diff env/lib/python3.7/site-packages/cwltool/stdfsaccess.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/cwltool/stdfsaccess.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-"""Abstracted IO access."""
-from __future__ import absolute_import
-
-import glob
-import os
-from io import open
-from typing import IO, Any, List
-
-from schema_salad.ref_resolver import file_uri, uri_file_path
-from six.moves import urllib
-from typing_extensions import Text
-# move to a regular typing import when Python 3.3-3.6 is no longer supported
-
-from .utils import onWindows
-
-
-def abspath(src, basedir):  # type: (Text, Text) -> Text
-    if src.startswith(u"file://"):
-        abpath = Text(uri_file_path(str(src)))
-    elif urllib.parse.urlsplit(src).scheme in ['http', 'https']:
-        return src
-    else:
-        if basedir.startswith(u"file://"):
-            abpath = src if os.path.isabs(src) else basedir+ '/'+ src
-        else:
-            abpath = src if os.path.isabs(src) else os.path.join(basedir, src)
-    return abpath
-
-class StdFsAccess(object):
-    """Local filesystem implementation."""
-
-    def __init__(self, basedir):  # type: (Text) -> None
-        """Perform operations with respect to a base directory."""
-        self.basedir = basedir
-
-    def _abs(self, p):  # type: (Text) -> Text
-        return abspath(p, self.basedir)
-
-    def glob(self, pattern):  # type: (Text) -> List[Text]
-        return [file_uri(str(self._abs(l))) for l in glob.glob(self._abs(pattern))]
-
-    def open(self, fn, mode):  # type: (Text, str) -> IO[Any]
-        return open(self._abs(fn), mode)
-
-    def exists(self, fn):  # type: (Text) -> bool
-        return os.path.exists(self._abs(fn))
-
-    def size(self, fn):    # type: (Text) -> int
-        return os.stat(self._abs(fn)).st_size
-
-    def isfile(self, fn):  # type: (Text) -> bool
-        return os.path.isfile(self._abs(fn))
-
-    def isdir(self, fn):  # type: (Text) -> bool
-        return os.path.isdir(self._abs(fn))
-
-    def listdir(self, fn):  # type: (Text) -> List[Text]
-        return [abspath(urllib.parse.quote(str(l)), fn) for l in os.listdir(self._abs(fn))]
-
-    def join(self, path, *paths):  # type: (Text, *Text) -> Text
-        return os.path.join(path, *paths)
-
-    def realpath(self, path):  # type: (Text) -> Text
-        return os.path.realpath(path)
-
-    # On windows os.path.realpath appends unecessary Drive, here we would avoid that
-    def docker_compatible_realpath(self, path):  # type: (Text) -> Text
-        if onWindows():
-            if path.startswith('/'):
-                return path
-            return '/'+path
-        return self.realpath(path)