Backport PR #6269: Implement atomic save

this should avoid issues with corrupted/lost notebooks when the disk is full

IPython/html/services/notebooks/filenbmanager.py

@@ -26,6 +26,7 b' from tornado import web'
 
 from .nbmanager import NotebookManager
 from IPython.nbformat import current
+from IPython.utils.io import atomic_writing
 from IPython.utils.traitlets import Unicode, Bool, TraitError
 from IPython.utils.py3compat import getcwd
 from IPython.utils import tz
@@ -304,7 +305,7 b' class FileNotebookManager(NotebookManager):'
             nb['metadata']['name'] = u''
         try:
             self.log.debug("Autosaving notebook %s", os_path)
-            with io.open(os_path, 'w', encoding='utf-8') as f:
+            with atomic_writing(os_path, encoding='utf-8') as f:
                 current.write(nb, f, u'json')
         except Exception as e:
             raise web.HTTPError(400, u'Unexpected error while autosaving notebook: %s %s' % (os_path, e))
@@ -314,7 +315,7 b' class FileNotebookManager(NotebookManager):'
             py_path = os.path.splitext(os_path)[0] + '.py'
             self.log.debug("Writing script %s", py_path)
             try:
-                with io.open(py_path, 'w', encoding='utf-8') as f:
+                with atomic_writing(py_path, encoding='utf-8') as f:
                     current.write(nb, f, u'py')
             except Exception as e:
                 raise web.HTTPError(400, u'Unexpected error while saving notebook as script: %s %s' % (py_path, e))

IPython/utils/io.py

@@ -16,6 +16,8 b' from __future__ import absolute_import'
 # Imports
 #-----------------------------------------------------------------------------
 import codecs
+from contextlib import contextmanager
+import io
 import os
 import sys
 import tempfile
@@ -217,6 +219,61 b" def temp_pyfile(src, ext='.py'):"
     f.flush()
     return fname, f
 
+@contextmanager
+def atomic_writing(path, text=True, encoding='utf-8', **kwargs):
+    """Context manager to write to a file only if the entire write is successful.
+
+    This works by creating a temporary file in the same directory, and renaming
+    it over the old file if the context is exited without an error. If the
+    target file is a symlink or a hardlink, this will not be preserved: it will
+    be replaced by a new regular file.
+
+    On Windows, there is a small chink in the atomicity: the target file is
+    deleted before renaming the temporary file over it. This appears to be
+    unavoidable.
+
+    Parameters
+    ----------
+    path : str
+      The target file to write to.
+
+    text : bool, optional
+      Whether to open the file in text mode (i.e. to write unicode). Default is
+      True.
+
+    encoding : str, optional
+      The encoding to use for files opened in text mode. Default is UTF-8.
+
+    **kwargs
+      Passed to :func:`io.open`.
+    """
+    dirname, basename = os.path.split(path)
+    handle, tmp_path = tempfile.mkstemp(prefix=basename, dir=dirname, text=text)
+    if text:
+        fileobj = io.open(handle, 'w', encoding=encoding, **kwargs)
+    else:
+        fileobj = io.open(handle, 'wb', **kwargs)
+
+    try:
+        yield fileobj
+    except:
+        fileobj.close()
+        os.remove(tmp_path)
+        raise
+
+    # Flush to disk
+    fileobj.flush()
+    os.fsync(fileobj.fileno())
+
+    # Written successfully, now rename it
+    fileobj.close()
+
+    if os.name == 'nt' and os.path.exists(path):
+        # Rename over existing file doesn't work on Windows
+        os.remove(path)
+
+    os.rename(tmp_path, path)
+
 
 def raw_print(*args, **kw):
     """Raw print to sys.__stdout__, otherwise identical interface to print()."""

IPython/utils/tests/test_io.py

@@ -15,6 +15,7 b' from __future__ import print_function'
 from __future__ import absolute_import
 
 import io as stdlib_io
+import os.path
 import sys
 
 from subprocess import Popen, PIPE
@@ -23,8 +24,11 b' import unittest'
 import nose.tools as nt
 
 from IPython.testing.decorators import skipif
-from IPython.utils.io import Tee, capture_output, unicode_std_stream
+from IPython.utils.io import (Tee, capture_output, unicode_std_stream,
+                              atomic_writing,
+                              )
 from IPython.utils.py3compat import doctest_refactor_print, PY3
+from IPython.utils.tempdir import TemporaryDirectory
 
 if PY3:
     from io import StringIO
@@ -121,4 +125,27 b' def test_UnicodeStdStream_nowrap():'
         nt.assert_is(unicode_std_stream(), sys.stdout)
         assert not sys.stdout.closed
     finally:
-        sys.stdout = orig_stdout
  No newline at end of file
+        sys.stdout = orig_stdout
+
+def test_atomic_writing():
+    class CustomExc(Exception): pass
+
+    with TemporaryDirectory() as td:
+        f1 = os.path.join(td, 'penguin')
+        with stdlib_io.open(f1, 'w') as f:
+            f.write(u'Before')
+
+        with nt.assert_raises(CustomExc):
+            with atomic_writing(f1) as f:
+                f.write(u'Failing write')
+                raise CustomExc
+
+        # Because of the exception, the file should not have been modified
+        with stdlib_io.open(f1, 'r') as f:
+            nt.assert_equal(f.read(), u'Before')
+
+        with atomic_writing(f1) as f:
+            f.write(u'Overwritten')
+
+        with stdlib_io.open(f1, 'r') as f:
+            nt.assert_equal(f.read(), u'Overwritten')