Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/io.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 from __future__ import print_function
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2 import contextlib
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3 import os
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4 import shutil
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5 import sys
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6 import tempfile
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7 import time
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8
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9 import click
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10 from galaxy.tools.deps import commands
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11 from galaxy.tools.deps.commands import which
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12
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13
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14 def communicate(cmds, **kwds):
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15 info(cmds)
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16 p = commands.shell_process(cmds, **kwds)
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17 ret_val = p.communicate()
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18 if p.returncode != 0:
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19 template = "Problem executing commands {0} - ({1}, {2})"
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20 msg = template.format(cmds, ret_val[0], ret_val[1])
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21 raise RuntimeError(msg)
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22 return ret_val
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23
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24
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25 def shell(cmds, **kwds):
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26 info(cmds)
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27 return commands.shell(cmds, **kwds)
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28
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29
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30 def info(message, *args):
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31 if args:
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32 message = message % args
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33 _echo(click.style(message, bold=True, fg='green'))
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34
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35
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36 def can_write_to_path(path, **kwds):
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37 if not kwds["force"] and os.path.exists(path):
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38 error("%s already exists, exiting." % path)
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39 return False
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40 return True
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41
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42
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43 def error(message, *args):
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44 if args:
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45 message = message % args
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46 _echo(click.style(message, bold=True, fg='red'), err=True)
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47
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48
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49 def warn(message, *args):
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50 if args:
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51 message = message % args
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52 _echo(click.style(message, fg='red'), err=True)
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53
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54
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55 def _echo(message, err=False):
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56 if sys.version_info[0] == 2:
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57 click.echo(message, err=err)
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58 else:
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59 print(message)
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60
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61
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62 def write_file(path, content):
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63 with open(path, "w") as f:
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64 f.write(content)
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65
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66
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67 def untar_to(url, path, tar_args):
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68 if which("wget"):
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69 download_cmd = "wget -q --recursive -O - '%s'"
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70 else:
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71 download_cmd = "curl '%s'"
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72 download_cmd = download_cmd % url
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73 if tar_args:
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74 if not os.path.exists(path):
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75 os.makedirs(path)
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76
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77 untar_cmd = "tar %s" % tar_args
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78 shell("%s | %s" % (download_cmd, untar_cmd))
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79 else:
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80 shell("%s > '%s'" % (download_cmd, path))
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81
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82
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83 @contextlib.contextmanager
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84 def temp_directory(prefix="planemo_tmp_"):
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85 temp_dir = tempfile.mkdtemp(prefix=prefix)
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86 try:
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87 yield temp_dir
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88 finally:
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89 shutil.rmtree(temp_dir)
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90
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91
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92 def kill_pid_file(pid_file):
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93 if not os.path.exists(pid_file):
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94 return
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95
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96 pid = int(open(pid_file, "r").read())
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97 kill_posix(pid)
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98
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99
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100 def kill_posix(pid):
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101 def _check_pid():
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102 try:
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103 os.kill(pid, 0)
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104 return True
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105 except OSError:
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106 return False
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107
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108 if _check_pid():
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109 for sig in [15, 9]:
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110 try:
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111 os.kill(pid, sig)
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112 except OSError:
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113 return
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114 time.sleep(1)
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115 if not _check_pid():
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116 return