Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/io.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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0
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1 from __future__ import absolute_import
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2 from __future__ import print_function
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3
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4 import contextlib
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5 import errno
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6 import fnmatch
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7 import os
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8 import shutil
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9 import subprocess
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10 import sys
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11 import tempfile
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12 import time
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13 from sys import platform as _platform
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14 from xml.sax.saxutils import escape
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15
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16 import click
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17 from galaxy.tool_util.deps import commands
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18 from galaxy.tool_util.deps.commands import download_command
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19 from six import (
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20 string_types,
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21 StringIO
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22 )
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23
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24 from .exit_codes import (
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25 EXIT_CODE_NO_SUCH_TARGET,
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26 EXIT_CODE_OK,
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27 )
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28
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29
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30 IS_OS_X = _platform == "darwin"
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31
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32
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33 def args_to_str(args):
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34 if args is None or isinstance(args, string_types):
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35 return args
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36 else:
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37 return commands.argv_to_str(args)
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38
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39
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40 def communicate(cmds, **kwds):
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41 cmd_string = args_to_str(cmds)
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42 info(cmd_string)
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43 p = commands.shell_process(cmds, **kwds)
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44 if kwds.get("stdout", None) is None and commands.redirecting_io(sys=sys):
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45 output = commands.redirect_aware_commmunicate(p)
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46 else:
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47 output = p.communicate()
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48
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49 if p.returncode != 0:
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50 template = "Problem executing commands {0} - ({1}, {2})"
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51 msg = template.format(cmd_string, output[0], output[1])
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52 raise RuntimeError(msg)
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53 return output
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54
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55
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56 def shell(cmds, **kwds):
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57 cmd_string = args_to_str(cmds)
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58 info(cmd_string)
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59 return commands.shell(cmds, **kwds)
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60
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61
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62 def info(message, *args):
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63 if args:
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64 message = message % args
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65 click.echo(click.style(message, bold=True, fg='green'))
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66
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67
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68 def can_write_to_path(path, **kwds):
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69 if not kwds["force"] and os.path.exists(path):
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70 error("%s already exists, exiting." % path)
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71 return False
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72 return True
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73
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74
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75 def error(message, *args):
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76 if args:
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77 message = message % args
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78 click.echo(click.style(message, bold=True, fg='red'), err=True)
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79
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80
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81 def warn(message, *args):
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82 if args:
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83 message = message % args
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84 click.echo(click.style(message, fg='red'), err=True)
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85
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86
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87 def shell_join(*args):
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88 """Join potentially empty commands together with '&&'."""
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89 return " && ".join(args_to_str(_) for _ in args if _)
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90
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91
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92 def write_file(path, content, force=True):
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93 if os.path.exists(path) and not force:
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94 return
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95
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96 with open(path, "w") as f:
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97 f.write(content)
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98
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99
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100 def untar_to(url, tar_args=None, path=None, dest_dir=None):
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101 if tar_args:
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102 assert not (path and dest_dir)
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103 if dest_dir:
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104 if not os.path.exists(dest_dir):
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105 os.makedirs(dest_dir)
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106 tar_args[0:0] = ['-C', dest_dir]
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107 if path:
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108 tar_args.insert(0, '-O')
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109
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110 download_cmd = download_command(url)
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111 download_p = commands.shell_process(download_cmd, stdout=subprocess.PIPE)
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112 untar_cmd = ['tar'] + tar_args
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113 if path:
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114 with open(path, 'wb') as fh:
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115 shell(untar_cmd, stdin=download_p.stdout, stdout=fh)
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116 else:
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117 shell(untar_cmd, stdin=download_p.stdout)
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118 download_p.wait()
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119 else:
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120 cmd = download_command(url, to=path)
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121 shell(cmd)
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122
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123
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124 def find_matching_directories(path, pattern, recursive):
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125 """Find directories below supplied path with file matching pattern.
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126
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127 Returns an empty list if no matches are found, and if recursive is False
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128 only the top directory specified by path will be considered.
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129 """
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130 dirs = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
131 if recursive:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
132 if not os.path.isdir(path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
133 template = "--recursive specified with non-directory path [%s]"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
134 message = template % (path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
135 raise Exception(message)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
136
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
137 for base_path, dirnames, filenames in os.walk(path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
138 dirnames.sort()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
139 for filename in fnmatch.filter(filenames, pattern):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
140 dirs.append(base_path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
141 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
142 if os.path.exists(os.path.join(path, pattern)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
143 dirs.append(path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
144 elif os.path.basename(path) == pattern:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
145 dirs.append(os.path.dirname(path))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
146 return dirs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
147
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
148
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
149 @contextlib.contextmanager
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
150 def real_io():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
151 """Ensure stdout and stderr have supported ``fileno()`` method.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
152
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
153 nosetests replaces these streams with :class:`StringIO` objects
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
154 that may not work the same in every situtation - :func:`subprocess.Popen`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
155 calls in particular.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
156 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
157 original_stdout = sys.stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
158 original_stderr = sys.stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
159 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
160 if commands.redirecting_io(sys=sys):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
161 sys.stdout = sys.__stdout__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
162 sys.stderr = sys.__stderr__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
163 yield
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
164 finally:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
165 sys.stdout = original_stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
166 sys.stderr = original_stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
167
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
168
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
169 @contextlib.contextmanager
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
170 def temp_directory(prefix="planemo_tmp_", dir=None, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
171 if dir is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
172 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
173 os.makedirs(dir)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
174 except OSError as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
175 if e.errno != errno.EEXIST:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
176 raise
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
177 temp_dir = tempfile.mkdtemp(prefix=prefix, dir=dir, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
178 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
179 yield temp_dir
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
180 finally:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
181 shutil.rmtree(temp_dir)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
182
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
183
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
184 def ps1_for_path(path, base="PS1"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
185 """ Used by environment commands to build a PS1 shell
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
186 variables for tool or directory of tools.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
187 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
188 file_name = os.path.basename(path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
189 base_name = os.path.splitext(file_name)[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
190 ps1 = "(%s)${%s}" % (base_name, base)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
191 return ps1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
192
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
193
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
194 def kill_pid_file(pid_file):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
195 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
196 os.stat(pid_file)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
197 except OSError as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
198 if e.errno == errno.ENOENT:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
199 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
201 with open(pid_file, "r") as fh:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
202 pid = int(fh.read())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
203 kill_posix(pid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
204 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
205 os.unlink(pid_file)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
206 except Exception:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
207 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
208
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
209
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
210 def kill_posix(pid):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
211 def _check_pid():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
212 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
213 os.kill(pid, 0)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
214 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
215 except OSError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
216 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
218 if _check_pid():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
219 for sig in [15, 9]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
220 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
221 os.kill(pid, sig)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
222 except OSError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
223 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
224 time.sleep(1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
225 if not _check_pid():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
226 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
227
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
228
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
229 @contextlib.contextmanager
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
230 def conditionally_captured_io(capture, tee=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
231 captured_std = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
232 if capture:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
233 with Capturing() as captured_std:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
234 yield captured_std
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
235 if tee:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
236 tee_captured_output(captured_std)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
237 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
238 yield
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
239
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
240
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
241 @contextlib.contextmanager
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
242 def captured_io_for_xunit(kwds, captured_io):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
243 captured_std = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
244 with_xunit = kwds.get('report_xunit', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
245 with conditionally_captured_io(with_xunit, tee=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
246 time1 = time.time()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
247 yield
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
248 time2 = time.time()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
249
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
250 if with_xunit:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
251 stdout = [escape(m['data']) for m in captured_std
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
252 if m['logger'] == 'stdout']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
253 stderr = [escape(m['data']) for m in captured_std
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
254 if m['logger'] == 'stderr']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
255 captured_io["stdout"] = stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
256 captured_io["stderr"] = stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
257 captured_io["time"] = (time2 - time1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
258 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
259 captured_io["stdout"] = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
260 captured_io["stderr"] = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
261 captured_io["time"] = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
262
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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263
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264 class Capturing(list):
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265 """Function context which captures stdout/stderr
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266
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267 This keeps planemo's codebase clean without requiring planemo to hold onto
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268 messages, or pass user-facing messages back at all. This could probably be
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269 solved by swapping planemo entirely to a logger and reading from/writing
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270 to that, but this is easier.
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271
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272 This swaps sys.std{out,err} with StringIOs and then makes that output
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273 available.
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274 """
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275 # http://stackoverflow.com/a/16571630
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276
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277 def __enter__(self):
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278 self._stdout = sys.stdout
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279 self._stderr = sys.stderr
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280 sys.stdout = self._stringio_stdout = StringIO()
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281 sys.stderr = self._stringio_stderr = StringIO()
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282 return self
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283
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284 def __exit__(self, *args):
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285 self.extend([{'logger': 'stdout', 'data': x} for x in
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286 self._stringio_stdout.getvalue().splitlines()])
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287 self.extend([{'logger': 'stderr', 'data': x} for x in
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288 self._stringio_stderr.getvalue().splitlines()])
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289
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290 sys.stdout = self._stdout
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291 sys.stderr = self._stderr
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292
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293
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294 def tee_captured_output(output):
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295 """For messages captured with Capturing, send them to their correct
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296 locations so as to not interfere with normal user experience.
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297 """
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298 for message in output:
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299 # Append '\n' due to `splitlines()` above
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300 if message['logger'] == 'stdout':
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301 sys.stdout.write(message['data'] + '\n')
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302 if message['logger'] == 'stderr':
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303 sys.stderr.write(message['data'] + '\n')
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304
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305
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306 def wait_on(function, desc, timeout=5, polling_backoff=0):
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307 """Wait on given function's readiness. Grow the polling
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308 interval incrementally by the polling_backoff."""
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309 delta = .25
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310 timing = 0
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311 while True:
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312 if timing > timeout:
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313 message = "Timed out waiting on %s." % desc
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314 raise Exception(message)
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315 timing += delta
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316 delta += polling_backoff
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317 value = function()
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318 if value is not None:
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319 return value
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320 time.sleep(delta)
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321
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322
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323 @contextlib.contextmanager
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324 def open_file_or_standard_output(path, *args, **kwds):
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325 if path == "-":
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326 yield sys.stdout
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327 else:
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328 yield open(path, *args, **kwds)
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329
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330
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331 def filter_paths(paths, cwd=None, **kwds):
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332 if cwd is None:
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333 cwd = os.getcwd()
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334
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335 def norm(path):
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336 if not os.path.isabs(path):
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337 path = os.path.join(cwd, path)
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338 return os.path.normpath(path)
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339
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340 def exclude_func(exclude_path):
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341 def path_startswith(p):
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342 """Check that p starts with exclude_path and that the first
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343 character of p not included in exclude_path (if any) is the
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344 directory separator.
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345 """
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346 norm_p = norm(p)
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347 norm_exclude_path = norm(exclude_path)
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348 if norm_p.startswith(norm_exclude_path):
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349 return norm_p[len(norm_exclude_path):len(norm_exclude_path) + 1] in ['', os.sep]
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350 return False
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351 return path_startswith
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352
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353 filters_as_funcs = []
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354 filters_as_funcs.extend(map(exclude_func, kwds.get("exclude", [])))
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355
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356 for exclude_paths_ins in kwds.get("exclude_from", []):
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357 with open(exclude_paths_ins, "r") as f:
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358 for line in f.readlines():
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359 line = line.strip()
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360 if not line or line.startswith("#"):
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361 continue
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362 filters_as_funcs.append(exclude_func(line))
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363
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364 return [p for p in paths if not any(f(p) for f in filters_as_funcs)]
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365
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366
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367 def coalesce_return_codes(ret_codes, assert_at_least_one=False):
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368 # Return 0 if everything is fine, otherwise pick the least
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369 # specific non-0 return code - preferring to report errors
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370 # to other non-0 exit codes.
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371 if assert_at_least_one and len(ret_codes) == 0:
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372 return EXIT_CODE_NO_SUCH_TARGET
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373
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374 coalesced_return_code = EXIT_CODE_OK
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375 for ret_code in ret_codes:
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376 # None is equivalent to 0 in these methods.
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377 ret_code = 0 if ret_code is None else ret_code
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378 if ret_code == 0:
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379 # Everything is fine, keep moving...
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380 pass
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381 elif coalesced_return_code == 0:
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382 coalesced_return_code = ret_code
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383 # At this point in logic both ret_code and coalesced_return_code are
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384 # are non-zero
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385 elif ret_code < 0:
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386 # Error state, this should override eveything else.
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387 coalesced_return_code = ret_code
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388 elif ret_code > 0 and coalesced_return_code < 0:
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389 # Keep error state recorded.
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390 pass
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391 elif ret_code > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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392 # Lets somewhat arbitrarily call the smaller exit code
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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393 # the less specific.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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394 coalesced_return_code = min(ret_code, coalesced_return_code)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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395
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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396 if coalesced_return_code < 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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397 # Map -1 => 254, -2 => 253, etc...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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398 # Not sure it is helpful to have negative error codes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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399 # this was a design and API mistake in planemo.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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400 coalesced_return_code = 255 + coalesced_return_code
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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401
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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402 return coalesced_return_code