fix(web): stop presenting an unscored case as a failed analysis, and four smaller things

From clicking through the redesigned UI:

- scoring a case without a model registry painted a red failure across a case that had in
  fact analysed fine. It is now a quiet note saying the model term contributes 0, because
  scoring is an optional fourth of the rank, not the analysis.
- the MLflow default moves to port 5001. On macOS, AirPlay Receiver owns 5000, which is why
  the registry answered "403" rather than refusing the connection; docker-compose publishes
  5001 to match.
- a funnel step that kept nothing drew a visible bar. Zero now draws zero.
- "1 candidates".
- the funnel's fixed grid columns forced a horizontal scrollbar on the report.

The report also lists the top undecided candidates now: the first thing anyone opens has no
decisions in it, and "Shortlisted (0)" alone said nothing about what the tool found.

Tests: api 77, web 32; ruff, mypy, svelte-check clean.

api/app/config.py

@@ -10,7 +10,8 @@ class Settings(BaseSettings):
     model_config = SettingsConfigDict(env_file=".env", extra="ignore")
 
     database_url: str = "postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens"
-    mlflow_tracking_uri: str = "http://localhost:5000"
+    # docker-compose publishes MLflow on 5001; macOS AirPlay Receiver owns 5000.
+    mlflow_tracking_uri: str = "http://localhost:5001"
     model_name: str = "rarelens-pathogenicity"
     # Registry alias set by `rarelens_ml.train --register` (stages are deprecated in MLflow 3).
     model_alias: str = "production"

api/app/routers/cases.py

@@ -36,6 +36,8 @@ from app.services.scoring import score_job
 logger = logging.getLogger(__name__)
 router = APIRouter()
 
+REPORT_TOP = 5
+
 
 async def _case_or_404(session: SessionDep, case_id: uuid.UUID) -> Case:
     case = await case_view.get_case(session, case_id)
@@ -208,6 +210,11 @@ async def report(case_id: uuid.UUID, session: SessionDep) -> ReportOut:
         ]
 
     shortlisted, dismissed = decided(DecisionState.shortlisted), decided(DecisionState.dismissed)
+    top = [
+        CandidateOut.from_candidate(c, labels)
+        for c in view.candidates
+        if c.variant.decision is None
+    ][:REPORT_TOP]
     prediction = next((c.variant.prediction for c in view.candidates if c.variant.prediction), None)
     return ReportOut(
         case=_as_case_out(case, view.job, len(shortlisted)),
@@ -222,4 +229,5 @@ async def report(case_id: uuid.UUID, session: SessionDep) -> ReportOut:
         ),
         shortlisted=shortlisted,
         dismissed=dismissed,
+        top=top,
     )

api/app/schemas.py

@@ -170,6 +170,8 @@ class ReportOut(BaseModel):
     provenance: ProvenanceOut
     shortlisted: list[CandidateOut]
     dismissed: list[CandidateOut]
+    # What a reviewer would look at next; a report with no decisions yet still says something.
+    top: list[CandidateOut]
 
 
 class ScoreOut(BaseModel):

api/tests/test_cases.py

@@ -113,6 +113,30 @@ async def test_the_report_is_the_decision_trail(client: AsyncClient) -> None:
     assert report["provenance"]["vep_version"] == "113.0"
 
 
+@pytest.mark.usefixtures("db")
+async def test_the_report_shows_the_top_candidates_before_anyone_decides(
+    client: AsyncClient,
+) -> None:
+    """The first thing anyone opens is a report with no decisions in it; it must still say something."""
+    case_id, _ = await a_case_with_candidates()
+
+    report = (await client.get(f"/api/cases/{case_id}/report")).json()
+    assert report["shortlisted"] == []
+    assert [c["variant"]["gene"] for c in report["top"]] == ["NF2", "CHEK2"]
+
+
+@pytest.mark.usefixtures("db")
+async def test_the_report_drops_decided_variants_from_the_top_list(client: AsyncClient) -> None:
+    case_id, _ = await a_case_with_candidates()
+    items = (await client.get(f"/api/cases/{case_id}/candidates")).json()["items"]
+    await client.post(f"/api/variants/{items[0]['variant']['id']}/decision",
+                      json={"state": "shortlisted", "reason": "fits"})
+
+    report = (await client.get(f"/api/cases/{case_id}/report")).json()
+    assert [c["variant"]["gene"] for c in report["shortlisted"]] == ["NF2"]
+    assert [c["variant"]["gene"] for c in report["top"]] == ["CHEK2"]
+
+
 @pytest.mark.usefixtures("db")
 async def test_candidates_can_still_be_filtered(client: AsyncClient) -> None:
     case_id, _ = await a_case_with_candidates()