edfcore 0.3.104 → 0.3.106

package/CHANGELOG.md

@@ -6,6 +6,39 @@ alone does not tell you whether you were affected.
 edfcore is pre-1.0. Patch releases have carried behaviour changes where the old behaviour was a
 defect; those are called out below.
 
+## 0.3.106
+
+- **Changed** `decodeAnnotations` and `readAnnotations` to throw `EdfChannelNotFoundError` for a
+  signal index the file does not have, matching the ten other entry points that take one.
+  - `resolveSignals` collapsed two different mistakes into one branch. An index outside
+    `header.signals` therefore produced a bare `RangeError` with no `selector` and no
+    `availableLabels`, `isEdfError` returned `false` for it, and the message read "signal 99 is not
+    an annotation signal" — which describes a signal that exists with the wrong kind. This is the
+    asymmetry 0.3.35 fixed for the envelope path, where `isEdfError` answered differently depending
+    on which read the caller had reached for.
+  - The plain `RangeError` stays for the case the docs actually describe and the carve-out's own
+    reason covers: a real data signal, whose samples this module exists to keep out of a text
+    parser. There are no samples at index 99.
+  - The test named for that rule only exercised index 0, which is how the two halves drifted apart.
+    It now covers both.
+
+## 0.3.105
+
+- **Fixed** a discarded TAL still reporting that it was kept.
+  - The `onset-unsigned` defect — "so the TAL was kept and the onset read as positive" — was logged
+    at the point the missing sign was recovered, which is upstream of the four branches that can
+    still throw the same TAL away: an out-of-range onset, an over-long duration field, a bad
+    duration grammar and an out-of-range duration. An unsigned onset combined with any of them
+    produced two `TAL_MALFORMED` entries about one TAL asserting opposite outcomes, and the one
+    that ran first was the false one. With an out-of-range onset the pair is indistinguishable by
+    anything but prose: same code, same offset, same length, same raw bytes, `occurrences` 1 each.
+  - It is now logged once the TAL is known to survive, ahead of the text scan so a kept TAL's
+    issues keep the order they had. Consequently its `occurrences` counts surviving unsigned
+    onsets, and its offset and raw bytes are the first surviving one's.
+  - 0.3.19 fixed the cross-TAL version of this by keying the log on the defect kind. That stops two
+    different TALs from describing each other and does nothing for one TAL describing itself twice;
+    both guards written for it build two TALs, so they passed throughout. The new guard builds one.
+
 ## 0.3.104
 
 - **Fixed** annotation text reaching a diagnostic message unescaped, which let a file forge a

package/dist/constants.d.ts

@@ -109,5 +109,5 @@ export declare const SIGNAL_FIELD_BLOCK_OFFSETS: {
     readonly reserved: 224;
 };
 /** Published package version. Kept in sync with package.json by a test. */
-export declare const VERSION = "0.3.104";
+export declare const VERSION = "0.3.106";
 //# sourceMappingURL=constants.d.ts.map

package/dist/constants.js

@@ -79,5 +79,5 @@ export const SIGNAL_FIELD_BLOCK_OFFSETS = {
     reserved: 224,
 };
 /** Published package version. Kept in sync with package.json by a test. */
-export const VERSION = '0.3.104';
+export const VERSION = '0.3.106';
 //# sourceMappingURL=constants.js.map

package/dist/tal/annotations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../src/tal/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AAMH,OAAO,KAAK,EACV,wBAAwB,EAExB,oBAAoB,EACpB,SAAS,EAET,WAAW,EACZ,MAAM,aAAa,CAAC;AAkWrB,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,UAAU,EACvB,OAAO,EAAE,WAAW,EACpB,OAAO,CAAC,EAAE,wBAAwB,GACjC,oBAAoB,CAsLtB"}
+{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../src/tal/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AAMH,OAAO,KAAK,EACV,wBAAwB,EAExB,oBAAoB,EACpB,SAAS,EAET,WAAW,EACZ,MAAM,aAAa,CAAC;AAiXrB,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,UAAU,EACvB,OAAO,EAAE,WAAW,EACpB,OAAO,CAAC,EAAE,wBAAwB,GACjC,oBAAoB,CAsLtB"}

package/dist/tal/annotations.js

@@ -34,7 +34,7 @@
 import { sliceBytes } from '../bytes/view.js';
 import { TICKS_PER_SECOND } from '../constants.js';
 import { DiagnosticSink } from '../diagnostics/collector.js';
-import { EdfRangeError } from '../errors.js';
+import { EdfChannelNotFoundError, EdfRangeError } from '../errors.js';
 import { escapeControls, parseTalRegion, previewBytes, splitChannelLabel, TAL_PREVIEW_MAX_BYTES, } from './grammar.js';
 import { saturateToInt64, ticksToSeconds } from './ticks.js';
 const ANNOTATIONS_SPEC = "EDF+ specification 2.2 (the 'EDF Annotations' signal)";
@@ -96,6 +96,13 @@ function assertRecordRange(header, recordBytes, records) {
  * A non-annotation index is refused with a plain `RangeError`, not an `EdfError`: parsing a data
  * signal's samples as text is exactly the garbage this module exists to prevent, and it can only
  * happen through a caller's mistake, never through a file's.
+ *
+ * That reason is about a signal the file HAS. An index the file does not have is a different
+ * mistake, and it throws `EdfChannelNotFoundError` like the ten other entry points that take a
+ * signal index — the same asymmetry 0.3.35 fixed for the envelope path, where `isEdfError`
+ * answered differently depending on which read the caller had reached for. The two were one
+ * branch, so index 99 into a 2-signal file was refused as "not an annotation signal", which
+ * describes a signal that exists with the wrong kind (fixed in 0.3.106).
  */
 function resolveSignals(header, requested) {
     const indices = requested ?? header.annotationSignalIndices;
@@ -106,7 +113,12 @@ function resolveSignals(header, requested) {
             continue;
         seen.add(index);
         const signal = header.signals[index];
-        if (signal === undefined || signal.kind !== 'annotations') {
+        if (signal === undefined) {
+            throw new EdfChannelNotFoundError(`signalIndex ${index} is outside the ${header.signals.length} signals this file ` +
+                'declares. Next: pass an index from header.annotationSignalIndices, or omit ' +
+                'signalIndices to read them all.', { selector: index, availableLabels: header.signals.map((one) => one.label) });
+        }
+        if (signal.kind !== 'annotations') {
             throw new RangeError(`decodeAnnotations(): signal ${index} is not an annotation signal. This file's ` +
                 `annotation signals are [${header.annotationSignalIndices.join(', ')}]. ` +
                 'Next: pass one of those, or omit signalIndices to read them all.');

package/dist/tal/annotations.js.map

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package/dist/tal/grammar.d.ts.map

@@ -1 +1 @@
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package/dist/tal/grammar.js

@@ -235,6 +235,7 @@ function scanTal(region, start, ordinal, log) {
     const onsetRaw = decodeHeaderLatin1(sliceBytes(region, start, onsetEnd - start));
     const signedOnset = parseSignedTicks(onsetRaw);
     let onsetTicks = signedOnset.ticks;
+    let onsetWasUnsigned = false;
     if (!signedOnset.ok) {
         // `parseSignedTicks` fails for a missing sign and for a bad magnitude alike. Only the first
         // is recoverable, and re-parsing without the sign is how they are told apart.
@@ -245,8 +246,11 @@ function scanTal(region, start, ordinal, log) {
             return { tal: undefined, next };
         }
         onsetTicks = unsignedOnset.ticks;
-        logIssue(log, 'TAL_MALFORMED', 'onset-unsigned', region, start, onsetEnd - start, `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
-            'kept and the onset read as positive');
+        // DEFERRED, not logged here. This is the one "the TAL was kept" message that sits upstream of
+        // a discard branch — four of them, in fact — so an unsigned onset combined with any of them
+        // reported two dispositions of the same TAL, and the one that ran first was the false one.
+        // See the flush below the duration checks (fixed in 0.3.105).
+        onsetWasUnsigned = true;
     }
     if (outsideInt64(onsetTicks)) {
         logIssue(log, 'TAL_MALFORMED', 'onset-out-of-range', region, start, onsetEnd - start, `the onset "${onsetRaw}" is outside the +/-2^63 tick range edfcore can represent, so the ` +
@@ -283,6 +287,13 @@ function scanTal(region, start, ordinal, log) {
         }
         durationTicks = duration.ticks;
     }
+    // Past every branch that can discard the TAL, so this is the first point at which "the TAL was
+    // kept" is true. It sits ahead of the text scan rather than beside the return so that a kept
+    // TAL's issues stay in the order they were in before 0.3.105 — onset, then text.
+    if (onsetWasUnsigned) {
+        logIssue(log, 'TAL_MALFORMED', 'onset-unsigned', region, start, onsetEnd - start, `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
+            'kept and the onset read as positive');
+    }
     const texts = [];
     let runStart = timestampEnd + 1;
     for (let i = runStart; i < bodyEnd; i += 1) {

package/dist/tal/grammar.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "edfcore",
-  "version": "0.3.104",
+  "version": "0.3.106",
   "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

@@ -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 = '0.3.104';
+export const VERSION = '0.3.106';

package/src/tal/annotations.ts

@@ -35,7 +35,7 @@
 import { sliceBytes } from '../bytes/view.js';
 import { TICKS_PER_SECOND } from '../constants.js';
 import { DiagnosticSink } from '../diagnostics/collector.js';
-import { EdfRangeError } from '../errors.js';
+import { EdfChannelNotFoundError, EdfRangeError } from '../errors.js';
 import type {
   DecodeAnnotationsOptions,
   EdfAnnotation,
@@ -173,6 +173,13 @@ function assertRecordRange(header: EdfHeader, recordBytes: Uint8Array, records:
  * A non-annotation index is refused with a plain `RangeError`, not an `EdfError`: parsing a data
  * signal's samples as text is exactly the garbage this module exists to prevent, and it can only
  * happen through a caller's mistake, never through a file's.
+ *
+ * That reason is about a signal the file HAS. An index the file does not have is a different
+ * mistake, and it throws `EdfChannelNotFoundError` like the ten other entry points that take a
+ * signal index — the same asymmetry 0.3.35 fixed for the envelope path, where `isEdfError`
+ * answered differently depending on which read the caller had reached for. The two were one
+ * branch, so index 99 into a 2-signal file was refused as "not an annotation signal", which
+ * describes a signal that exists with the wrong kind (fixed in 0.3.106).
  */
 function resolveSignals(
   header: EdfHeader,
@@ -185,7 +192,15 @@ function resolveSignals(
     if (seen.has(index)) continue;
     seen.add(index);
     const signal = header.signals[index];
-    if (signal === undefined || signal.kind !== 'annotations') {
+    if (signal === undefined) {
+      throw new EdfChannelNotFoundError(
+        `signalIndex ${index} is outside the ${header.signals.length} signals this file ` +
+          'declares. Next: pass an index from header.annotationSignalIndices, or omit ' +
+          'signalIndices to read them all.',
+        { selector: index, availableLabels: header.signals.map((one) => one.label) },
+      );
+    }
+    if (signal.kind !== 'annotations') {
       throw new RangeError(
         `decodeAnnotations(): signal ${index} is not an annotation signal. This file's ` +
           `annotation signals are [${header.annotationSignalIndices.join(', ')}]. ` +

package/src/tal/grammar.ts

@@ -272,6 +272,13 @@ export function rawBytesText(bytes: Uint8Array, offset: number, length: number):
  * bytes they found — `the onset "??" is not …` — and keying on those would be unbounded. The
  * per-region issue count stays bounded by the number of KINDS, which is what the collapsing
  * exists to protect.
+ *
+ * Keying by kind stops two DIFFERENT TALs from describing each other; it does nothing for one TAL
+ * describing itself twice, which is what `onset-unsigned` did until 0.3.105 — it was logged before
+ * the four branches that can still discard the TAL, so a region could carry two `TAL_MALFORMED`
+ * entries with the same offset, length and raw bytes asserting opposite dispositions. It is now
+ * logged only once the TAL is known to survive, which means its `occurrences` counts SURVIVING
+ * unsigned onsets and its offset is the first surviving one.
  */
 type TalIssueKind =
   | 'text-not-utf8'
@@ -433,6 +440,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
   const onsetRaw = decodeHeaderLatin1(sliceBytes(region, start, onsetEnd - start));
   const signedOnset = parseSignedTicks(onsetRaw);
   let onsetTicks = signedOnset.ticks;
+  let onsetWasUnsigned = false;
   if (!signedOnset.ok) {
     // `parseSignedTicks` fails for a missing sign and for a bad magnitude alike. Only the first
     // is recoverable, and re-parsing without the sign is how they are told apart.
@@ -451,16 +459,11 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
       return { tal: undefined, next };
     }
     onsetTicks = unsignedOnset.ticks;
-    logIssue(
-      log,
-      'TAL_MALFORMED',
-      'onset-unsigned',
-      region,
-      start,
-      onsetEnd - start,
-      `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
-        'kept and the onset read as positive',
-    );
+    // DEFERRED, not logged here. This is the one "the TAL was kept" message that sits upstream of
+    // a discard branch — four of them, in fact — so an unsigned onset combined with any of them
+    // reported two dispositions of the same TAL, and the one that ran first was the false one.
+    // See the flush below the duration checks (fixed in 0.3.105).
+    onsetWasUnsigned = true;
   }
   if (outsideInt64(onsetTicks)) {
     logIssue(
@@ -531,6 +534,22 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     durationTicks = duration.ticks;
   }
 
+  // Past every branch that can discard the TAL, so this is the first point at which "the TAL was
+  // kept" is true. It sits ahead of the text scan rather than beside the return so that a kept
+  // TAL's issues stay in the order they were in before 0.3.105 — onset, then text.
+  if (onsetWasUnsigned) {
+    logIssue(
+      log,
+      'TAL_MALFORMED',
+      'onset-unsigned',
+      region,
+      start,
+      onsetEnd - start,
+      `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
+        'kept and the onset read as positive',
+    );
+  }
+
   const texts: TalText[] = [];
   let runStart = timestampEnd + 1;
   for (let i = runStart; i < bodyEnd; i += 1) {