Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/run.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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1 """Utilities for calling Galaxy scripts."""
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2 import os
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3 import string
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4
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5 from galaxy.tool_util.deps.commands import shell
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6 from six.moves import shlex_quote
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7
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8 from planemo.io import info, shell_join
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9 from planemo.virtualenv import (
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10 create_command,
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11 DEFAULT_PYTHON_VERSION,
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12 )
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14
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15 # Activate galaxy's virtualenv if present (needed for tests say but not for
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16 # server because run.sh does this).
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17 ACTIVATE_COMMAND = 'if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi'
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18 CREATE_COMMAND_TEMPLATE = string.Template(
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19 'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi',
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20 )
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21 PRINT_VENV_COMMAND = shell_join(
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22 r'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
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23 ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; '
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24 'then echo "Virtual environment directory exists."; '
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25 'else echo "Virtual environment directory does not exist."; fi'),
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26 )
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29 CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ]; "
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30 "then GALAXY_VIRTUAL_ENV=.venv; "
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31 "else GALAXY_VIRTUAL_ENV=%s; fi")
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32 UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
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33
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34
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35 def setup_venv(ctx, kwds):
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36 if kwds.get("skip_venv", False):
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37 return ""
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38
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39 create_template_params = {
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40 'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV", kwds.get('galaxy_python_version'))
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41 }
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42 return shell_join(
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43 locate_galaxy_virtualenv(ctx, kwds),
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44 PRINT_VENV_COMMAND if ctx.verbose else None,
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45 CREATE_COMMAND_TEMPLATE.safe_substitute(create_template_params),
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46 PRINT_VENV_COMMAND if ctx.verbose else None,
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47 ACTIVATE_COMMAND,
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48 )
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49
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50
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51 def locate_galaxy_virtualenv(ctx, kwds):
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52 if os.environ.get("GALAXY_VIRTUAL_ENV"):
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53 venv_command = ""
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54 elif not kwds.get("no_cache_galaxy", False):
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55 workspace = ctx.workspace
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56 galaxy_branch = kwds.get("galaxy_branch") or "master"
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57 shared_venv_path = os.path.join(workspace, "gx_venv")
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58 galaxy_python_version = kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION
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59 if galaxy_python_version != DEFAULT_PYTHON_VERSION:
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60 shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_python_version)
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61 if galaxy_branch != "master":
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62 shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_branch)
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63 venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex_quote(shared_venv_path)
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64 else:
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65 venv_command = UNCACHED_VIRTUAL_ENV_COMMAND
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66 return shell_join(
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67 venv_command,
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68 "export GALAXY_VIRTUAL_ENV",
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69 )
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70
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71
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72 def shell_if_wheels(command):
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73 """ Take a shell command and convert it to shell command that runs
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74 only if Galaxy is new enough to use wheels.
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75 """
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76 return "$(grep -q 'skip-venv' run_tests.sh) && %s" % command
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77
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78
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79 def setup_common_startup_args():
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80 return _set_variable_if_wheels(
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81 "COMMON_STARTUP_ARGS", "--dev-wheels"
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82 )
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83
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84
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85 def _set_variable_if_wheels(var, if_wheels_val, else_val=""):
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86 var_command = '${var}=${else_val}; '
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87 var_command += shell_if_wheels(
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88 '${var}="${if_wheels_val}"; '
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89 )
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90 var_command += "export ${var}"
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91 var_command += '; echo "Set ${var} to ${${var}}"'
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92 return string.Template(var_command).safe_substitute(
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93 var=var,
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94 if_wheels_val=if_wheels_val,
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95 else_val=else_val,
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96 )
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97
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98
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99 def run_galaxy_command(ctx, command, env, action):
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100 """Run Galaxy command with informative verbose logging."""
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101 message = "%s with command [%s]" % (action, command)
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102 info(message)
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103 ctx.vlog("With environment variables:")
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104 ctx.vlog("============================")
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105 for key, value in env.items():
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106 ctx.vlog('%s="%s"' % (key, value))
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107 ctx.vlog("============================")
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108 exit_code = shell(command, env=env)
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109 ctx.vlog("run command exited with return code %s" % exit_code)
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110 return exit_code
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111
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112
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113 __all__ = (
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114 "setup_venv",
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115 "run_galaxy_command",
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116 "setup_common_startup_args",
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117 )