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* A local file as a {@link ByteSource} — the private path (spec §11).
*
* Nothing here leaves the machine. A file dropped on the page is mounted into
* the Emscripten FS and opened from there; nothing is uploaded, which is what
* makes "no accounts, no storage, no GDPR review" a property of the code rather
* than a promise in the UI.
*
* Three inputs are supported because the same class has to serve a browser and
* the Node test suite:
*
* | input | mount |
* |---|---|
* | `File` / `Blob` in a worker | **lazy** FS node, slices read on demand |
* | `Uint8Array` / `ArrayBuffer` | bytes copied into the FS |
* | filesystem path (Node only) | used as-is |
*
* The path case costs nothing: `h5wasm/node` is built with NODERAWFS, so its
* `FS` *is* the real filesystem and HDF5 reads the file in place. That is why
* the 26 MB reference file can be opened in a unit test without a 26 MB copy.
*
* The `Blob` case now costs nothing either, and for the same reason: a
* `FileReaderSync` over `blob.slice()` behind a bounded LRU is exactly what
* `RemoteRangeSource` does with range requests, so a dropped file is read a
* slice at a time instead of entirely, twice, before the first byte is parsed.
* The fallback below it is for a runtime with no `FileReaderSync` — the main
* thread, and the Node tests, neither of which is where the app does I/O.
*/
import type { ByteSource, SourceStats } from '../types'
import { ViewerError } from '../errors'
import type { H5FSNode, H5Module } from '../h5/bootstrap'
import { getH5, isNodeRuntime } from '../h5/bootstrap'
/** Bytes per cached slice. Matches the remote source's, for the same reasons. */
const LOCAL_CHUNK_SIZE = 1 << 20
/** Upper bound on retained slice bytes; least-recently-used are dropped. */
const LOCAL_CACHE_BYTES = 64 << 20
/** Anything {@link LocalFileSource} knows how to mount. */
export type LocalFileInput = Blob | Uint8Array | ArrayBuffer | ArrayBufferView | string
/**
* A file already on disk, with its size resolved. Produced by
* {@link LocalFileSource.fromPath}; the constructor accepts it so that the
* path case shares one code path with the in-memory cases, without forcing
* every caller through an async factory.
*/
export interface LocalPathRef {
readonly path: string
readonly size: number
}
export interface LocalFileOptions {
/** Overrides the name used for the mount point and for `id`. */
name?: string
/**
* Directory the temporary copy is written to when the input is in-memory and
* we are running under Node. Defaults to `$TMPDIR` (then `/tmp`). Ignored in
* the browser, where MEMFS has no such notion.
*/
tempDir?: string
}
let counter = 0
export class LocalFileSource implements ByteSource {
readonly id: string
readonly size: number
/** Always: the bytes are on this machine, and seeking is free. */
readonly isRemote = false
private readonly bytes: Uint8Array | null
private readonly blob: Blob | null
private readonly existingPath: string | null
private readonly tempDir: string | undefined
private mountPath: string | null = null
private ownsMount = false
private requests = 0
private bytesRead = 0
/** Slice cache for the lazy mount; insertion-ordered, so first key is LRU. */
private readonly cache = new Map<number, Uint8Array>()
private cachedBytes = 0
private syncReader: FileReaderSync | null = null
/** Resolved at mount, so {@link readBytes} has an FS to read a path through. */
private module: H5Module | null = null
/**
* An exact read, for a dropped file only — see {@link readBlobExact}. A file
* held in memory, or read by path, is read exactly already, and a walk
* reads it the ordinary way.
*/
readonly readExact?: (position: number, length: number) => Promise<Uint8Array>
/**
* Wrap a `File`, a `Blob`, raw bytes, or a {@link LocalPathRef}.
*
* Synchronous, because `size` is knowable without I/O for every one of those
* — and a `ByteSource` must report its size before `mount()`. Bytes are not
* touched here: a `Blob` is only read when {@link mount} is called, so
* constructing one is free.
*
* A bare filesystem path is *not* accepted, because its size cannot be
* learnt synchronously; use {@link LocalFileSource.fromPath}.
*/
constructor(
input: Blob | Uint8Array | ArrayBuffer | ArrayBufferView | LocalPathRef,
options: LocalFileOptions = {},
) {
this.tempDir = options.tempDir
this.bytes = null
this.blob = null
this.existingPath = null
if (isBlob(input)) {
const named = typeof File !== 'undefined' && input instanceof File ? input.name : null
this.blob = input
this.size = input.size
this.id = options.name ?? named ?? `blob-${nextId()}`
this.readExact = (position, length) => this.readBlobExact(input, position, length)
return
}
if (isPathRef(input)) {
this.existingPath = input.path
this.size = input.size
this.id = options.name ?? input.path
return
}
const bytes = asUint8Array(input)
this.bytes = bytes
this.size = bytes.byteLength
this.id = options.name ?? `bytes-${nextId()}`
}
/**
* Wrap a file already on disk. Node only.
*
* Async because the size is read through h5wasm's `FS.stat` rather than
* `node:fs` — that keeps this module free of Node built-in imports, which is
* what lets it be bundled for the browser unchanged.
*/
static async fromPath(path: string, options: LocalFileOptions = {}): Promise<LocalFileSource> {
if (!isNodeRuntime()) {
throw new ViewerError(
'bad-uri',
`cannot open the filesystem path ${path} in a browser; pass the File object instead`,
{ path },
)
}
const h5 = await getH5()
let size: number
try {
size = h5.FS.stat(path).size
} catch (cause) {
throw new ViewerError(
'not-hdf5',
`cannot stat ${path}: ${cause instanceof Error ? cause.message : String(cause)}`,
{ path },
)
}
return new LocalFileSource({ path, size }, { name: options.name ?? path, ...options })
}
/** Dispatch on whatever the caller has. */
static async open(
input: LocalFileInput,
options: LocalFileOptions = {},
): Promise<LocalFileSource> {
if (typeof input === 'string') return LocalFileSource.fromPath(input, options)
return new LocalFileSource(input, options)
}
async mount(): Promise<string> {
if (this.mountPath !== null) return this.mountPath
const h5 = await getH5()
this.module = h5
if (this.existingPath !== null) {
// NODERAWFS: the file is already visible to HDF5 where it lies. No copy,
// no request, nothing to clean up.
this.mountPath = this.existingPath
this.ownsMount = false
return this.mountPath
}
// A `Blob` in a worker is read *lazily*, a slice at a time.
//
// Reading it whole put the file in memory twice — once as the ArrayBuffer
// and once as the MEMFS copy — before a single byte of HDF5 was parsed, so
// opening a 5 GB file to look at one 2 Mb region cost 5 GB of reading and up
// to 10 GB of heap, and a large enough file could not be opened at all. The
// remote path has never done that: it mounts an FS node whose `read` fetches
// on demand behind an LRU. `FileReaderSync` is the same shape for a local
// file — synchronous, worker-only, which is where all I/O already lives — so
// the two sources differ in their byte accessor and in nothing else, and a
// local file is now bounded by its *reads* rather than by its size.
if (this.blob !== null && typeof FileReaderSync !== 'undefined') {
this.mountPath = this.mountLazy(h5, this.blob)
this.ownsMount = true
return this.mountPath
}
const bytes = this.bytes ?? new Uint8Array(await (this.blob as Blob).arrayBuffer())
const target = this.mountTarget()
h5.FS.writeFile(target, bytes)
this.mountPath = target
this.ownsMount = true
this.requests += 1
this.bytesRead += bytes.byteLength
return target
}
/**
* Create the lazy FS node, mirroring `RemoteRangeSource.mount`.
*
* `usedBytes` has to be a getter over `contents.length` or MEMFS's `getattr`
* reports a zero-length file and HDF5 refuses to open it; `stream_ops` is
* copied rather than mutated because MEMFS shares one object across every file
* it created.
*/
private mountLazy(h5: H5Module, blob: Blob): string {
const leaf = this.mountTarget().replace(/^\//, '')
const node: H5FSNode = h5.FS.createFile('/', leaf, {}, true, false)
const contents = { length: this.size }
node.contents = contents
Object.defineProperty(node, 'usedBytes', { get: () => contents.length })
node.stream_ops = {
...node.stream_ops,
read: (
_stream: unknown,
buffer: Uint8Array,
offset: number,
length: number,
position: number,
): number => {
if (position >= this.size) return 0
const n = Math.min(this.size - position, length)
this.copyInto(blob, buffer, offset, position, n)
return n
},
mmap: (_stream: unknown, length: number, position: number): { ptr: number; allocated: boolean } => {
const ptr = h5.Module._malloc(length)
if (ptr === 0) throw new Error('mmap allocation failed')
const n = Math.max(0, Math.min(this.size - position, length))
if (n > 0) this.copyInto(blob, h5.Module.HEAPU8, ptr, position, n)
return { ptr, allocated: true }
},
}
return `/${leaf}`
}
/**
* Read `[position, position + length)`, whatever this source is backed by.
*
* The three cases are the three constructor inputs, and each takes the
* cheapest route it has: in-memory bytes are a `subarray` copy, a `Blob` goes
* through the same slice cache the lazy mount uses — so a `.hic`'s block
* index and the blocks beside it are paid for once — and a path is read
* through the Emscripten FS, which under NODERAWFS is a real bounded read.
*
* The path case needs {@link mount} to have been called, because that is
* where the module is resolved and there is nowhere in a synchronous method
* to await it. Every caller mounts first; the throw is for the one that
* forgets, and says so rather than returning zeroes.
*/
readBytes(position: number, length: number): Uint8Array {
const n = Math.max(0, Math.min(this.size - position, length))
if (n <= 0) return new Uint8Array(0)
if (this.bytes !== null) {
return this.bytes.subarray(position, position + n).slice()
}
if (this.blob !== null) {
const out = new Uint8Array(n)
this.copyInto(this.blob, out, 0, position, n)
return out
}
const h5 = this.module
if (this.existingPath === null || h5 === null) {
throw new ViewerError(
'unsupported',
`${this.id} cannot be read directly before it has been mounted.`,
{ id: this.id },
)
}
const out = new Uint8Array(n)
const stream = h5.FS.open(this.existingPath, 'r')
try {
let done = 0
while (done < n) {
const got = h5.FS.read(stream, out, done, n - done, position + done)
if (got <= 0) break
done += got
}
this.requests += 1
this.bytesRead += done
return done === n ? out : out.subarray(0, done)
} finally {
h5.FS.close(stream)
}
}
/**
* Read `[position, position + length)` of a dropped file exactly: a `.hic`
* walk's read (`ByteSource.readExact`).
*
* Through the slice cache, a walk paid a 1 MiB slice of the disk for most of
* its reads: the 630 matrix records of a 4DN chicken map, read for its whole
* genome at 2.5 Mb, lie a median 146 KB apart, and their heads and blocks came
* to 222 MiB of slices; read exactly, they are 11 MB. So, as the
* remote source does it, the cache is consulted and never filled: a range
* whose slices are all held is copied out of them, and any other is read as
* asked for and handed over whole. Asynchronous, through `Blob.arrayBuffer`,
* so the worker answers other requests while a walk's reads are out.
*/
private async readBlobExact(blob: Blob, position: number, length: number): Promise<Uint8Array> {
const n = Math.max(0, Math.min(this.size - position, length))
if (n === 0) return new Uint8Array(0)
const first = Math.floor(position / LOCAL_CHUNK_SIZE)
const last = Math.floor((position + n - 1) / LOCAL_CHUNK_SIZE)
let held = true
for (let i = first; i <= last && held; i++) held = this.cache.has(i)
if (held) return this.readBytes(position, n)
const bytes = new Uint8Array(await blob.slice(position, position + n).arrayBuffer())
this.requests += 1
this.bytesRead += bytes.byteLength
return bytes
}
/**
* Copy `length` bytes at `position` out of the blob, through a chunk cache.
*
* The same bounded LRU the remote source uses, for the same reason: HDF5's
* metadata walk reads a few dozen bytes at a time from a handful of places,
* and a `FileReaderSync` call per read would be thousands of them.
*/
private copyInto(
blob: Blob,
buffer: Uint8Array,
offset: number,
position: number,
length: number,
): void {
let done = 0
while (done < length) {
const at = position + done
const index = Math.floor(at / LOCAL_CHUNK_SIZE)
let chunk = this.cache.get(index)
if (chunk === undefined) {
const from = index * LOCAL_CHUNK_SIZE
const to = Math.min(from + LOCAL_CHUNK_SIZE, this.size)
chunk = new Uint8Array(this.reader().readAsArrayBuffer(blob.slice(from, to)))
this.store(index, chunk)
this.requests += 1
this.bytesRead += chunk.byteLength
} else {
// Reinsert at the back: `Map` keeps insertion order, so the first key
// is the least recently used.
this.cache.delete(index)
this.cache.set(index, chunk)
}
const start = at - index * LOCAL_CHUNK_SIZE
const n = Math.min(chunk.length - start, length - done)
if (n <= 0) throw new Error(`short read of ${this.id} at ${at}`)
buffer.set(chunk.subarray(start, start + n), offset + done)
done += n
}
}
private store(index: number, chunk: Uint8Array): void {
this.cache.set(index, chunk)
this.cachedBytes += chunk.byteLength
for (const key of this.cache.keys()) {
if (this.cachedBytes <= LOCAL_CACHE_BYTES) break
if (key === index) continue
const evicted = this.cache.get(key)
if (evicted) this.cachedBytes -= evicted.byteLength
this.cache.delete(key)
}
}
private reader(): FileReaderSync {
this.syncReader ??= new FileReaderSync()
return this.syncReader
}
close(): void {
this.cache.clear()
this.cachedBytes = 0
if (this.mountPath === null) return
const path = this.mountPath
this.mountPath = null
if (!this.ownsMount) return
this.ownsMount = false
void getH5().then(
(h5) => {
try {
h5.FS.unlink(path)
} catch {
// Already gone, or the FS was torn down with the worker. Either way
// there is nothing a viewer can do about it and nothing to report.
}
},
() => undefined,
)
}
/**
* Bytes materialised and copies made.
*
* There is no network here, so `requests` counts FS materialisations: `0` for
* a path mount, `1` once an in-memory source has been written. The §12
* budget tests read this to prove that opening a local file costs no
* requests at all.
*/
stats(): SourceStats {
return { requests: this.requests, bytes: this.bytesRead }
}
/** Slices currently retained — a cache-behaviour assertion for tests. */
cachedChunkCount(): number {
return this.cache.size
}
/** Zero the counters, so a budget test can measure one operation. */
resetStats(): void {
this.requests = 0
this.bytesRead = 0
}
private mountTarget(): string {
const safe = this.id.replace(/[^A-Za-z0-9._-]+/g, '_').slice(-100)
const leaf = `chromosomix-${nextId()}-${safe}`
if (!isNodeRuntime()) return `/${leaf}`
// Under NODERAWFS a "mount" is a real file, so it needs a real writable
// directory; MEMFS's root does not exist on the host filesystem.
const env = (globalThis as { process?: { env?: Record<string, string | undefined> } }).process
?.env
const dir = this.tempDir ?? env?.TMPDIR ?? env?.TMP ?? env?.TEMP ?? '/tmp'
return `${dir.replace(/\/+$/, '')}/${leaf}`
}
}
function nextId(): string {
counter += 1
return `${Date.now().toString(36)}${counter.toString(36)}`
}
function isBlob(value: unknown): value is Blob {
return typeof Blob !== 'undefined' && value instanceof Blob
}
function isPathRef(value: unknown): value is LocalPathRef {
return (
typeof value === 'object' &&
value !== null &&
typeof (value as LocalPathRef).path === 'string' &&
typeof (value as LocalPathRef).size === 'number'
)
}
function asUint8Array(data: Uint8Array | ArrayBuffer | ArrayBufferView): Uint8Array {
if (data instanceof Uint8Array) return data
if (data instanceof ArrayBuffer) return new Uint8Array(data)
return new Uint8Array(data.buffer, data.byteOffset, data.byteLength)
}
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