refactor: address CodeRabbit nitpicks for Phase 10

- Centralize SourceName type alias in models.py
- Update search_handler.py to use SourceName (reduces cast brittleness)
- Update app.py intro text to mention ClinicalTrials.gov
- Update run_search.py docstring for multi-source search
- DRY test setup with mock_requests_get fixture
- Speed up error test by patching tenacity retry stop condition

examples/search_demo/run_search.py

@@ -2,8 +2,9 @@
 """
 Demo: Search for drug repurposing evidence.
 
-This script demonstrates Phase 2 functionality:
+This script demonstrates multi-source search functionality:
 - PubMed search (biomedical literature)
+- ClinicalTrials.gov search (clinical trial evidence)
 - SearchHandler (parallel scatter-gather orchestration)
 
 Usage:

src/app.py

@@ -128,7 +128,7 @@ def create_demo() -> Any:
         ## AI-Powered Drug Repurposing Research Agent
 
         Ask questions about potential drug repurposing opportunities.
-        The agent will search PubMed, evaluate evidence, and provide recommendations.
+        The agent searches PubMed & ClinicalTrials.gov to provide recommendations.
 
         **Example questions:**
         - "What drugs could be repurposed for Alzheimer's disease?"

src/tools/search_handler.py

@@ -1,13 +1,13 @@
 """Search handler - orchestrates multiple search tools."""
 
 import asyncio
-from typing import Literal, cast
+from typing import cast
 
 import structlog
 
 from src.tools.base import SearchTool
 from src.utils.exceptions import SearchError
-from src.utils.models import Evidence, SearchResult
+from src.utils.models import Evidence, SearchResult, SourceName
 
 logger = structlog.get_logger()
 
@@ -49,7 +49,7 @@ class SearchHandler:
 
         # Process results
         all_evidence: list[Evidence] = []
-        sources_searched: list[Literal["pubmed", "clinicaltrials"]] = []
+        sources_searched: list[SourceName] = []
         errors: list[str] = []
 
         for tool, result in zip(self.tools, results, strict=True):
@@ -61,8 +61,8 @@ class SearchHandler:
                 success_result = cast(list[Evidence], result)
                 all_evidence.extend(success_result)
 
-                # Cast tool.name to the expected Literal
-                tool_name = cast(Literal["pubmed", "clinicaltrials"], tool.name)
+                # Cast tool.name to SourceName (centralized type from models)
+                tool_name = cast(SourceName, tool.name)
                 sources_searched.append(tool_name)
                 logger.info("Search tool succeeded", tool=tool.name, count=len(success_result))
 

src/utils/models.py

@@ -5,11 +5,14 @@ from typing import Any, ClassVar, Literal
 
 from pydantic import BaseModel, Field
 
+# Centralized source type - add new sources here (e.g., "biorxiv" in Phase 11)
+SourceName = Literal["pubmed", "clinicaltrials"]
+
 
 class Citation(BaseModel):
     """A citation to a source document."""
 
-    source: Literal["pubmed", "clinicaltrials"] = Field(description="Where this came from")
+    source: SourceName = Field(description="Where this came from")
     title: str = Field(min_length=1, max_length=500)
     url: str = Field(description="URL to the source")
     date: str = Field(description="Publication date (YYYY-MM-DD or 'Unknown')")
@@ -41,7 +44,7 @@ class SearchResult(BaseModel):
 
     query: str
     evidence: list[Evidence]
-    sources_searched: list[Literal["pubmed", "clinicaltrials"]]
+    sources_searched: list[SourceName]
     total_found: int
     errors: list[str] = Field(default_factory=list)
 

tests/unit/tools/test_clinicaltrials.py

@@ -1,5 +1,7 @@
 """Unit tests for ClinicalTrials.gov tool."""
 
+from collections.abc import Generator
+from typing import Any
 from unittest.mock import MagicMock, patch
 
 import pytest
@@ -11,7 +13,7 @@ from src.utils.models import Evidence
 
 
 @pytest.fixture
-def mock_clinicaltrials_response() -> dict:
+def mock_clinicaltrials_response() -> dict[str, Any]:
     """Mock ClinicalTrials.gov API response."""
     return {
         "studies": [
@@ -39,6 +41,19 @@ def mock_clinicaltrials_response() -> dict:
     }
 
 
+@pytest.fixture
+def mock_requests_get(
+    mock_clinicaltrials_response: dict[str, Any],
+) -> Generator[MagicMock, None, None]:
+    """Fixture to mock requests.get with a successful response."""
+    with patch("src.tools.clinicaltrials.requests.get") as mock_get:
+        mock_response = MagicMock()
+        mock_response.json.return_value = mock_clinicaltrials_response
+        mock_response.raise_for_status = MagicMock()
+        mock_get.return_value = mock_response
+        yield mock_get
+
+
 class TestClinicalTrialsTool:
     """Tests for ClinicalTrialsTool."""
 
@@ -48,50 +63,32 @@ class TestClinicalTrialsTool:
         assert tool.name == "clinicaltrials"
 
     @pytest.mark.asyncio
-    async def test_search_returns_evidence(self, mock_clinicaltrials_response: dict) -> None:
+    async def test_search_returns_evidence(self, mock_requests_get: MagicMock) -> None:
         """Search should return Evidence objects."""
-        with patch("src.tools.clinicaltrials.requests.get") as mock_get:
-            mock_response = MagicMock()
-            mock_response.json.return_value = mock_clinicaltrials_response
-            mock_response.raise_for_status = MagicMock()
-            mock_get.return_value = mock_response
-
-            tool = ClinicalTrialsTool()
-            results = await tool.search("metformin alzheimer", max_results=5)
+        tool = ClinicalTrialsTool()
+        results = await tool.search("metformin alzheimer", max_results=5)
 
-            assert len(results) == 1
-            assert isinstance(results[0], Evidence)
-            assert results[0].citation.source == "clinicaltrials"
-            assert "NCT04098666" in results[0].citation.url
-            assert "Metformin" in results[0].citation.title
+        assert len(results) == 1
+        assert isinstance(results[0], Evidence)
+        assert results[0].citation.source == "clinicaltrials"
+        assert "NCT04098666" in results[0].citation.url
+        assert "Metformin" in results[0].citation.title
 
     @pytest.mark.asyncio
-    async def test_search_extracts_phase(self, mock_clinicaltrials_response: dict) -> None:
+    async def test_search_extracts_phase(self, mock_requests_get: MagicMock) -> None:
         """Search should extract trial phase."""
-        with patch("src.tools.clinicaltrials.requests.get") as mock_get:
-            mock_response = MagicMock()
-            mock_response.json.return_value = mock_clinicaltrials_response
-            mock_response.raise_for_status = MagicMock()
-            mock_get.return_value = mock_response
-
-            tool = ClinicalTrialsTool()
-            results = await tool.search("metformin alzheimer")
+        tool = ClinicalTrialsTool()
+        results = await tool.search("metformin alzheimer")
 
-            assert "PHASE2" in results[0].content
+        assert "PHASE2" in results[0].content
 
     @pytest.mark.asyncio
-    async def test_search_extracts_status(self, mock_clinicaltrials_response: dict) -> None:
+    async def test_search_extracts_status(self, mock_requests_get: MagicMock) -> None:
         """Search should extract trial status."""
-        with patch("src.tools.clinicaltrials.requests.get") as mock_get:
-            mock_response = MagicMock()
-            mock_response.json.return_value = mock_clinicaltrials_response
-            mock_response.raise_for_status = MagicMock()
-            mock_get.return_value = mock_response
-
-            tool = ClinicalTrialsTool()
-            results = await tool.search("metformin alzheimer")
+        tool = ClinicalTrialsTool()
+        results = await tool.search("metformin alzheimer")
 
-            assert "Recruiting" in results[0].content
+        assert "Recruiting" in results[0].content
 
     @pytest.mark.asyncio
     async def test_search_empty_results(self) -> None:
@@ -109,13 +106,18 @@ class TestClinicalTrialsTool:
 
     @pytest.mark.asyncio
     async def test_search_api_error(self) -> None:
-        """Search should raise SearchError on API failure."""
+        """Search should raise SearchError on API failure.
+
+        Note: We patch the retry decorator to avoid 3x backoff delay in tests.
+        """
         with patch("src.tools.clinicaltrials.requests.get") as mock_get:
             mock_response = MagicMock()
             mock_response.raise_for_status.side_effect = requests.HTTPError("500 Server Error")
             mock_get.return_value = mock_response
 
             tool = ClinicalTrialsTool()
+            # Patch the retry decorator's stop condition to fail immediately
+            tool.search.retry.stop = lambda _: True  # type: ignore[attr-defined]
 
             with pytest.raises(SearchError):
                 await tool.search("metformin alzheimer")