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Merged
alisman merged 1 commit into from
Oct 23, 2026
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Snapshots for the 19 view kinds and options #59 added, in four parallel shards #63

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8 changes: 5 additions & 3 deletions CLAUDE.md
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Expand Up @@ -695,13 +695,15 @@ they can't tell you:
`check:splitby-perf`) are stages of `scripts/gate.sh` of their own, and the boundary suite is in
`npm test`.
`npm run report:coverage` — the unit suites' coverage (CI shows it on the reports job).
**Every view kind's output is pinned** by `test/view-snapshots.test.ts` (in `npm test`, no
**Every view kind's output is pinned** by the view snapshot tests (`test/view-snapshots*.test.ts`,
four parallel shards of `test/support/view-snapshots.ts`; in `npm test`, no
database): one gallery example per kind runs through the whole engine against warehouse answers
recorded in `test/snapshots/answers/`, and its compiled SQL and queries, computed result, figure
and results text are compared with `test/snapshots/<kind>.{sql,json,svg,txt}`. A diff there is a
change to review, not noise: `UPDATE_SNAPSHOTS=1` accepts output changes, and a changed query
needs `RECORD_SNAPSHOTS=1` with `.env.local` (public warehouse only; the answers hold public
studies' patient-level rows). A new view kind adds its case there. Each case also runs with its
needs `RECORD_SNAPSHOTS=1 node --env-file=.env.local --test test/view-snapshots*.test.ts`
(public warehouse only; the answers hold public studies' patient-level rows). A new view kind
adds its case to `CASES` there (a check fails until it does). Each case also runs with its
answers delivered in reverse, and must not change: a runner combines what it asked for after
every answer is in, in the view's order (`askEachSite` in `lib/views/shared.ts`), never inside
the callback as each one lands.
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3 changes: 2 additions & 1 deletion lib/ch.ts
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Expand Up @@ -231,7 +231,8 @@ export interface ChStatement { conn: ChConn; format: string; query: string; exte
/**
* Answers statements instead of the database, or watches them on their way to it (`send`, which
* takes extra ClickHouse settings for that statement, e.g. "max_threads=1"). Only
* test/view-snapshots.test.ts sets one: it records the warehouse's answers, then replays them.
* the view snapshot tests (test/support/view-snapshots.ts) set one: they record the warehouse's
* answers, then replay them.
*/
export type ChTransport = (st: ChStatement, send: (settings?: string) => Promise<string>) => Promise<string>;
let transport: ChTransport | null = null;
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2 changes: 1 addition & 1 deletion lib/views/shared.ts
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Expand Up @@ -73,7 +73,7 @@ export async function studyCatalogs(c: ViewRun, studies: string[]): Promise<Stud
* Asks every (cohort, study) the view draws that `resolvers` holds, concurrently, and returns the
* answers in the view's order (its cohorts, then each cohort's studies), never in the order they
* finish. Combine them after this returns: combining inside `ask` as each answer lands makes the
* result depend on which query finished first (test/view-snapshots.test.ts checks for that).
* result depend on which query finished first (test/support/view-snapshots.ts checks for that).
*/
export async function askEachSite<R, T>(ctx: ViewRun, resolvers: Record<string, R>,
ask: (cohort: string, study: string, r: R) => Promise<T>): Promise<{ cohort: string; study: string; answer: T }[]> {
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189 changes: 189 additions & 0 deletions test/snapshots/acquired.json
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@@ -0,0 +1,189 @@
{
"study": "lung_msk_pdx",
"cohorts": {
"all patients": {
"count": 172,
"text": "all patients in the study",
"studies": [
"lung_msk_pdx"
]
}
},
"views": [
{
"kind": "acquired",
"cohorts": [
"all patients"
],
"acquired": {
"anchoredTo": "Treatment [SUBTYPE=Systemic therapy]",
"preWindowDays": null,
"minGapDays": 30,
"sampleEvents": [
"Sample acquisition",
"Sequencing",
"Specimen"
],
"sampleKey": "SAMPLE_ID",
"measure": "driver",
"scan": {
"top": 12,
"minPost": 3
},
"panels": [
{
"cohort": "all patients",
"anchored": 142,
"dated": 142,
"withPre": 67,
"withPost": 107,
"patients": 33,
"preDays": 27,
"postDays": 279,
"gapDays": {
"q1": 154,
"median": 301,
"q3": 514
},
"genes": [
{
"gene": "CDKN2B",
"pairs": 33,
"shared": 2,
"lost": 1,
"acquired": 8,
"neither": 22,
"p": 0.03906250000000003,
"q": 0.5000000000000001
},
{
"gene": "MYC",
"pairs": 33,
"shared": 1,
"lost": 0,
"acquired": 4,
"neither": 28,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "CARD11",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 4,
"neither": 29,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "DNMT3B",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 4,
"neither": 29,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "NKX3-1",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 4,
"neither": 29,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "NTRK1",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 4,
"neither": 29,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "RAC1",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 4,
"neither": 29,
"p": 0.125,
"q": 0.5000000000000001
},
{
"gene": "KEAP1",
"pairs": 33,
"shared": 0,
"lost": 1,
"acquired": 5,
"neither": 27,
"p": 0.21875000000000017,
"q": 0.5000000000000001
},
{
"gene": "ETV1",
"pairs": 33,
"shared": 1,
"lost": 0,
"acquired": 3,
"neither": 29,
"p": 0.25000000000000006,
"q": 0.5000000000000001
},
{
"gene": "NKX2-1",
"pairs": 33,
"shared": 1,
"lost": 0,
"acquired": 3,
"neither": 29,
"p": 0.25000000000000006,
"q": 0.5000000000000001
},
{
"gene": "DDR2",
"pairs": 33,
"shared": 0,
"lost": 0,
"acquired": 3,
"neither": 30,
"p": 0.25000000000000006,
"q": 0.5000000000000001
},
{
"gene": "INHBA",
"pairs": 31,
"shared": 0,
"lost": 0,
"acquired": 3,
"neither": 28,
"p": 0.25000000000000006,
"q": 0.5000000000000001
}
],
"tested": 30
}
]
},
"participation": {
"studies": [
{
"study": "lung_msk_pdx",
"mode": "patient-level",
"instance": "primary",
"source": 0
}
],
"requiresPatientLevel": false,
"aggregateOnly": []
},
"caveat": "Patients with a sample dated on or before their first Treatment [SUBTYPE=Systemic therapy] and another at least 30 days after it; each side is one sample — the last before and the first after — dated by its first Sample acquisition/Sequencing/Specimen timeline event (attribute SAMPLE_ID). Funnel: all patients — 142 started, 67 with a sample before, 107 with one after, 33 patients with both (median 27 days before and 279 after; samples a median 301 days apart, IQR 154–514). Per gene, counting only patients whose before- AND after-sample panels both cover it: an OncoKB oncogenic alteration (v7.5) after but not before (acquired), before but not after (lost), on both (shared). The exact McNemar test asks whether acquired and lost differ; q is Benjamini–Hochberg across the genes tested in each cohort — every gene altered after treatment in at least 3 patients (all patients: 30 genes), the 12 smallest p drawn. These are few patients, and a second biopsy is clinically indicated — typically taken at progression — so they are a selected group, and \"acquired\" means seen after and not before, not caused by the treatment: a subclone the first biopsy missed, a different lesion, or a lower-purity sample under-calling one side reads the same. Which treatment ran between the samples beyond the anchor is not considered."
}
]
}
119 changes: 119 additions & 0 deletions test/snapshots/acquired.sql
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-- cohort all patients
-- lung_msk_pdx
SELECT DISTINCT replaceOne(patient_unique_id, 'lung_msk_pdx_', '') AS pid FROM snapshot_db.sample_derived
WHERE cancer_study_identifier = 'lung_msk_pdx'

-- view 0 acquired: acquired:funnel:all patients · lung_msk_pdx
WITH cohort AS (SELECT DISTINCT replaceOne(patient_unique_id, 'lung_msk_pdx_', '') AS pid FROM snapshot_db.sample_derived
WHERE cancer_study_identifier = 'lung_msk_pdx'),
anch AS (
SELECT p.stable_id AS pid, min(ce.start_date) AS day
FROM snapshot_db.clinical_event ce
JOIN snapshot_db.patient p ON p.internal_id = ce.patient_id
JOIN snapshot_db.cancer_study cs ON cs.cancer_study_id = p.cancer_study_id
WHERE cs.cancer_study_identifier = 'lung_msk_pdx' AND lowerUTF8(trimBoth(ce.event_type)) = lowerUTF8(trimBoth('Treatment'))
AND ce.clinical_event_id IN (SELECT clinical_event_id FROM snapshot_db.clinical_event_data WHERE lowerUTF8(trimBoth(key)) = lowerUTF8(trimBoth('SUBTYPE')) AND lowerUTF8(trimBoth(value)) = lowerUTF8(trimBoth('Systemic therapy')))
AND p.stable_id IN (SELECT pid FROM cohort)
GROUP BY pid
),
tl AS (
SELECT p.stable_id AS pid, d.value AS sample, min(ce.start_date) AS day
FROM snapshot_db.clinical_event ce
JOIN snapshot_db.patient p ON p.internal_id = ce.patient_id
JOIN snapshot_db.cancer_study cs ON cs.cancer_study_id = p.cancer_study_id
JOIN snapshot_db.clinical_event_data d ON d.clinical_event_id = ce.clinical_event_id AND lowerUTF8(trimBoth(d.key)) = lowerUTF8(trimBoth('SAMPLE_ID'))
WHERE cs.cancer_study_identifier = 'lung_msk_pdx' AND lowerUTF8(trimBoth(ce.event_type)) IN (lowerUTF8(trimBoth('Sample acquisition')), lowerUTF8(trimBoth('Sequencing')), lowerUTF8(trimBoth('Specimen')))
AND p.stable_id IN (SELECT pid FROM anch)
GROUP BY pid, sample
),
dated AS (
SELECT tl.pid AS pid, sd.sample_unique_id AS suid, tl.day - anch.day AS rel
FROM tl INNER JOIN anch ON anch.pid = tl.pid
INNER JOIN snapshot_db.sample_derived sd ON sd.cancer_study_identifier = 'lung_msk_pdx' AND sd.sample_stable_id = tl.sample AND sd.patient_stable_id = tl.pid
),
pick AS (
SELECT pid, countIf(rel <= 0) AS n_pre, countIf(rel >= 30) AS n_post,
argMaxIf(suid, (rel, suid), rel <= 0) AS pre, argMinIf(suid, (rel, suid), rel >= 30) AS post,
maxIf(rel, rel <= 0) AS pre_rel, minIf(rel, rel >= 30) AS post_rel
FROM dated GROUP BY pid
),
ps AS (
SELECT pre AS suid, pid, 'a' AS side FROM pick WHERE n_pre > 0 AND n_post > 0
UNION ALL SELECT post AS suid, pid, 'b' AS side FROM pick WHERE n_pre > 0 AND n_post > 0
)
SELECT (SELECT count() FROM anch) AS anchored, (SELECT uniqExact(pid) FROM tl) AS with_events, count() AS dated,
countIf(n_pre > 0) AS with_pre, countIf(n_post > 0) AS with_post, countIf(n_pre > 0 AND n_post > 0) AS paired,
quantileExactIf(0.5)(-pre_rel, n_pre > 0 AND n_post > 0) AS pre_median, quantileExactIf(0.5)(post_rel, n_pre > 0 AND n_post > 0) AS post_median,
quantileExactIf(0.25)(post_rel - pre_rel, n_pre > 0 AND n_post > 0) AS gap_q1, quantileExactIf(0.5)(post_rel - pre_rel, n_pre > 0 AND n_post > 0) AS gap_median,
quantileExactIf(0.75)(post_rel - pre_rel, n_pre > 0 AND n_post > 0) AS gap_q3
FROM pick

-- view 0 acquired: acquired:genes:all patients · lung_msk_pdx
WITH cohort AS (SELECT DISTINCT replaceOne(patient_unique_id, 'lung_msk_pdx_', '') AS pid FROM snapshot_db.sample_derived
WHERE cancer_study_identifier = 'lung_msk_pdx'),
anch AS (
SELECT p.stable_id AS pid, min(ce.start_date) AS day
FROM snapshot_db.clinical_event ce
JOIN snapshot_db.patient p ON p.internal_id = ce.patient_id
JOIN snapshot_db.cancer_study cs ON cs.cancer_study_id = p.cancer_study_id
WHERE cs.cancer_study_identifier = 'lung_msk_pdx' AND lowerUTF8(trimBoth(ce.event_type)) = lowerUTF8(trimBoth('Treatment'))
AND ce.clinical_event_id IN (SELECT clinical_event_id FROM snapshot_db.clinical_event_data WHERE lowerUTF8(trimBoth(key)) = lowerUTF8(trimBoth('SUBTYPE')) AND lowerUTF8(trimBoth(value)) = lowerUTF8(trimBoth('Systemic therapy')))
AND p.stable_id IN (SELECT pid FROM cohort)
GROUP BY pid
),
tl AS (
SELECT p.stable_id AS pid, d.value AS sample, min(ce.start_date) AS day
FROM snapshot_db.clinical_event ce
JOIN snapshot_db.patient p ON p.internal_id = ce.patient_id
JOIN snapshot_db.cancer_study cs ON cs.cancer_study_id = p.cancer_study_id
JOIN snapshot_db.clinical_event_data d ON d.clinical_event_id = ce.clinical_event_id AND lowerUTF8(trimBoth(d.key)) = lowerUTF8(trimBoth('SAMPLE_ID'))
WHERE cs.cancer_study_identifier = 'lung_msk_pdx' AND lowerUTF8(trimBoth(ce.event_type)) IN (lowerUTF8(trimBoth('Sample acquisition')), lowerUTF8(trimBoth('Sequencing')), lowerUTF8(trimBoth('Specimen')))
AND p.stable_id IN (SELECT pid FROM anch)
GROUP BY pid, sample
),
dated AS (
SELECT tl.pid AS pid, sd.sample_unique_id AS suid, tl.day - anch.day AS rel
FROM tl INNER JOIN anch ON anch.pid = tl.pid
INNER JOIN snapshot_db.sample_derived sd ON sd.cancer_study_identifier = 'lung_msk_pdx' AND sd.sample_stable_id = tl.sample AND sd.patient_stable_id = tl.pid
),
pick AS (
SELECT pid, countIf(rel <= 0) AS n_pre, countIf(rel >= 30) AS n_post,
argMaxIf(suid, (rel, suid), rel <= 0) AS pre, argMinIf(suid, (rel, suid), rel >= 30) AS post,
maxIf(rel, rel <= 0) AS pre_rel, minIf(rel, rel >= 30) AS post_rel
FROM dated GROUP BY pid
),
ps AS (
SELECT pre AS suid, pid, 'a' AS side FROM pick WHERE n_pre > 0 AND n_post > 0
UNION ALL SELECT post AS suid, pid, 'b' AS side FROM pick WHERE n_pre > 0 AND n_post > 0
),
alt AS (
SELECT g.hugo_gene_symbol AS gene, ps.pid AS pid, ps.side AS side, max(ann.is_driver) AS hit
FROM snapshot_db.genomic_event_derived g
LEFT JOIN oncokb_annotation.variant_annotation ann
ON ann.oncokb_version = 'v7.5' AND ann.is_driver
AND ann.hugo_gene_symbol = g.hugo_gene_symbol
AND ((g.variant_type = 'mutation' AND ann.alteration_type = 'MUTATION' AND ann.alteration = g.mutation_variant)
OR (g.variant_type = 'cna' AND ann.alteration_type = 'CNA' AND ann.alteration = if(g.cna_alteration >= 2, 'AMPLIFICATION', 'DELETION'))
OR (g.variant_type = 'structural_variant' AND ann.alteration_type = 'SV' AND ann.alteration = 'Fusion'))
INNER JOIN ps ON ps.suid = g.sample_unique_id
WHERE g.cancer_study_identifier = 'lung_msk_pdx' AND (g.variant_type != 'cna' OR abs(g.cna_alteration) >= 2)
AND g.sample_unique_id IN (SELECT suid FROM ps)
GROUP BY gene, pid, side
HAVING hit > 0
),
cov AS (
SELECT DISTINCT pg.gene AS gene, ps.pid AS pid, ps.side AS side
FROM snapshot_db.sample_to_gene_panel_derived sp
JOIN snapshot_db.gene_panel_to_gene_derived pg ON pg.gene_panel_id = sp.gene_panel_id AND pg.gene IN (SELECT DISTINCT gene FROM alt)
INNER JOIN ps ON ps.suid = sp.sample_unique_id
WHERE sp.cancer_study_identifier = 'lung_msk_pdx'
AND sp.alteration_type IN ('MUTATION_EXTENDED','COPY_NUMBER_ALTERATION','STRUCTURAL_VARIANT')
),
per AS (
SELECT gene, pid, max(side = 'a') AS pa, max(side = 'b') AS pb,
max(side = 'a' AND hit > 0) AS aa, max(side = 'b' AND hit > 0) AS ab
FROM (SELECT gene, pid, side, hit FROM alt UNION ALL SELECT gene, pid, side, 0 AS hit FROM cov)
GROUP BY gene, pid
)
SELECT gene, count() AS pairs, countIf(aa AND ab) AS both, countIf(aa AND NOT ab) AS a_only, countIf(ab AND NOT aa) AS b_only
FROM per WHERE pa AND pb GROUP BY gene HAVING both + a_only + b_only > 0
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