diff env/lib/python3.9/site-packages/cwltool/stdfsaccess.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/cwltool/stdfsaccess.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,74 @@
+"""Abstracted IO access."""
+
+import glob
+import os
+import urllib
+from typing import IO, Any, List
+
+from schema_salad.ref_resolver import file_uri, uri_file_path
+
+from .utils import onWindows
+
+
+def abspath(src: str, basedir: str) -> str:
+    if src.startswith("file://"):
+        abpath = uri_file_path(src)
+    elif urllib.parse.urlsplit(src).scheme in ["http", "https"]:
+        return src
+    else:
+        if basedir.startswith("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:
+    """Local filesystem implementation."""
+
+    def __init__(self, basedir: str) -> None:
+        """Perform operations with respect to a base directory."""
+        self.basedir = basedir
+
+    def _abs(self, p: str) -> str:
+        return abspath(p, self.basedir)
+
+    def glob(self, pattern: str) -> List[str]:
+        return [
+            file_uri(str(self._abs(line))) for line in glob.glob(self._abs(pattern))
+        ]
+
+    def open(self, fn: str, mode: str) -> IO[Any]:
+        return open(self._abs(fn), mode)
+
+    def exists(self, fn: str) -> bool:
+        return os.path.exists(self._abs(fn))
+
+    def size(self, fn: str) -> int:
+        return os.stat(self._abs(fn)).st_size
+
+    def isfile(self, fn: str) -> bool:
+        return os.path.isfile(self._abs(fn))
+
+    def isdir(self, fn: str) -> bool:
+        return os.path.isdir(self._abs(fn))
+
+    def listdir(self, fn: str) -> List[str]:
+        return [
+            abspath(urllib.parse.quote(entry), fn)
+            for entry in os.listdir(self._abs(fn))
+        ]
+
+    def join(self, path, *paths):  # type: (str, *str) -> str
+        return os.path.join(path, *paths)
+
+    def realpath(self, path: str) -> str:
+        return os.path.realpath(path)
+
+    # On windows os.path.realpath appends unecessary Drive, here we would avoid that
+    def docker_compatible_realpath(self, path: str) -> str:
+        if onWindows():
+            if path.startswith("/"):
+                return path
+            return "/" + path
+        return self.realpath(path)