edf2csv 0.4.2 → 0.4.4

package/CHANGELOG.md

@@ -3,6 +3,69 @@
 Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
 major version is 0, a minor bump may contain breaking changes.
 
+## 0.4.4
+
+### Fixed: a symlinked recording inside a folder was skipped without a word
+
+0.4.3 took a folder as input, and left out any recording that was a symbolic link. A recursive
+`readdir` reports a link as a link and never as a file, so the extension test never saw it:
+
+```
+study/
+  plain.edf
+  link.edf -> /data/real/actual.edf     skipped
+  linkdir  -> /data/real/               skipped, and everything inside it
+```
+
+The run then said `Converted 1 of 1 recordings` — describing what it had noticed rather than
+what the folder held. Linking recordings into a working directory is an ordinary way to arrange
+data, and naming the same link directly on the command line always worked, which made the
+omission harder to notice rather than easier. Converting fewer files than were asked for, and
+reporting a total that agrees with itself, is the failure this tool exists to avoid.
+
+Links are now followed, to recordings and to folders alike. Two consequences, both deliberate:
+
+- **A cycle terminates.** `study/sub/loop -> study` is legal and would otherwise be walked
+  forever. Directories are recorded by their resolved identity and visited once.
+- **A recording reachable two ways is converted once.** Where `find -L` lists both `link.edf`
+  and `linkdir/actual.edf`, this converts the one recording behind them. The alternative is
+  two output directories holding identical data, and a count that overstates what was there.
+
+The walk is written out rather than delegated to `readdir`'s recursive mode, which cannot
+express either of those.
+
+## 0.4.3
+
+### Added: a folder as input
+
+```bash
+edf2csv /data/study --out ./converted --jobs auto
+```
+
+Every `.edf` and `.bdf` inside is converted, at any depth. Recordings arrive organised into
+folders and a shell has no tidy way to reach them, which is why the recipes here carried a
+`find` incantation to do it. Passing the folder is the obvious thing to try, and until now it
+failed with "is a directory, not an EDF file".
+
+**The layout is kept.** A recording at `study/night-1/rec.edf` comes out at
+`converted/night-1/rec`. That is not only tidiness: one folder per night with the file always
+called `rec.edf` is a normal way to lay out a study, and flattening those onto their file names
+would have every one of them claim `converted/rec` — which 0.4.0 correctly refuses, so the
+whole run would have stopped before writing anything.
+
+Anything in the folder that is not a recording is skipped, and a folder holding none says so
+rather than converting nothing in silence:
+
+```
+No EDF or BDF recordings found in "/data/empty".
+```
+
+A path that is not a directory is passed through untouched, so a file named on the command line
+that does not exist still reports itself instead of quietly vanishing from the list.
+
+Folders and files can be mixed in one command, and everything else — `--jobs`, `--out`,
+`--channels`, the time window — applies to the lot.
+
 ## 0.4.2
 
 ### Added: `--jobs`, converting several recordings at once

package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAaH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA2F9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAoQnE;AAmXD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAcH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA+F9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAgRnE;AA0cD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}

package/dist/cli.js

@@ -10,6 +10,7 @@
 import { parseArgs } from 'node:util';
 import { pathToFileURL, fileURLToPath } from 'node:url';
 import { realpathSync } from 'node:fs';
+import { readdir, realpath, stat } from 'node:fs/promises';
 import { cpus } from 'node:os';
 import { fork } from 'node:child_process';
 import path from 'node:path';
@@ -22,12 +23,13 @@ import { ChannelSelectionError } from './convert/channels.js';
 import { TimeRangeError, parseTimeSpec } from './convert/time-range.js';
 import { deriveRecordStarts } from './convert/timing.js';
 import { formatDiagnostics, formatInfo, infoJson, formatSummary, printable, printableLines, summaryJson } from './cli/report.js';
+import { listed } from './format/list.js';
 import { VERSION } from './version.js';
 const USAGE = `edf2csv ${VERSION}
 Convert EDF, EDF+ and BDF recordings to CSV
 
 Usage
-  edf2csv <recording.edf> [more.edf ...] [options]
+  edf2csv <recording.edf | folder> [more ...] [options]
 
 Options
   -i, --info             Show the recording's structure and estimated output size,
@@ -53,6 +55,8 @@ Options
   -V, --version          Show the version
 
 Several recordings
+  A folder is expanded to every .edf and .bdf inside it, at any depth, and the
+  layout is kept: recordings in sub-folders come out in sub-folders.
   Pass more than one and each is converted in turn. Without --out each lands
   beside itself as usual; with --out that directory becomes the parent and each
   recording gets its own inside it. A file that cannot be read is reported and
@@ -74,6 +78,7 @@ Examples
   edf2csv recording.edf --annotations-only
   edf2csv /data/*.edf --out ./converted
   edf2csv /data/*.edf --out ./converted --jobs auto
+  edf2csv /data/study --out ./converted --jobs auto
 `;
 /** A problem with how the command was invoked, as opposed to a problem with the file. */
 class OptionError extends Error {
@@ -153,7 +158,18 @@ export async function main(argv) {
         process.stderr.write(`No input file given.\n\n${USAGE}`);
         return EXIT_USAGE;
     }
-    const inputs = positionals;
+    let expanded;
+    try {
+        expanded = await expandInputs(positionals);
+    }
+    catch (error) {
+        return reportError(error);
+    }
+    if (expanded.length === 0) {
+        process.stderr.write(`No EDF or BDF recordings found in ${listed(positionals.map((p) => `"${p}"`))}.\n`);
+        return EXIT_USAGE;
+    }
+    const inputs = expanded.map((entry) => entry.path);
     const batch = inputs.length > 1;
     const quiet = values['quiet'] === true;
     const asJson = values['json'] === true;
@@ -190,7 +206,7 @@ export async function main(argv) {
     const jsonIndent = batch ? null : 2;
     try {
         const outOption = typeof values['out'] === 'string' ? values['out'] : undefined;
-        const destinations = destinationsFor(inputs, outOption);
+        const destinations = destinationsFor(expanded, outOption);
         assertDistinct(inputs, destinations);
         const shared = {
             channels: splitChannels(values['channels']),
@@ -449,6 +465,78 @@ async function convertOne(input, destination, options, emit = writeThrough) {
         process.off('SIGTERM', onInterrupt);
     }
 }
+/**
+ * Recordings to convert, with directories expanded to what is inside them.
+ *
+ * A directory yields every `.edf` and `.bdf` beneath it, at any depth. Recordings arrive
+ * organised into folders, and a shell has no tidy way to reach them — which is why the
+ * recipes here carried a `find` incantation to do it. Passing the folder is the obvious
+ * thing to try, and it used to fail with "is a directory, not an EDF file".
+ */
+async function expandInputs(positionals) {
+    const found = [];
+    for (const given of positionals) {
+        const info = await stat(given).catch(() => null);
+        if (info === null || !info.isDirectory()) {
+            // Anything that is not a directory is passed through untouched, so a file that does
+            // not exist still reports itself rather than vanishing from the list.
+            found.push({ path: given, name: path.basename(given) });
+            continue;
+        }
+        for (const file of await walk(given)) {
+            found.push({ path: file, name: path.relative(given, file) });
+        }
+    }
+    // A directory hands its entries back in whatever order the filesystem stored them.
+    found.sort((a, b) => (a.path < b.path ? -1 : a.path > b.path ? 1 : 0));
+    return found;
+}
+/**
+ * Every recording under a directory, following symbolic links.
+ *
+ * Written by hand rather than with a recursive `readdir` because that reports a symlink as
+ * a symlink and never as a file, so a linked recording was skipped without a word — and the
+ * closing "converted 3 of 3" then described the three it had noticed rather than what was in
+ * the folder. Data organised by linking recordings into a working directory is ordinary, and
+ * quietly converting fewer files than were asked for is the failure this tool exists to
+ * avoid. Naming the same link on the command line always worked, which made the omission
+ * harder to notice rather than easier.
+ *
+ * Following links means they can form a cycle, so directories are recorded by their resolved
+ * identity and visited once. A link to a file already reached another way is likewise
+ * converted once.
+ */
+async function walk(root) {
+    const files = [];
+    const seen = new Set();
+    const queue = [root];
+    while (queue.length > 0) {
+        const directory = queue.pop();
+        const real = await realpath(directory).catch(() => directory);
+        if (seen.has(real))
+            continue;
+        seen.add(real);
+        const entries = await readdir(directory, { withFileTypes: true }).catch(() => []);
+        for (const entry of entries) {
+            const full = path.join(directory, entry.name);
+            // stat, not the dirent: a dirent describes the link, and what matters is its target.
+            const info = await stat(full).catch(() => null);
+            if (info === null)
+                continue;
+            if (info.isDirectory()) {
+                queue.push(full);
+            }
+            else if (info.isFile() && /\.(edf|bdf)$/iu.test(entry.name)) {
+                const identity = await realpath(full).catch(() => full);
+                if (seen.has(identity))
+                    continue;
+                seen.add(identity);
+                files.push(full);
+            }
+        }
+    }
+    return files;
+}
 /**
  * Where each recording's output goes.
  *
@@ -462,16 +550,16 @@ async function convertOne(input, destination, options, emit = writeThrough) {
  */
 function destinationsFor(inputs, out) {
     if (out === undefined)
-        return inputs.map((input) => defaultOutputDir(input));
+        return inputs.map((input) => defaultOutputDir(input.path));
     if (inputs.length === 1)
         return [out];
-    return inputs.map((input) => path.join(out, stemOf(input)));
+    return inputs.map((input) => path.join(out, stemOf(input.name)));
 }
-/** File name without its extension, keeping a leading dot: `.hidden.edf` -> `.hidden`. */
-function stemOf(file) {
-    const base = path.basename(file);
-    const dot = base.lastIndexOf('.');
-    return dot > 0 ? base.slice(0, dot) : base;
+/** A name without its extension, keeping a leading dot: `.hidden.edf` -> `.hidden`. */
+function stemOf(name) {
+    const dot = name.lastIndexOf('.');
+    const slash = Math.max(name.lastIndexOf('/'), name.lastIndexOf('\\'));
+    return dot > slash + 1 ? name.slice(0, dot) : name;
 }
 /**
  * Refuse a batch in which two recordings would land in the same directory.

package/dist/cli.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.4.2",
+  "version": "0.4.4",
   "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",