def apply_patch(original, patchfile, reverse=False, fuzz=2):
"""Apply a patch with optional fuzz - uses the commandline 'patch' utility."""
result = tempfile.NamedTemporaryFile(delete=False)
try:
# We open the file again to avoid race-conditions with multithreaded reads
with open(original.name) as fp:
shutil.copyfileobj(fp, result)
result.close()
cmdline = ["patch", "--no-backup-if-mismatch", "--force", "--silent", "-r", "-"]
if reverse: cmdline.append("--reverse")
if fuzz != 2: cmdline.append("--fuzz=%d" % fuzz)
cmdline += [result.name, patchfile.name]
exitcode = subprocess.call(cmdline, stdout=_devnull, stderr=_devnull)
if exitcode != 0:
raise PatchApplyError("Failed to apply patch (exitcode %d)." % exitcode)
# Hack - we can't keep the file open while patching ('patch' might rename/replace
# the file), so create a new _TemporaryFileWrapper object for the existing path.
return tempfile._TemporaryFileWrapper(file=open(result.name, 'r+b'), \
name=result.name, delete=True)
except:
os.unlink(result.name)
raise
def apply_patch(original, patchfile, reverse=False, fuzz=2):
"""Apply a patch with optional fuzz - uses the commandline 'patch' utility."""
result = tempfile.NamedTemporaryFile(delete=False)
try:
# We open the file again to avoid race-conditions with multithreaded reads
with open(original.name) as fp:
shutil.copyfileobj(fp, result)
result.close()
cmdline = [
"patch", "--no-backup-if-mismatch", "--force", "--silent", "-r",
"-"
]
if reverse: cmdline.append("--reverse")
if fuzz != 2: cmdline.append("--fuzz=%d" % fuzz)
cmdline += [result.name, patchfile.name]
exitcode = subprocess.call(cmdline, stdout=_devnull, stderr=_devnull)
if exitcode != 0:
raise PatchApplyError("Failed to apply patch (exitcode %d)." %
exitcode)
# Hack - we can't keep the file open while patching ('patch' might rename/replace
# the file), so create a new _TemporaryFileWrapper object for the existing path.
return tempfile._TemporaryFileWrapper(file=open(result.name, 'r+b'), \
name=result.name, delete=True)
except:
os.unlink(result.name)
raise
def hardlink(path, suffix='', prefix='didjvu.', dir=None):
new_path = name(suffix=suffix, prefix=prefix, dir=dir)
os.link(path, new_path)
return tempfile._TemporaryFileWrapper(
open(new_path, 'r+b'),
new_path
)
def _tempfile(self):
w, name = self.temp_maker()
r = os.open(name, os.O_RDONLY)
self._set_cloexec_flag(w)
# TODO: bufsize?
r = open(name, 'rU' if self.universal_newlines else 'rb', 0)
r = tempfile._TemporaryFileWrapper(r, name)
self._set_cloexec_flag(r.fileno())
return r, w
def _tempfile(self):
w, name = self.temp_maker()
r = os.open(name, os.O_RDONLY)
self._set_cloexec_flag(w)
# TODO: bufsize?
r = open(name, 'rU' if self.universal_newlines else 'rb', 0)
r = tempfile._TemporaryFileWrapper(r, name)
self._set_cloexec_flag(r.fileno())
return r, w
def _try_create_desired_file(mode, bufsize, dir_path, desired_name, delete):
# try to match desired_name directly
# most of this code is adapted from the tempfile source
# pylint: disable=W0212
if 'b' in mode:
flags = tempfile._bin_openflags
else:
flags = tempfile._text_openflags
fd = os.open(os.path.join(dir_path, desired_name), flags, 0600)
tempfile._set_cloexec(fd)
file_name = os.path.abspath(os.path.join(dir_path, desired_name))
file_handle = os.fdopen(fd, mode, bufsize)
return tempfile._TemporaryFileWrapper(file_handle, file_name, delete)
def open_concrete(self, delete: bool = True) -> IO[bytes]:
if self._concrete_path and os.path.isfile(self._concrete_path):
return open(self._concrete_path, "rb") # noqa: SIM115
file_path = os.path.join(self.parent_file.container_temp_root,
self.path_in_container)
os.makedirs(os.path.dirname(file_path), exist_ok=True)
tf = open(file_path, "wb") # noqa: SIM115
self.extract(tf)
tf.seek(0)
self._concrete_path = tf.name
return tempfile._TemporaryFileWrapper(tf, tf.name,
delete=delete) # type: ignore
def _try_create_desired_file(mode, bufsize, dir_path, desired_name, delete):
# try to match desired_name directly
# most of this code is adapted from the tempfile source
# pylint: disable=W0212
if 'b' in mode:
flags = tempfile._bin_openflags
else:
flags = tempfile._text_openflags
fd = os.open(os.path.join(dir_path, desired_name), flags, 0600)
tempfile._set_cloexec(fd)
file_name = os.path.abspath(os.path.join(dir_path, desired_name))
file_handle = os.fdopen(fd, mode, bufsize)
return tempfile._TemporaryFileWrapper(file_handle, file_name, delete)
def __init__(self, mode='w+b', bufsize=-1, suffix=["shp", "dbf", "shx"],
prefix=tmp.template, dir=None, delete=True):
from collections import Counter
super(NamedTemporaryFiles, self).__init__()
# first check whether no invalid suffix is part
suffix = list(suffix)
for s in (s for s in suffix if not s):
raise ValueError("Empty suffixes are not allowed!")
# now check whether one suffix occurs multiple times
for item in (item for item in Counter(suffix).items() if item[1] > 1):
raise ValueError("Found suffix %s multiple (%i) times!" % item)
suffix = ['.'+s for s in suffix]
files = [0] * len(suffix)
success = False
for _ in xrange(tmp.TMP_MAX):
f = tmp.NamedTemporaryFile(
mode=mode, bufsize=bufsize, suffix=suffix[0], prefix=prefix,
dir=dir, delete=delete)
basename = os.path.splitext(f.name)[0]
success = all(not os.path.exists(basename+s) for s in suffix[1:])
if success:
break
if not success:
f.close()
raise IOError("No usable temporary file name found")
if 'b' in mode:
flags = tmp._bin_openflags
else:
flags = tmp._text_openflags
# Setting O_TEMPORARY in the flags causes the OS to delete
# the file when it is closed. This is only supported by Windows.
if os.name == 'nt' and delete:
flags |= os.O_TEMPORARY
files[0] = f
for i, s in enumerate(suffix[1:], start=1):
fd = os.open(basename+s, flags, 0600)
tmp._set_cloexec(fd)
f = os.fdopen(fd, mode, bufsize)
files[i] = tmp._TemporaryFileWrapper(f, basename+s, delete=delete)
self.name = basename
self.update(zip([s[1:] for s in suffix], files))
def tmpfile(self, prefix=None, suffix=".tmp", fullname=None,
delete=None):
if delete is None:
delete = self.delete
if fullname is not None:
path = self.pathname(fullname)
f = open(path, "w+")
if delete:
f = _TemporaryFileWrapper(f, f.name)
else:
if prefix is None:
prefix = self.name + "_"
else:
prefix = "{0}_{1}_".format(self.name, prefix)
f = NamedTemporaryFile(prefix=prefix, suffix=suffix,
dir=self.directory, delete=delete)
self.memory.append(f)
return f
def tmpfile(self, prefix=None, suffix=".tmp", fullname=None, delete=None):
if delete is None:
delete = self.delete
if fullname is not None:
path = self.pathname(fullname)
f = open(path, "w+")
if delete:
f = _TemporaryFileWrapper(f, f.name)
else:
if prefix is None:
prefix = self.name + "_"
else:
prefix = "{0}_{1}_".format(self.name, prefix)
f = NamedTemporaryFile(prefix=prefix,
suffix=suffix,
dir=self.directory,
delete=delete)
self.memory.append(f)
return f
def get_named_tempfile(delete):
try:
return tempfile.NamedTemporaryFile(delete=delete)
except TypeError:
if os.name == "nt":
dir_ = tempfile.gettempdir()
flags = tempfile._bin_openflags
if delete:
flags |= os.O_TEMPORARY
(fd, name) = tempfile._mkstemp_inner(dir_, "tmp", "", flags)
f = os.fdopen(fd, "w+b", -1)
return tempfile._TemporaryFileWrapper(f, name)
else:
f = tempfile.NamedTemporaryFile()
if not delete:
def close():
f.close_called = True
f.file.close()
f.close = close
return f
def SharedTemporaryFile(
mode="w+b",
buffering=-1,
encoding=None,
newline=None,
suffix="",
prefix=template,
dir=None,
delete=True,
communicator=parallelComm,
):
"""Create a temporary file shared by all MPI ranks.
The file is created as `NamedTemporaryFile` would do it.
The name of the returned file-like object is accessible as its
``name`` attribute. The file will be automatically deleted when it
is closed unless the `delete` argument is set to False.
>>> from fipy.tools import SharedTemporaryFile, parallelComm
>>> with SharedTemporaryFile(mode='w+', suffix=".tmp") as tmpFile:
... # write on processor 0
... if parallelComm.procID == 0:
... _ = tmpFile.write("shared text")
...
... parallelComm.Barrier()
...
... # read on all processors
... _ = tmpFile.seek(0)
... txt = tmpFile.read()
>>> print(txt)
shared text
Parameters
----------
prefix, suffix, dir : str
As for mkstemp
mode : str
The mode argument to io.open (default "w+b")
buffering : int
The buffer size argument to io.open (default -1)
encoding : str or None
The encoding argument to io.open (default None)
newline : str or None
The newline argument to io.open (default None)
delete : bool
Whether the file is deleted on close (default True)
communicator : ~fipy.tools.comms.commWrapper.CommWrapper
MPI communicator describing ranks to share with. A duck-typed
object with `procID` and `Nproc` attributes is sufficient.
Returns
-------
file-like object
See Also
--------
tempfile.NamedTemporaryFile, tempfile.mkstemp, io.open
"""
if communicator.procID == 0:
file = NamedTemporaryFile(
mode=mode,
buffering=buffering,
encoding=encoding,
newline=newline,
suffix=suffix,
prefix=prefix,
dir=dir,
delete=delete,
)
fname = file.name
else:
fname = None
fname = communicator.bcast(fname)
if communicator.procID != 0:
file = _io.open(fname,
mode,
buffering=buffering,
newline=newline,
encoding=encoding)
# let procID 0 handle delete
file = _TemporaryFileWrapper(file, fname, delete=False)
return file