Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/pathmapper.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 from __future__ import absolute_import
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2
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3 import collections
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4 import logging
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5 import os
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6 import stat
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7 import uuid
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8 from functools import partial # pylint: disable=unused-import
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9 from tempfile import NamedTemporaryFile
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10 from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
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11 Optional, Set, Tuple, Union)
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12
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13 import requests
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14 from cachecontrol import CacheControl
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15 from cachecontrol.caches import FileCache
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16 from schema_salad import validate
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17 from schema_salad.ref_resolver import uri_file_path
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18 from schema_salad.sourceline import SourceLine
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19 from six.moves import urllib
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20 from typing_extensions import Text # pylint: disable=unused-import
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21 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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22
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23 from .loghandler import _logger
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24 from .stdfsaccess import StdFsAccess, abspath # pylint: disable=unused-import
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25 from .utils import Directory # pylint: disable=unused-import
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26 from .utils import convert_pathsep_to_unix, visit_class
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27
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28
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29 CONTENT_LIMIT = 64 * 1024
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30
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31 MapperEnt = collections.namedtuple("MapperEnt", ["resolved", "target", "type", "staged"])
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32
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33
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34 def adjustFiles(rec, op): # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
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35 """Apply a mapping function to each File path in the object `rec`."""
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36 if isinstance(rec, MutableMapping):
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37 if rec.get("class") == "File":
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38 rec["path"] = op(rec["path"])
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39 for d in rec:
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40 adjustFiles(rec[d], op)
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41 if isinstance(rec, MutableSequence):
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42 for d in rec:
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43 adjustFiles(d, op)
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44
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45
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46 def adjustFileObjs(rec, op): # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
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47 """Apply an update function to each File object in the object `rec`."""
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48 visit_class(rec, ("File",), op)
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49
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50 def adjustDirObjs(rec, op):
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51 # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
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52 """Apply an update function to each Directory object in the object `rec`."""
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53 visit_class(rec, ("Directory",), op)
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54
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55 def normalizeFilesDirs(job):
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56 # type: (Optional[Union[List[Dict[Text, Any]], MutableMapping[Text, Any], Directory]]) -> None
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57 def addLocation(d): # type: (Dict[Text, Any]) -> None
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58 if "location" not in d:
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59 if d["class"] == "File" and ("contents" not in d):
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60 raise validate.ValidationException("Anonymous file object must have 'contents' and 'basename' fields.")
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61 if d["class"] == "Directory" and ("listing" not in d or "basename" not in d):
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62 raise validate.ValidationException(
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63 "Anonymous directory object must have 'listing' and 'basename' fields.")
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64 d["location"] = "_:" + Text(uuid.uuid4())
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65 if "basename" not in d:
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66 d["basename"] = d["location"][2:]
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67
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68 parse = urllib.parse.urlparse(d["location"])
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69 path = parse.path
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70 # strip trailing slash
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71 if path.endswith("/"):
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72 if d["class"] != "Directory":
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73 raise validate.ValidationException(
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74 "location '%s' ends with '/' but is not a Directory" % d["location"])
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75 path = path.rstrip("/")
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76 d["location"] = urllib.parse.urlunparse((parse.scheme, parse.netloc, path, parse.params, parse.query, parse.fragment))
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77
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78 if not d.get("basename"):
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79 if path.startswith("_:"):
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80 d["basename"] = Text(path[2:])
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81 else:
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82 d["basename"] = Text(os.path.basename(urllib.request.url2pathname(path)))
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83
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84 if d["class"] == "File":
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85 nr, ne = os.path.splitext(d["basename"])
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86 if d.get("nameroot") != nr:
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87 d["nameroot"] = Text(nr)
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88 if d.get("nameext") != ne:
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89 d["nameext"] = Text(ne)
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90
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91 contents = d.get("contents")
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92 if contents and len(contents) > CONTENT_LIMIT:
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93 if len(contents) > CONTENT_LIMIT:
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94 raise validate.ValidationException("File object contains contents with number of bytes that exceeds CONTENT_LIMIT length (%d)" % CONTENT_LIMIT)
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95
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96 visit_class(job, ("File", "Directory"), addLocation)
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97
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98
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99 def dedup(listing): # type: (List[Any]) -> List[Any]
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100 marksub = set()
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101
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102 def mark(d): # type: (Dict[Text, Text]) -> None
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103 marksub.add(d["location"])
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104
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105 for l in listing:
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106 if l["class"] == "Directory":
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107 for e in l.get("listing", []):
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108 adjustFileObjs(e, mark)
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109 adjustDirObjs(e, mark)
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110
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111 dd = []
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112 markdup = set() # type: Set[Text]
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113 for r in listing:
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114 if r["location"] not in marksub and r["location"] not in markdup:
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115 dd.append(r)
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116 markdup.add(r["location"])
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117
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118 return dd
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119
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120 def get_listing(fs_access, rec, recursive=True):
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121 # type: (StdFsAccess, MutableMapping[Text, Any], bool) -> None
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122 if rec.get("class") != "Directory":
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123 finddirs = [] # type: List[MutableMapping[Text, Text]]
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124 visit_class(rec, ("Directory",), finddirs.append)
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125 for f in finddirs:
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126 get_listing(fs_access, f, recursive=recursive)
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127 return
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128 if "listing" in rec:
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129 return
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130 listing = []
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131 loc = rec["location"]
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132 for ld in fs_access.listdir(loc):
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133 parse = urllib.parse.urlparse(ld)
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134 bn = os.path.basename(urllib.request.url2pathname(parse.path))
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135 if fs_access.isdir(ld):
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136 ent = {u"class": u"Directory",
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137 u"location": ld,
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138 u"basename": bn}
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139 if recursive:
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140 get_listing(fs_access, ent, recursive)
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141 listing.append(ent)
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142 else:
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143 listing.append({"class": "File", "location": ld, "basename": bn})
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144 rec["listing"] = listing
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145
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146 def trim_listing(obj): # type: (Dict[Text, Any]) -> None
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147 """
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148 Remove 'listing' field from Directory objects that are file references.
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149
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150 It redundant and potentially expensive to pass fully enumerated Directory
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151 objects around if not explicitly needed, so delete the 'listing' field when
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152 it is safe to do so.
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153 """
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154 if obj.get("location", "").startswith("file://") and "listing" in obj:
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155 del obj["listing"]
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156
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157 # Download http Files
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158 def downloadHttpFile(httpurl):
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159 # type: (Text) -> Text
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160 cache_session = None
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161 if "XDG_CACHE_HOME" in os.environ:
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162 directory = os.environ["XDG_CACHE_HOME"]
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163 elif "HOME" in os.environ:
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164 directory = os.environ["HOME"]
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165 else:
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166 directory = os.path.expanduser('~')
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167
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168 cache_session = CacheControl(
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169 requests.Session(),
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170 cache=FileCache(
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171 os.path.join(directory, ".cache", "cwltool")))
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172
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173 r = cache_session.get(httpurl, stream=True)
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174 with NamedTemporaryFile(mode='wb', delete=False) as f:
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175 for chunk in r.iter_content(chunk_size=16384):
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176 if chunk: # filter out keep-alive new chunks
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177 f.write(chunk)
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178 r.close()
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179 return str(f.name)
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180
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181 def ensure_writable(path): # type: (Text) -> None
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182 if os.path.isdir(path):
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183 for root, dirs, files in os.walk(path):
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184 for name in files:
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185 j = os.path.join(root, name)
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186 st = os.stat(j)
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187 mode = stat.S_IMODE(st.st_mode)
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188 os.chmod(j, mode | stat.S_IWUSR)
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189 for name in dirs:
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190 j = os.path.join(root, name)
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191 st = os.stat(j)
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192 mode = stat.S_IMODE(st.st_mode)
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193 os.chmod(j, mode | stat.S_IWUSR)
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194 else:
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195 st = os.stat(path)
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196 mode = stat.S_IMODE(st.st_mode)
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197 os.chmod(path, mode | stat.S_IWUSR)
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198
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199 def ensure_non_writable(path): # type: (Text) -> None
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200 if os.path.isdir(path):
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201 for root, dirs, files in os.walk(path):
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202 for name in files:
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203 j = os.path.join(root, name)
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204 st = os.stat(j)
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205 mode = stat.S_IMODE(st.st_mode)
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206 os.chmod(j,
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207 mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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208 for name in dirs:
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209 j = os.path.join(root, name)
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210 st = os.stat(j)
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211 mode = stat.S_IMODE(st.st_mode)
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212 os.chmod(j,
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213 mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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214 else:
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215 st = os.stat(path)
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216 mode = stat.S_IMODE(st.st_mode)
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217 os.chmod(path, mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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218
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219 class PathMapper(object):
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220 """
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221 Mapping of files from relative path provided in the file to a tuple.
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222
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223 (absolute local path, absolute container path)
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224
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225 The tao of PathMapper:
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226
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227 The initializer takes a list of File and Directory objects, a base
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228 directory (for resolving relative references) and a staging directory
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229 (where the files are mapped to).
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230
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231 The purpose of the setup method is to determine where each File or
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232 Directory should be placed on the target file system (relative to
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233 stagedir).
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234
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235 If separatedirs=True, unrelated files will be isolated in their own
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236 directories under stagedir. If separatedirs=False, files and directories
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237 will all be placed in stagedir (with the possibility for name
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238 collisions...)
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239
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240 The path map maps the "location" of the input Files and Directory objects
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241 to a tuple (resolved, target, type). The "resolved" field is the "real"
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242 path on the local file system (after resolving relative paths and
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243 traversing symlinks). The "target" is the path on the target file system
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244 (under stagedir). The type is the object type (one of File, Directory,
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245 CreateFile, WritableFile, CreateWritableFile).
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246
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247 The latter three (CreateFile, WritableFile, CreateWritableFile) are used by
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248 InitialWorkDirRequirement to indicate files that are generated on the fly
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249 (CreateFile and CreateWritableFile, in this case "resolved" holds the file
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250 contents instead of the path because they file doesn't exist) or copied
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251 into the output directory so they can be opened for update ("r+" or "a")
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252 (WritableFile and CreateWritableFile).
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253
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254 """
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255
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256 def __init__(self, referenced_files, basedir, stagedir, separateDirs=True):
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257 # type: (List[Any], Text, Text, bool) -> None
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258 """Initialize the PathMapper."""
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259 self._pathmap = {} # type: Dict[Text, MapperEnt]
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260 self.stagedir = stagedir
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261 self.separateDirs = separateDirs
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262 self.setup(dedup(referenced_files), basedir)
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263
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264 def visitlisting(self, listing, stagedir, basedir, copy=False, staged=False):
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265 # type: (List[Dict[Text, Any]], Text, Text, bool, bool) -> None
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266 for ld in listing:
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267 self.visit(ld, stagedir, basedir, copy=ld.get("writable", copy), staged=staged)
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268
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269 def visit(self, obj, stagedir, basedir, copy=False, staged=False):
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270 # type: (Dict[Text, Any], Text, Text, bool, bool) -> None
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271 tgt = convert_pathsep_to_unix(
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272 os.path.join(stagedir, obj["basename"]))
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273 if obj["location"] in self._pathmap:
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274 return
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275 if obj["class"] == "Directory":
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276 if obj["location"].startswith("file://"):
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277 resolved = uri_file_path(obj["location"])
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278 else:
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279 resolved = obj["location"]
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280 self._pathmap[obj["location"]] = MapperEnt(resolved, tgt, "WritableDirectory" if copy else "Directory", staged)
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281 if obj["location"].startswith("file://"):
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282 staged = False
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283 self.visitlisting(obj.get("listing", []), tgt, basedir, copy=copy, staged=staged)
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284 elif obj["class"] == "File":
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285 path = obj["location"]
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286 ab = abspath(path, basedir)
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287 if "contents" in obj and obj["location"].startswith("_:"):
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288 self._pathmap[obj["location"]] = MapperEnt(
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289 obj["contents"], tgt,
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290 "CreateWritableFile" if copy else "CreateFile", staged)
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291 else:
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292 with SourceLine(obj, "location", validate.ValidationException, _logger.isEnabledFor(logging.DEBUG)):
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293 deref = ab
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294 if urllib.parse.urlsplit(deref).scheme in ['http', 'https']:
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295 deref = downloadHttpFile(path)
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296 else:
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297 # Dereference symbolic links
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298 st = os.lstat(deref)
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299 while stat.S_ISLNK(st.st_mode):
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300 rl = os.readlink(deref)
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301 deref = rl if os.path.isabs(rl) else os.path.join(
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302 os.path.dirname(deref), rl)
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303 st = os.lstat(deref)
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304
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305 self._pathmap[path] = MapperEnt(
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306 deref, tgt, "WritableFile" if copy else "File", staged)
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307 self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir,
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308 copy=copy, staged=staged)
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309
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310 def setup(self, referenced_files, basedir):
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311 # type: (List[Any], Text) -> None
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312
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313 # Go through each file and set the target to its own directory along
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314 # with any secondary files.
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315 stagedir = self.stagedir
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316 for fob in referenced_files:
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317 if self.separateDirs:
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318 stagedir = os.path.join(self.stagedir, "stg%s" % uuid.uuid4())
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319 self.visit(fob, stagedir, basedir, copy=fob.get("writable"), staged=True)
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320
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321 def mapper(self, src): # type: (Text) -> MapperEnt
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322 if u"#" in src:
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323 i = src.index(u"#")
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324 p = self._pathmap[src[:i]]
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325 return MapperEnt(p.resolved, p.target + src[i:], p.type, p.staged)
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326 return self._pathmap[src]
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327
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328 def files(self): # type: () -> List[Text]
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329 return list(self._pathmap.keys())
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330
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331 def items(self): # type: () -> List[Tuple[Text, MapperEnt]]
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332 return list(self._pathmap.items())
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333
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334 def reversemap(self,
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335 target # type: Text
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336 ): # type: (...) -> Optional[Tuple[Text, Text]]
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337 for k, v in self._pathmap.items():
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338 if v[1] == target:
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339 return (k, v[0])
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340 return None
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341
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342 def update(self, key, resolved, target, ctype, stage):
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343 # type: (Text, Text, Text, Text, bool) -> MapperEnt
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344 m = MapperEnt(resolved, target, ctype, stage)
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345 self._pathmap[key] = m
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346 return m
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347
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348 def __contains__(self, key): # type: (Text) -> bool
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349 """Test for the presence of the given relative path in this mapper."""
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350 return key in self._pathmap