Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/planemo/galaxy/run.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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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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13 |
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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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27 |
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28 |
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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 ) |