
+)
+
+
+@pytest.fixture
+def client():
+    """Create a test client for the FastAPI app."""
+    return TestClient(app)
+
+
+class TestHealthEndpoint:
+    def test_health_check_returns_healthy(self, client: TestClient) -> None:
+        response = client.get("/health")
+        assert response.status_code == 200
+        assert response.json() == {"status": "healthy"}
+
+
+class TestSearchRequestModel:
+    def test_default_values(self) -> None:
+        req = SearchRequest(query="test")
+        assert req.query == "test"
+        assert req.limit == 5
+        assert req.mode == "graphrag"
+
+    def test_custom_values(self) -> None:
+        req = SearchRequest(query="BRCA1", limit=3, mode="dense")
+        assert req.limit == 3
+        assert req.mode == "dense"
+
+    def test_limit_validation_max(self) -> None:
+        from pydantic import ValidationError
+
+        with pytest.raises(ValidationError):
+            SearchRequest(query="test", limit=10)
+
+    def test_limit_validation_min(self) -> None:
+        from pydantic import ValidationError
+
+        with pytest.raises(ValidationError):
+            SearchRequest(query="test", limit=0)
+
+
+class TestResponseModels:
+    def test_search_response_defaults(self) -> None:
+        resp = SearchResponse()
+        assert resp.summary is None
+        assert resp.results == []
+        assert resp.trace == []
+        assert resp.metadata == {}
+
+    def test_trace_step_creation(self) -> None:
+        step = TraceStep(name="qdrant_search", arguments={"query": "test"}, result_count=5)
+        assert step.name == "qdrant_search"
+        assert step.arguments == {"query": "test"}
+        assert step.result_count == 5
+
+    def test_health_response(self) -> None:
+        resp = HealthResponse()
+        assert resp.status == "healthy"
+
+
+class TestSearchEndpoint:
+    def test_search_missing_query(self, client: TestClient) -> None:
+        response = client.post("/api/graphrag-query", json={})
+        assert response.status_code == 422
+
+    def test_search_invalid_limit(self, client: TestClient) -> None:
+        response = client.post("/api/graphrag-query", json={"query": "test", "limit": -1})
+        assert response.status_code == 422