test: update tests for evidence-linked mock data and new features

- Update NCT ID references from NCT04000xxx to MOCK-NCT-* across all tests
- Update MCP test mocks from streaming to regular POST response
- Add live test fixtures (Gemini, MCP, MedGemma) in conftest.py
- Load .env in conftest for live test API key access
- Test "would match IF" phrasing in gap analysis page
- Test patient profile inclusion in MedGemma criterion evaluation
- Patch direct_pipeline in profile review advance test

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app/tests/test_gap_analysis_page.py

@@ -30,8 +30,11 @@ def test_page_renders_without_error(gap_app):
 
 
 def test_displays_gaps(gap_app):
+    expander_labels = [str(e.label) for e in gap_app.expander]
+    all_labels = " ".join(expander_labels)
     all_md = " ".join(str(m.value) for m in gap_app.markdown)
-    assert "Brain MRI" in all_md or "KRAS" in all_md
+    combined = all_labels + " " + all_md
+    assert "Brain MRI" in combined or "EGFR" in combined
 
 
 def test_displays_recommended_actions(gap_app):
@@ -39,6 +42,13 @@ def test_displays_recommended_actions(gap_app):
     assert "upload" in all_md.lower() or "request" in all_md.lower()
 
 
+def test_displays_would_match_phrasing(gap_app):
+    """PRD core value proposition: 'You would match [trial] IF you had' phrasing."""
+    all_md = " ".join(str(m.value) for m in gap_app.markdown)
+    assert "You would match" in all_md
+    assert "IF you had" in all_md
+
+
 def test_has_summary_button(gap_app):
     labels = [str(b.label) for b in gap_app.button]
     assert any("summary" in lbl.lower() or "generate" in lbl.lower() for lbl in labels)

app/tests/test_profile_review_page.py

@@ -1,9 +1,15 @@
 """Tests for app/pages/2_profile_review.py — PRESCREEN state."""
 
+from unittest.mock import patch
+
 import pytest
 from streamlit.testing.v1 import AppTest
 
-from app.services.mock_data import MOCK_PATIENT_PROFILE
+from app.services.mock_data import (
+    MOCK_ELIGIBILITY_LEDGERS,
+    MOCK_PATIENT_PROFILE,
+    MOCK_TRIAL_CANDIDATES,
+)
 
 
 @pytest.fixture
@@ -52,7 +58,11 @@ def test_has_confirm_button(profile_app):
     assert any("confirm" in lbl.lower() or "search" in lbl.lower() for lbl in labels)
 
 
-def test_confirm_advances_to_validate_trials(profile_app):
+@patch(
+    "app.services.direct_pipeline.run_trial_search_and_evaluate",
+    return_value=(MOCK_TRIAL_CANDIDATES, MOCK_ELIGIBILITY_LEDGERS),
+)
+def test_confirm_advances_to_validate_trials(mock_pipeline, profile_app):
     confirm_btns = [
         b
         for b in profile_app.button

app/tests/test_trial_matching_page.py

@@ -38,8 +38,8 @@ def test_displays_trial_nct_ids(matching_app):
     # NCT IDs are in expander labels, not in markdown body text
     expander_labels = [str(e.label) for e in matching_app.expander]
     all_labels = " ".join(expander_labels)
-    assert "NCT04000001" in all_labels
-    assert "NCT04000002" in all_labels
+    assert "MOCK-NCT-KEYNOTE999" in all_labels
+    assert "MOCK-NCT-FLAURA2" in all_labels
 
 
 def test_displays_traffic_light_colors(matching_app):

conftest.py

@@ -2,10 +2,18 @@
 
 from __future__ import annotations
 
+import os
 from unittest.mock import AsyncMock, MagicMock, patch
 
 import pytest
 
+try:
+    from dotenv import load_dotenv
+
+    load_dotenv()
+except ImportError:
+    pass
+
 from app.services.mock_data import (
     MOCK_ELIGIBILITY_LEDGERS,
     MOCK_PATIENT_PROFILE,
@@ -146,3 +154,42 @@ def mock_mcp():
         instance.get_study.return_value = MOCK_TRIAL_CANDIDATES[0].model_dump()
         cls.return_value = instance
         yield instance
+
+
+# ---------------------------------------------------------------------------
+# Live service fixtures (require real API keys / running servers)
+# ---------------------------------------------------------------------------
+
+
+@pytest.fixture(scope="session")
+def live_env():
+    """Ensure env vars are loaded; skip the entire session block if missing."""
+    if not os.environ.get("GEMINI_API_KEY"):
+        pytest.skip("GEMINI_API_KEY not set — skipping live tests")
+
+
+@pytest.fixture(scope="session")
+def live_gemini(live_env):
+    """Return a real GeminiPlanner wired to the Gemini API."""
+    from trialpath.services.gemini_planner import GeminiPlanner
+
+    return GeminiPlanner()
+
+
+@pytest.fixture(scope="session")
+def live_mcp_client(live_env):
+    """Return a real ClinicalTrialsMCPClient."""
+    from trialpath.services.mcp_client import ClinicalTrialsMCPClient
+
+    return ClinicalTrialsMCPClient()
+
+
+@pytest.fixture(scope="session")
+def live_medgemma(live_env):
+    """Return a real MedGemmaExtractor (skip if no HF_TOKEN)."""
+    if not os.environ.get("HF_TOKEN"):
+        pytest.skip("HF_TOKEN not set — skipping MedGemma live tests")
+
+    from trialpath.services.medgemma_extractor import MedGemmaExtractor
+
+    return MedGemmaExtractor()

tests/test_integration.py

@@ -72,15 +72,15 @@ class TestComponentModelIntegration:
         assert len(spec["biomarkers"]) == 3
 
     def test_trial_card_renders_green_trial(self):
-        # NCT04000002 is LIKELY_ELIGIBLE -> green
+        # MOCK-NCT-FLAURA2 is LIKELY_ELIGIBLE -> green
         trial = MOCK_TRIAL_CANDIDATES[1]
         ledger = MOCK_ELIGIBILITY_LEDGERS[1]
         spec = render_trial_card(trial, ledger)
         assert spec["traffic_light"] == "green"
-        assert spec["nct_id"] == "NCT04000002"
+        assert spec["nct_id"] == "MOCK-NCT-FLAURA2"
 
     def test_trial_card_renders_yellow_trial(self):
-        # NCT04000001 is UNCERTAIN -> yellow
+        # MOCK-NCT-KEYNOTE999 is UNCERTAIN -> yellow
         trial = MOCK_TRIAL_CANDIDATES[0]
         ledger = MOCK_ELIGIBILITY_LEDGERS[0]
         spec = render_trial_card(trial, ledger)
@@ -88,7 +88,7 @@ class TestComponentModelIntegration:
         assert len(spec["gaps"]) == 1
 
     def test_trial_card_renders_red_trial(self):
-        # NCT04000003 is LIKELY_INELIGIBLE -> red
+        # MOCK-NCT-CM817 is LIKELY_INELIGIBLE -> red
         trial = MOCK_TRIAL_CANDIDATES[2]
         ledger = MOCK_ELIGIBILITY_LEDGERS[2]
         spec = render_trial_card(trial, ledger)
@@ -97,7 +97,7 @@ class TestComponentModelIntegration:
     def test_gap_card_renders_from_ledger_gap(self):
         ledger = MOCK_ELIGIBILITY_LEDGERS[0]
         gap = ledger.gaps[0]
-        spec = render_gap_card(gap, affected_trials=["NCT04000001"])
+        spec = render_gap_card(gap, affected_trials=["MOCK-NCT-KEYNOTE999"])
         assert "Brain MRI" in spec["description"]
         assert spec["importance_color"] == "red"  # high importance
 
@@ -153,7 +153,7 @@ class TestDoctorPacketGeneration:
     def test_all_trial_nct_ids_in_packet(self):
         ledgers = MOCK_ELIGIBILITY_LEDGERS
         packet_ids = [lg.nct_id for lg in ledgers]
-        expected_ids = ["NCT04000001", "NCT04000002", "NCT04000003"]
+        expected_ids = ["MOCK-NCT-KEYNOTE999", "MOCK-NCT-FLAURA2", "MOCK-NCT-CM817"]
         assert packet_ids == expected_ids
 
 

trialpath/tests/test_mcp.py

@@ -33,21 +33,14 @@ class TestMCPClient:
     def _mock_httpx(self, MockHTTP, response_data):
         import json as _json
 
-        # Mock the streaming response (async context manager from client.stream())
-        mock_stream_response = MagicMock()
-        mock_stream_response.raise_for_status = MagicMock()
-        mock_stream_response.aread = AsyncMock(
-            return_value=_json.dumps(response_data).encode("utf-8")
-        )
-        mock_stream_response.headers = {"content-type": "application/json"}
-
-        # client.stream() returns an async context manager
-        mock_stream_ctx = MagicMock()
-        mock_stream_ctx.__aenter__ = AsyncMock(return_value=mock_stream_response)
-        mock_stream_ctx.__aexit__ = AsyncMock(return_value=None)
+        # Mock the response from client.post()
+        mock_response = MagicMock()
+        mock_response.raise_for_status = MagicMock()
+        mock_response.text = _json.dumps(response_data)
+        mock_response.headers = {"content-type": "application/json"}
 
         mock_client = MagicMock()
-        mock_client.stream = MagicMock(return_value=mock_stream_ctx)
+        mock_client.post = AsyncMock(return_value=mock_response)
 
         # AsyncClient() itself is an async context manager
         mock_client_ctx = MagicMock()
@@ -64,7 +57,7 @@ class TestMCPClient:
 
             await client.search(sample_anchors)
 
-            call_args = mock_client.stream.call_args
+            call_args = mock_client.post.call_args
             body = call_args.kwargs.get("json", call_args[1].get("json", {}))
             query = body["params"]["arguments"]["query"]
 
@@ -79,7 +72,7 @@ class TestMCPClient:
 
             await client.search(sample_anchors)
 
-            call_args = mock_client.stream.call_args
+            call_args = mock_client.post.call_args
             body = call_args.kwargs.get("json", call_args[1].get("json", {}))
             args = body["params"]["arguments"]
 
@@ -93,7 +86,7 @@ class TestMCPClient:
 
             await client.search(sample_anchors)
 
-            call_args = mock_client.stream.call_args
+            call_args = mock_client.post.call_args
             body = call_args.kwargs.get("json", call_args[1].get("json", {}))
             filter_str = body["params"]["arguments"].get("filter", "")
 
@@ -135,7 +128,7 @@ class TestMCPClient:
                 country="United States",
             )
 
-            call_args = mock_client.stream.call_args
+            call_args = mock_client.post.call_args
             body = call_args.kwargs.get("json", call_args[1].get("json", {}))
             args = body["params"]["arguments"]
 

trialpath/tests/test_medgemma.py

@@ -160,9 +160,13 @@ class TestMedGemmaHFEndpoint:
         """evaluate_medical_criterion should return decision dict."""
         decision_data = {
             "decision": "met",
-            "reasoning": "Patient has EGFR exon 19 del",
+            "reasoning": "Patient has EGFR exon 19 del per biomarkers",
             "confidence": 0.95,
         }
+        patient_profile = {
+            "diagnosis": {"primary_condition": "NSCLC", "stage": "IIIA"},
+            "biomarkers": [{"name": "EGFR", "result": "exon 19 del"}],
+        }
         mock_choice = MagicMock()
         mock_choice.message.content = json.dumps(decision_data)
         mock_response = MagicMock()
@@ -171,10 +175,19 @@ class TestMedGemmaHFEndpoint:
         with patch("trialpath.services.medgemma_extractor.InferenceClient") as MockClient:
             MockClient.return_value.chat_completion.return_value = mock_response
             extractor = MedGemmaExtractor(endpoint_url="http://test", hf_token="tok")
-            result = await extractor.evaluate_medical_criterion("EGFR mutation positive", {}, [])
+            result = await extractor.evaluate_medical_criterion(
+                "EGFR mutation positive", patient_profile, []
+            )
 
             assert result["decision"] == "met"
             assert result["confidence"] == 0.95
+            # Verify patient profile was included in the prompt
+            call_args = MockClient.return_value.chat_completion.call_args
+            user_content = call_args[1]["messages"][1]["content"]
+            prompt_text = user_content[0]["text"]
+            assert "Patient Profile" in prompt_text
+            assert "EGFR" in prompt_text
+            assert "exon 19 del" in prompt_text
 
     @pytest.mark.asyncio
     async def test_retry_on_cold_start(self):