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* Files named by an address: read by range where their format allows it, and
* fetched to disk where it does not.
*
* ## By range, as the app reads one
*
* The app reads an address a megabyte at a time through `RemoteRangeSource`,
* whose reads are synchronous because HDF5's are. A browser worker has a
* synchronous request and Node does not, so for a long time the command fetched
* every address whole first — seven gigabytes of `.mcool` to read one rung of
* it. It has one now (`cli/syncFetch.ts`), and so a map — a cooler, an
* `.mcool`, a `.hic`, an `.scool`, a `.pairs` — and a bigWig, a `.2bit` or an
* indexed FASTA are read where they are, by the same source and the same
* coalescing and read-ahead the app reads them with ({@link Downloads.ranged},
* {@link Downloads.where}). Nothing is written to disk for them.
*
* A host that will not serve a range — that answers `200` with the whole object,
* or compresses what it sends — is said so on stderr, and the file is fetched
* whole instead, as it always was: the command works on the hosts it worked on.
*
* ## Whole, for what is read whole anyway
*
* A feature file, a bedGraph, a HiC-Pro matrix, a workspace: every one is parsed
* from all of its bytes, so there is nothing a range would save, and the copy
* is what the roads that read a name — a HiC-Pro matrix's bin file beside it —
* read. These are fetched to disk ({@link Downloads.local}).
*
* ## Three decisions about a copy
*
* - **Streamed to disk, never held.** A 4DN `.mcool` is seven gigabytes, and a
* download that passes through memory is a download that ends the process.
* Each chunk is written as it arrives, and the progress goes to stderr unless
* `--quiet` says otherwise, because a command that sits silent for twenty
* minutes reads as a hang.
* - **The copy keeps its name.** Several roads read a name rather than bytes —
* a HiC-Pro matrix is one by its `.matrix`, a FASTA is read by range where
* `<name>.fai` lies beside it, a feature file's sniffers look at its
* extension — so the copy is `<slot>/<name>`, one slot per address so that two
* addresses ending in the same name cannot meet, and the sidecar each of those
* formats reads beside itself is fetched beside it wherever the server has one.
* - **Gone when the command ends.** One directory per command, under the
* system's temporary directory (`$TMPDIR`), removed on success, on failure and
* on Ctrl-C. A batch lets each map go once its run is done, so a command over
* two hundred addresses holds one map at a time rather than two hundred; what
* every run reads — a `--sequence`, a `--tracks`, an `--against` — is kept to
* the end.
*
* Only `http` and `https`. An `s3://` address needs credentials this command
* has not got, and any other scheme is refused by name rather than handed to
* `stat` as a path.
*/
import { existsSync, rmSync } from 'node:fs'
import { mkdir, mkdtemp, open, readFile, rm } from 'node:fs/promises'
import { tmpdir } from 'node:os'
import { basename, dirname, join } from 'node:path'
import type {
BufferEncoding,
FilehandleOptions,
GenericFilehandle,
Stats,
} from 'generic-filehandle2'
import { FASTA_NAME, hicProBinsNames, isHicProMatrix } from '../annotations/sidecar'
import { ViewerError } from '../errors'
import { RemoteRangeSource } from '../sources/RemoteRangeSource'
import { closeSyncFetch, identityFetch, nodeSyncFetch } from './syncFetch'
/** Whether a string the reader typed is an address this command fetches. */
export function isAddress(text: string): boolean {
return /^https?:\/\//i.test(text.trim())
}
/** The scheme of an address this command does not fetch — `s3`, `gs`, `file` — or `null`. */
function otherScheme(text: string): string | null {
if (isAddress(text)) return null
return /^([a-z][a-z0-9+.-]*):\/\//i.exec(text.trim())?.[1] ?? null
}
/** The file half of `file::group`, as `parseUri` splits it, without its refusal of an empty one. */
function fileHalf(text: string): string {
const sep = text.indexOf('::')
return (sep < 0 ? text : text.slice(0, sep)).trim()
}
/**
* What a file is called, whether a path or an address names it: the `::` group,
* an address's query and its percent-encoding taken off.
*
* `basename` of an address keeps the query — a presigned link's
* `sample.mcool?X-Amz-Signature=…` — and a name made of that is no name. So an
* address is read as one, and its last segment decoded. What decoding can put
* back that a file name must not hold — a `/`, a `\`, a control character — is
* replaced, because the name becomes a path under `--out` and under the
* download directory, and `%2F..%2F` must walk out of neither.
*/
export function fileNameOf(text: string): string {
const file = fileHalf(text)
if (!isAddress(file)) return basename(file)
let last: string
try {
last = new URL(file).pathname.split('/').filter((part) => part !== '').pop() ?? ''
} catch {
return 'download'
}
let name = last
try {
name = decodeURIComponent(last)
} catch {
// A `%` that begins no escape: the segment as it was written is the better name.
}
const safe = [...name].map((char) => (char === '/' || char === '\\' || char < ' ' ? '_' : char)).join('')
return safe === '' || safe === '.' || safe === '..' ? 'download' : safe
}
/**
* The directories an address's file sits in, nearest first, then its host —
* what the outputs of two addresses ending in one name are told apart by.
* Empty for a path, whose directories are the filesystem's to say.
*/
export function addressDirectories(text: string): string[] {
const file = fileHalf(text)
if (!isAddress(file)) return []
try {
const url = new URL(file)
const parts = url.pathname.split('/').filter((part) => part !== '').slice(0, -1)
return [...parts.reverse(), url.host].map((part) => {
try {
return decodeURIComponent(part)
} catch {
return part
}
})
} catch {
return []
}
}
/**
* The sidecars a format reads beside itself, by the names a server would serve
* them under: a FASTA's `samtools faidx` index, without which a genome past
* 2 GiB cannot be read at all (`cli/reference.ts`), and the bin file a HiC-Pro
* matrix has no coordinates without (§3.9).
*/
function companionsOf(name: string): string[] {
if (FASTA_NAME.test(name)) return [`${name}.fai`]
if (isHicProMatrix(name)) return hicProBinsNames(name)
return []
}
/** `7.0 GB`, `512.0 MB`, `40 kB` — decimal, as `cli/reference.ts` writes a size. */
export function sizeText(bytes: number): string {
if (bytes >= 1e9) return `${(bytes / 1e9).toFixed(1)} GB`
if (bytes >= 1e6) return `${(bytes / 1e6).toFixed(1)} MB`
if (bytes >= 1e3) return `${Math.round(bytes / 1e3)} kB`
return `${bytes} B`
}
/**
* An address as a sentence about it names it: without its query, which on a
* presigned link is the signature, and has no business in a log.
*/
function shownOf(address: string): string {
try {
const url = new URL(address)
return `${url.origin}${url.pathname}${url.search === '' ? '' : '?…'}`
} catch {
return address
}
}
/**
* What stderr calls a file named on the line: a path as it was typed, and an
* address as {@link shownOf} has it, its `::` group kept.
*/
export function displayOf(typed: string): string {
if (!isAddress(typed)) return typed
const sep = typed.indexOf('::')
return sep < 0 ? shownOf(typed.trim()) : `${shownOf(fileHalf(typed))}${typed.slice(sep).trim()}`
}
/** What `fetch` threw, with the cause it hides: `fetch failed` names nothing. */
function reasonOf(error: unknown): string {
if (!(error instanceof Error)) return String(error)
const cause = (error as { cause?: unknown }).cause
return cause instanceof Error && cause.message !== ''
? `${error.message} (${cause.message})`
: error.message
}
/**
* Whether a refusal to open an address by range says the host *has* the file
* and will not serve it in pieces — a `200` with the whole object, or a body
* compressed in transit — which a whole download answers. A `404` or a `403`
* to the range probe a signed link is opened with is not that: it is the
* address's answer, and fetching it whole would only get it again.
*/
function servedWhole(error: unknown): error is ViewerError {
if (!(error instanceof ViewerError)) return false
if (error.code === 'remote-compressed') return true
if (error.code !== 'remote-no-ranges') return false
const status = (error.detail as { status?: unknown }).status
return typeof status !== 'number' || (status >= 200 && status < 300)
}
/**
* What opening an address by range was refused with, as this command says it.
*
* `RemoteRangeSource` speaks to a page — a bucket's CORS, *connect a bucket…*
* — and names the address whole, signature and all. A shell's
* sentence names the status, or the cause of a request that got no answer, and
* the address as {@link shownOf} has it.
*/
function refusalOf(address: string, error: unknown): string {
const shown = shownOf(address)
if (error instanceof ViewerError) {
const detail = error.detail as { status?: unknown; cause?: unknown }
if (typeof detail.status === 'number') return `${shown} answered ${detail.status}.`
if (typeof detail.cause === 'string') return `${shown} could not be fetched: ${detail.cause}.`
}
const message = error instanceof Error ? reasonOf(error) : String(error)
return `${shown}: ${message.split(address).join(shown)}`
}
/** How a {@link Downloads} fetches, and whether it says so. */
export interface DownloadOptions {
/** Nothing on stderr: the command's own `--quiet`. */
quiet: boolean
/** The `fetch` to fetch with — the global one, unless a test hands another. */
fetch?: typeof fetch
}
interface Held {
/** The copy on disk, once it is there. */
readonly at: Promise<string>
/** Kept to the end of the command, rather than let go after one run. */
keep: boolean
}
/**
* Where a file's bytes are read from: a path on this machine — the file the
* reader named, or the copy of an address fetched whole — or a source reading
* an address by range.
*/
export type Where = { kind: 'disk'; path: string } | { kind: 'range'; source: RemoteRangeSource }
/**
* What a range source keeps of a track or a reference, rather than a map's
* 64 MiB: a run over two hundred bigWigs holds two hundred of them, and a track
* is read a few blocks at a time.
*/
export const SIDE_CACHE_BYTES = 8 << 20
/** A sidecar's address beside its file's: the same directory, the query left off. */
export function besideAddress(address: string, name: string): string {
return new URL(encodeURIComponent(name), fileHalf(address)).href
}
/** Every byte of a file, wherever it is: one exact request for a ranged address. */
export async function wholeBytes(where: Where): Promise<Uint8Array> {
if (where.kind === 'disk') return new Uint8Array(await readFile(where.path))
const { source } = where
return source.readExact === undefined ? source.readBytes(0, source.size) : source.readExact(0, source.size)
}
/**
* A ranged source as the filehandle `@gmod/bbi` and the `.2bit` reader take:
* each read through the source's cache, coalescing and read-ahead — the reads
* the annotations worker makes of a bigWig at an address.
*/
export class SourceHandle implements GenericFilehandle {
constructor(private readonly source: RemoteRangeSource) {}
async read(length: number, position = 0): Promise<Uint8Array<ArrayBuffer>> {
return this.source.readBytes(position, length) as Uint8Array<ArrayBuffer>
}
readFile(options?: Omit<FilehandleOptions, 'encoding'>): Promise<Uint8Array<ArrayBuffer>>
readFile(
options: BufferEncoding | (Omit<FilehandleOptions, 'encoding'> & { encoding: BufferEncoding }),
): Promise<string>
async readFile(options?: BufferEncoding | FilehandleOptions): Promise<Uint8Array<ArrayBuffer> | string> {
const bytes = (await wholeBytes({ kind: 'range', source: this.source })) as Uint8Array<ArrayBuffer>
// Text as UTF-8, whichever spelling asked: nothing here reads another.
const encoding = typeof options === 'string' ? options : options?.encoding
return encoding === undefined ? bytes : new TextDecoder().decode(bytes)
}
async stat(): Promise<Stats> {
return { size: this.source.size } as Stats
}
async close(): Promise<void> {
this.source.close()
}
}
/**
* Every address one command fetched, and the directory they are in.
*
* One per command, closed by `main` whatever way the command ended. An address
* is fetched once however often it is named — `x.mcool::/resolutions/1000` and
* `x.mcool::/resolutions/5000` are one file — and a path is left alone.
*/
export class Downloads {
private made: Promise<string> | null = null
private root: string | null = null
private slots = 0
private readonly held = new Map<string, Held>()
/** Addresses whose host would not serve a range, said once and fetched whole from then on. */
private readonly whole = new Set<string>()
constructor(private readonly options: DownloadOptions) {}
/**
* A source reading `typed`'s address by range — a new one each call, each
* the caller's to close — or `null` where its host will not serve a range,
* which is said on stderr the first time and is the caller's cue to fetch it
* whole with {@link local}.
*
* Every other refusal is a sentence about the address, its query left off:
* a `404`, a host that cannot be reached.
*/
async ranged(typed: string, maxCacheBytes?: number): Promise<RemoteRangeSource | null> {
this.refuseScheme(typed)
const address = fileHalf(typed)
if (!isAddress(address)) throw new Error(`${address} is not an address.`)
if (this.whole.has(address)) return null
const doFetch = this.options.fetch ?? identityFetch
// What a request that got no answer was refused with — `ECONNREFUSED`, a
// name that does not resolve — which the source's own refusal folds into
// `fetch failed`.
let unanswered: string | null = null
try {
return await RemoteRangeSource.open(address, {
fetchImpl: (input, init) =>
doFetch(input, init).catch((error: unknown) => {
unanswered ??= reasonOf(error)
throw error
}),
syncFetch: nodeSyncFetch,
...(maxCacheBytes === undefined ? {} : { maxCacheBytes }),
})
} catch (error) {
if (unanswered !== null) throw new Error(`${shownOf(address)} could not be fetched: ${unanswered}.`)
if (servedWhole(error)) {
this.whole.add(address)
if (!this.options.quiet) {
process.stderr.write(
` ${shownOf(address)} is not served by range ` +
`(${error.code === 'remote-compressed' ? 'it is compressed in transit' : 'it ignores Range'}); ` +
'fetching it whole\n',
)
}
return null
}
throw new Error(refusalOf(address, error))
}
}
/**
* Where `typed`'s bytes are read from: the path itself, an address by range,
* or — where its host serves no range — the copy {@link local} fetched.
*/
async where(typed: string, keep: boolean, maxCacheBytes?: number): Promise<Where> {
this.refuseScheme(typed)
const file = fileHalf(typed)
if (!isAddress(file)) return { kind: 'disk', path: file }
const source = await this.ranged(file, maxCacheBytes)
if (source !== null) return { kind: 'range', source }
return { kind: 'disk', path: (await this.local(file, keep)) ?? file }
}
/**
* A sidecar's text beside the file `typed` names — a FASTA's `.fai` — or
* `null` where there is none. An address's is fetched beside it, and a
* missing one is no error: its format reads the file without it.
*/
async sidecarText(typed: string, name: string): Promise<string | null> {
const file = fileHalf(typed)
if (!isAddress(file)) {
const path = join(dirname(file), name)
return existsSync(path) ? readFile(path, 'utf8') : null
}
try {
const response = await (this.options.fetch ?? identityFetch)(besideAddress(file, name))
if (!response.ok) {
await response.body?.cancel().catch(() => undefined)
return null
}
return await response.text()
} catch {
return null
}
}
/**
* A sidecar beside an address as a ranged source — a `.pairs` file's `.px2`
* — or `null` where there is none to range over. Quietly: an index that is
* not there is an index the reader did not make, and the file is read
* without it.
*/
async sidecarRanged(typed: string, name: string): Promise<RemoteRangeSource | null> {
try {
return await RemoteRangeSource.open(besideAddress(typed, name), {
fetchImpl: this.options.fetch ?? identityFetch,
syncFetch: nodeSyncFetch,
})
} catch {
return null
}
}
/**
* Make sure a map every run reads can be had, before the first run: a range
* opened and let go, or the copy fetched where it is read whole — a HiC-Pro
* matrix, or a host that serves no range. A path is the filesystem's to say.
*/
async reach(typed: string, keep: boolean): Promise<void> {
this.refuseScheme(typed)
const file = fileHalf(typed)
if (!isAddress(file)) return
if (!isHicProMatrix(fileNameOf(file))) {
const source = await this.ranged(file)
if (source !== null) {
source.close()
return
}
}
await this.local(file, keep)
}
/** Refuse a scheme this command does not fetch, by name, rather than `stat` it as a path. */
refuseScheme(typed: string): void {
const scheme = otherScheme(typed)
if (scheme !== null) {
throw new Error(
`${fileHalf(typed)}: this command fetches http and https addresses, and ${scheme}:// is ` +
'neither. Copy the file to disk and name the copy.',
)
}
}
/**
* Where the bytes of the file `typed` names are on this machine: `undefined`
* for a path, which is read where it lies, and the copy for an address.
*
* `keep` is for what every run of the command reads. A map named as a
* positional is fetched without it and let go by {@link release} once its
* run is done, so a batch holds one at a time.
*/
async local(typed: string, keep: boolean): Promise<string | undefined> {
this.refuseScheme(typed)
if (!isAddress(typed)) return undefined
const address = fileHalf(typed)
const held = this.held.get(address)
if (held !== undefined) {
held.keep ||= keep
return held.at
}
const at = this.fetchOne(address)
this.held.set(address, { at, keep })
try {
return await at
} catch (error) {
this.held.delete(address)
throw error
}
}
/** Let go of a copy one run read, unless something every run reads holds it too. */
async release(typed: string): Promise<void> {
if (!isAddress(typed)) return
const address = fileHalf(typed)
const held = this.held.get(address)
if (held === undefined || held.keep) return
this.held.delete(address)
const at = await held.at.catch(() => null)
if (at !== null) await rm(dirname(at), { recursive: true, force: true }).catch(() => undefined)
}
/** Remove every copy, and the directory they were in, and stop the request thread. Safe to call twice. */
async close(): Promise<void> {
await closeSyncFetch()
this.unwatch()
const root = this.root
this.root = null
this.made = null
this.held.clear()
if (root !== null) await rm(root, { recursive: true, force: true })
}
/** The command's directory, made on the first fetch and not before. */
private directory(): Promise<string> {
this.made ??= mkdtemp(join(tmpdir(), 'chromosomix-')).then((root) => {
this.root = root
process.once('SIGINT', this.interrupted)
process.once('SIGTERM', this.interrupted)
return root
})
return this.made
}
/**
* Ctrl-C in the middle of a seven-gigabyte download: the copies go, and then
* the signal does what it would have done had nothing been listening.
*/
private readonly interrupted = (signal: NodeJS.Signals): void => {
this.unwatch()
if (this.root !== null) rmSync(this.root, { recursive: true, force: true })
process.kill(process.pid, signal)
}
private unwatch(): void {
process.off('SIGINT', this.interrupted)
process.off('SIGTERM', this.interrupted)
}
private async fetchOne(address: string): Promise<string> {
this.slots += 1
const slot = join(await this.directory(), String(this.slots))
await mkdir(slot)
const name = fileNameOf(address)
const to = join(slot, name)
await this.fetchTo(address, to, name, !this.options.quiet)
for (const companion of companionsOf(name)) {
// Taken where the server has one, and nothing said where it has not: each
// is a sidecar its format looks for beside the file, and a format that
// cannot do without one says so in its own words.
await this.fetchTo(
new URL(encodeURIComponent(companion), address).href,
join(slot, companion),
companion,
false,
).catch(() => undefined)
}
return to
}
private async fetchTo(address: string, to: string, name: string, report: boolean): Promise<void> {
let response: Response
try {
// `identity`, so the bytes are the file's: a server that compressed the
// response on the way out would hand back a count its length does not
// match, and a `.gz` decompressed in transit is a file misnamed on disk.
response = await (this.options.fetch ?? fetch)(address, {
headers: { 'accept-encoding': 'identity' },
})
} catch (error) {
throw new Error(`${shownOf(address)} could not be fetched: ${reasonOf(error)}.`)
}
if (!response.ok || response.body === null) {
await response.body?.cancel().catch(() => undefined)
const status = `${response.status} ${response.statusText}`.trim()
throw new Error(`${shownOf(address)} answered ${status}.`)
}
const announced = Number(response.headers.get('content-length') ?? Number.NaN)
const total = Number.isFinite(announced) && announced > 0 ? announced : null
const encoded = (response.headers.get('content-encoding') ?? 'identity').toLowerCase() !== 'identity'
const shown = report ? progressOf(name, total) : null
const body = response.body
const handle = await open(to, 'w').catch(async (error: unknown) => {
await body.cancel().catch(() => undefined)
throw error
})
const reader = body.getReader()
let received = 0
try {
for (;;) {
const { done, value } = await reader.read()
if (done) break
await handle.write(value)
received += value.byteLength
shown?.step(received)
}
} catch (error) {
// A disk that filled is a stream still open, and a socket held for it.
await reader.cancel().catch(() => undefined)
await handle.close().catch(() => undefined)
await rm(to, { force: true })
if (shown !== null) process.stderr.write('\n')
throw new Error(`${shownOf(address)} stopped after ${sizeText(received)}: ${reasonOf(error)}.`)
}
await handle.close()
// A length is a promise about the bytes, and a copy that fell short of it
// is a map that fails later with a sentence about HDF5 rather than about
// the download. Not where the server compressed anyway: its length is then
// of the compressed body, and `fetch` has already undone the compression.
if (total !== null && !encoded && received !== total) {
await rm(to, { force: true })
if (shown !== null) process.stderr.write('\n')
throw new Error(
`${shownOf(address)} sent ${sizeText(received)} of the ${sizeText(total)} it announced.`,
)
}
shown?.done(received)
}
}
/**
* A download's line on stderr, redrawn in place.
*
* On a change of percent, or of 8 MB where the server named no length: a line
* per chunk is a terminal redrawn ten thousand times a gigabyte.
*/
function progressOf(
name: string,
total: number | null,
): { step(received: number): void; done(received: number): void } {
let shown = -1
return {
step: (received) => {
const mark = total === null ? Math.floor(received / 8e6) : Math.floor((received / total) * 100)
if (mark === shown) return
shown = mark
process.stderr.write(
total === null
? `\r downloading ${name}: ${sizeText(received)} `
: `\r downloading ${name}: ${mark}% of ${sizeText(total)} `,
)
},
done: (received) => {
process.stderr.write(`\r downloaded ${name}, ${sizeText(received)}${' '.repeat(12)}\n`)
},
}
}
|