Kemal Yaylali
3ab404ebe5
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.
162 lines
7.3 KiB
Python
162 lines
7.3 KiB
Python
"""The triage workflow: a case with a phenotype, ranked candidates, decisions, a report."""
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import uuid
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import pytest
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from factories import seed_case
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from httpx import AsyncClient
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NF2_TERMS = [("HP:0000365", "Hearing impairment"), ("HP:0009592", "Vestibular schwannoma")]
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CASE_TERMS = [*NF2_TERMS, ("HP:0002321", "Vertigo")]
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async def a_case_with_candidates() -> tuple[uuid.UUID, uuid.UUID]:
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return await seed_case(
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phenotypes=CASE_TERMS,
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gene_terms={"NF2": NF2_TERMS},
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variants=[
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{"id": 1, "gene": "NF2", "pos": 1000, "impact": "HIGH", "score": 0.94,
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"clinvar_sig": "pathogenic"},
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{"id": 2, "gene": "CHEK2", "pos": 2000, "impact": "MODERATE", "gnomad_af": 0.0004,
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"score": 0.55},
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{"id": 3, "gene": "TTN", "pos": 3000, "impact": "MODIFIER", "gnomad_af": None},
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{"id": 4, "gene": "APOE", "pos": 4000, "impact": "HIGH", "gnomad_af": 0.3},
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],
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)
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@pytest.mark.usefixtures("db")
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async def test_a_case_keeps_its_phenotype(client: AsyncClient) -> None:
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body = {
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"name": "PROBAND-01",
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"vcf_uri": "gs://bucket/proband.vcf.gz",
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"phenotypes": [{"hpo_id": h, "label": lab} for h, lab in NF2_TERMS],
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}
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r = await client.post("/api/cases", json=body)
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assert r.status_code == 201, r.text
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assert [p["label"] for p in r.json()["phenotypes"]] == [lab for _, lab in NF2_TERMS]
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listed = (await client.get("/api/cases")).json()
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assert listed[0]["name"] == "PROBAND-01"
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assert listed[0]["shortlisted"] == 0
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@pytest.mark.usefixtures("db")
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async def test_the_funnel_shows_the_narrowing(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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page = (await client.get(f"/api/cases/{case_id}/candidates")).json()
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# 4 variants -> 3 rare -> 2 rare and coding -> 1 of those in a phenotype-matched gene
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assert page["funnel"] == {"total": 4, "rare": 3, "candidates": 2, "phenotype_matched": 1}
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@pytest.mark.usefixtures("db")
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async def test_the_phenotype_matched_variant_ranks_first_with_its_reasons(
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client: AsyncClient,
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) -> None:
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case_id, _ = await a_case_with_candidates()
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page = (await client.get(f"/api/cases/{case_id}/candidates")).json()
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assert [c["variant"]["gene"] for c in page["items"]] == ["NF2", "CHEK2"]
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top = page["items"][0]
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assert [t["label"] for t in top["matched_terms"]] == ["Hearing impairment", "Vestibular schwannoma"]
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assert top["components"]["phenotype"] == pytest.approx(2 / 3, abs=1e-4)
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assert top["components"]["rarity"] == 1.0
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assert page["weights"]["phenotype"] == 0.35
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# ClinVar is evidence, not an input to the rank.
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assert top["variant"]["clinvar_sig"] == "pathogenic"
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@pytest.mark.usefixtures("db")
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async def test_a_reviewer_decides_and_the_decision_sticks(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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variant_id = (await client.get(f"/api/cases/{case_id}/candidates")).json()["items"][0]["variant"]["id"]
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r = await client.post(
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f"/api/variants/{variant_id}/decision",
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json={"state": "shortlisted", "reason": "fits the phenotype", "note": "confirm by Sanger"},
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)
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assert r.status_code == 200, r.text
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# Changing your mind replaces the decision rather than failing.
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r = await client.post(f"/api/variants/{variant_id}/decision", json={"state": "dismissed"})
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assert r.status_code == 200
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detail = (await client.get(f"/api/variants/{variant_id}")).json()
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assert detail["decision"]["state"] == "dismissed"
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assert (await client.get("/api/cases")).json()[0]["shortlisted"] == 0
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@pytest.mark.usefixtures("db")
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async def test_the_variant_panel_carries_the_evidence(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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variant_id = (await client.get(f"/api/cases/{case_id}/candidates")).json()["items"][0]["variant"]["id"]
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detail = (await client.get(f"/api/variants/{variant_id}")).json()
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assert detail["variant"]["hgvsp"] is None or isinstance(detail["variant"]["hgvsp"], str)
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assert detail["score"] > 0
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assert [t["hpo_id"] for t in detail["matched_terms"]] == [h for h, _ in NF2_TERMS]
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assert "annotations" in detail
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@pytest.mark.usefixtures("db")
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async def test_the_report_is_the_decision_trail(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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items = (await client.get(f"/api/cases/{case_id}/candidates")).json()["items"]
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await client.post(f"/api/variants/{items[0]['variant']['id']}/decision",
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json={"state": "shortlisted", "reason": "fits the phenotype"})
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await client.post(f"/api/variants/{items[1]['variant']['id']}/decision",
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json={"state": "dismissed", "reason": "gene unrelated to phenotype"})
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report = (await client.get(f"/api/cases/{case_id}/report")).json()
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assert report["funnel"]["candidates"] == 2
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assert [v["variant"]["gene"] for v in report["shortlisted"]] == ["NF2"]
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assert report["shortlisted"][0]["decision"]["reason"] == "fits the phenotype"
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assert [v["variant"]["gene"] for v in report["dismissed"]] == ["CHEK2"]
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assert report["provenance"]["vep_version"] == "113.0"
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@pytest.mark.usefixtures("db")
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async def test_the_report_shows_the_top_candidates_before_anyone_decides(
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client: AsyncClient,
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) -> None:
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"""The first thing anyone opens is a report with no decisions in it; it must still say something."""
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case_id, _ = await a_case_with_candidates()
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report = (await client.get(f"/api/cases/{case_id}/report")).json()
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assert report["shortlisted"] == []
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assert [c["variant"]["gene"] for c in report["top"]] == ["NF2", "CHEK2"]
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@pytest.mark.usefixtures("db")
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async def test_the_report_drops_decided_variants_from_the_top_list(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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items = (await client.get(f"/api/cases/{case_id}/candidates")).json()["items"]
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await client.post(f"/api/variants/{items[0]['variant']['id']}/decision",
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json={"state": "shortlisted", "reason": "fits"})
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report = (await client.get(f"/api/cases/{case_id}/report")).json()
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assert [c["variant"]["gene"] for c in report["shortlisted"]] == ["NF2"]
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assert [c["variant"]["gene"] for c in report["top"]] == ["CHEK2"]
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@pytest.mark.usefixtures("db")
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async def test_candidates_can_still_be_filtered(client: AsyncClient) -> None:
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case_id, _ = await a_case_with_candidates()
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page = (await client.get(f"/api/cases/{case_id}/candidates", params={"gene": "chek2"})).json()
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assert [c["variant"]["gene"] for c in page["items"]] == ["CHEK2"]
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# The funnel still describes the whole case, not the filtered view.
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assert page["funnel"]["total"] == 4
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@pytest.mark.usefixtures("db")
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async def test_phenotype_search_backs_the_picker(client: AsyncClient) -> None:
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await seed_case(gene_terms={"NF2": NF2_TERMS}, variants=[])
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found = (await client.get("/api/phenotypes", params={"q": "vestibular"})).json()
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assert found == [{"hpo_id": "HP:0009592", "label": "Vestibular schwannoma"}]
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@pytest.mark.usefixtures("db")
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async def test_candidates_before_the_pipeline_has_run(client: AsyncClient) -> None:
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r = await client.post("/api/cases", json={"name": "empty", "vcf_uri": "gs://bucket/x.vcf.gz"})
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page = (await client.get(f"/api/cases/{r.json()['id']}/candidates")).json()
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assert page["items"] == []
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assert page["funnel"]["total"] == 0
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