npm - edf2csv - Versions diffs - 0.2.29 → 0.2.31 - Mend

edf2csv 0.2.29 → 0.2.31

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 (8) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -3,6 +3,55 @@
 Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
 major version is 0, a minor bump may contain breaking changes.
+## 0.2.31
+### Fixed: asking for more of a recording returned fewer annotations
+0.2.4 stopped a plain conversion from dropping events that sit at or past the last sample — an
+end-of-recording marker lives at exactly `duration`. But the filter used the window *after* it was
+clamped to the recording, so any request that extended past the data collapsed back onto `[0, duration)`:
+```
+edf2csv edges.edf                 ->  2.5, 3, 3.5     (all three)
+edf2csv edges.edf --end 999h      ->  2.5             two lost
+edf2csv edges.edf --start 0       ->  2.5             two lost
+```
+Both of those mean "everything", and both returned less than asking for nothing at all.
+Annotations are now filtered against the bounds actually given. An end the caller did not supply is
+unbounded rather than "the end of the data", so `--end 999h` and `--start 0` behave like a bare run.
+An explicit bound is unchanged: `--end 3` still keeps only the event at 2.5, because 3 is outside a
+half-open `[.., 3)`.
+## 0.2.30
+### Fixed: `--stdout` piped into `head` reported a write failure
+The most ordinary thing you would do with `--stdout` broke it:
+```
+$ edf2csv big.edf --stdout | head -1
+time_s,ch1
+error: Writing to stdout failed: write EPIPE
+       The files written so far are incomplete and should not be used. Free up space or
+       choose another destination with --out, then run the conversion again.
+exit 1
+```
+Three things wrong at once — exit 1 for a routine shell idiom, a claim about files that were never
+written, and advice about disk space and `--out` that had nothing to do with it.
+`EPIPE` is the reader hanging up, not a write failure, and a file stream cannot raise it. The
+buffered writer now treats it as a clean end: writing stops, the run exits 0, and whatever the reader
+did take is intact. Genuine write failures — a full disk, an unwritable path — are unaffected and
+still exit 1 with their message.
+It needed handling in two places. The writer's `error` listener catches a pipe that closes during a
+write; a separate listener, registered only while waiting for `drain`, sees one that closes while the
+consumer is behind. Only the first was obvious, and a long conversion is precisely the case that
+reaches the second.
 ## 0.2.29
 ### Docs: the scripting advice caught up with `--strict`, `--info --json` and `--stdout`

package/dist/convert/run.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/convert/run.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AASH,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAE3C,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAMnD,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAa,MAAM,WAAW,CAAC;AAGxE,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,eAAe,CAAC;AAExD,OAAO,EAAE,YAAY,EAAE,CAAC;AAExB,MAAM,MAAM,mBAAmB,GAC3B,eAAe,GACf,mBAAmB,GACnB,wBAAwB,GACxB,cAAc,CAAC;AAEnB,qBAAa,eAAgB,SAAQ,KAAK;IACxC,QAAQ,CAAC,IAAI,EAAE,mBAAmB,CAAC;IACnC,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;gBACtB,IAAI,EAAE,mBAAmB,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,MAAM;CAMtE;AAED,MAAM,WAAW,cAAe,SAAQ,WAAW;IACjD,sFAAsF;IACtF,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,8CAA8C;IAC9C,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,wFAAwF;IACxF,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC/B;;;;;;OAMG;IACH,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC/B,UAAU,CAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,kBAAkB,KAAK,IAAI,CAAC,GAAG,SAAS,CAAC;CACnE;AAED,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,WAAW,EAAE,CAAC;IACrB,eAAe,EAAE,MAAM,CAAC;IACxB,WAAW,EAAE,UAAU,EAAE,CAAC;IAC1B,IAAI,EAAE,cAAc,CAAC;IACrB,IAAI,EAAE,OAAO,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;CACnB;AASD,wBAAsB,OAAO,CAAC,SAAS,EAAE,MAAM,EAAE,OAAO,GAAE,cAAmB,GAAG,OAAO,CAAC,aAAa,CAAC,~~CA0GrG~~;AAqDD,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAG1D"}
1	+ {"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/convert/run.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AASH,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAE3C,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAMnD,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAa,MAAM,WAAW,CAAC;AAGxE,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,eAAe,CAAC;AAExD,OAAO,EAAE,YAAY,EAAE,CAAC;AAExB,MAAM,MAAM,mBAAmB,GAC3B,eAAe,GACf,mBAAmB,GACnB,wBAAwB,GACxB,cAAc,CAAC;AAEnB,qBAAa,eAAgB,SAAQ,KAAK;IACxC,QAAQ,CAAC,IAAI,EAAE,mBAAmB,CAAC;IACnC,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;gBACtB,IAAI,EAAE,mBAAmB,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,MAAM;CAMtE;AAED,MAAM,WAAW,cAAe,SAAQ,WAAW;IACjD,sFAAsF;IACtF,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,8CAA8C;IAC9C,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,wFAAwF;IACxF,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC/B;;;;;;OAMG;IACH,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC/B,UAAU,CAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,kBAAkB,KAAK,IAAI,CAAC,GAAG,SAAS,CAAC;CACnE;AAED,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,WAAW,EAAE,CAAC;IACrB,eAAe,EAAE,MAAM,CAAC;IACxB,WAAW,EAAE,UAAU,EAAE,CAAC;IAC1B,IAAI,EAAE,cAAc,CAAC;IACrB,IAAI,EAAE,OAAO,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;CACnB;AASD,wBAAsB,OAAO,CAAC,SAAS,EAAE,MAAM,EAAE,OAAO,GAAE,cAAmB,GAAG,OAAO,CAAC,aAAa,CAAC,CAyGrG;AAqDD,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAG1D"}

package/dist/convert/run.js CHANGED Viewed

@@ -87,7 +87,7 @@ export async function convert(inputPath, options = {}) {
         }
         let annotationsWritten = 0;
         if (file.annotationSignals.length > 0) {
-            const result = await writeAnnotationsCsv(outputDir, annotationData.annotations, plan, options.start !== undefined || options.end !== undefined || options.duration !== undefined);
+            const result = await writeAnnotationsCsv(outputDir, annotationData.annotations, requestedAnnotationWindow(options));
             written.push(result);
             annotationsWritten = result.rows;
         }
@@ -375,23 +375,30 @@ async function writeChannelsCsv(outputDir, file, plan) {
     await writeOutputFile(outputDir, 'channels.csv', lines.join('\n') + '\n');
     return { name: 'channels.csv', rows: lines.length - 1 };
 }
-async function writeAnnotationsCsv(outputDir, annotations, plan, windowRequested) {
-    const { startSeconds, endSeconds } = plan.range;
-    /*
-      Filter only when the caller actually asked for a window.
-      EDF+ does not oblige an annotation's onset to fall inside the data span: a marker for
-      the end of a recording sits at exactly `duration`, and files carry markers at negative
-      onsets ahead of the first record. The window on a whole-file conversion is
-      [0, duration), so filtering by it unconditionally dropped both from a plain
-      `edf2csv recording.edf` with no time options given, and no flag could ask for them back.
-      The test is whether a window was requested, not whether the resolved one happens to
-      cover everything: `--end 3` on a three-second recording resolves to the whole file but
-      is still an explicit request for [0, 3), and an event at exactly 3 belongs outside it.
-    */
+/*
+  The bounds an annotation is filtered against: what the caller actually asked for, not the
+  window that survived being clamped to the recording.
+  Filtering by the resolved window meant an unbounded request still lost events. `--end 999h`
+  on a three-second file clamps to 3, and `--start 0` gets its end from the recording, so
+  both filtered to [0, 3) and dropped the markers at 3.0 and 3.5 that a bare invocation
+  keeps — asking for more of a recording returned less of it.
+  An end the caller did not give is unbounded, not "the end of the data": EDF+ lets an
+  annotation sit past the last sample, which is exactly where an end-of-recording marker is.
+*/
+function requestedAnnotationWindow(options) {
+    const from = options.start ?? -Infinity;
+    const to = options.end !== undefined
+        ? options.end
+        : options.duration !== undefined
+            ? (options.start ?? 0) + options.duration
+            : Infinity;
+    return { from, to };
+}
+async function writeAnnotationsCsv(outputDir, annotations, window) {
     const inWindow = annotations
-        .filter((a) => !windowRequested || (a.onset >= startSeconds && a.onset < endSeconds))
+        .filter((a) => a.onset >= window.from && a.onset < window.to)
         .sort((a, b) => a.onset - b.onset || a.recordIndex - b.recordIndex);
     const lines = [csvRow(['onset_s', 'duration_s', 'description', 'record_index'])];
     for (const annotation of inWindow) {

package/dist/convert/run.js.map CHANGED Viewed

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

	@@ -1 +1 @@
1	- {"version":3,"file":"csv.d.ts","sourceRoot":"","sources":["../../src/format/csv.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAQ5C,6EAA6E;AAC7E,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAIpD;AAED,wBAAgB,MAAM,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAEvD;AAED;;;;;GAKG;AACH,qBAAa,kBAAkB;;~~gBASjB~~,MAAM,EAAE,QAAQ,EAAE,SAAS,GAAE,MAAgC;~~IAWzE~~,8EAA8E;IAC9E,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,IAAI,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAKxB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAK5B,qEAAqE;IAC/D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAI3B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;~~IA2C5B~~,gDAAgD;IAC1C,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;IAe1B,oEAAoE;IACpE,OAAO,IAAI,IAAI;CAOhB"}
1	+ {"version":3,"file":"csv.d.ts","sourceRoot":"","sources":["../../src/format/csv.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAQ5C,6EAA6E;AAC7E,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAIpD;AAED,wBAAgB,MAAM,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAEvD;AAED;;;;;GAKG;AACH,qBAAa,kBAAkB;;gBAWjB,MAAM,EAAE,QAAQ,EAAE,SAAS,GAAE,MAAgC;IAwBzE,8EAA8E;IAC9E,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,IAAI,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAKxB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAK5B,qEAAqE;IAC/D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAI3B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAsD5B,gDAAgD;IAC1C,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;IAe1B,oEAAoE;IACpE,OAAO,IAAI,IAAI;CAOhB"}

package/dist/format/csv.js CHANGED Viewed

@@ -34,6 +34,8 @@ export class BufferedLineWriter {
     #threshold;
     #bytesWritten = 0;
     #ended = false;
+    /** The reader closed the pipe; there is nowhere left to write, but this is not a failure. */
+    #hungUp = false;
     #failure = null;
     constructor(stream, threshold = DEFAULT_FLUSH_THRESHOLD) {
         this.#stream = stream;
@@ -42,6 +44,19 @@ export class BufferedLineWriter {
         // process down with a raw stack trace. Capturing the error here lets the next
         // flush surface it as a normal failure with a usable message.
         this.#stream.on('error', (error) => {
+            /*
+              EPIPE is the reader hanging up, not a write failure.
+              `edf2csv recording.edf --stdout | head -1` closes the pipe while the conversion is
+              still writing, and treating that as an error produced exit 1 and a message about
+              files that do not exist and disk space that is not the problem. A file stream
+              cannot raise EPIPE, so this only ever means "the consumer stopped reading", which
+              is what a shell pipeline does routinely and on purpose.
+            */
+            if (error.code === 'EPIPE') {
+                this.#hungUp = true;
+                return;
+            }
             this.#failure ??= error;
         });
     }
@@ -65,6 +80,10 @@ export class BufferedLineWriter {
     async flush() {
         if (this.#failure)
             throw this.#failure;
+        // The reader hung up (see the EPIPE note above); there is nowhere left to write.
+        // Deliberately not `#ended`, which end() sets before its own final flush.
+        if (this.#hungUp)
+            return;
         if (this.#parts.length === 0)
             return;
         const chunk = this.#parts.join('');
@@ -93,6 +112,14 @@ export class BufferedLineWriter {
             };
             const onError = (error) => {
                 cleanup();
+                // A pipe closing while we wait for drain is the same benign hang-up as one
+                // closing during a write, and has to be handled here too: this listener is
+                // registered for the duration of the wait and sees the error first.
+                if (error.code === 'EPIPE') {
+                    this.#hungUp = true;
+                    resolve();
+                    return;
+                }
                 reject(error);
             };
             const onClose = () => {

package/dist/format/csv.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.2.29",
+  "version": "0.2.31",
   "description": "Convert EDF, EDF+ and BDF biosignal recordings (European Data Format) to CSV from the command line. Local, streaming, and never resamples or alters units.",
   "keywords": [
     "edf",