Fix dup in nodefs

Backport of emscripten-core/emscripten#21399. Resolves pyodide#4541

emsdk/patches/0001-Fix-dup-in-nodefs-by-refcounting-nodefs-file-descrip.patch

@@ -0,0 +1,166 @@
+From 135baa3d4cc211c0145d2e1df116e39f60df4f91 Mon Sep 17 00:00:00 2001
+From: Hood Chatham <roberthoodchatham@gmail.com>
+Date: Thu, 22 Feb 2024 21:47:13 -0800
+Subject: [PATCH] Fix dup in nodefs by refcounting nodefs file descriptors
+ (#21399)
+
+---
+ src/library_fs.js         |  5 +++++
+ src/library_nodefs.js     |  6 +++++-
+ src/library_syscall.js    |  6 +++---
+ test/fs/test_nodefs_dup.c | 45 +++++++++++++++++++++++++++++++++++++++
+ test/test_core.py         |  8 +++++++
+ 5 files changed, 66 insertions(+), 4 deletions(-)
+ create mode 100644 test/fs/test_nodefs_dup.c
+
+diff --git a/src/library_fs.js b/src/library_fs.js
+index f5d16b86c..379e65268 100644
+--- a/src/library_fs.js
++++ b/src/library_fs.js
+@@ -471,6 +471,11 @@ FS.staticInit();` +
+     closeStream(fd) {
+       FS.streams[fd] = null;
+     },
++    dupStream(origStream, fd = -1) {
++      var stream = FS.createStream(origStream, fd);
++      stream.stream_ops?.dup?.(stream);
++      return stream;
++    },
+
+     //
+     // devices
+diff --git a/src/library_nodefs.js b/src/library_nodefs.js
+index 81864ffcc..ace50458c 100644
+--- a/src/library_nodefs.js
++++ b/src/library_nodefs.js
+@@ -251,6 +251,7 @@ addToLibrary({
+         var path = NODEFS.realPath(stream.node);
+         try {
+           if (FS.isFile(stream.node.mode)) {
++            stream.shared.refcount = 1;
+             stream.nfd = fs.openSync(path, NODEFS.flagsForNode(stream.flags));
+           }
+         } catch (e) {
+@@ -260,7 +261,7 @@ addToLibrary({
+       },
+       close(stream) {
+         try {
+-          if (FS.isFile(stream.node.mode) && stream.nfd) {
++          if (FS.isFile(stream.node.mode) && stream.nfd && --stream.shared.refcount === 0) {
+             fs.closeSync(stream.nfd);
+           }
+         } catch (e) {
+@@ -268,6 +269,9 @@ addToLibrary({
+           throw new FS.ErrnoError(NODEFS.convertNodeCode(e));
+         }
+       },
++      dup(stream) {
++        stream.shared.refcount++;
++      },
+       read(stream, buffer, offset, length, position) {
+         // Node.js < 6 compatibility: node errors on 0 length reads
+         if (length === 0) return 0;
+diff --git a/src/library_syscall.js b/src/library_syscall.js
+index b078bd71c..69ea6f8b2 100644
+--- a/src/library_syscall.js
++++ b/src/library_syscall.js
+@@ -183,7 +183,7 @@ var SyscallsLibrary = {
+   },
+   __syscall_dup: (fd) => {
+     var old = SYSCALLS.getStreamFromFD(fd);
+-    return FS.createStream(old).fd;
++    return FS.dupStream(old).fd;
+   },
+   __syscall_pipe__deps: ['$PIPEFS'],
+   __syscall_pipe: (fdPtr) => {
+@@ -760,7 +760,7 @@ var SyscallsLibrary = {
+           arg++;
+         }
+         var newStream;
+-        newStream = FS.createStream(stream, arg);
++        newStream = FS.dupStream(stream, arg);
+         return newStream.fd;
+       }
+       case {{{ cDefs.F_GETFD }}}:
+@@ -1007,7 +1007,7 @@ var SyscallsLibrary = {
+     if (old.fd === newfd) return -{{{ cDefs.EINVAL }}};
+     var existing = FS.getStream(newfd);
+     if (existing) FS.close(existing);
+-    return FS.createStream(old, newfd).fd;
++    return FS.dupStream(old, newfd).fd;
+   },
+ };
+
+diff --git a/test/fs/test_nodefs_dup.c b/test/fs/test_nodefs_dup.c
+new file mode 100644
+index 000000000..abf34935b
+--- /dev/null
++++ b/test/fs/test_nodefs_dup.c
+@@ -0,0 +1,45 @@
++/*
++ * Copyright 2018 The Emscripten Authors.  All rights reserved.
++ * Emscripten is available under two separate licenses, the MIT license and the
++ * University of Illinois/NCSA Open Source License.  Both these licenses can be
++ * found in the LICENSE file.
++ */
++
++#include <assert.h>
++#include <emscripten.h>
++#include <fcntl.h>
++#include <stdio.h>
++#include <unistd.h>
++
++#ifdef NODERAWFS
++#define CWD ""
++#else
++#define CWD "/working/"
++#endif
++
++int main(void)
++{
++    EM_ASM(
++#ifdef NODERAWFS
++        FS.close(FS.open('test.txt', 'w'));
++#else
++        FS.mkdir('/working');
++        FS.mount(NODEFS, {root: '.'}, '/working');
++        FS.close(FS.open('/working/test.txt', 'w'));
++#endif
++    );
++    int fd1 = open(CWD "test.txt", O_WRONLY);
++    int fd2 = dup(fd1);
++    int fd3 = fcntl(fd1, F_DUPFD_CLOEXEC, 0);
++
++    assert(fd1 == 3);
++    assert(fd2 == 4);
++    assert(fd3 == 5);
++    assert(close(fd1) == 0);
++    assert(write(fd2, "abcdef", 6) == 6);
++    assert(close(fd2) == 0);
++    assert(write(fd3, "ghijkl", 6) == 6);
++    assert(close(fd3) == 0);
++    printf("success\n");
++    return 0;
++}
+diff --git a/test/test_core.py b/test/test_core.py
+index 3f21eb5ef..f304f1366 100644
+--- a/test/test_core.py
++++ b/test/test_core.py
+@@ -5745,6 +5745,14 @@ Module = {
+     self.emcc_args += ['-lnodefs.js']
+     self.do_runf('fs/test_nodefs_cloexec.c', 'success')
+
++  @also_with_noderawfs
++  @requires_node
++  def test_fs_nodefs_dup(self):
++    if self.get_setting('WASMFS'):
++      self.set_setting('FORCE_FILESYSTEM')
++    self.emcc_args += ['-lnodefs.js']
++    self.do_runf('fs/test_nodefs_dup.c', 'success')
++
+   @requires_node
+   def test_fs_nodefs_home(self):
+     self.set_setting('FORCE_FILESYSTEM')
+-- 
+2.34.1
+