Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/io.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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0
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1 """Planemo I/O abstractions and utilities."""
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2 from __future__ import absolute_import
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3 from __future__ import print_function
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4
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5 import contextlib
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6 import errno
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7 import fnmatch
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8 import os
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9 import shutil
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10 import subprocess
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11 import sys
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12 import tempfile
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13 import time
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14 from sys import platform as _platform
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15 from xml.sax.saxutils import escape
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16
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17 import click
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18 from galaxy.util import commands
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19 from galaxy.util.commands import download_command
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20 from six import (
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21 string_types,
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22 StringIO
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23 )
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24
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25 from .exit_codes import (
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26 EXIT_CODE_NO_SUCH_TARGET,
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27 EXIT_CODE_OK,
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28 )
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29
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30
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31 IS_OS_X = _platform == "darwin"
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32
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33
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34 def args_to_str(args):
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35 """Collapse list of arguments in a commmand-line string."""
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36 if args is None or isinstance(args, string_types):
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37 return args
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38 else:
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39 return commands.argv_to_str(args)
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40
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41
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42 def communicate(cmds, **kwds):
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43 """Execute shell command and wait for output.
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44
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45 With click-aware I/O handling, pretty display of the command being executed,
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46 and formatted exception if the exit code is not 0.
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47 """
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48 cmd_string = args_to_str(cmds)
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49 info(cmd_string)
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50 p = commands.shell_process(cmds, **kwds)
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51 if kwds.get("stdout", None) is None and commands.redirecting_io(sys=sys):
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52 output = commands.redirect_aware_commmunicate(p)
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53 else:
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54 output = p.communicate()
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55
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56 if p.returncode != 0:
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57 template = "Problem executing commands {0} - ({1}, {2})"
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58 msg = template.format(cmd_string, output[0], output[1])
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59 raise RuntimeError(msg)
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60 return output
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61
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62
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63 def shell(cmds, **kwds):
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64 """Print and execute shell command."""
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65 cmd_string = args_to_str(cmds)
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66 info(cmd_string)
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67 return commands.shell(cmds, **kwds)
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68
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69
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70 def info(message, *args):
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71 """Print stylized info message to the screen."""
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72 if args:
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73 message = message % args
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74 click.echo(click.style(message, bold=True, fg='green'))
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75
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76
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77 def error(message, *args):
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78 """Print stylized error message to the screen."""
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79 if args:
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80 message = message % args
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81 click.echo(click.style(message, bold=True, fg='red'), err=True)
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82
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83
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84 def warn(message, *args):
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85 """Print stylized warning message to the screen."""
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86 if args:
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87 message = message % args
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88 click.echo(click.style(message, fg='red'), err=True)
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89
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90
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91 def can_write_to_path(path: str, **kwds):
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92 """Implement -f/--force logic.
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93
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94 If supplied path exists, print an error message and return False
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95 unless --force caused the 'force' keyword argument to be True.
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96 """
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97 if not kwds["force"] and os.path.exists(path):
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98 error("%s already exists, exiting." % path)
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99 return False
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100 return True
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101
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102
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103 def shell_join(*args):
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104 """Join potentially empty commands together with '&&'."""
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105 return " && ".join(args_to_str(_) for _ in args if _)
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106
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107
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108 def write_file(path, content, force=True):
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109 if os.path.exists(path) and not force:
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110 return
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111
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112 with open(path, "w") as f:
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113 f.write(content)
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114
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115
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116 def untar_to(url, tar_args=None, path=None, dest_dir=None):
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117 if tar_args:
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118 assert not (path and dest_dir)
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119 if dest_dir:
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120 if not os.path.exists(dest_dir):
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121 os.makedirs(dest_dir)
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122 tar_args[0:0] = ['-C', dest_dir]
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123 if path:
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124 tar_args.insert(0, '-O')
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125
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126 download_cmd = download_command(url)
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127 download_p = commands.shell_process(download_cmd, stdout=subprocess.PIPE)
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128 untar_cmd = ['tar'] + tar_args
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shellac
parents:
diff changeset
129 if path:
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shellac
parents:
diff changeset
130 with open(path, 'wb') as fh:
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shellac
parents:
diff changeset
131 shell(untar_cmd, stdin=download_p.stdout, stdout=fh)
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shellac
parents:
diff changeset
132 else:
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shellac
parents:
diff changeset
133 shell(untar_cmd, stdin=download_p.stdout)
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shellac
parents:
diff changeset
134 download_p.wait()
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shellac
parents:
diff changeset
135 else:
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shellac
parents:
diff changeset
136 cmd = download_command(url, to=path)
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shellac
parents:
diff changeset
137 shell(cmd)
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shellac
parents:
diff changeset
138
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shellac
parents:
diff changeset
139
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parents:
diff changeset
140 def find_matching_directories(path, pattern, recursive):
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shellac
parents:
diff changeset
141 """Find directories below supplied path with file matching pattern.
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shellac
parents:
diff changeset
142
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shellac
parents:
diff changeset
143 Returns an empty list if no matches are found, and if recursive is False
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parents:
diff changeset
144 only the top directory specified by path will be considered.
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shellac
parents:
diff changeset
145 """
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shellac
parents:
diff changeset
146 dirs = []
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shellac
parents:
diff changeset
147 if recursive:
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shellac
parents:
diff changeset
148 if not os.path.isdir(path):
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shellac
parents:
diff changeset
149 template = "--recursive specified with non-directory path [%s]"
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shellac
parents:
diff changeset
150 message = template % (path)
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shellac
parents:
diff changeset
151 raise Exception(message)
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shellac
parents:
diff changeset
152
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shellac
parents:
diff changeset
153 for base_path, dirnames, filenames in os.walk(path):
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shellac
parents:
diff changeset
154 dirnames.sort()
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shellac
parents:
diff changeset
155 for filename in fnmatch.filter(filenames, pattern):
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shellac
parents:
diff changeset
156 dirs.append(base_path)
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shellac
parents:
diff changeset
157 else:
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shellac
parents:
diff changeset
158 if os.path.exists(os.path.join(path, pattern)):
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shellac
parents:
diff changeset
159 dirs.append(path)
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shellac
parents:
diff changeset
160 elif os.path.basename(path) == pattern:
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shellac
parents:
diff changeset
161 dirs.append(os.path.dirname(path))
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shellac
parents:
diff changeset
162 return dirs
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shellac
parents:
diff changeset
163
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shellac
parents:
diff changeset
164
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shellac
parents:
diff changeset
165 @contextlib.contextmanager
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shellac
parents:
diff changeset
166 def real_io():
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shellac
parents:
diff changeset
167 """Ensure stdout and stderr have supported ``fileno()`` method.
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shellac
parents:
diff changeset
168
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shellac
parents:
diff changeset
169 nosetests replaces these streams with :class:`StringIO` objects
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shellac
parents:
diff changeset
170 that may not work the same in every situtation - :func:`subprocess.Popen`
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shellac
parents:
diff changeset
171 calls in particular.
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shellac
parents:
diff changeset
172 """
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shellac
parents:
diff changeset
173 original_stdout = sys.stdout
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shellac
parents:
diff changeset
174 original_stderr = sys.stderr
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shellac
parents:
diff changeset
175 try:
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shellac
parents:
diff changeset
176 if commands.redirecting_io(sys=sys):
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shellac
parents:
diff changeset
177 sys.stdout = sys.__stdout__
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shellac
parents:
diff changeset
178 sys.stderr = sys.__stderr__
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
179 yield
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
180 finally:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
181 sys.stdout = original_stdout
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shellac
parents:
diff changeset
182 sys.stderr = original_stderr
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shellac
parents:
diff changeset
183
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shellac
parents:
diff changeset
184
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shellac
parents:
diff changeset
185 @contextlib.contextmanager
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shellac
parents:
diff changeset
186 def temp_directory(prefix="planemo_tmp_", dir=None, **kwds):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
187 if dir is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
188 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
189 os.makedirs(dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
190 except OSError as e:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
191 if e.errno != errno.EEXIST:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
192 raise
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
193 temp_dir = tempfile.mkdtemp(prefix=prefix, dir=dir, **kwds)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
194 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
195 yield temp_dir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
196 finally:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
197 shutil.rmtree(temp_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
198
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
199
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
200 def ps1_for_path(path, base="PS1"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
201 """ Used by environment commands to build a PS1 shell
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
202 variables for tool or directory of tools.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
203 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
204 file_name = os.path.basename(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
205 base_name = os.path.splitext(file_name)[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
206 ps1 = "(%s)${%s}" % (base_name, base)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
207 return ps1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
208
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
209
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
210 def kill_pid_file(pid_file: str):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
211 """Kill process group corresponding to specified pid file."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
212 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
213 os.stat(pid_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
214 except OSError as e:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
215 if e.errno == errno.ENOENT:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
216 return False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
217
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
218 with open(pid_file, "r") as fh:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
219 pid = int(fh.read())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
220 kill_posix(pid)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
221 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
222 os.unlink(pid_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
223 except Exception:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
224 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
225
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
226
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
227 def kill_posix(pid: int):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
228 """Kill process group corresponding to specified pid."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
229 def _check_pid():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
230 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
231 os.kill(pid, 0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
232 return True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
233 except OSError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
234 return False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
235
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
236 if _check_pid():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
237 for sig in [15, 9]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
238 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
239 # gunicorn (unlike paste), seem to require killing process
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
240 # group
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
241 os.killpg(os.getpgid(pid), sig)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
242 except OSError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
243 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
244 time.sleep(1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
245 if not _check_pid():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
246 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
247
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
248
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
249 @contextlib.contextmanager
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
250 def conditionally_captured_io(capture, tee=False):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
251 """If capture is True, capture stdout and stderr for logging."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
252 captured_std = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
253 if capture:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
254 with _Capturing() as captured_std:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
255 yield captured_std
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
256 if tee:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
257 tee_captured_output(captured_std)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
258 else:
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259 yield
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260
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261
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262 @contextlib.contextmanager
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263 def captured_io_for_xunit(kwds, captured_io):
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264 """Capture Planemo I/O and timing for outputting to an xUnit report."""
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265 captured_std = []
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266 with_xunit = kwds.get('report_xunit', False)
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267 with conditionally_captured_io(with_xunit, tee=True):
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268 time1 = time.time()
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269 yield
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270 time2 = time.time()
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271
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272 if with_xunit:
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273 stdout = [escape(m['data']) for m in captured_std
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274 if m['logger'] == 'stdout']
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275 stderr = [escape(m['data']) for m in captured_std
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276 if m['logger'] == 'stderr']
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277 captured_io["stdout"] = stdout
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278 captured_io["stderr"] = stderr
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279 captured_io["time"] = (time2 - time1)
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280 else:
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281 captured_io["stdout"] = None
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282 captured_io["stderr"] = None
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283 captured_io["time"] = None
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284
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285
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286 class _Capturing(list):
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287 """Function context which captures stdout/stderr
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288
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289 This keeps planemo's codebase clean without requiring planemo to hold onto
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290 messages, or pass user-facing messages back at all. This could probably be
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291 solved by swapping planemo entirely to a logger and reading from/writing
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292 to that, but this is easier.
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293
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294 This swaps sys.std{out,err} with StringIOs and then makes that output
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295 available.
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296 """
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297 # http://stackoverflow.com/a/16571630
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298
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299 def __enter__(self):
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300 self._stdout = sys.stdout
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301 self._stderr = sys.stderr
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302 sys.stdout = self._stringio_stdout = StringIO()
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303 sys.stderr = self._stringio_stderr = StringIO()
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304 return self
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305
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306 def __exit__(self, *args):
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307 self.extend([{'logger': 'stdout', 'data': x} for x in
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308 self._stringio_stdout.getvalue().splitlines()])
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309 self.extend([{'logger': 'stderr', 'data': x} for x in
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310 self._stringio_stderr.getvalue().splitlines()])
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311
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312 sys.stdout = self._stdout
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313 sys.stderr = self._stderr
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314
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315
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316 def tee_captured_output(output):
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317 """tee captured standard output and standard error if needed.
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318
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319 For messages captured with Capturing, send them to their correct
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320 locations so as to not interfere with normal user experience.
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321 """
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322 for message in output:
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323 # Append '\n' due to `splitlines()` above
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324 if message['logger'] == 'stdout':
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325 sys.stdout.write(message['data'] + '\n')
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326 if message['logger'] == 'stderr':
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327 sys.stderr.write(message['data'] + '\n')
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328
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329
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330 def wait_on(function, desc, timeout=5, polling_backoff=0):
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331 """Wait on given function's readiness.
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332
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333 Grow the polling interval incrementally by the polling_backoff.
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334 """
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335 delta = .25
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336 timing = 0
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337 while True:
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338 if timing > timeout:
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339 message = "Timed out waiting on %s." % desc
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340 raise Exception(message)
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341 timing += delta
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342 delta += polling_backoff
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343 value = function()
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344 if value is not None:
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345 return value
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346 time.sleep(delta)
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347
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348
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349 @contextlib.contextmanager
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350 def open_file_or_standard_output(path, *args, **kwds):
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351 """Open file but respect '-' as referring to stdout."""
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352 if path == "-":
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353 yield sys.stdout
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354 else:
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355 yield open(path, *args, **kwds)
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356
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357
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358 def filter_paths(paths, cwd=None, **kwds):
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359 if cwd is None:
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360 cwd = os.getcwd()
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361
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362 def norm(path):
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363 if not os.path.isabs(path):
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364 path = os.path.join(cwd, path)
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365 return os.path.normpath(path)
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366
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367 def exclude_func(exclude_path):
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368 def path_startswith(p):
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369 """Check that p starts with exclude_path and that the first
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370 character of p not included in exclude_path (if any) is the
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371 directory separator.
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372 """
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373 norm_p = norm(p)
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374 norm_exclude_path = norm(exclude_path)
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375 if norm_p.startswith(norm_exclude_path):
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376 return norm_p[len(norm_exclude_path):len(norm_exclude_path) + 1] in ['', os.sep]
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377 return False
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378 return path_startswith
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379
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380 filters_as_funcs = []
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381 filters_as_funcs.extend(map(exclude_func, kwds.get("exclude", [])))
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382
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383 for exclude_paths_ins in kwds.get("exclude_from", []):
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384 with open(exclude_paths_ins, "r") as f:
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385 for line in f.readlines():
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386 line = line.strip()
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387 if not line or line.startswith("#"):
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388 continue
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389 filters_as_funcs.append(exclude_func(line))
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390
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391 return [p for p in paths if not any(f(p) for f in filters_as_funcs)]
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392
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393
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394 def coalesce_return_codes(ret_codes, assert_at_least_one=False):
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395 # Return 0 if everything is fine, otherwise pick the least
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396 # specific non-0 return code - preferring to report errors
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397 # to other non-0 exit codes.
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398 if assert_at_least_one and len(ret_codes) == 0:
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399 return EXIT_CODE_NO_SUCH_TARGET
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400
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401 coalesced_return_code = EXIT_CODE_OK
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402 for ret_code in ret_codes:
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403 # None is equivalent to 0 in these methods.
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404 ret_code = 0 if ret_code is None else ret_code
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405 if ret_code == 0:
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406 # Everything is fine, keep moving...
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407 pass
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408 elif coalesced_return_code == 0:
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409 coalesced_return_code = ret_code
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410 # At this point in logic both ret_code and coalesced_return_code are
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411 # are non-zero
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412 elif ret_code < 0:
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413 # Error state, this should override eveything else.
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414 coalesced_return_code = ret_code
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415 elif ret_code > 0 and coalesced_return_code < 0:
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416 # Keep error state recorded.
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417 pass
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418 elif ret_code > 0:
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419 # Lets somewhat arbitrarily call the smaller exit code
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420 # the less specific.
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421 coalesced_return_code = min(ret_code, coalesced_return_code)
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422
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423 if coalesced_return_code < 0:
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424 # Map -1 => 254, -2 => 253, etc...
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425 # Not sure it is helpful to have negative error codes
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426 # this was a design and API mistake in planemo.
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427 coalesced_return_code = 255 + coalesced_return_code
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428
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429 return coalesced_return_code