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* The analysis worker — the thread a job runs on, and nothing else.
*
* It is the third thread of the arrangement `analysis/worker/protocol.ts`
* argues for: the reader worker answers the frames, the annotations worker
* answers the tracks, and this one takes the work that is measured in seconds
* and minutes, so that neither of the other two ever queues behind it (§18.3).
*
* Two things follow from that and are worth stating as properties rather than
* as intentions.
*
* **It is a second mount of the same file, not a second reader.** It opens the
* source for itself through the same `worker/sources.ts` the reader uses, so a
* dropped `File` costs nothing at all here and a remote object costs a second
* range cache. It answers no view request, holds no dense block and reports no
* byte statistics; everything it produces is a {@link TaskResult}.
*
* **It knows nothing about the task catalogue.** A `run` names a task id and
* this module looks it up in `analysis/run/index.ts` — the descriptors in
* `analysis/tasks/` are a main-thread concern (`analysis/job.ts` says why the
* split is load-bearing), and importing the registry here to read one number off
* a descriptor would drag the panel's half of the subtree into this bundle. The
* one place that costs anything is `provenance.taskVersion`, and it is paid for
* below.
*
* Like `worker/reader.worker.ts`, this module names `MetaCooler`; unlike it,
* nothing in `src/worker/` or `src/ui/` does, so the reader's claim to be the
* only such module *there* is untouched.
*/
import { yieldToEventLoop } from '../../async'
import { LOAD_REPORT_MS, startBusyProbe } from '../../perf/busy'
import { ViewerError } from '../../errors'
import { MetaCooler } from '../../metacooler/MetaCooler'
import type { ByteSource } from '../../types'
import { COMMIT, VERSION } from '../../version'
import { serialiseError } from '../../worker/protocol'
import { createDetachedSource, releaseSources } from '../../worker/sources'
import { openMap } from '../../worker/open'
import { correlationField, type CorrelationField } from '../compartments'
import { useCorrelationThreads } from '../pearsonThreads'
import { spawnGramWorker } from './spawnGram'
import { useLikelihoodThreads } from '../likelihoodThreads'
import { spawnLikelihoodWorker } from './spawnLikelihood'
import { adaptiveSmoothValues } from '../../render/smooth'
import { abortError, type JobContext } from '../job'
import { RUNNERS } from '../run/index'
import type { TaskResult } from '../types'
import {
analysisTransfers,
type ResampleTarget,
type AnalysisRequest,
type AnalysisResponse,
type AnalysisResultMap,
} from './protocol'
import type { SmoothedField } from '../../render/derive'
/**
* `lib` includes both DOM and WebWorker, so `self` is typed as a window here.
* One cast, at the top, rather than a cast per `postMessage`.
*/
const ctx = self as unknown as DedicatedWorkerGlobalScope
// The correlation matrix — the map's correlation and the compartment chain's —
// shares its bands with helper workers, one fewer than the cores, since this
// thread computes a stretch of its own (`pearsonThreads.ts`). Seven at most:
// past that the copies of the rows cost more than the cores give back.
const HELPERS = Math.max(0, Math.min(7, (typeof navigator === 'undefined' ? 1 : navigator.hardwareConcurrency || 1) - 1))
useCorrelationThreads(spawnGramWorker, HELPERS)
// pastis-NB's likelihood shares its bands the same way, as many helpers, and
// gives the same bits on any number of them (`likelihoodThreads.ts`).
useLikelihoodThreads(spawnLikelihoodWorker, HELPERS)
// The reader worker starts fetching h5wasm at module scope, while the user is
// still choosing a file, because it is certain to need it within the second.
// This worker deliberately does not, and the difference is not an oversight: it
// may never open anything at all. A reader who folds the Analysis panel open,
// reads the list of tasks and folds it again has just been charged a 4.8 MB
// async chunk — download, parse and instantiate — for a mount that was never
// made, which is the exact opposite of the lazy mount §18.3 promises. `getH5()`
// is reached from `MetaCooler.open` below, on the first task that needs a file,
// and memoises from there.
interface Session {
mc: MetaCooler
/**
* The mount's byte source, held for its lifetime.
*
* Not read by anything here — this worker publishes no statistics — but the
* handle `mc` closes is a lent view of it (`worker/sources.ts`), so the thing
* that actually owns the bytes has to be somewhere until `releaseSources`.
*/
source: ByteSource
}
let session: Session | null = null
const cancelled = new Set<number>()
function requireSession(): Session {
// Not an implicit mount: a `run` names a task and carries no uri and no
// source, so there is nothing here to open a file *from*. A run before an open
// is a fault in the main-thread runner's ordering, and says so.
if (session === null) throw new Error('no file is open in the analysis worker')
return session
}
function post(response: AnalysisResponse, transfers: Transferable[] = []): void {
ctx.postMessage(response, transfers)
}
// ---------------------------------------------------------------------------
// Handlers
// ---------------------------------------------------------------------------
async function handleOpen(
request: Extract<AnalysisRequest, { kind: 'open' }>,
): Promise<AnalysisResultMap['open']> {
session?.mc.close()
session = null
// A cancel that arrives after its target finished leaves its id behind, since
// the `finally` that would have removed it has already run. Harmless
// individually and unbounded over a session, so it is cleared with the file
// the ids belonged to.
cancelled.clear()
// Through `openMap`, not `MetaCooler.open`: a HiC-Pro pair is two text files
// and no HDF5 at all, and calling the HDF5 road directly reached h5wasm with a
// `.matrix` and failed inside it — `error - name not defined!` — for every
// task on a map that was on screen and perfectly fine (`worker/open.ts`).
const opened = await openMap(request.uri, request.source, {
report: (done, total, note) => post({ type: 'progress', id: request.id, done, total, note }),
cancelled: () => cancelled.has(request.id),
// Carried rather than re-asked: a contact list has no resolution of its own
// and the reader chose one when the *first* worker opened it (§3.7).
...(request.binning === undefined ? {} : { binning: request.binning }),
})
const source = opened.source
let mc = opened.mc
// Through the edit the reader's map is drawn through (§27.7), before anything
// reads it: a task on an edited map measures the edited assembly. Refused by
// name where it cannot be, rather than measuring the file as it was under a
// view that says otherwise.
if (request.edit !== undefined) {
const seen = MetaCooler.withLens(mc, request.edit)
if (seen.refusal !== null) {
mc.close()
throw new ViewerError('unsupported', seen.refusal)
}
mc = seen.map
}
// The cells the reader has ticked, not the file's whole set. A task measures
// what is on screen, and an scool with two cells selected draws two: opening
// the pseudo-bulk here would answer a question about four thousand cells with
// the same number every time and no way to tell (§3.8).
if (request.cells !== undefined && mc.cells.length > 0) mc.selectCells(request.cells)
// Drawn as the reader drew it, before any task reads it (§6.5). Awaited here,
// so a refusal fails the mount by name rather than every task after it.
if (request.resample !== undefined) await drawnAs(mc, request.resample, request.id)
// At the resolution the reader added, where the map is drawn at one (§3.4):
// last, so it sums the map as drawn — through the edit, at the total — as the
// reader's own read does.
if (request.coarsen !== undefined) {
try {
mc = atResolution(mc, request.coarsen)
} catch (error) {
mc.close()
throw error
}
}
session = { mc, source }
// Two numbers and no table. Everything else about the file is already on the
// main thread from the reader's own open, and answering with a second copy of
// it would be a second thing to keep in step; these two are here because
// `toBins` below is defined in terms of one of them and the caller has a right
// to check that the two mounts agree about the file.
return { nBins: mc.nBins, binsize: mc.binsize }
}
/**
* A map read at `binsize` (§3.4): its own bins summed, a whole number at a time,
* or the map itself where they are already that size. Refused by name rather
* than read at the nearest resolution it has — a task measured at another
* resolution than the one its framing names is the wrong number with the right
* label.
*/
function atResolution(mc: MetaCooler, binsize: number): MetaCooler {
if (binsize === mc.binsize) return mc
const factor = binsize / mc.binsize
if (!Number.isInteger(factor) || factor < 1) {
throw new ViewerError(
'unsupported',
`This map's bins are ${mc.binsize.toLocaleString('en-US')} bp, and ` +
`${binsize.toLocaleString('en-US')} bp is not a whole number of them, so it is not measured at that resolution.`,
)
}
const seen = MetaCooler.coarsened(mc, factor)
if (seen.refusal !== null) throw new ViewerError('unsupported', seen.refusal)
return seen.map
}
/**
* Draw a mount to the reader's total (§6.5), with the reader's census where it
* was handed one — the same pixels, without walking the file a second time.
*/
async function drawnAs(mc: MetaCooler, target: ResampleTarget, id: number): Promise<void> {
await mc.resample(
{
contacts: target.contacts,
...(target.seed === undefined ? {} : { seed: target.seed }),
...(target.alpha === undefined ? {} : { alpha: target.alpha }),
},
{
...(target.census === undefined ? {} : { census: target.census }),
onProgress: (done, total) => post({ type: 'progress', id, done, total, note: 'counting contacts' }),
cancelled: () => cancelled.has(id),
},
)
}
/**
* The version stamped on a result produced here.
*
* The descriptor that owns the real number lives in `analysis/registry.ts` on
* the main thread, and this worker does not import it (see the module docstring)
* — so the field is filled with a placeholder and **overwritten by the
* main-thread runner** as the result comes back, before anything stores it,
* draws it or writes it into an export. A result that reached a reader still
* carrying `0` would mean the runner skipped that step.
*/
const UNSTAMPED_TASK_VERSION = 0
/**
* The build that produced a number, for the `#` provenance line above it.
*
* `VERSION` alone on a build with no git behind it — a source tarball, or
* `vitest`, which applies none of the `define` block — rather than a trailing
* separator with nothing after it. Not `buildLine()`: that is composed for the
* about dialog and carries the commit date and the target as well, which is more
* than a provenance header needs and one more thing to diff when comparing two
* results.
*/
const APP = [VERSION, COMMIT].filter((part) => part !== '').join(' ')
async function handleRun(
request: Extract<AnalysisRequest, { kind: 'run' }>,
): Promise<TaskResult> {
const runner = RUNNERS[request.task]
if (runner === undefined) {
// Named, because the id is the only thing that distinguishes this from a
// registry that is simply empty — and a task offered by the panel and absent
// from `RUNNERS` is exactly the mismatch `test/unit/analysis-registry.test.ts`
// exists to catch before a reader ever clicks the row.
throw new Error(`no analysis runner is registered for the task ${request.task}`)
}
const { mc } = requireSession()
const id = request.id
const notes: string[] = []
const started = performance.now()
const job: JobContext = {
mc,
params: request.params,
framing: request.framing,
inputs: request.inputs,
cancelled: () => cancelled.has(id),
throwIfCancelled: () => {
if (cancelled.has(id)) throw abortError()
},
// The event loop first and the flag second, in that order: the whole point
// is to let the `cancel` message that is already queued be *delivered*, and
// reading the flag before yielding would read it exactly as stale as
// `throwIfCancelled` does. See `analysis/job.ts`.
breathe: async () => {
await yieldToEventLoop()
if (cancelled.has(id)) throw abortError()
},
progress: (done, total, note) => post({ type: 'progress', id, done, total, note }),
note: (text) => {
notes.push(text)
},
toBp: (bins) => bins * mc.binsize,
// At least one bin, because every caller of this is sizing a window, and a
// window of zero bins is a kernel that reads nothing and returns a clean
// number. A flank smaller than the bin size is a question this file cannot
// answer at the resolution asked for; the honest floor is the resolution it
// has.
toBins: (bp) => Math.max(1, Math.round(bp / mc.binsize)),
// A **second** mount inside this worker, for the length of one computation.
// Detached from the source cache the first one uses, because that cache
// holds one local and one remote mount and releasing the held one is how it
// makes room — which on the local road would close the file this very task
// is reading through (`worker/sources.ts`).
// Bytes rather than a container, for a file this application reads and does
// not mount — see `JobContext.openBytes`. Detached from the mount cache for
// the same reason `peer` is.
openBytes: async (url) => await createDetachedSource({ kind: 'remote', url }),
// And a file the form was handed rather than told the address of — a
// dropped `File`, or a picked row carrying what authorises it.
openSource: async (spec) => await createDetachedSource(spec),
peer: async (map) => {
const opened = await openMap(map.uri, map.source, {
report: (done, total, note) => post({ type: 'progress', id, done, total, note }),
cancelled: () => cancelled.has(id),
detached: true,
...(map.binning === undefined ? {} : { binning: map.binning }),
})
if (map.cells !== undefined && opened.mc.cells.length > 0) {
opened.mc.selectCells(map.cells)
}
if (map.resample !== undefined) {
try {
await drawnAs(opened.mc, map.resample, id)
} catch (error) {
opened.mc.close()
opened.source.close()
throw error
}
}
// At the resolution the map it is compared with is read at, where its own
// bins sum to it; where they do not, as it is — and the task, which
// compares bin sizes before it compares anything, says so (§3.4).
let mc = opened.mc
if (map.coarsen !== undefined) {
try {
mc = atResolution(opened.mc, map.coarsen)
} catch {
mc = opened.mc
}
}
return {
mc,
close: () => {
mc.close()
opened.source.close()
},
}
},
}
const outputs = await runner(job)
// A runner whose last loop finished just as the cancel landed would otherwise
// deliver a complete result to a reader who has already dismissed the drawer.
job.throwIfCancelled()
return {
outputs,
provenance: {
task: request.task,
taskVersion: UNSTAMPED_TASK_VERSION,
// The parameters and the framing as they arrived, not as the runner read
// them: provenance is a record of what was asked for, and a runner's
// fallback for a key an older session did not have is part of the answer
// rather than part of the question.
params: request.params,
framing: request.framing,
app: APP,
createdAt: new Date().toISOString(),
},
notes,
ms: performance.now() - started,
}
}
/**
* The correlation of a square the view handed over.
*
* The one handler that needs **no mount**, and the only one: everything it works
* on arrived in the message. So it deliberately does not call `requireSession`
* — a reader who turns the map's correlation toggle on should not thereby open a
* second HDF5 handle on their file, and would be very surprised to be told the
* worker had not been opened yet.
*
* Progress and cancellation come from the row hook `correlationMatrix` already
* takes for exactly this, and the yield is what makes the cancel real: a `cancel`
* message cannot be *delivered* to a thread that never returns to its event
* loop, so a check without a yield asks about a message that could not have
* arrived (`analysis/job.ts`). Every sixty-fourth row, which is the same batch
* size the task runner breathes on — the round trip is paid once a batch instead
* of `m` times.
*/
async function handleCorrelate(request: Extract<AnalysisRequest, { kind: 'correlate' }>): Promise<
CorrelationField
> {
const id = request.id
const total = request.n
const field = await correlationField(request.values, request.n, async (row) => {
if (row % CORRELATE_BATCH_ROWS !== 0) return
await yieldToEventLoop()
if (cancelled.has(id)) throw abortError()
post({ type: 'progress', id, done: row, total, note: 'correlating' })
})
// As `handleRun` does, and for its reason: a job whose last row finished just
// as the cancel landed would otherwise deliver a full square to a reader who
// has already switched the toggle off.
if (cancelled.has(id)) throw abortError()
return field
}
/**
* Rows between yields while correlating.
*
* The trade is the same one everywhere in this file: yielding per row turns an
* `m`-row job into `m` round trips through the event loop, and yielding never
* makes the cancel a lie. Sixty-four rows of a thousand-bin square is a few tens
* of milliseconds, which is the granularity a reader experiences as "it stopped
* when I asked".
*/
const CORRELATE_BATCH_ROWS = 64
/**
* The adaptive despeckle of one block.
*
* Synchronous, unlike the correlation beside it, and that is a deliberate
* difference rather than an omission. The filter's two passes are banded over
* rows and each band's tables are built and thrown away together; there is no
* consistent state to stop at partway through one, and threading a yield through
* both passes would buy a cancel that lands a few hundred milliseconds sooner on
* a job the reader is no longer waiting for anyway.
*
* What that costs is that a superseded job runs to completion instead of being
* cut short. It is bounded: the cancel is checked **before** the work as well as
* after, so a job cancelled while it sat in the queue never starts, and only the
* one already running is wasted.
*/
function handleSmooth(
request: Extract<AnalysisRequest, { kind: 'smooth' }>,
): SmoothedField {
if (cancelled.has(request.id)) throw abortError()
const smoothed = adaptiveSmoothValues(
{ nrows: request.nrows, ncols: request.ncols, values: request.values },
request.counts,
request.spec,
request.over ?? undefined,
)
// As `handleRun` does, and for its reason: a job whose last band finished just
// as the cancel landed would otherwise deliver a picture to a reader who has
// already moved the picker.
if (cancelled.has(request.id)) throw abortError()
return {
values: smoothed.values,
over: smoothed.over,
applied: smoothed.applied,
scope: smoothed.scope,
}
}
// ---------------------------------------------------------------------------
// Dispatch
// ---------------------------------------------------------------------------
async function dispatch(request: AnalysisRequest): Promise<unknown> {
switch (request.kind) {
case 'open':
return handleOpen(request)
case 'run':
return handleRun(request)
case 'correlate':
return handleCorrelate(request)
case 'smooth':
return handleSmooth(request)
case 'cancel':
cancelled.add(request.target)
return null
case 'close':
session?.mc.close()
session = null
cancelled.clear()
// The handle's `close` returns the *borrowed* source; this is what
// actually releases the mount and its chunk cache (`worker/sources.ts`).
releaseSources()
return null
}
}
async function handle(request: AnalysisRequest): Promise<void> {
try {
const payload = await dispatch(request)
post(
{ type: 'result', id: request.id, kind: request.kind, payload },
analysisTransfers(payload),
)
} catch (err) {
post({ type: 'error', id: request.id, error: serialiseError(err) })
} finally {
cancelled.delete(request.id)
}
}
ctx.onmessage = (event: MessageEvent<AnalysisRequest>): void => {
void handle(event.data)
}
// How busy this thread has been, once a second, unasked — the same probe the
// other two workers run. It matters most here: a job is the longest thing this
// tab does, and it is the one stretch during which a CPU figure taken from the
// main thread alone would read 0%.
const probe = startBusyProbe()
setInterval(() => post({ type: 'busy', fraction: probe.busy() }), LOAD_REPORT_MS)
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