guppy_basecaller: env/lib/python3.7/site-packages/setuptools/sandbox.py comparison

comparison env/lib/python3.7/site-packages/setuptools/sandbox.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

author	shellac
date	Sat, 02 May 2020 07:14:21 -0400
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:26e78fe6e8c4
+import os
+import sys
+import tempfile
+import operator
+import functools
+import itertools
+import re
+import contextlib
+import pickle
+import textwrap
+from setuptools.extern import six
+from setuptools.extern.six.moves import builtins, map
+import pkg_resources.py31compat
+if sys.platform.startswith('java'):
+import org.python.modules.posix.PosixModule as _os
+else:
+_os = sys.modules[os.name]
+try:
+_file = file
+except NameError:
+_file = None
+_open = open
+from distutils.errors import DistutilsError
+from pkg_resources import working_set
+__all__ = [
+"AbstractSandbox", "DirectorySandbox", "SandboxViolation", "run_setup",
+]
+def _execfile(filename, globals, locals=None):
+"""
+Python 3 implementation of execfile.
+"""
+mode = 'rb'
+with open(filename, mode) as stream:
+script = stream.read()
+if locals is None:
+locals = globals
+code = compile(script, filename, 'exec')
+exec(code, globals, locals)
+@contextlib.contextmanager
+def save_argv(repl=None):
+saved = sys.argv[:]
+if repl is not None:
+sys.argv[:] = repl
+try:
+yield saved
+finally:
+sys.argv[:] = saved
+@contextlib.contextmanager
+def save_path():
+saved = sys.path[:]
+try:
+yield saved
+finally:
+sys.path[:] = saved
+@contextlib.contextmanager
+def override_temp(replacement):
+"""
+Monkey-patch tempfile.tempdir with replacement, ensuring it exists
+"""
+pkg_resources.py31compat.makedirs(replacement, exist_ok=True)
+saved = tempfile.tempdir
+tempfile.tempdir = replacement
+try:
+yield
+finally:
+tempfile.tempdir = saved
+@contextlib.contextmanager
+def pushd(target):
+saved = os.getcwd()
+os.chdir(target)
+try:
+yield saved
+finally:
+os.chdir(saved)
+class UnpickleableException(Exception):
+"""
+An exception representing another Exception that could not be pickled.
+"""
+@staticmethod
+def dump(type, exc):
+"""
+Always return a dumped (pickled) type and exc. If exc can't be pickled,
+wrap it in UnpickleableException first.
+"""
+try:
+return pickle.dumps(type), pickle.dumps(exc)
+except Exception:
+# get UnpickleableException inside the sandbox
+from setuptools.sandbox import UnpickleableException as cls
+return cls.dump(cls, cls(repr(exc)))
+class ExceptionSaver:
+"""
+A Context Manager that will save an exception, serialized, and restore it
+later.
+"""
+def __enter__(self):
+return self
+def __exit__(self, type, exc, tb):
+if not exc:
+return
+# dump the exception
+self._saved = UnpickleableException.dump(type, exc)
+self._tb = tb
+# suppress the exception
+return True
+def resume(self):
+"restore and re-raise any exception"
+if '_saved' not in vars(self):
+return
+type, exc = map(pickle.loads, self._saved)
+six.reraise(type, exc, self._tb)
+@contextlib.contextmanager
+def save_modules():
+"""
+Context in which imported modules are saved.
+Translates exceptions internal to the context into the equivalent exception
+outside the context.
+"""
+saved = sys.modules.copy()
+with ExceptionSaver() as saved_exc:
+yield saved
+sys.modules.update(saved)
+# remove any modules imported since
+del_modules = (
+mod_name for mod_name in sys.modules
+if mod_name not in saved
+# exclude any encodings modules. See #285
+and not mod_name.startswith('encodings.')
+)
+_clear_modules(del_modules)
+saved_exc.resume()
+def _clear_modules(module_names):
+for mod_name in list(module_names):
+del sys.modules[mod_name]
+@contextlib.contextmanager
+def save_pkg_resources_state():
+saved = pkg_resources.__getstate__()
+try:
+yield saved
+finally:
+pkg_resources.__setstate__(saved)
+@contextlib.contextmanager
+def setup_context(setup_dir):
+temp_dir = os.path.join(setup_dir, 'temp')
+with save_pkg_resources_state():
+with save_modules():
+hide_setuptools()
+with save_path():
+with save_argv():
+with override_temp(temp_dir):
+with pushd(setup_dir):
+# ensure setuptools commands are available
+__import__('setuptools')
+yield
+def _needs_hiding(mod_name):
+"""
+>>> _needs_hiding('setuptools')
+True
+>>> _needs_hiding('pkg_resources')
+True
+>>> _needs_hiding('setuptools_plugin')
+False
+>>> _needs_hiding('setuptools.__init__')
+True
+>>> _needs_hiding('distutils')
+True
+>>> _needs_hiding('os')
+False
+>>> _needs_hiding('Cython')
+True
+"""
+pattern = re.compile(r'(setuptools|pkg_resources|distutils|Cython)(\.|$)')
+return bool(pattern.match(mod_name))
+def hide_setuptools():
+"""
+Remove references to setuptools' modules from sys.modules to allow the
+invocation to import the most appropriate setuptools. This technique is
+necessary to avoid issues such as #315 where setuptools upgrading itself
+would fail to find a function declared in the metadata.
+"""
+modules = filter(_needs_hiding, sys.modules)
+_clear_modules(modules)
+def run_setup(setup_script, args):
+"""Run a distutils setup script, sandboxed in its directory"""
+setup_dir = os.path.abspath(os.path.dirname(setup_script))
+with setup_context(setup_dir):
+try:
+sys.argv[:] = [setup_script] + list(args)
+sys.path.insert(0, setup_dir)
+# reset to include setup dir, w/clean callback list
+working_set.__init__()
+working_set.callbacks.append(lambda dist: dist.activate())
+# __file__ should be a byte string on Python 2 (#712)
+dunder_file = (
+setup_script
+if isinstance(setup_script, str) else
+setup_script.encode(sys.getfilesystemencoding())
+)
+with DirectorySandbox(setup_dir):
+ns = dict(__file__=dunder_file, __name__='__main__')
+_execfile(setup_script, ns)
+except SystemExit as v:
+if v.args and v.args[0]:
+raise
+# Normal exit, just return
+class AbstractSandbox:
+"""Wrap 'os' module and 'open()' builtin for virtualizing setup scripts"""
+_active = False
+def __init__(self):
+self._attrs = [
+name for name in dir(_os)
+if not name.startswith('_') and hasattr(self, name)
+]
+def _copy(self, source):
+for name in self._attrs:
+setattr(os, name, getattr(source, name))
+def __enter__(self):
+self._copy(self)
+if _file:
+builtins.file = self._file
+builtins.open = self._open
+self._active = True
+def __exit__(self, exc_type, exc_value, traceback):
+self._active = False
+if _file:
+builtins.file = _file
+builtins.open = _open
+self._copy(_os)
+def run(self, func):
+"""Run 'func' under os sandboxing"""
+with self:
+return func()
+def _mk_dual_path_wrapper(name):
+original = getattr(_os, name)
+def wrap(self, src, dst, *args, **kw):
+if self._active:
+src, dst = self._remap_pair(name, src, dst, *args, **kw)
+return original(src, dst, *args, **kw)
+return wrap
+for name in ["rename", "link", "symlink"]:
+if hasattr(_os, name):
+locals()[name] = _mk_dual_path_wrapper(name)
+def _mk_single_path_wrapper(name, original=None):
+original = original or getattr(_os, name)
+def wrap(self, path, *args, **kw):
+if self._active:
+path = self._remap_input(name, path, *args, **kw)
+return original(path, *args, **kw)
+return wrap
+if _file:
+_file = _mk_single_path_wrapper('file', _file)
+_open = _mk_single_path_wrapper('open', _open)
+for name in [
+"stat", "listdir", "chdir", "open", "chmod", "chown", "mkdir",
+"remove", "unlink", "rmdir", "utime", "lchown", "chroot", "lstat",
+"startfile", "mkfifo", "mknod", "pathconf", "access"
+]:
+if hasattr(_os, name):
+locals()[name] = _mk_single_path_wrapper(name)
+def _mk_single_with_return(name):
+original = getattr(_os, name)
+def wrap(self, path, *args, **kw):
+if self._active:
+path = self._remap_input(name, path, *args, **kw)
+return self._remap_output(name, original(path, *args, **kw))
+return original(path, *args, **kw)
+return wrap
+for name in ['readlink', 'tempnam']:
+if hasattr(_os, name):
+locals()[name] = _mk_single_with_return(name)
+def _mk_query(name):
+original = getattr(_os, name)
+def wrap(self, *args, **kw):
+retval = original(*args, **kw)
+if self._active:
+return self._remap_output(name, retval)
+return retval
+return wrap
+for name in ['getcwd', 'tmpnam']:
+if hasattr(_os, name):
+locals()[name] = _mk_query(name)
+def _validate_path(self, path):
+"""Called to remap or validate any path, whether input or output"""
+return path
+def _remap_input(self, operation, path, *args, **kw):
+"""Called for path inputs"""
+return self._validate_path(path)
+def _remap_output(self, operation, path):
+"""Called for path outputs"""
+return self._validate_path(path)
+def _remap_pair(self, operation, src, dst, *args, **kw):
+"""Called for path pairs like rename, link, and symlink operations"""
+return (
+self._remap_input(operation + '-from', src, *args, **kw),
+self._remap_input(operation + '-to', dst, *args, **kw)
+)
+if hasattr(os, 'devnull'):
+_EXCEPTIONS = [os.devnull,]
+else:
+_EXCEPTIONS = []
+class DirectorySandbox(AbstractSandbox):
+"""Restrict operations to a single subdirectory - pseudo-chroot"""
+write_ops = dict.fromkeys([
+"open", "chmod", "chown", "mkdir", "remove", "unlink", "rmdir",
+"utime", "lchown", "chroot", "mkfifo", "mknod", "tempnam",
+])
+_exception_patterns = [
+# Allow lib2to3 to attempt to save a pickled grammar object (#121)
+r'.*lib2to3.*\.pickle$',
+]
+"exempt writing to paths that match the pattern"
+def __init__(self, sandbox, exceptions=_EXCEPTIONS):
+self._sandbox = os.path.normcase(os.path.realpath(sandbox))
+self._prefix = os.path.join(self._sandbox, '')
+self._exceptions = [
+os.path.normcase(os.path.realpath(path))
+for path in exceptions
+]
+AbstractSandbox.__init__(self)
+def _violation(self, operation, *args, **kw):
+from setuptools.sandbox import SandboxViolation
+raise SandboxViolation(operation, args, kw)
+if _file:
+def _file(self, path, mode='r', *args, **kw):
+if mode not in ('r', 'rt', 'rb', 'rU', 'U') and not self._ok(path):
+self._violation("file", path, mode, *args, **kw)
+return _file(path, mode, *args, **kw)
+def _open(self, path, mode='r', *args, **kw):
+if mode not in ('r', 'rt', 'rb', 'rU', 'U') and not self._ok(path):
+self._violation("open", path, mode, *args, **kw)
+return _open(path, mode, *args, **kw)
+def tmpnam(self):
+self._violation("tmpnam")
+def _ok(self, path):
+active = self._active
+try:
+self._active = False
+realpath = os.path.normcase(os.path.realpath(path))
+return (
+self._exempted(realpath)
+or realpath == self._sandbox
+or realpath.startswith(self._prefix)
+)
+finally:
+self._active = active
+def _exempted(self, filepath):
+start_matches = (
+filepath.startswith(exception)
+for exception in self._exceptions
+)
+pattern_matches = (
+re.match(pattern, filepath)
+for pattern in self._exception_patterns
+)
+candidates = itertools.chain(start_matches, pattern_matches)
+return any(candidates)
+def _remap_input(self, operation, path, *args, **kw):
+"""Called for path inputs"""
+if operation in self.write_ops and not self._ok(path):
+self._violation(operation, os.path.realpath(path), *args, **kw)
+return path
+def _remap_pair(self, operation, src, dst, *args, **kw):
+"""Called for path pairs like rename, link, and symlink operations"""
+if not self._ok(src) or not self._ok(dst):
+self._violation(operation, src, dst, *args, **kw)
+return (src, dst)
+def open(self, file, flags, mode=0o777, *args, **kw):
+"""Called for low-level os.open()"""
+if flags & WRITE_FLAGS and not self._ok(file):
+self._violation("os.open", file, flags, mode, *args, **kw)
+return _os.open(file, flags, mode, *args, **kw)
+WRITE_FLAGS = functools.reduce(
+operator.or_, [getattr(_os, a, 0) for a in
+"O_WRONLY O_RDWR O_APPEND O_CREAT O_TRUNC O_TEMPORARY".split()]
+)
+class SandboxViolation(DistutilsError):
+"""A setup script attempted to modify the filesystem outside the sandbox"""
+tmpl = textwrap.dedent("""
+SandboxViolation: {cmd}{args!r} {kwargs}
+The package setup script has attempted to modify files on your system
+that are not within the EasyInstall build area, and has been aborted.
+This package cannot be safely installed by EasyInstall, and may not
+support alternate installation locations even if you run its setup
+script by hand.  Please inform the package's author and the EasyInstall
+maintainers to find out if a fix or workaround is available.
+""").lstrip()
+def __str__(self):
+cmd, args, kwargs = self.args
+return self.tmpl.format(**locals())

Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/setuptools/sandbox.py @ 0:26e78fe6e8c4 draft