FIX Patch emscripten to fix problems with dup (#1823)

docs/project/changelog.md

@@ -69,6 +69,13 @@ substitutions:
 
 - {{Fix}} pillow now correctly encodes/decodes JPEG image format. {pr}`1818`
 
+### Micellaneous
+
+- {{Fix}} Patched emscripten to make the system calls to duplicate file
+  descriptors closer to posix-compliant. In particular, this fixes the use of
+  `dup` on pipes and temporary files, as needed by `pytest`.
+  {pr}`1823`
+
 ## Version 0.18.0
 
 _August 3rd, 2021_

emsdk/patches/fix-dup.patch

@@ -0,0 +1,75 @@
+From 52c0b163bad96cde2081c734680b9ec485fea908 Mon Sep 17 00:00:00 2001
+From: Hood <hood@mit.edu>
+Date: Wed, 8 Sep 2021 17:49:15 -0700
+Subject: [PATCH] Fix dup
+
+---
+ src/library_syscall.js           | 12 ++++++------
+ tests/third_party/posixtestsuite |  2 +-
+ 2 files changed, 7 insertions(+), 7 deletions(-)
+
+This should fix two problems with the `dup` system calls:
+1. Pipes cannot be duplicated (https://github.com/emscripten-core/emscripten/issues/14640)
+2. `TemporaryFiles` cannot be duplicated (https://github.com/emscripten-core/emscripten/issues/15012)
+
+Both of these issues cause trouble with pytest. There is an upstream pull request that would fix this problem:
+https://github.com/emscripten-core/emscripten/pull/9396/files
+
+This patch only partially resolves the problems with `dup` (it doesn't fully duplicate the changes in the emscripten PR) but I think it will be good enough to fix pytest.
+
+diff --git a/emsdk/upstream/emscripten/src/library_syscall.js b/emsdk/upstream/emscripten/src/library_syscall.js
+index 96d2ec0c3..0001624ec 100644
+--- a/emsdk/upstream/emscripten/src/library_syscall.js
++++ b/emsdk/upstream/emscripten/src/library_syscall.js
+@@ -137,10 +137,10 @@ var SyscallsLibrary = {
+       }
+       return 0;
+     },
+-    doDup: function(path, flags, suggestFD) {
++    doDup: function(stream, suggestFD) {
+       var suggest = FS.getStream(suggestFD);
+       if (suggest) FS.close(suggest);
+-      return FS.open(path, flags, 0, suggestFD, suggestFD).fd;
++      return FS.createStream(stream, suggestFD, suggestFD).fd;
+     },
+     doReadv: function(stream, iov, iovcnt, offset) {
+       var ret = 0;
+@@ -380,7 +380,7 @@ var SyscallsLibrary = {
+   },
+   __sys_dup: function(fd) {
+     var old = SYSCALLS.getStreamFromFD(fd);
+-    return FS.open(old.path, old.flags, 0).fd;
++    return FS.createStream(old, 0).fd;
+   },
+   __sys_pipe__deps: ['$PIPEFS'],
+   __sys_pipe: function(fdPtr) {
+@@ -472,7 +472,7 @@ var SyscallsLibrary = {
+   __sys_dup2: function(oldfd, suggestFD) {
+     var old = SYSCALLS.getStreamFromFD(oldfd);
+     if (old.fd === suggestFD) return suggestFD;
+-    return SYSCALLS.doDup(old.path, old.flags, suggestFD);
++    return SYSCALLS.doDup(old, suggestFD);
+   },
+   __sys_getppid__nothrow: true,
+   __sys_getppid__proxy: false,
+@@ -1167,7 +1167,7 @@ var SyscallsLibrary = {
+           return -{{{ cDefine('EINVAL') }}};
+         }
+         var newStream;
+-        newStream = FS.open(stream.path, stream.flags, 0, arg);
++        newStream = FS.createStream(stream, arg);
+         return newStream.fd;
+       }
+       case {{{ cDefine('F_GETFD') }}}:
+@@ -1403,7 +1403,7 @@ var SyscallsLibrary = {
+     assert(!flags);
+ #endif
+     if (old.fd === suggestFD) return -{{{ cDefine('EINVAL') }}};
+-    return SYSCALLS.doDup(old.path, old.flags, suggestFD);
++    return SYSCALLS.doDup(old, suggestFD);
+   },
+   __sys_pipe2__nothrow: true,
+   __sys_pipe2__proxy: false,
+-- 
+2.17.1
+

src/tests/test_pyodide.py

@@ -2,6 +2,7 @@ import pytest
 from pathlib import Path
 import sys
 from textwrap import dedent
+from pyodide_build.testing import run_in_pyodide
 
 sys.path.append(str(Path(__file__).resolve().parents[2] / "src" / "py"))
 
@@ -158,6 +159,41 @@ def test_eval_code_locals():
     eval_code("invalidate_caches()", globals, locals)
 
 
+@run_in_pyodide
+def test_dup_pipe():
+    # See https://github.com/emscripten-core/emscripten/issues/14640
+    import os
+
+    [fdr1, fdw1] = os.pipe()
+    fdr2 = os.dup(fdr1)
+    fdw2 = os.dup2(fdw1, 50)
+    # Closing any of fdr, fdr2, fdw, or fdw2 will currently destroy the pipe.
+    # This bug is fixed upstream:
+    # https://github.com/emscripten-core/emscripten/pull/14685
+    s1 = b"some stuff"
+    s2 = b"other stuff to write"
+    os.write(fdw1, s1)
+    assert os.read(fdr2, 100) == s1
+    os.write(fdw2, s2)
+    assert os.read(fdr1, 100) == s2
+
+
+@run_in_pyodide
+def test_dup_temp_file():
+    # See https://github.com/emscripten-core/emscripten/issues/15012
+    import os
+    from tempfile import TemporaryFile
+
+    tf = TemporaryFile(buffering=0)
+    fd1 = os.dup(tf.fileno())
+    fd2 = os.dup2(tf.fileno(), 50)
+    s = b"hello there!"
+    tf.write(s)
+    # This next assertion actually demonstrates a bug in dup: the correct value
+    # to return should be b"".
+    assert os.read(fd1, 50) == s
+
+
 @pytest.mark.skip_pyproxy_check
 def test_monkeypatch_eval_code(selenium):
     try: