Merge pull request #256 from psafont/win32

Win32 compatibility

Author: mr-c

cwltool/load_tool.py

@@ -6,12 +6,14 @@
 import logging
 import re
 import urlparse
+import pathlib2
 
 from typing import Any, AnyStr, Callable, cast, Dict, Text, Tuple, Union
 from ruamel.yaml.comments import CommentedSeq, CommentedMap
 from avro.schema import Names
 import requests.sessions
 
+
 from schema_salad.ref_resolver import Loader, Fetcher
 import schema_salad.validate as validate
 from schema_salad.validate import ValidationException
@@ -42,7 +44,7 @@ def fetch_document(argsworkflow,   # type: Union[Text, dict[Text, Any]]
         if split.scheme:
             uri = argsworkflow
         elif os.path.exists(os.path.abspath(argsworkflow)):
-            uri = "file://" + os.path.abspath(argsworkflow)
+            uri = pathlib2.Path(os.path.abspath(argsworkflow)).as_uri()
         elif resolver:
             uri = resolver(document_loader, argsworkflow)
 

cwltool/pathmapper.py

@@ -3,6 +3,7 @@
 import stat
 import collections
 import uuid
+import urllib
 import urlparse
 from functools import partial
 from typing import Any, Callable, Set, Text, Tuple, Union
@@ -72,7 +73,7 @@ def addLocation(d):
 
 def abspath(src, basedir):  # type: (Text, Text) -> Text
     if src.startswith(u"file://"):
-        ab = src[7:]
+        ab = urllib.url2pathname(urlparse.urlparse(src).path)
     else:
         ab = src if os.path.isabs(src) else os.path.join(basedir, src)
     return ab

requirements.txt

@@ -6,3 +6,4 @@ shellescape==3.4.1
 schema-salad>=2.1.20161216210732,<3
 cwltest>=1.0.20160907111242
 typing==3.5.2.2 ; python_version>="2.7"
+pathlib2==2.1.0

setup.py

@@ -49,7 +49,9 @@
           'shellescape >= 3.4.1, < 3.5',
           'schema-salad >= 2.1.20161216210732, < 3',
           'typing >= 3.5.2, < 3.6',
-          'cwltest >= 1.0.20160907111242'],
+          'cwltest >= 1.0.20160907111242',
+          'pathlib2 >= 2.1.0'
+      ],
       test_suite='tests',
       tests_require=[],
       entry_points={

typeshed/2.7/pathlib2.pyi

@@ -0,0 +1,188 @@
+# Stubs for pathlib2 (Python 2)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+
+from typing import Any, AnyStr, Type, TypeVar, Optional, Union
+from collections import Sequence
+
+_P = TypeVar('_P', bound='PurePath')
+
+intern = ...  # type: Any
+basestring = ...  # type: Any
+supports_symlinks = ...  # type: bool
+nt = ...  # type: Any
+
+class _Flavour:
+    join = ...  # type: Any
+    def __init__(self) -> None: ...
+    def parse_parts(self, parts): ...
+    def join_parsed_parts(self, drv, root, parts, drv2, root2, parts2): ...
+
+class _WindowsFlavour(_Flavour):
+    sep = ...  # type: str
+    altsep = ...  # type: str
+    has_drv = ...  # type: bool
+    pathmod = ...  # type: Any
+    is_supported = ...  # type: Any
+    drive_letters = ...  # type: Any
+    ext_namespace_prefix = ...  # type: str
+    reserved_names = ...  # type: Any
+    def splitroot(self, part, sep: Any = ...): ...
+    def casefold(self, s): ...
+    def casefold_parts(self, parts): ...
+    def resolve(self, path): ...
+    def is_reserved(self, parts): ...
+    def make_uri(self, path): ...
+    def gethomedir(self, username): ...
+
+class _PosixFlavour(_Flavour):
+    sep = ...  # type: str
+    altsep = ...  # type: str
+    has_drv = ...  # type: bool
+    pathmod = ...  # type: Any
+    is_supported = ...  # type: Any
+    def splitroot(self, part, sep: Any = ...): ...
+    def casefold(self, s): ...
+    def casefold_parts(self, parts): ...
+    def resolve(self, path): ...
+    def is_reserved(self, parts): ...
+    def make_uri(self, path): ...
+    def gethomedir(self, username): ...
+
+class _Accessor: ...
+
+class _NormalAccessor(_Accessor):
+    stat = ...  # type: Any
+    lstat = ...  # type: Any
+    open = ...  # type: Any
+    listdir = ...  # type: Any
+    chmod = ...  # type: Any
+    lchmod = ...  # type: Any
+    #def lchmod(self, pathobj, mode): ...
+    mkdir = ...  # type: Any
+    unlink = ...  # type: Any
+    rmdir = ...  # type: Any
+    rename = ...  # type: Any
+    replace = ...  # type: Any
+    symlink = ...  # type: Any
+    #def symlink(a, b, target_is_directory): ...
+    #@staticmethod
+    #def symlink(a, b, target_is_directory): ...
+    utime = ...  # type: Any
+    def readlink(self, path): ...
+
+class _Selector:
+    child_parts = ...  # type: Any
+    successor = ...  # type: Any
+    def __init__(self, child_parts) -> None: ...
+    def select_from(self, parent_path): ...
+
+class _TerminatingSelector: ...
+
+class _PreciseSelector(_Selector):
+    name = ...  # type: Any
+    def __init__(self, name, child_parts) -> None: ...
+
+class _WildcardSelector(_Selector):
+    pat = ...  # type: Any
+    def __init__(self, pat, child_parts) -> None: ...
+
+class _RecursiveWildcardSelector(_Selector):
+    def __init__(self, pat, child_parts) -> None: ...
+
+class _PathParents(Sequence):
+    def __init__(self, path) -> None: ...
+    def __len__(self): ...
+    def __getitem__(self, idx): ...
+
+class PurePath:
+    def __new__(cls, *args): ...
+    def __reduce__(self): ...
+    def as_posix(self): ...
+    def __bytes__(self): ...
+    def as_uri(self) -> str: ...
+    def __eq__(self, other): ...
+    def __ne__(self, other): ...
+    def __hash__(self): ...
+    def __lt__(self, other): ...
+    def __le__(self, other): ...
+    def __gt__(self, other): ...
+    def __ge__(self, other): ...
+    drive = ...  # type: Any
+    root = ...  # type: Any
+    @property
+    def anchor(self): ...
+    @property
+    def name(self): ...
+    @property
+    def suffix(self): ...
+    @property
+    def suffixes(self): ...
+    @property
+    def stem(self): ...
+    def with_name(self, name): ...
+    def with_suffix(self, suffix): ...
+    def relative_to(self, *other): ...
+    @property
+    def parts(self): ...
+    def joinpath(self, *args): ...
+    def __truediv__(self, key): ...
+    def __rtruediv__(self, key): ...
+    __div__ = ...  # type: Any
+    __rdiv__ = ...  # type: Any
+    @property
+    def parent(self): ...
+    @property
+    def parents(self): ...
+    def is_absolute(self): ...
+    def is_reserved(self): ...
+    def match(self, path_pattern): ...
+
+class PurePosixPath(PurePath): ...
+class PureWindowsPath(PurePath): ...
+
+class Path(PurePath):
+    def __new__(cls: Type[_P], *args: Union[AnyStr, PurePath],
+	**kwargs: Any) -> _P: ...
+    def __enter__(self): ...
+    def __exit__(self, t, v, tb): ...
+    @classmethod
+    def cwd(cls): ...
+    @classmethod
+    def home(cls): ...
+    def samefile(self, other_path): ...
+    def iterdir(self): ...
+    def glob(self, pattern): ...
+    def rglob(self, pattern): ...
+    def absolute(self): ...
+    def resolve(self): ...
+    def stat(self): ...
+    def owner(self): ...
+    def group(self): ...
+    def open(self, mode: str = ..., buffering: int = ..., encoding: Optional[Any] = ..., errors: Optional[Any] = ..., newline: Optional[Any] = ...): ...
+    def read_bytes(self): ...
+    def read_text(self, encoding: Optional[Any] = ..., errors: Optional[Any] = ...): ...
+    def write_bytes(self, data): ...
+    def write_text(self, data, encoding: Optional[Any] = ..., errors: Optional[Any] = ...): ...
+    def touch(self, mode: int = ..., exist_ok: bool = ...): ...
+    def mkdir(self, mode: int = ..., parents: bool = ..., exist_ok: bool = ...): ...
+    def chmod(self, mode): ...
+    def lchmod(self, mode): ...
+    def unlink(self): ...
+    def rmdir(self): ...
+    def lstat(self): ...
+    def rename(self, target): ...
+    def replace(self, target): ...
+    def symlink_to(self, target, target_is_directory: bool = ...): ...
+    def exists(self): ...
+    def is_dir(self): ...
+    def is_file(self): ...
+    def is_symlink(self): ...
+    def is_block_device(self): ...
+    def is_char_device(self): ...
+    def is_fifo(self): ...
+    def is_socket(self): ...
+    def expanduser(self): ...
+
+class PosixPath(Path, PurePosixPath): ...
+class WindowsPath(Path, PureWindowsPath): ...

typeshed/2.7/urllib.pyi

@@ -0,0 +1,135 @@
+# Stubs for urllib (Python 2)
+# NOTE: This dynamically typed stub was originally automatically generated by stubgen.
+
+from typing import Any, AnyStr, Mapping, Union, Tuple, Sequence, IO
+
+def url2pathname(pathname: AnyStr) -> AnyStr: ...
+def pathname2url(pathname: str) -> str: ...
+def urlopen(url: str, data=..., proxies: Mapping[str, str] = ..., context=...) -> IO[Any]: ...
+def urlretrieve(url, filename=..., reporthook=..., data=..., context=...): ...
+def urlcleanup() -> None: ...
+
+class ContentTooShortError(IOError):
+    content = ...  # type: Any
+    def __init__(self, message, content) -> None: ...
+
+class URLopener:
+    version = ...  # type: Any
+    proxies = ...  # type: Any
+    key_file = ...  # type: Any
+    cert_file = ...  # type: Any
+    context = ...  # type: Any
+    addheaders = ...  # type: Any
+    tempcache = ...  # type: Any
+    ftpcache = ...  # type: Any
+    def __init__(self, proxies: Mapping[str, str] = ..., context=..., **x509) -> None: ...
+    def __del__(self): ...
+    def close(self): ...
+    def cleanup(self): ...
+    def addheader(self, *args): ...
+    type = ...  # type: Any
+    def open(self, fullurl: str, data=...): ...
+    def open_unknown(self, fullurl, data=...): ...
+    def open_unknown_proxy(self, proxy, fullurl, data=...): ...
+    def retrieve(self, url, filename=..., reporthook=..., data=...): ...
+    def open_http(self, url, data=...): ...
+    def http_error(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def http_error_default(self, url, fp, errcode, errmsg, headers): ...
+    def open_https(self, url, data=...): ...
+    def open_file(self, url): ...
+    def open_local_file(self, url): ...
+    def open_ftp(self, url): ...
+    def open_data(self, url, data=...): ...
+
+class FancyURLopener(URLopener):
+    auth_cache = ...  # type: Any
+    tries = ...  # type: Any
+    maxtries = ...  # type: Any
+    def __init__(self, *args, **kwargs) -> None: ...
+    def http_error_default(self, url, fp, errcode, errmsg, headers): ...
+    def http_error_302(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def redirect_internal(self, url, fp, errcode, errmsg, headers, data): ...
+    def http_error_301(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def http_error_303(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def http_error_307(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def http_error_401(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def http_error_407(self, url, fp, errcode, errmsg, headers, data=...): ...
+    def retry_proxy_http_basic_auth(self, url, realm, data=...): ...
+    def retry_proxy_https_basic_auth(self, url, realm, data=...): ...
+    def retry_http_basic_auth(self, url, realm, data=...): ...
+    def retry_https_basic_auth(self, url, realm, data=...): ...
+    def get_user_passwd(self, host, realm, clear_cache=...): ...
+    def prompt_user_passwd(self, host, realm): ...
+
+class ftpwrapper:
+    user = ...  # type: Any
+    passwd = ...  # type: Any
+    host = ...  # type: Any
+    port = ...  # type: Any
+    dirs = ...  # type: Any
+    timeout = ...  # type: Any
+    refcount = ...  # type: Any
+    keepalive = ...  # type: Any
+    def __init__(self, user, passwd, host, port, dirs, timeout=..., persistent=...) -> None: ...
+    busy = ...  # type: Any
+    ftp = ...  # type: Any
+    def init(self): ...
+    def retrfile(self, file, type): ...
+    def endtransfer(self): ...
+    def close(self): ...
+    def file_close(self): ...
+    def real_close(self): ...
+
+class addbase:
+    fp = ...  # type: Any
+    read = ...  # type: Any
+    readline = ...  # type: Any
+    readlines = ...  # type: Any
+    fileno = ...  # type: Any
+    __iter__ = ...  # type: Any
+    next = ...  # type: Any
+    def __init__(self, fp) -> None: ...
+    def close(self): ...
+
+class addclosehook(addbase):
+    closehook = ...  # type: Any
+    hookargs = ...  # type: Any
+    def __init__(self, fp, closehook, *hookargs) -> None: ...
+    def close(self): ...
+
+class addinfo(addbase):
+    headers = ...  # type: Any
+    def __init__(self, fp, headers) -> None: ...
+    def info(self): ...
+
+class addinfourl(addbase):
+    headers = ...  # type: Any
+    url = ...  # type: Any
+    code = ...  # type: Any
+    def __init__(self, fp, headers, url, code=...) -> None: ...
+    def info(self): ...
+    def getcode(self): ...
+    def geturl(self): ...
+
+def unwrap(url): ...
+def splittype(url): ...
+def splithost(url): ...
+def splituser(host): ...
+def splitpasswd(user): ...
+def splitport(host): ...
+def splitnport(host, defport=...): ...
+def splitquery(url): ...
+def splittag(url): ...
+def splitattr(url): ...
+def splitvalue(attr): ...
+def unquote(s: str) -> str: ...
+def unquote_plus(s: str) -> str: ...
+def quote(s: str, safe=...) -> str: ...
+def quote_plus(s: str, safe=...) -> str: ...
+def urlencode(query: Union[Sequence[Tuple[Any, Any]], Mapping[Any, Any]], doseq=...) -> str: ...
+
+def getproxies() -> Mapping[str, str]: ...
+def proxy_bypass(host): ...
+
+# Names in __all__ with no definition:
+#   basejoin