edf2csv 0.4.3 → 0.4.4

package/CHANGELOG.md

@@ -3,6 +3,37 @@
 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

package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"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;AAiaD,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

@@ -10,7 +10,7 @@
 import { parseArgs } from 'node:util';
 import { pathToFileURL, fileURLToPath } from 'node:url';
 import { realpathSync } from 'node:fs';
-import { readdir, stat } from 'node:fs/promises';
+import { readdir, realpath, stat } from 'node:fs/promises';
 import { cpus } from 'node:os';
 import { fork } from 'node:child_process';
 import path from 'node:path';
@@ -483,19 +483,60 @@ async function expandInputs(positionals) {
             found.push({ path: given, name: path.basename(given) });
             continue;
         }
-        for (const entry of await readdir(given, { recursive: true, withFileTypes: true })) {
-            if (!entry.isFile() || !/\.(edf|bdf)$/iu.test(entry.name))
-                continue;
-            // parentPath is the directory the entry was found in, which for a recursive read is
-            // below the one that was asked for.
-            const full = path.join(entry.parentPath ?? given, entry.name);
-            found.push({ path: full, name: path.relative(given, full) });
+        for (const file of await walk(given)) {
+            found.push({ path: file, name: path.relative(given, file) });
         }
     }
-    // A directory hands them back in whatever order the filesystem stored them.
+    // 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.
  *

package/dist/cli.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.4.3",
+  "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",