Merge branch 'main' into dev

src/tools/clinicaltrials.py

@@ -30,6 +30,9 @@ class ClinicalTrialsTool:
         "InterventionName",
         "StartDate",
         "BriefSummary",
+        # NEW: Outcome measures
+        "OutcomesModule",
+        "HasResults",
     ]
 
     # Status filter: Only active/completed studies with potential data
@@ -89,6 +92,20 @@ class ClinicalTrialsTool:
         except requests.RequestException as e:
             raise SearchError(f"ClinicalTrials.gov request failed: {e}") from e
 
+    def _extract_primary_outcome(self, outcomes_module: dict[str, Any]) -> str:
+        """Extract and format primary outcome from outcomes module."""
+        primary_outcomes = outcomes_module.get("primaryOutcomes", [])
+        if not primary_outcomes:
+            return ""
+        # Get first primary outcome measure and timeframe
+        first = primary_outcomes[0]
+        measure = first.get("measure", "")
+        timeframe = first.get("timeFrame", "")
+        # Build full outcome string first, then truncate
+        result = f"{measure} (measured at {timeframe})" if timeframe else measure
+        # Truncate long outcome descriptions with ellipsis
+        return result[:197] + "..." if len(result) > 200 else result
+
     def _study_to_evidence(self, study: dict[str, Any]) -> Evidence:
         """Convert a clinical trial study to Evidence."""
         # Navigate nested structure
@@ -99,6 +116,7 @@ class ClinicalTrialsTool:
         design_module = protocol.get("designModule", {})
         conditions_module = protocol.get("conditionsModule", {})
         arms_module = protocol.get("armsInterventionsModule", {})
+        outcomes_module = protocol.get("outcomesModule", {})
 
         nct_id = id_module.get("nctId", "Unknown")
         title = id_module.get("briefTitle", "Untitled Study")
@@ -121,14 +139,42 @@ class ClinicalTrialsTool:
         # Get summary
         summary = desc_module.get("briefSummary", "No summary available.")
 
+        # Extract outcome measures
+        primary_outcome_str = self._extract_primary_outcome(outcomes_module)
+        secondary_count = len(outcomes_module.get("secondaryOutcomes", []))
+
+        # Check if results are available (hasResults is TOP-LEVEL, not in protocol!)
+        has_results = study.get("hasResults", False)
+
+        # Results date is in statusModule (nested inside date struct)
+        results_date_struct = status_module.get("resultsFirstPostDateStruct", {})
+        results_date = results_date_struct.get("date", "")
+
         # Build content with key trial info
-        content = (
-            f"{summary[:500]}... "
-            f"Trial Phase: {phase}. "
-            f"Status: {status}. "
-            f"Conditions: {conditions_str}. "
-            f"Interventions: {interventions_str}."
-        )
+        summary_text = summary[:400] + "..." if len(summary) > 400 else summary
+        content_parts = [
+            summary_text,
+            f"Trial Phase: {phase}.",
+            f"Status: {status}.",
+            f"Conditions: {conditions_str}.",
+            f"Interventions: {interventions_str}.",
+        ]
+
+        if primary_outcome_str:
+            content_parts.append(f"Primary Outcome: {primary_outcome_str}.")
+
+        if secondary_count > 0:
+            content_parts.append(f"Secondary Outcomes: {secondary_count} additional endpoints.")
+
+        if has_results:
+            results_info = "Results Available: Yes"
+            if results_date:
+                results_info += f" (posted {results_date})"
+            content_parts.append(results_info + ".")
+        else:
+            content_parts.append("Results Available: Not yet posted.")
+
+        content = " ".join(content_parts)
 
         return Evidence(
             content=content[:2000],
@@ -139,5 +185,5 @@ class ClinicalTrialsTool:
                 date=start_date,
                 authors=[],  # Trials don't have traditional authors
             ),
-            relevance=0.85,  # Trials are highly relevant for repurposing
+            relevance=0.90 if has_results else 0.85,  # Boost relevance for trials with results
         )

tests/unit/tools/test_clinicaltrials.py

@@ -128,6 +128,150 @@ class TestClinicalTrialsTool:
             assert results == []
 
 
+@pytest.mark.unit
+class TestClinicalTrialsOutcomes:
+    """Tests for outcome measure extraction."""
+
+    @pytest.fixture
+    def tool(self) -> ClinicalTrialsTool:
+        return ClinicalTrialsTool()
+
+    @pytest.mark.asyncio
+    async def test_extracts_primary_outcome(self, tool: ClinicalTrialsTool) -> None:
+        """Test that primary outcome is extracted from response."""
+        mock_study = {
+            "protocolSection": {
+                "identificationModule": {"nctId": "NCT12345678", "briefTitle": "Test"},
+                "statusModule": {"overallStatus": "COMPLETED", "startDateStruct": {"date": "2023"}},
+                "descriptionModule": {"briefSummary": "Summary"},
+                "designModule": {"phases": ["PHASE3"]},
+                "conditionsModule": {"conditions": ["ED"]},
+                "armsInterventionsModule": {"interventions": []},
+                "outcomesModule": {
+                    "primaryOutcomes": [
+                        {"measure": "Change in IIEF-EF score", "timeFrame": "Week 12"}
+                    ]
+                },
+            },
+            "hasResults": True,
+        }
+
+        mock_response = MagicMock()
+        mock_response.json.return_value = {"studies": [mock_study]}
+        mock_response.raise_for_status = MagicMock()
+
+        with patch("requests.get", return_value=mock_response):
+            results = await tool.search("test", max_results=1)
+
+            assert len(results) == 1
+            assert "Primary Outcome" in results[0].content
+            assert "IIEF-EF" in results[0].content
+            assert "Week 12" in results[0].content
+
+    @pytest.mark.asyncio
+    async def test_includes_results_status(self, tool: ClinicalTrialsTool) -> None:
+        """Test that results availability is shown."""
+        mock_study = {
+            "protocolSection": {
+                "identificationModule": {"nctId": "NCT12345678", "briefTitle": "Test"},
+                "statusModule": {
+                    "overallStatus": "COMPLETED",
+                    "startDateStruct": {"date": "2023"},
+                    # Note: resultsFirstPostDateStruct, not resultsFirstSubmitDate
+                    "resultsFirstPostDateStruct": {"date": "2024-06-15"},
+                },
+                "descriptionModule": {"briefSummary": "Summary"},
+                "designModule": {"phases": ["PHASE3"]},
+                "conditionsModule": {"conditions": ["ED"]},
+                "armsInterventionsModule": {"interventions": []},
+                "outcomesModule": {},
+            },
+            "hasResults": True,  # Note: hasResults is TOP-LEVEL
+        }
+
+        mock_response = MagicMock()
+        mock_response.json.return_value = {"studies": [mock_study]}
+        mock_response.raise_for_status = MagicMock()
+
+        with patch("requests.get", return_value=mock_response):
+            results = await tool.search("test", max_results=1)
+
+            assert "Results Available: Yes" in results[0].content
+            assert "2024-06-15" in results[0].content
+
+    @pytest.mark.asyncio
+    async def test_shows_no_results_when_missing(self, tool: ClinicalTrialsTool) -> None:
+        """Test that missing results are indicated."""
+        mock_study = {
+            "protocolSection": {
+                "identificationModule": {
+                    "nctId": "NCT99999999",
+                    "briefTitle": "Test Study",
+                },
+                "statusModule": {
+                    "overallStatus": "RECRUITING",
+                    "startDateStruct": {"date": "2024"},
+                },
+                "descriptionModule": {"briefSummary": "Summary"},
+                "designModule": {"phases": ["PHASE2"]},
+                "conditionsModule": {"conditions": ["ED"]},
+                "armsInterventionsModule": {"interventions": []},
+                "outcomesModule": {},
+            },
+            "hasResults": False,
+        }
+
+        mock_response = MagicMock()
+        mock_response.json.return_value = {"studies": [mock_study]}
+        mock_response.raise_for_status = MagicMock()
+
+        with patch("requests.get", return_value=mock_response):
+            results = await tool.search("test", max_results=1)
+
+            assert "Results Available: Not yet posted" in results[0].content
+
+    @pytest.mark.asyncio
+    async def test_boosts_relevance_for_results(self, tool: ClinicalTrialsTool) -> None:
+        """Trials with results should have higher relevance score."""
+        with_results = {
+            "protocolSection": {
+                "identificationModule": {"nctId": "NCT11111111", "briefTitle": "With Results"},
+                "statusModule": {"overallStatus": "COMPLETED", "startDateStruct": {"date": "2023"}},
+                "descriptionModule": {"briefSummary": "Summary"},
+                "designModule": {"phases": []},
+                "conditionsModule": {"conditions": []},
+                "armsInterventionsModule": {"interventions": []},
+                "outcomesModule": {},
+            },
+            "hasResults": True,
+        }
+        without_results = {
+            "protocolSection": {
+                "identificationModule": {"nctId": "NCT22222222", "briefTitle": "No Results"},
+                "statusModule": {
+                    "overallStatus": "RECRUITING",
+                    "startDateStruct": {"date": "2024"},
+                },
+                "descriptionModule": {"briefSummary": "Summary"},
+                "designModule": {"phases": []},
+                "conditionsModule": {"conditions": []},
+                "armsInterventionsModule": {"interventions": []},
+                "outcomesModule": {},
+            },
+            "hasResults": False,
+        }
+
+        mock_response = MagicMock()
+        mock_response.json.return_value = {"studies": [with_results, without_results]}
+        mock_response.raise_for_status = MagicMock()
+
+        with patch("requests.get", return_value=mock_response):
+            results = await tool.search("test", max_results=2)
+
+            assert results[0].relevance == 0.90  # With results
+            assert results[1].relevance == 0.85  # Without results
+
+
 @pytest.mark.integration
 class TestClinicalTrialsIntegration:
     """Integration tests with real API."""
@@ -150,3 +294,21 @@ class TestClinicalTrialsIntegration:
             or "phase" in all_content
         )
         assert has_intervention
+
+    @pytest.mark.asyncio
+    async def test_real_completed_trial_has_outcome(self) -> None:
+        """Real completed Phase 3 trials should have outcome measures."""
+        tool = ClinicalTrialsTool()
+
+        # Search for completed Phase 3 ED trials (likely to have outcomes)
+        results = await tool.search(
+            "sildenafil erectile dysfunction Phase 3 COMPLETED", max_results=3
+        )
+
+        # Skip if API returns no results (external dependency)
+        if not results:
+            pytest.skip("API returned no results for this query")
+
+        # At least one should have primary outcome
+        has_outcome = any("Primary Outcome" in r.content for r in results)
+        assert has_outcome, "No completed trials with outcome measures found"