Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/stdfsaccess.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Abstracted IO access."""
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2 from __future__ import absolute_import
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3
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4 import glob
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5 import os
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6 from io import open
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7 from typing import IO, Any, List
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8
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9 from schema_salad.ref_resolver import file_uri, uri_file_path
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10 from six.moves import urllib
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11 from typing_extensions import Text
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12 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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13
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14 from .utils import onWindows
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15
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16
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17 def abspath(src, basedir): # type: (Text, Text) -> Text
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18 if src.startswith(u"file://"):
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19 abpath = Text(uri_file_path(str(src)))
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20 elif urllib.parse.urlsplit(src).scheme in ['http', 'https']:
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21 return src
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22 else:
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23 if basedir.startswith(u"file://"):
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24 abpath = src if os.path.isabs(src) else basedir+ '/'+ src
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25 else:
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26 abpath = src if os.path.isabs(src) else os.path.join(basedir, src)
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27 return abpath
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28
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29 class StdFsAccess(object):
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30 """Local filesystem implementation."""
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31
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32 def __init__(self, basedir): # type: (Text) -> None
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33 """Perform operations with respect to a base directory."""
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34 self.basedir = basedir
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35
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36 def _abs(self, p): # type: (Text) -> Text
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37 return abspath(p, self.basedir)
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38
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39 def glob(self, pattern): # type: (Text) -> List[Text]
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40 return [file_uri(str(self._abs(l))) for l in glob.glob(self._abs(pattern))]
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41
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42 def open(self, fn, mode): # type: (Text, str) -> IO[Any]
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43 return open(self._abs(fn), mode)
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44
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45 def exists(self, fn): # type: (Text) -> bool
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46 return os.path.exists(self._abs(fn))
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47
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48 def size(self, fn): # type: (Text) -> int
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49 return os.stat(self._abs(fn)).st_size
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50
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51 def isfile(self, fn): # type: (Text) -> bool
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52 return os.path.isfile(self._abs(fn))
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53
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54 def isdir(self, fn): # type: (Text) -> bool
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55 return os.path.isdir(self._abs(fn))
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56
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57 def listdir(self, fn): # type: (Text) -> List[Text]
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58 return [abspath(urllib.parse.quote(str(l)), fn) for l in os.listdir(self._abs(fn))]
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59
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60 def join(self, path, *paths): # type: (Text, *Text) -> Text
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61 return os.path.join(path, *paths)
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62
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63 def realpath(self, path): # type: (Text) -> Text
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64 return os.path.realpath(path)
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65
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66 # On windows os.path.realpath appends unecessary Drive, here we would avoid that
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67 def docker_compatible_realpath(self, path): # type: (Text) -> Text
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68 if onWindows():
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69 if path.startswith('/'):
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70 return path
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71 return '/'+path
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72 return self.realpath(path)