edfcore 0.3.18 → 0.3.19

package/CHANGELOG.md

@@ -6,6 +6,35 @@ 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.
 
+## 0.3.19
+
+**Two places where content was dropped under a diagnostic saying it was not.** Both are annotation
+data going missing quietly, which is the failure this package exists to refuse.
+
+- **Fixed** a timekeeping TAL carrying a duration AND text being classified as harmless. A writer
+  that merges a scored epoch into the timekeeping TAL writes
+  `+onset 0x15 30 0x14 Sleep stage W 0x14 0x14 0x00`, and every one of those epochs is dropped.
+  edfcore reported **one** diagnostic, naming record 0, blaming the duration field, and ending
+  "nothing was lost". Remove the duration from the same file and it correctly emitted six, each
+  naming the event it lost — so adding a duration turned six loud reports into one misleading one.
+  `timekeepingDefect` returns at the first matching branch and asked about the benign duration
+  before the destructive text; the text check now comes first, and a stray duration is mentioned
+  inside that same message.
+- 0.2.33 fixed the same swallowing by splitting the once-per-call flag between the two kinds and
+  left the check ORDER alone. Its test builds a merged TAL with text and no duration, so the
+  combination was never exercised. Both fixtures now live in that file.
+- **Fixed** `TAL_MALFORMED` collapsing nine structurally different defects onto one report.
+  Their dispositions are opposites: a 0x15 inside a text run and a missing onset sign KEEP the TAL,
+  while a bad onset, an over-long field, an out-of-range onset, a bad duration and an unterminated
+  timestamp DISCARD it. Whichever came first in a region won the `detail`, the offset and the raw
+  bytes, so a region holding one of each reported *"the text was kept verbatim"* with occurrences 2
+  while an annotation had in fact been thrown away — and reversing the two TALs produced the
+  mirror-image lie. `TalIssue.detail` promises to state "what was wrong AND what was done about it".
+- The issue log is keyed on the defect KIND rather than the code, from a closed set of twelve. Not
+  on the `detail` string: several details interpolate the bytes they found, so keying on those
+  would be unbounded — and bounding the per-region issue count is the whole reason the collapsing
+  exists. Many occurrences of the same defect still collapse to one entry with a count.
+
 ## 0.3.18
 
 - **Fixed** `inspectEdf` discarding every diagnostic the parse had already found when a fatal check

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 = "0.3.18";
+export declare const VERSION = "0.3.19";
 //# 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 = '0.3.18';
+export const VERSION = '0.3.19';
 //# 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;AAyUrB,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,UAAU,EACvB,OAAO,EAAE,WAAW,EACpB,OAAO,CAAC,EAAE,wBAAwB,GACjC,oBAAoB,CAmKtB"}
+{"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;AAoVrB,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EACjB,WAAW,EAAE,UAAU,EACvB,OAAO,EAAE,WAAW,EACpB,OAAO,CAAC,EAAE,wBAAwB,GACjC,oBAAoB,CAmKtB"}

package/dist/tal/annotations.js

@@ -157,6 +157,24 @@ function reportTimekeepingMissing(sink, context) {
     });
 }
 function timekeepingDefect(tal) {
+    // TEXT IS TESTED FIRST, and the order is the whole point. A TAL can be wrong in more than one
+    // way at once, and this returns at the first match — so asking about the benign duration before
+    // the destructive text classified a TAL that loses an annotation as one that loses nothing. It
+    // was then capped at one report per call, under a message ending "nothing was lost".
+    //
+    // 0.2.33 fixed the same swallowing by splitting the once-per-call flag between the two kinds,
+    // and left this order alone; the test written for it builds a timekeeping TAL with text and NO
+    // duration, so the combination stayed uncovered. A writer that merges a scored epoch into the
+    // timekeeping TAL writes both (fixed in 0.3.19).
+    const texts = tal.texts.map((run) => run.text).filter((text) => text.length > 0);
+    if (texts.length > 0) {
+        const strayDuration = tal.durationRaw === undefined ? '' : ` (and the duration "${tal.durationRaw}")`;
+        return {
+            reason: `carries the text ${texts.map((text) => `"${text}"`).join(', ')}${strayDuration}, which ` +
+                'is dropped: the timekeeping TAL is not an annotation',
+            destructive: true,
+        };
+    }
     if (tal.durationRaw !== undefined) {
         return {
             reason: `carries the duration "${tal.durationRaw}", which a timekeeping TAL never has`,
@@ -170,14 +188,6 @@ function timekeepingDefect(tal) {
             destructive: false,
         };
     }
-    const texts = tal.texts.map((run) => run.text).filter((text) => text.length > 0);
-    if (texts.length > 0) {
-        return {
-            reason: `carries the text ${texts.map((text) => `"${text}"`).join(', ')}, which is dropped: the ` +
-                'timekeeping TAL is not an annotation',
-            destructive: true,
-        };
-    }
     if (tal.texts.length > 1) {
         return {
             reason: `carries ${tal.texts.length} empty texts, where the grammar allows exactly one`,

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

@@ -102,13 +102,14 @@ export function previewBytes(bytes, offset, length) {
     const text = escapeControls(decodeHeaderLatin1(sliceBytes(bytes, offset, shown)));
     return length > shown ? `${text}...` : text;
 }
-function logIssue(log, code, region, offset, length, detail) {
-    const existing = log.get(code);
+function logIssue(log, code, kind, region, offset, length, detail) {
+    const key = `${code}|${kind}`;
+    const existing = log.get(key);
     if (existing !== undefined) {
         existing.occurrences += 1;
         return;
     }
-    log.set(code, {
+    log.set(key, {
         code,
         byteOffsetInRegion: offset,
         byteLength: length,
@@ -150,7 +151,7 @@ function decodeTextRun(region, start, length, log) {
             // A fatal decoder rejects invalid UTF-8 with a TypeError. Fall through to Latin-1.
         }
     }
-    logIssue(log, 'ANNOTATION_TEXT_NOT_UTF8', region, start, length, decoder === null
+    logIssue(log, 'ANNOTATION_TEXT_NOT_UTF8', 'text-not-utf8', region, start, length, decoder === null
         ? 'this runtime has no TextDecoder, so the text run could not be verified as UTF-8 and ' +
             'was decoded as ISO-8859-1'
         : 'the text run is not valid UTF-8 and was decoded as ISO-8859-1 instead');
@@ -175,20 +176,20 @@ function scanTal(region, start, ordinal, log) {
     const regionLength = region.length;
     const bodyEnd = indexOfByte(region, start, regionLength, TAL_TERMINATOR);
     if (bodyEnd < 0) {
-        logIssue(log, 'TAL_TRUNCATED_AT_REGION_END', region, start, regionLength - start, 'a TAL begins here and has no terminating 0x00 inside the region, so it was discarded ' +
+        logIssue(log, 'TAL_TRUNCATED_AT_REGION_END', 'tal-unterminated', region, start, regionLength - start, 'a TAL begins here and has no terminating 0x00 inside the region, so it was discarded ' +
             "rather than continued into the following signal's samples");
         return { tal: undefined, next: regionLength };
     }
     const next = bodyEnd + 1;
     const timestampEnd = indexOfByte(region, start, bodyEnd, TAL_FIELD_TERMINATOR);
     if (timestampEnd < 0) {
-        logIssue(log, 'TAL_MALFORMED', region, start, bodyEnd - start, 'the timestamp is not terminated by 0x14, so the TAL was skipped');
+        logIssue(log, 'TAL_MALFORMED', 'timestamp-unterminated', region, start, bodyEnd - start, 'the timestamp is not terminated by 0x14, so the TAL was skipped');
         return { tal: undefined, next };
     }
     const separator = indexOfByte(region, start, timestampEnd, TAL_ONSET_DURATION_SEPARATOR);
     const onsetEnd = separator < 0 ? timestampEnd : separator;
     if (onsetEnd - start > MAX_TIMESTAMP_FIELD_CHARS) {
-        logIssue(log, 'TAL_MALFORMED', region, start, onsetEnd - start, `the onset field is ${onsetEnd - start} bytes long, which no time in 100 ns ticks needs; ` +
+        logIssue(log, 'TAL_MALFORMED', 'onset-field-too-long', region, start, onsetEnd - start, `the onset field is ${onsetEnd - start} bytes long, which no time in 100 ns ticks needs; ` +
             'the TAL was skipped');
         return { tal: undefined, next };
     }
@@ -200,16 +201,16 @@ function scanTal(region, start, ordinal, log) {
         // is recoverable, and re-parsing without the sign is how they are told apart.
         const unsignedOnset = parseUnsignedTicks(onsetRaw);
         if (!unsignedOnset.ok) {
-            logIssue(log, 'TAL_MALFORMED', region, start, Math.max(onsetEnd - start, 1), `the onset "${onsetRaw}" is not ("+" / "-") 1*DIGIT [ "." 1*DIGIT ], so the TAL was ` +
+            logIssue(log, 'TAL_MALFORMED', 'onset-grammar', region, start, Math.max(onsetEnd - start, 1), `the onset "${onsetRaw}" is not ("+" / "-") 1*DIGIT [ "." 1*DIGIT ], so the TAL was ` +
                 'skipped');
             return { tal: undefined, next };
         }
         onsetTicks = unsignedOnset.ticks;
-        logIssue(log, 'TAL_MALFORMED', region, start, onsetEnd - start, `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
+        logIssue(log, 'TAL_MALFORMED', 'onset-unsigned', region, start, onsetEnd - start, `the onset "${onsetRaw}" has no mandatory sign; the value is unambiguous, so the TAL was ` +
             'kept and the onset read as positive');
     }
     if (outsideInt64(onsetTicks)) {
-        logIssue(log, 'TAL_MALFORMED', region, start, onsetEnd - start, `the onset "${onsetRaw}" is outside the +/-2^63 tick range edfcore can represent, so the ` +
+        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 ` +
             'TAL was skipped');
         return { tal: undefined, next };
     }
@@ -219,14 +220,14 @@ function scanTal(region, start, ordinal, log) {
         const durationStart = separator + 1;
         const durationLength = timestampEnd - durationStart;
         if (durationLength > MAX_TIMESTAMP_FIELD_CHARS) {
-            logIssue(log, 'TAL_MALFORMED', region, durationStart, durationLength, `the duration field is ${durationLength} bytes long, which no time in 100 ns ticks ` +
+            logIssue(log, 'TAL_MALFORMED', 'duration-field-too-long', region, durationStart, durationLength, `the duration field is ${durationLength} bytes long, which no time in 100 ns ticks ` +
                 'needs; the TAL was skipped');
             return { tal: undefined, next };
         }
         durationRaw = decodeHeaderLatin1(sliceBytes(region, durationStart, durationLength));
         const duration = parseUnsignedTicks(durationRaw);
         if (!duration.ok || outsideInt64(duration.ticks)) {
-            logIssue(log, 'TAL_MALFORMED', region, durationStart, Math.max(durationLength, 1), `0x15 is present but the duration "${durationRaw}" is not 1*DIGIT [ "." 1*DIGIT ] — a ` +
+            logIssue(log, 'TAL_MALFORMED', 'duration-grammar', region, durationStart, Math.max(durationLength, 1), `0x15 is present but the duration "${durationRaw}" is not 1*DIGIT [ "." 1*DIGIT ] — a ` +
                 'duration is never signed — so the TAL was skipped');
             return { tal: undefined, next };
         }
@@ -243,7 +244,7 @@ function scanTal(region, start, ordinal, log) {
     if (runStart < bodyEnd) {
         // The grammar terminates every text with 0x14, so a run left over here means the last text
         // ran straight into the TAL terminator. The bytes are unambiguous, so the text is kept.
-        logIssue(log, 'TAL_MALFORMED', region, runStart, bodyEnd - runStart, 'the last text of the TAL is not terminated by 0x14; the text was kept verbatim');
+        logIssue(log, 'TAL_MALFORMED', 'last-text-unterminated', region, runStart, bodyEnd - runStart, 'the last text of the TAL is not terminated by 0x14; the text was kept verbatim');
         texts.push(readTextRun(region, runStart, bodyEnd, log));
     }
     return {
@@ -262,7 +263,7 @@ function scanTal(region, start, ordinal, log) {
 }
 function readTextRun(region, start, end, log) {
     if (indexOfByte(region, start, end, TAL_ONSET_DURATION_SEPARATOR) >= 0) {
-        logIssue(log, 'TAL_MALFORMED', region, start, end - start, 'a text run contains 0x15, which the grammar reserves for the onset/duration separator; ' +
+        logIssue(log, 'TAL_MALFORMED', 'text-contains-separator', region, start, end - start, 'a text run contains 0x15, which the grammar reserves for the onset/duration separator; ' +
             'the text was kept verbatim');
     }
     return decodeTextRun(region, start, end - start, log);
@@ -290,7 +291,7 @@ export function parseTalRegion(bytes, regionStart, regionBytes) {
                 scan += 1;
             if (scan === regionBytes)
                 break;
-            logIssue(log, 'TAL_REGION_NOT_NUL_TERMINATED', region, scan, regionBytes - scan, 'the region tail after the last TAL is not all 0x00; parsing resumed at this byte');
+            logIssue(log, 'TAL_REGION_NOT_NUL_TERMINATED', 'region-tail-not-nul', region, scan, regionBytes - scan, 'the region tail after the last TAL is not all 0x00; parsing resumed at this byte');
             // A TAL found after padding did not begin the region, so it must never be promoted into
             // the timekeeping role: slot 0 is a position, not "the first TAL we managed to parse".
             if (ordinal === 0)

package/dist/tal/grammar.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "edfcore",
-  "version": "0.3.18",
+  "version": "0.3.19",
   "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 = '0.3.18';
+export const VERSION = '0.3.19';

package/src/tal/annotations.ts

@@ -273,6 +273,26 @@ interface TimekeepingDefect {
 }
 
 function timekeepingDefect(tal: ParsedTal): TimekeepingDefect | undefined {
+  // TEXT IS TESTED FIRST, and the order is the whole point. A TAL can be wrong in more than one
+  // way at once, and this returns at the first match — so asking about the benign duration before
+  // the destructive text classified a TAL that loses an annotation as one that loses nothing. It
+  // was then capped at one report per call, under a message ending "nothing was lost".
+  //
+  // 0.2.33 fixed the same swallowing by splitting the once-per-call flag between the two kinds,
+  // and left this order alone; the test written for it builds a timekeeping TAL with text and NO
+  // duration, so the combination stayed uncovered. A writer that merges a scored epoch into the
+  // timekeeping TAL writes both (fixed in 0.3.19).
+  const texts = tal.texts.map((run) => run.text).filter((text) => text.length > 0);
+  if (texts.length > 0) {
+    const strayDuration =
+      tal.durationRaw === undefined ? '' : ` (and the duration "${tal.durationRaw}")`;
+    return {
+      reason:
+        `carries the text ${texts.map((text) => `"${text}"`).join(', ')}${strayDuration}, which ` +
+        'is dropped: the timekeeping TAL is not an annotation',
+      destructive: true,
+    };
+  }
   if (tal.durationRaw !== undefined) {
     return {
       reason: `carries the duration "${tal.durationRaw}", which a timekeeping TAL never has`,
@@ -287,15 +307,6 @@ function timekeepingDefect(tal: ParsedTal): TimekeepingDefect | undefined {
       destructive: false,
     };
   }
-  const texts = tal.texts.map((run) => run.text).filter((text) => text.length > 0);
-  if (texts.length > 0) {
-    return {
-      reason:
-        `carries the text ${texts.map((text) => `"${text}"`).join(', ')}, which is dropped: the ` +
-        'timekeeping TAL is not an annotation',
-      destructive: true,
-    };
-  }
   if (tal.texts.length > 1) {
     return {
       reason: `carries ${tal.texts.length} empty texts, where the grammar allows exactly one`,

package/src/tal/grammar.ts

@@ -133,7 +133,8 @@ interface MutableTalIssue {
   raw: string;
 }
 
-type IssueLog = Map<TalIssueCode, MutableTalIssue>;
+/** Keyed by `${code}|${kind}`, not by code alone. See `TalIssueKind`. */
+type IssueLog = Map<string, MutableTalIssue>;
 
 interface TalScan {
   readonly tal: ParsedTal | undefined;
@@ -210,20 +211,53 @@ export function previewBytes(bytes: Uint8Array, offset: number, length: number):
   return length > shown ? `${text}...` : text;
 }
 
+/**
+ * Which defect this is, within its code. A FIXED, closed set.
+ *
+ * `TAL_MALFORMED` covers nine structurally different defects, and their dispositions are
+ * opposites: a 0x15 inside a text run and a missing onset sign KEEP the TAL, while a bad onset, an
+ * over-long field, an out-of-range onset, a bad duration and an unterminated timestamp DISCARD it.
+ * Collapsing on the code alone let the first one in a region win the `detail`, the offset and the
+ * `raw`, so a region holding one of each reported "the text was kept verbatim" with occurrences 2
+ * while an annotation had in fact been thrown away — and reversing the two TALs produced the
+ * mirror-image lie. `TalIssue.detail` promises to state "what was wrong AND what was done about
+ * it", which is exactly what that broke (fixed in 0.3.19).
+ *
+ * The key is this tag rather than the `detail` string, because several details interpolate the
+ * 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.
+ */
+type TalIssueKind =
+  | 'text-not-utf8'
+  | 'tal-unterminated'
+  | 'timestamp-unterminated'
+  | 'onset-field-too-long'
+  | 'onset-grammar'
+  | 'onset-unsigned'
+  | 'onset-out-of-range'
+  | 'duration-field-too-long'
+  | 'duration-grammar'
+  | 'last-text-unterminated'
+  | 'text-contains-separator'
+  | 'region-tail-not-nul';
+
 function logIssue(
   log: IssueLog,
   code: TalIssueCode,
+  kind: TalIssueKind,
   region: Uint8Array,
   offset: number,
   length: number,
   detail: string,
 ): void {
-  const existing = log.get(code);
+  const key = `${code}|${kind}`;
+  const existing = log.get(key);
   if (existing !== undefined) {
     existing.occurrences += 1;
     return;
   }
-  log.set(code, {
+  log.set(key, {
     code,
     byteOffsetInRegion: offset,
     byteLength: length,
@@ -271,6 +305,7 @@ function decodeTextRun(region: Uint8Array, start: number, length: number, log: I
   logIssue(
     log,
     'ANNOTATION_TEXT_NOT_UTF8',
+    'text-not-utf8',
     region,
     start,
     length,
@@ -306,6 +341,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_TRUNCATED_AT_REGION_END',
+      'tal-unterminated',
       region,
       start,
       regionLength - start,
@@ -321,6 +357,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'timestamp-unterminated',
       region,
       start,
       bodyEnd - start,
@@ -336,6 +373,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'onset-field-too-long',
       region,
       start,
       onsetEnd - start,
@@ -356,6 +394,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
       logIssue(
         log,
         'TAL_MALFORMED',
+        'onset-grammar',
         region,
         start,
         Math.max(onsetEnd - start, 1),
@@ -368,6 +407,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'onset-unsigned',
       region,
       start,
       onsetEnd - start,
@@ -379,6 +419,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'onset-out-of-range',
       region,
       start,
       onsetEnd - start,
@@ -397,6 +438,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
       logIssue(
         log,
         'TAL_MALFORMED',
+        'duration-field-too-long',
         region,
         durationStart,
         durationLength,
@@ -411,6 +453,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
       logIssue(
         log,
         'TAL_MALFORMED',
+        'duration-grammar',
         region,
         durationStart,
         Math.max(durationLength, 1),
@@ -435,6 +478,7 @@ function scanTal(region: Uint8Array, start: number, ordinal: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'last-text-unterminated',
       region,
       runStart,
       bodyEnd - runStart,
@@ -463,6 +507,7 @@ function readTextRun(region: Uint8Array, start: number, end: number, log: IssueL
     logIssue(
       log,
       'TAL_MALFORMED',
+      'text-contains-separator',
       region,
       start,
       end - start,
@@ -502,6 +547,7 @@ export function parseTalRegion(
       logIssue(
         log,
         'TAL_REGION_NOT_NUL_TERMINATED',
+        'region-tail-not-nul',
         region,
         scan,
         regionBytes - scan,