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annotate env/lib/python3.9/site-packages/galaxy/util/commands.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Generic I/O and shell processing code used by Galaxy tool dependencies."""
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2 import logging
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3 import os
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4 import shlex
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5 import subprocess
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6 import sys as _sys
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7
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8 from galaxy.util import (
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9 unicodify,
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10 which
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11 )
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12
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13 log = logging.getLogger(__name__)
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14
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15 STDOUT_INDICATOR = "-"
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16
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17
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18 def redirecting_io(sys=_sys):
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19 """Predicate to determine if we are redicting stdout in process."""
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20 assert sys is not None
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21 try:
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22 # Need to explicitly call fileno() because sys.stdout could be a
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23 # io.StringIO object, which has a fileno() method but only raises an
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24 # io.UnsupportedOperation exception
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25 sys.stdout.fileno()
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26 except Exception:
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27 return True
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28 else:
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29 return False
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30
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31
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32 def redirect_aware_commmunicate(p, sys=_sys):
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33 """Variant of process.communicate that works with in process I/O redirection."""
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34 assert sys is not None
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35 out, err = p.communicate()
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36 if redirecting_io(sys=sys):
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37 if out:
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38 # We don't unicodify in Python2 because sys.stdout may be a
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39 # cStringIO.StringIO object, which does not accept Unicode strings
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40 out = unicodify(out)
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41 sys.stdout.write(out)
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42 out = None
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43 if err:
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44 err = unicodify(err)
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45 sys.stderr.write(err)
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46 err = None
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47 return out, err
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48
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49
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50 def shell(cmds, env=None, **kwds):
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51 """Run shell commands with `shell_process` and wait."""
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52 sys = kwds.get("sys", _sys)
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53 assert sys is not None
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54 p = shell_process(cmds, env, **kwds)
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55 if redirecting_io(sys=sys):
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56 redirect_aware_commmunicate(p, sys=sys)
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57 exit = p.returncode
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58 return exit
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59 else:
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60 return p.wait()
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61
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62
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63 def shell_process(cmds, env=None, **kwds):
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64 """A high-level method wrapping subprocess.Popen.
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65
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66 Handles details such as environment extension and in process I/O
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67 redirection.
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68 """
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69 sys = kwds.get("sys", _sys)
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70 popen_kwds = dict()
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71 if isinstance(cmds, str):
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72 log.warning("Passing program arguments as a string may be a security hazard if combined with untrusted input")
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73 popen_kwds['shell'] = True
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74 if kwds.get("stdout", None) is None and redirecting_io(sys=sys):
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75 popen_kwds["stdout"] = subprocess.PIPE
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76 if kwds.get("stderr", None) is None and redirecting_io(sys=sys):
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77 popen_kwds["stderr"] = subprocess.PIPE
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78
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79 popen_kwds.update(**kwds)
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80 if env:
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81 new_env = os.environ.copy()
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82 new_env.update(env)
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83 popen_kwds["env"] = new_env
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84 p = subprocess.Popen(cmds, **popen_kwds)
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85 return p
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86
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87
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88 def execute(cmds, input=None):
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89 """Execute commands and throw an exception on a non-zero exit.
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90 if input is not None then the string is sent to the process' stdin.
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91
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92 Return the standard output if the commands are successful
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93 """
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94 return _wait(cmds, input=input, shell=False, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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95
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96
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97 def argv_to_str(command_argv, quote=True):
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98 """Convert an argv command list to a string for shell subprocess.
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99
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100 If None appears in the command list it is simply excluded.
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101
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102 Arguments are quoted with shlex.quote(). That said, this method is not meant to be
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103 used in security critical paths of code and should not be used to sanitize
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104 code.
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105 """
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106 map_func = shlex.quote if quote else lambda x: x
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107 return " ".join(map_func(c) for c in command_argv if c is not None)
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108
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109
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110 def _wait(cmds, input=None, **popen_kwds):
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111 p = subprocess.Popen(cmds, **popen_kwds)
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112 stdout, stderr = p.communicate(input)
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113 stdout, stderr = unicodify(stdout), unicodify(stderr)
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114 if p.returncode != 0:
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115 raise CommandLineException(argv_to_str(cmds), stdout, stderr, p.returncode)
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116 return stdout
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117
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118
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119 def download_command(url, to=STDOUT_INDICATOR):
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120 """Build a command line to download a URL.
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121
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122 By default the URL will be downloaded to standard output but a specific
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123 file can be specified with the `to` argument.
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124 """
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125 if which("wget"):
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126 download_cmd = ["wget", "-q"]
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127 if to == STDOUT_INDICATOR:
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128 download_cmd.extend(["-O", STDOUT_INDICATOR, url])
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129 else:
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130 download_cmd.extend(["--recursive", "-O", to, url])
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131 else:
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132 download_cmd = ["curl", "-L", url]
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133 if to != STDOUT_INDICATOR:
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134 download_cmd.extend(["-o", to])
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135 return download_cmd
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136
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137
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138 class CommandLineException(Exception):
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139 """An exception indicating a non-zero command-line exit."""
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140
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141 def __init__(self, command, stdout, stderr, returncode):
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142 """Construct a CommandLineException from command and standard I/O."""
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143 self.command = command
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144 self.stdout = stdout
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145 self.stderr = stderr
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146 self.returncode = returncode
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147 self.message = ("Failed to execute command-line %s, stderr was:\n"
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148 "-------->>begin stderr<<--------\n"
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149 "%s\n"
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150 "-------->>end stderr<<--------\n"
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151 "-------->>begin stdout<<--------\n"
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152 "%s\n"
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153 "-------->>end stdout<<--------\n"
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154 ) % (command, stderr, stdout)
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155
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156 def __str__(self):
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157 """Return a verbose error message indicating the command problem."""
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158 return self.message
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159
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160
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161 __all__ = (
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162 'argv_to_str',
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163 'CommandLineException',
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164 'download_command',
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165 'execute',
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166 'redirect_aware_commmunicate',
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167 'redirecting_io',
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168 'shell',
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169 'shell_process',
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170 'which',
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171 )