npm - edfcore - Versions diffs - 0.1.2 → 0.1.4 - Mend

edfcore 0.1.2 → 0.1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (36) hide show

package/dist/constants.d.ts +1 -1
package/dist/constants.js +1 -1
package/dist/io/cached.d.ts.map +1 -1
package/dist/io/cached.js +3 -3
package/dist/io/cached.js.map +1 -1
package/dist/io/http.d.ts.map +1 -1
package/dist/io/http.js +95 -22
package/dist/io/http.js.map +1 -1
package/dist/io/source.d.ts +24 -1
package/dist/io/source.d.ts.map +1 -1
package/dist/io/source.js +34 -1
package/dist/io/source.js.map +1 -1
package/dist/record-index.d.ts.map +1 -1
package/dist/record-index.js +18 -4
package/dist/record-index.js.map +1 -1
package/dist/recording.d.ts.map +1 -1
package/dist/recording.js +8 -1
package/dist/recording.js.map +1 -1
package/dist/tal/annotations.d.ts.map +1 -1
package/dist/tal/annotations.js +7 -1
package/dist/tal/annotations.js.map +1 -1
package/dist/types.d.ts +15 -0
package/dist/types.d.ts.map +1 -1
package/dist/validate.d.ts.map +1 -1
package/dist/validate.js +28 -4
package/dist/validate.js.map +1 -1
package/package.json +1 -1
package/src/constants.ts +1 -1
package/src/io/cached.ts +9 -3
package/src/io/http.ts +111 -24
package/src/io/source.ts +41 -2
package/src/record-index.ts +24 -5
package/src/recording.ts +8 -1
package/src/tal/annotations.ts +7 -1
package/src/types.ts +15 -0
package/src/validate.ts +32 -4

package/dist/tal/annotations.js.map CHANGED Viewed

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package/dist/types.d.ts CHANGED Viewed

@@ -375,6 +375,21 @@ export interface WindowSelection {
 export interface DecodeAnnotationsOptions extends ParseOptions {
     /** Defaults to every annotation signal. Only the first carries timekeeping. */
     readonly signalIndices?: readonly number[];
+    /**
+     * The recording's own time origin, for deriving the onset of a record whose timekeeping TAL
+     * is missing.
+     *
+     * A missing timekeeping TAL is a warning, not a fatal error, and such a record is documented
+     * to get `start + recordIndex * recordDuration`. That `start` can only be known by a caller
+     * who has already seen record 0. Without it the derivation falls back to an origin of zero,
+     * which is right only for a file whose first record starts at zero — and makes the answer
+     * depend on which records happened to share the call, because a range containing no observed
+     * onset at all gets a different origin from one that contains one.
+     *
+     * Pass `timeline.startOffsetTicks` whenever it is known. Decoding a range in isolation, as
+     * `openEdf` does before any timeline exists, correctly omits it.
+     */
+    readonly originTicks?: bigint;
 }
 /** Header-only triage. Reads at most 128 KiB and never throws on malformed content. */
 export interface EdfInspection {

package/dist/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/validate.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/validate.js CHANGED Viewed

@@ -18,9 +18,10 @@
  * 9, they can never be fatal, and a consumer's `switch` keeps its `default` branch.
  */
 import { trimEdfField } from './bytes/latin1.js';
-import { EDF_RECOMMENDED_MAX_RECORD_BYTES } from './constants.js';
+import { DEFAULT_MAX_MATERIALIZE_BYTES, EDF_RECOMMENDED_MAX_RECORD_BYTES } from './constants.js';
 import { decodeDigitalCounted } from './decode/digital.js';
 import { createDiagnostic } from './diagnostics/collector.js';
+import { EdfBudgetError } from './errors.js';
 import { calendarDatesEqual, formatCalendarDate, isValidCalendarDate } from './header/dates.js';
 import { signalFieldOffset } from './header/signals.js';
 import { readRecordBytes } from './io/read.js';
@@ -30,6 +31,8 @@ import { buildSegmentation } from './time/segments.js';
 import { assertMonotonicOnsetArray } from './time/timeline.js';
 const LABEL_SPEC = 'EDF+ additional specification 9 (standard texts and labels)';
 const TIMEKEEPING_SPEC = 'EDF+ specification 2.2.1 (time keeping of data records)';
+/** The sample-scan scratch buffer is an `Int32Array`, so four bytes per sample. */
+const BYTES_PER_SCRATCH_SAMPLE = 4;
 /**
  * The signal types EDF+ additional specification 9 names.
  *
@@ -371,8 +374,17 @@ async function traverse(recording, options, scanSamples) {
         }))
         : [];
     const chunkRecords = scanChunkRecords(header, options?.maxMaterializeBytes);
-    // One scratch array for every signal and every chunk. Bounded by chunkRecords *
-    // max(samplesPerRecord) * 4 bytes, which is at most twice the chunk's own byte size.
+    /*
+     * One scratch array for every signal and every chunk.
+     *
+     * This is normally bounded by the chunk's own byte size, because `scanChunkRecords` fits the
+     * chunk into a scan block. That bound fails for a single record larger than the whole block:
+     * the record count floors to 1 and the scratch size becomes `samplesPerRecord` unclamped, up
+     * to the 99,999,999 an 8-byte EDF field can hold — a 400 MB allocation reachable from one
+     * corrupted digit in a 512-byte file, made before any read, so no downstream check can catch
+     * it. Validation exists to be pointed at untrusted files, so it is exactly the caller who
+     * needs the budget honoured rather than a documented cap that only the read path respects.
+     */
     let scratch;
     if (scanSamples) {
         let maxSamplesPerRecord = 0;
@@ -382,6 +394,15 @@ async function traverse(recording, options, scanSamples) {
                 maxSamplesPerRecord = Math.max(maxSamplesPerRecord, signal.samplesPerRecord);
             }
         }
+        const scratchBytes = chunkRecords * maxSamplesPerRecord * BYTES_PER_SCRATCH_SAMPLE;
+        const budgetBytes = options?.maxMaterializeBytes ?? DEFAULT_MAX_MATERIALIZE_BYTES;
+        if (scratchBytes > budgetBytes) {
+            throw new EdfBudgetError(`Scanning samples needs a ${scratchBytes}-byte scratch buffer for ${chunkRecords} ` +
+                `record(s) of up to ${maxSamplesPerRecord} samples, above the ${budgetBytes}-byte ` +
+                'maxMaterializeBytes budget, so the scan was refused before anything was allocated. ' +
+                'Next: raise options.maxMaterializeBytes, or drop scanSamples and validate the ' +
+                'header alone.', { requiredBytes: scratchBytes, budgetBytes });
+        }
         scratch = new Int32Array(chunkRecords * maxSamplesPerRecord);
     }
     let recordsScanned = 0;
@@ -394,7 +415,10 @@ async function traverse(recording, options, scanSamples) {
         const bytes = await readRecordBytes(source, header, records, options);
         bytesRead += bytes.length;
         // Never strict: a sweep whose job is to list every defect must not stop at the first one.
-        const decoded = decodeAnnotations(header, bytes, records);
+        // The origin is the recording's, so the sweep's verdict does not depend on its chunk size.
+        const decoded = decodeAnnotations(header, bytes, records, {
+            originTicks: recording.timeline.startOffsetTicks,
+        });
         onsets.set(decoded.recordOnsetTicks, records.start);
         diagnostics.push(...decoded.diagnostics);
         for (const accumulator of accumulators) {

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "edfcore",
-  "version": "0.1.2",
+  "version": "0.1.4",
   "description": "Modern, typed, zero-dependency reader for EDF, EDF+, BDF and BDF+ biosignal files. Works in browsers and Node with true random access.",
   "keywords": [
     "edf",

package/src/constants.ts CHANGED Viewed

@@ -93,4 +93,4 @@ export const SIGNAL_FIELD_BLOCK_OFFSETS = {
 } as const;
 /** Published package version. Kept in sync with package.json by a test. */
-export const VERSION = '0.1.2';
+export const VERSION = '0.1.4';

package/src/io/cached.ts CHANGED Viewed

@@ -16,7 +16,7 @@
  */
 import type { ByteSource, CacheOptions, ReadOptions } from '../types.js';
-import { assertExactRead, assertReadRange, throwIfAborted } from './source.js';
+import { assertExactRead, assertReadRange, requireFiniteOption, throwIfAborted } from './source.js';
 const DEFAULT_BLOCK_BYTES = 1024 * 1024;
 const DEFAULT_MAX_BYTES = 64 * 1024 * 1024;
@@ -36,8 +36,14 @@ function passThrough(source: ByteSource): ByteSource {
 export function cachedSource(source: ByteSource, options?: CacheOptions): ByteSource {
   const byteLength = source.byteLength;
-  const maxBytes = Math.max(0, Math.floor(options?.maxBytes ?? DEFAULT_MAX_BYTES));
-  const requestedBlockBytes = Math.max(1, Math.floor(options?.blockBytes ?? DEFAULT_BLOCK_BYTES));
+  const maxBytes = Math.max(
+    0,
+    Math.floor(requireFiniteOption(options?.maxBytes, 'maxBytes', DEFAULT_MAX_BYTES)),
+  );
+  const requestedBlockBytes = Math.max(
+    1,
+    Math.floor(requireFiniteOption(options?.blockBytes, 'blockBytes', DEFAULT_BLOCK_BYTES)),
+  );
   // A block wider than the whole budget would evict itself on every insert, so the block is
   // clamped to the budget rather than the cache being left in a state that can never hold one.
   const blockBytes = Math.min(requestedBlockBytes, maxBytes);

package/src/io/http.ts CHANGED Viewed

@@ -23,7 +23,12 @@ import type {
   HttpSourceOptions,
   ReadOptions,
 } from '../types.js';
-import { assertExactRead, assertReadRange, throwIfAborted } from './source.js';
+import {
+  assertExactRead,
+  assertReadRange,
+  requireFiniteOption,
+  throwIfSignalAborted,
+} from './source.js';
 /** Small enough to stay polite to a shared origin, large enough to hide latency. */
 const DEFAULT_MAX_CONCURRENCY = 4;
@@ -122,7 +127,7 @@ function resolveFetch(options: HttpSourceOptions | undefined): FetchLike {
  *
  * It is attached only when it carries `addEventListener`, i.e. when it genuinely is an
  * `AbortSignal`. The platform `fetch` throws a `TypeError` on anything else, and a caller who
- * passed a bare `{ aborted }` shim is still served by the `throwIfAborted` polls around the
+ * passed a bare `{ aborted }` shim is still served by the `throwIfSignalAborted` polls around the
  * request.
  */
 function attachSignal(init: RequestInitLike, signal: AbortSignalLike | undefined): void {
@@ -170,6 +175,9 @@ async function resolveSource(
   options: HttpSourceOptions | undefined,
 ): Promise<ResolvedSource> {
   const signal = options?.signal;
+  // Resolution issues its own HEAD and probe requests, so an already-aborted source signal has
+  // to be caught here too — otherwise httpSource() itself does network work after cancellation.
+  throwIfSignalAborted(signal);
   const declared = options?.byteLength;
   if (declared !== undefined) {
@@ -232,13 +240,37 @@ export async function httpSource(
   const fetchImpl = resolveFetch(options);
   const baseHeaders: Record<string, string> = { ...options?.headers };
   const gate = createGate(
-    Math.max(1, Math.floor(options?.maxConcurrency ?? DEFAULT_MAX_CONCURRENCY)),
+    Math.max(
+      1,
+      Math.floor(
+        requireFiniteOption(options?.maxConcurrency, 'maxConcurrency', DEFAULT_MAX_CONCURRENCY),
+      ),
+    ),
   );
   const resolved = await resolveSource(fetchImpl, href, baseHeaders, options);
   const byteLength = resolved.byteLength;
   /** Set once, and only ever when the server ignored Range and the caller allowed it. */
   let fullBody: Uint8Array | undefined = resolved.body;
+  /**
+   * The one in-flight full download, so a server that ignores Range costs one transfer.
+   *
+   * Without it, every read that had already entered `fetchRange` issued its own GET, each
+   * buffering the whole resource — N concurrent block reads downloaded the file N times and held
+   * up to `maxConcurrency` copies at once. That turns a large remote recording into an
+   * out-of-memory crash rather than a slow read.
+   */
+  let fullBodyInflight: Promise<Uint8Array> | undefined;
+  /**
+   * Settles once one request has revealed whether this server honours Range.
+   *
+   * Only used when `allowFullDownload` is on. Until the answer is known, a request is a gamble:
+   * if the server ignores Range it answers with the entire resource, and `maxConcurrency`
+   * requests issued in parallel each pay for a whole copy before any of them can warn the
+   * others. Sending the first one alone costs one round trip on the first read and bounds the
+   * worst case at a single transfer instead of `maxConcurrency` of them.
+   */
+  let rangeSupportProbe: Promise<void> | undefined;
   async function fetchRange(
     offset: number,
@@ -251,43 +283,98 @@ export async function httpSource(
     await gate.acquire();
     try {
-      throwIfAborted(readOptions);
-      const response = await request(fetchImpl, href, headers, 'GET', signal);
-      if (response.status === HTTP_PARTIAL_CONTENT) {
-        const bytes = new Uint8Array(await response.arrayBuffer());
-        return assertExactRead(bytes, offset, length);
+      throwIfSignalAborted(signal);
+      // Waiting for a gate slot can take arbitrarily long, and in that time another read may
+      // have discovered that the server ignores Range. Re-checking here is what stops every
+      // queued read from repeating the download the first one already made.
+      if (fullBody !== undefined) return sliceFullBody(fullBody, offset, length);
+      if (fullBodyInflight !== undefined) {
+        return sliceFullBody(await fullBodyInflight, offset, length);
       }
-      if (response.status === HTTP_OK) {
-        if (options?.allowFullDownload !== true) throw rangeIgnoredError(href, offset, length);
-        const body = new Uint8Array(await response.arrayBuffer());
-        // A concurrent read may have won the race; either copy is the same resource, so keep
-        // whichever landed first and let this one be collected.
-        if (fullBody === undefined) fullBody = body;
-        return sliceFullBody(fullBody, offset, length);
+      let announceProbeDone: (() => void) | undefined;
+      if (options?.allowFullDownload === true) {
+        if (rangeSupportProbe === undefined) {
+          rangeSupportProbe = new Promise<void>((resolve) => {
+            announceProbeDone = resolve;
+          });
+        } else {
+          // Someone else is finding out. Their answer is ours too.
+          await rangeSupportProbe;
+          if (fullBody !== undefined) return sliceFullBody(fullBody, offset, length);
+          if (fullBodyInflight !== undefined) {
+            return sliceFullBody(await fullBodyInflight, offset, length);
+          }
+        }
       }
-      throw new EdfSourceError(
-        `Reading bytes ${offset}..${offset + length - 1} of ${href} failed: the server ` +
-          `answered HTTP ${response.status}. Next: check the URL, its authentication headers ` +
-          'and whether a signed URL has expired.',
-        { offset, requestedLength: length },
-      );
+      try {
+        return await issueRequest(offset, length, headers, signal);
+      } finally {
+        announceProbeDone?.();
+      }
     } finally {
       gate.release();
     }
   }
+  async function issueRequest(
+    offset: number,
+    length: number,
+    headers: Record<string, string>,
+    signal: AbortSignalLike | undefined,
+  ): Promise<Uint8Array> {
+    const response = await request(fetchImpl, href, headers, 'GET', signal);
+    if (response.status === HTTP_PARTIAL_CONTENT) {
+      const bytes = new Uint8Array(await response.arrayBuffer());
+      return assertExactRead(bytes, offset, length);
+    }
+    if (response.status === HTTP_OK) {
+      if (options?.allowFullDownload !== true) throw rangeIgnoredError(href, offset, length);
+      if (fullBody !== undefined) return sliceFullBody(fullBody, offset, length);
+      // A read that raced us to the same discovery already owns the transfer. Abandon this
+      // response body unread and take theirs — either copy is the same resource.
+      if (fullBodyInflight === undefined) {
+        fullBodyInflight = response
+          .arrayBuffer()
+          .then((buffer) => {
+            const body = new Uint8Array(buffer);
+            fullBody = body;
+            return body;
+          })
+          .catch((error: unknown) => {
+            // A failed transfer must not poison every later read with a rejected promise.
+            fullBodyInflight = undefined;
+            throw error;
+          });
+      }
+      return sliceFullBody(await fullBodyInflight, offset, length);
+    }
+    throw new EdfSourceError(
+      `Reading bytes ${offset}..${offset + length - 1} of ${href} failed: the server ` +
+        `answered HTTP ${response.status}. Next: check the URL, its authentication headers ` +
+        'and whether a signed URL has expired.',
+      { offset, requestedLength: length },
+    );
+  }
   return {
     byteLength,
     async read(offset: number, length: number, readOptions?: ReadOptions): Promise<Uint8Array> {
-      throwIfAborted(readOptions);
+      // The effective signal, not just the per-read one. A source-level signal is documented as
+      // "the default for every request", and honouring it only inside `attachSignal` meant it
+      // worked for a real AbortSignal and was a silent no-op for the published
+      // `AbortSignalLike` shim, which has no addEventListener to attach to.
+      const signal = readOptions?.signal ?? options?.signal;
+      throwIfSignalAborted(signal);
       assertReadRange(offset, length, byteLength);
       if (length === 0) return new Uint8Array(0);
       if (fullBody !== undefined) return sliceFullBody(fullBody, offset, length);
       const bytes = await fetchRange(offset, length, readOptions);
-      throwIfAborted(readOptions);
+      throwIfSignalAborted(signal);
       return bytes;
     },
   };

package/src/io/source.ts CHANGED Viewed

@@ -12,7 +12,7 @@
  */
 import { EdfSourceError } from '../errors.js';
-import type { ReadOptions } from '../types.js';
+import type { AbortSignalLike, ReadOptions } from '../types.js';
 /**
  * A misbehaving source may resolve with something that is not a byte array at all, which is
@@ -80,8 +80,47 @@ export function assertReadRange(offset: number, length: number, byteLength: numb
  * on is `error.name === 'AbortError'`, so that is what this produces.
  */
 export function throwIfAborted(options?: ReadOptions): void {
-  if (options?.signal?.aborted !== true) return;
+  throwIfSignalAborted(options?.signal);
+}
+/**
+ * The same check against a signal that was resolved by the caller.
+ *
+ * A source can carry its own signal as well as the one passed per read, and the effective signal
+ * is `readOptions?.signal ?? sourceOptions?.signal`. That cannot be handed back to
+ * `throwIfAborted` as an object literal, because `exactOptionalPropertyTypes` refuses
+ * `{ signal: undefined }` where the property is declared optional.
+ */
+export function throwIfSignalAborted(signal?: AbortSignalLike): void {
+  if (signal?.aborted !== true) return;
   const error = new Error('The read was aborted through options.signal.');
   error.name = 'AbortError';
   throw error;
 }
+/**
+ * A numeric source option, rejected rather than silently coerced when it is not a finite number.
+ *
+ * These options are typed `number`, which admits `NaN` and `Infinity`, and both arrive easily:
+ * `Number(process.env.EDFCORE_CACHE_MIB)`, `Number(searchParams.get('block'))` and any absent
+ * key in a JSON config all produce `NaN`. Left alone they do not fail loudly — `Math.max(1, NaN)`
+ * is `NaN` and every subsequent comparison against it is false, so guards written as
+ * `if (value < 1)` simply do not fire and the caller gets fabricated data or a read that never
+ * settles. Refusing at construction keeps the failure at the line that holds the bad value.
+ *
+ * A plain `RangeError`, not an `EdfError`: this is a bug in the calling code rather than a
+ * problem with the file, which is the same split `isEdfError` documents.
+ */
+export function requireFiniteOption(
+  value: number | undefined,
+  name: string,
+  fallback: number,
+): number {
+  if (value === undefined) return fallback;
+  if (Number.isFinite(value)) return value;
+  throw new RangeError(
+    `options.${name} must be a finite number, but was ${String(value)}. Next: check the ` +
+      'expression that produced it — Number() on an absent environment variable, query ' +
+      'parameter or config key yields NaN.',
+  );
+}