Mercurial > repos > shellac > guppy_basecaller
comparison 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 |
comparison
equal
deleted
inserted
replaced
| 4:79f47841a781 | 5:9b1c78e6ba9c |
|---|---|
| 1 """Abstracted IO access.""" | |
| 2 from __future__ import absolute_import | |
| 3 | |
| 4 import glob | |
| 5 import os | |
| 6 from io import open | |
| 7 from typing import IO, Any, List | |
| 8 | |
| 9 from schema_salad.ref_resolver import file_uri, uri_file_path | |
| 10 from six.moves import urllib | |
| 11 from typing_extensions import Text | |
| 12 # move to a regular typing import when Python 3.3-3.6 is no longer supported | |
| 13 | |
| 14 from .utils import onWindows | |
| 15 | |
| 16 | |
| 17 def abspath(src, basedir): # type: (Text, Text) -> Text | |
| 18 if src.startswith(u"file://"): | |
| 19 abpath = Text(uri_file_path(str(src))) | |
| 20 elif urllib.parse.urlsplit(src).scheme in ['http', 'https']: | |
| 21 return src | |
| 22 else: | |
| 23 if basedir.startswith(u"file://"): | |
| 24 abpath = src if os.path.isabs(src) else basedir+ '/'+ src | |
| 25 else: | |
| 26 abpath = src if os.path.isabs(src) else os.path.join(basedir, src) | |
| 27 return abpath | |
| 28 | |
| 29 class StdFsAccess(object): | |
| 30 """Local filesystem implementation.""" | |
| 31 | |
| 32 def __init__(self, basedir): # type: (Text) -> None | |
| 33 """Perform operations with respect to a base directory.""" | |
| 34 self.basedir = basedir | |
| 35 | |
| 36 def _abs(self, p): # type: (Text) -> Text | |
| 37 return abspath(p, self.basedir) | |
| 38 | |
| 39 def glob(self, pattern): # type: (Text) -> List[Text] | |
| 40 return [file_uri(str(self._abs(l))) for l in glob.glob(self._abs(pattern))] | |
| 41 | |
| 42 def open(self, fn, mode): # type: (Text, str) -> IO[Any] | |
| 43 return open(self._abs(fn), mode) | |
| 44 | |
| 45 def exists(self, fn): # type: (Text) -> bool | |
| 46 return os.path.exists(self._abs(fn)) | |
| 47 | |
| 48 def size(self, fn): # type: (Text) -> int | |
| 49 return os.stat(self._abs(fn)).st_size | |
| 50 | |
| 51 def isfile(self, fn): # type: (Text) -> bool | |
| 52 return os.path.isfile(self._abs(fn)) | |
| 53 | |
| 54 def isdir(self, fn): # type: (Text) -> bool | |
| 55 return os.path.isdir(self._abs(fn)) | |
| 56 | |
| 57 def listdir(self, fn): # type: (Text) -> List[Text] | |
| 58 return [abspath(urllib.parse.quote(str(l)), fn) for l in os.listdir(self._abs(fn))] | |
| 59 | |
| 60 def join(self, path, *paths): # type: (Text, *Text) -> Text | |
| 61 return os.path.join(path, *paths) | |
| 62 | |
| 63 def realpath(self, path): # type: (Text) -> Text | |
| 64 return os.path.realpath(path) | |
| 65 | |
| 66 # On windows os.path.realpath appends unecessary Drive, here we would avoid that | |
| 67 def docker_compatible_realpath(self, path): # type: (Text) -> Text | |
| 68 if onWindows(): | |
| 69 if path.startswith('/'): | |
| 70 return path | |
| 71 return '/'+path | |
| 72 return self.realpath(path) |