Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/job.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
parents
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0
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1 import datetime
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2 import functools
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3 import itertools
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4 import logging
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5 import os
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6 import re
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7 import shutil
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8 import subprocess # nosec
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9 import sys
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10 import tempfile
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11 import threading
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12 import time
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13 import uuid
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14 from abc import ABCMeta, abstractmethod
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15 from io import IOBase
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16 from threading import Timer
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17 from typing import (
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18 IO,
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19 Callable,
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20 Iterable,
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21 List,
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22 Match,
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23 MutableMapping,
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24 MutableSequence,
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25 Optional,
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26 TextIO,
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27 Tuple,
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28 Union,
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29 cast,
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30 )
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31
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32 import psutil
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33 import shellescape
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34 from prov.model import PROV
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35 from schema_salad.sourceline import SourceLine
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36 from schema_salad.utils import json_dump, json_dumps
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37 from typing_extensions import TYPE_CHECKING
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38
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39 from .builder import Builder, HasReqsHints
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40 from .context import RuntimeContext
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41 from .errors import UnsupportedRequirement, WorkflowException
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42 from .loghandler import _logger
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43 from .pathmapper import MapperEnt, PathMapper
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44 from .process import stage_files
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45 from .secrets import SecretStore
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46 from .utils import (
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47 CWLObjectType,
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48 CWLOutputType,
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49 DirectoryType,
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50 OutputCallbackType,
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51 bytes2str_in_dicts,
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52 copytree_with_merge,
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53 create_tmp_dir,
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54 ensure_non_writable,
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55 ensure_writable,
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56 onWindows,
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57 processes_to_kill,
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58 )
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59
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60 if TYPE_CHECKING:
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61 from .provenance_profile import ProvenanceProfile # pylint: disable=unused-import
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62 needs_shell_quoting_re = re.compile(r"""(^$|[\s|&;()<>\'"$@])""")
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63
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64 FORCE_SHELLED_POPEN = os.getenv("CWLTOOL_FORCE_SHELL_POPEN", "0") == "1"
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65
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66 SHELL_COMMAND_TEMPLATE = """#!/bin/bash
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67 python "run_job.py" "job.json"
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68 """
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69
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70 PYTHON_RUN_SCRIPT = """
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71 import json
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72 import os
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73 import sys
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74 if os.name == 'posix':
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75 try:
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76 import subprocess32 as subprocess # type: ignore
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77 except Exception:
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78 import subprocess
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79 else:
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80 import subprocess # type: ignore
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81
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82 with open(sys.argv[1], "r") as f:
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83 popen_description = json.load(f)
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84 commands = popen_description["commands"]
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85 cwd = popen_description["cwd"]
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86 env = popen_description["env"]
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87 env["PATH"] = os.environ.get("PATH")
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88 stdin_path = popen_description["stdin_path"]
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89 stdout_path = popen_description["stdout_path"]
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90 stderr_path = popen_description["stderr_path"]
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91 if stdin_path is not None:
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92 stdin = open(stdin_path, "rb")
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93 else:
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94 stdin = subprocess.PIPE
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95 if stdout_path is not None:
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96 stdout = open(stdout_path, "wb")
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97 else:
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98 stdout = sys.stderr
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99 if stderr_path is not None:
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100 stderr = open(stderr_path, "wb")
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101 else:
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102 stderr = sys.stderr
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103 if os.name == 'nt':
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104 close_fds = False
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105 for key, value in env.items():
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106 env[key] = str(value)
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107 else:
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108 close_fds = True
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109 sp = subprocess.Popen(commands,
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110 shell=False,
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111 close_fds=close_fds,
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112 stdin=stdin,
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113 stdout=stdout,
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114 stderr=stderr,
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115 env=env,
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116 cwd=cwd)
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117 if sp.stdin:
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118 sp.stdin.close()
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119 rcode = sp.wait()
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120 if stdin is not subprocess.PIPE:
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121 stdin.close()
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122 if stdout is not sys.stderr:
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123 stdout.close()
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124 if stderr is not sys.stderr:
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125 stderr.close()
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126 sys.exit(rcode)
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127 """
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128
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129
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130 def relink_initialworkdir(
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131 pathmapper: PathMapper,
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132 host_outdir: str,
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133 container_outdir: str,
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134 inplace_update: bool = False,
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135 ) -> None:
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136 for _, vol in pathmapper.items():
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137 if not vol.staged:
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138 continue
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139
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140 if vol.type in ("File", "Directory") or (
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141 inplace_update and vol.type in ("WritableFile", "WritableDirectory")
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142 ):
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143 if not vol.target.startswith(container_outdir):
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144 # this is an input file written outside of the working
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145 # directory, so therefor ineligable for being an output file.
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146 # Thus, none of our business
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147 continue
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148 host_outdir_tgt = os.path.join(
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149 host_outdir, vol.target[len(container_outdir) + 1 :]
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150 )
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151 if os.path.islink(host_outdir_tgt) or os.path.isfile(host_outdir_tgt):
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152 try:
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153 os.remove(host_outdir_tgt)
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154 except PermissionError:
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155 pass
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156 elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
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157 shutil.rmtree(host_outdir_tgt)
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158 if onWindows():
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159 # If this becomes a big issue for someone then we could
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160 # refactor the code to process output from a running container
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161 # and avoid all the extra IO below
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162 if vol.type in ("File", "WritableFile"):
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163 shutil.copy(vol.resolved, host_outdir_tgt)
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164 elif vol.type in ("Directory", "WritableDirectory"):
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165 copytree_with_merge(vol.resolved, host_outdir_tgt)
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166 elif not vol.resolved.startswith("_:"):
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167 try:
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168 os.symlink(vol.resolved, host_outdir_tgt)
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169 except FileExistsError:
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170 pass
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171
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172
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173 def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str]]:
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174 return None
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175
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176
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177 CollectOutputsType = Union[Callable[[str, int], CWLObjectType], functools.partial]
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178
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179
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180 class JobBase(HasReqsHints, metaclass=ABCMeta):
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181 def __init__(
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182 self,
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183 builder: Builder,
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184 joborder: CWLObjectType,
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185 make_path_mapper: Callable[..., PathMapper],
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186 requirements: List[CWLObjectType],
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187 hints: List[CWLObjectType],
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188 name: str,
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189 ) -> None:
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190 """Initialize the job object."""
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191 super().__init__()
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192 self.builder = builder
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193 self.joborder = joborder
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194 self.stdin = None # type: Optional[str]
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195 self.stderr = None # type: Optional[str]
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196 self.stdout = None # type: Optional[str]
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197 self.successCodes = [] # type: Iterable[int]
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198 self.temporaryFailCodes = [] # type: Iterable[int]
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199 self.permanentFailCodes = [] # type: Iterable[int]
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200 self.requirements = requirements
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201 self.hints = hints
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202 self.name = name
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203 self.command_line = [] # type: List[str]
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204 self.pathmapper = PathMapper([], "", "")
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205 self.make_path_mapper = make_path_mapper
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206 self.generatemapper = None # type: Optional[PathMapper]
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207
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208 # set in CommandLineTool.job(i)
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209 self.collect_outputs = cast(CollectOutputsType, None)
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210 self.output_callback = None # type: Optional[OutputCallbackType]
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211 self.outdir = ""
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212 self.tmpdir = ""
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213
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214 self.environment = {} # type: MutableMapping[str, str]
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215 self.generatefiles = {
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216 "class": "Directory",
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217 "listing": [],
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218 "basename": "",
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219 } # type: DirectoryType
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220 self.stagedir = None # type: Optional[str]
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221 self.inplace_update = False
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222 self.prov_obj = None # type: Optional[ProvenanceProfile]
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223 self.parent_wf = None # type: Optional[ProvenanceProfile]
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224 self.timelimit = None # type: Optional[int]
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225 self.networkaccess = False # type: bool
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226 self.mpi_procs = None # type: Optional[int]
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227
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228 def __repr__(self): # type: () -> str
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229 """Represent this Job object."""
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230 return "CommandLineJob(%s)" % self.name
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231
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232 @abstractmethod
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233 def run(
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234 self,
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235 runtimeContext: RuntimeContext,
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236 tmpdir_lock: Optional[threading.Lock] = None,
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237 ) -> None:
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238 pass
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239
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240 def _setup(self, runtimeContext: RuntimeContext) -> None:
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241 if not os.path.exists(self.outdir):
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242 os.makedirs(self.outdir)
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243
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244 for knownfile in self.pathmapper.files():
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245 p = self.pathmapper.mapper(knownfile)
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246 if p.type == "File" and not os.path.isfile(p[0]) and p.staged:
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247 raise WorkflowException(
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248 "Input file %s (at %s) not found or is not a regular "
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249 "file." % (knownfile, self.pathmapper.mapper(knownfile)[0])
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250 )
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251
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252 if "listing" in self.generatefiles:
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253 runtimeContext = runtimeContext.copy()
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254 runtimeContext.outdir = self.outdir
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255 self.generatemapper = self.make_path_mapper(
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256 self.generatefiles["listing"],
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257 self.builder.outdir,
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258 runtimeContext,
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259 False,
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260 )
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261 if _logger.isEnabledFor(logging.DEBUG):
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262 _logger.debug(
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263 "[job %s] initial work dir %s",
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264 self.name,
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265 json_dumps(
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266 {
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267 p: self.generatemapper.mapper(p)
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268 for p in self.generatemapper.files()
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269 },
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270 indent=4,
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271 ),
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272 )
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273
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274 def _execute(
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275 self,
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276 runtime: List[str],
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277 env: MutableMapping[str, str],
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278 runtimeContext: RuntimeContext,
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279 monitor_function=None, # type: Optional[Callable[[subprocess.Popen[str]], None]]
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280 ) -> None:
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281
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282 scr = self.get_requirement("ShellCommandRequirement")[0]
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283
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284 shouldquote = needs_shell_quoting_re.search
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285 if scr is not None:
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286 shouldquote = neverquote
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287
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288 # If mpi_procs (is not None and > 0) then prepend the
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289 # appropriate MPI job launch command and flags before the
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290 # execution.
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291 if self.mpi_procs:
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292 menv = runtimeContext.mpi_config
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293 mpi_runtime = [
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294 menv.runner,
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295 menv.nproc_flag,
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296 str(self.mpi_procs),
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297 ] + menv.extra_flags
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298 runtime = mpi_runtime + runtime
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299 menv.pass_through_env_vars(env)
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300 menv.set_env_vars(env)
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301
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302 _logger.info(
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303 "[job %s] %s$ %s%s%s%s",
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304 self.name,
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305 self.outdir,
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306 " \\\n ".join(
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307 [
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308 shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
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309 for arg in (runtime + self.command_line)
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310 ]
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311 ),
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312 " < %s" % self.stdin if self.stdin else "",
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313 " > %s" % os.path.join(self.outdir, self.stdout) if self.stdout else "",
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314 " 2> %s" % os.path.join(self.outdir, self.stderr) if self.stderr else "",
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315 )
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316 if self.joborder is not None and runtimeContext.research_obj is not None:
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317 job_order = self.joborder
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318 if (
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319 runtimeContext.process_run_id is not None
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320 and runtimeContext.prov_obj is not None
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321 and isinstance(job_order, (list, dict))
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322 ):
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323 runtimeContext.prov_obj.used_artefacts(
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324 job_order, runtimeContext.process_run_id, str(self.name)
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325 )
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326 else:
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327 _logger.warning(
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328 "research_obj set but one of process_run_id "
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diff changeset
329 "or prov_obj is missing from runtimeContext: "
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diff changeset
330 "{}".format(runtimeContext)
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331 )
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332 outputs = {} # type: CWLObjectType
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333 try:
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334 stdin_path = None
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335 if self.stdin is not None:
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336 rmap = self.pathmapper.reversemap(self.stdin)
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337 if rmap is None:
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338 raise WorkflowException(f"{self.stdin} missing from pathmapper")
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339 else:
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340 stdin_path = rmap[1]
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341
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342 stderr_path = None
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343 if self.stderr is not None:
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344 abserr = os.path.join(self.outdir, self.stderr)
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345 dnerr = os.path.dirname(abserr)
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346 if dnerr and not os.path.exists(dnerr):
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347 os.makedirs(dnerr)
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348 stderr_path = abserr
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349
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350 stdout_path = None
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351 if self.stdout is not None:
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352 absout = os.path.join(self.outdir, self.stdout)
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353 dnout = os.path.dirname(absout)
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diff changeset
354 if dnout and not os.path.exists(dnout):
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355 os.makedirs(dnout)
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356 stdout_path = absout
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357
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358 commands = [str(x) for x in runtime + self.command_line]
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359 if runtimeContext.secret_store is not None:
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360 commands = cast(
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361 List[str],
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362 runtimeContext.secret_store.retrieve(cast(CWLOutputType, commands)),
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363 )
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364 env = cast(
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365 MutableMapping[str, str],
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366 runtimeContext.secret_store.retrieve(cast(CWLOutputType, env)),
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367 )
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368
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369 job_script_contents = None # type: Optional[str]
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370 builder = getattr(self, "builder", None) # type: Builder
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371 if builder is not None:
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372 job_script_contents = builder.build_job_script(commands)
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parents:
diff changeset
373 rcode = _job_popen(
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374 commands,
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375 stdin_path=stdin_path,
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376 stdout_path=stdout_path,
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377 stderr_path=stderr_path,
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diff changeset
378 env=env,
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379 cwd=self.outdir,
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diff changeset
380 make_job_dir=lambda: runtimeContext.create_outdir(),
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381 job_script_contents=job_script_contents,
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382 timelimit=self.timelimit,
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383 name=self.name,
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parents:
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384 monitor_function=monitor_function,
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385 default_stdout=runtimeContext.default_stdout,
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386 default_stderr=runtimeContext.default_stderr,
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387 )
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388
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389 if rcode in self.successCodes:
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390 processStatus = "success"
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391 elif rcode in self.temporaryFailCodes:
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392 processStatus = "temporaryFail"
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393 elif rcode in self.permanentFailCodes:
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394 processStatus = "permanentFail"
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395 elif rcode == 0:
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396 processStatus = "success"
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397 else:
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398 processStatus = "permanentFail"
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399
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400 if "listing" in self.generatefiles:
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401 if self.generatemapper:
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402 relink_initialworkdir(
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403 self.generatemapper,
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404 self.outdir,
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405 self.builder.outdir,
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406 inplace_update=self.inplace_update,
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407 )
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408 else:
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409 raise ValueError(
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410 "'listing' in self.generatefiles but no "
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411 "generatemapper was setup."
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412 )
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413
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414 outputs = self.collect_outputs(self.outdir, rcode)
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415 outputs = bytes2str_in_dicts(outputs) # type: ignore
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416 except OSError as e:
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417 if e.errno == 2:
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418 if runtime:
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419 _logger.error("'%s' not found: %s", runtime[0], str(e))
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420 else:
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421 _logger.error("'%s' not found: %s", self.command_line[0], str(e))
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422 else:
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423 _logger.exception("Exception while running job")
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424 processStatus = "permanentFail"
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425 except WorkflowException as err:
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426 _logger.error("[job %s] Job error:\n%s", self.name, str(err))
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427 processStatus = "permanentFail"
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428 except Exception:
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429 _logger.exception("Exception while running job")
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430 processStatus = "permanentFail"
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431 if (
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432 runtimeContext.research_obj is not None
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433 and self.prov_obj is not None
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434 and runtimeContext.process_run_id is not None
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435 ):
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436 # creating entities for the outputs produced by each step (in the provenance document)
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437 self.prov_obj.record_process_end(
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438 str(self.name),
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439 runtimeContext.process_run_id,
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440 outputs,
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441 datetime.datetime.now(),
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442 )
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443 if processStatus != "success":
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444 _logger.warning("[job %s] completed %s", self.name, processStatus)
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445 else:
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446 _logger.info("[job %s] completed %s", self.name, processStatus)
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447
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448 if _logger.isEnabledFor(logging.DEBUG):
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449 _logger.debug(
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450 "[job %s] outputs %s", self.name, json_dumps(outputs, indent=4)
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451 )
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452
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453 if self.generatemapper is not None and runtimeContext.secret_store is not None:
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454 # Delete any runtime-generated files containing secrets.
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diff changeset
455 for _, p in self.generatemapper.items():
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parents:
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456 if p.type == "CreateFile":
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diff changeset
457 if runtimeContext.secret_store.has_secret(p.resolved):
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458 host_outdir = self.outdir
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diff changeset
459 container_outdir = self.builder.outdir
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parents:
diff changeset
460 host_outdir_tgt = p.target
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parents:
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461 if p.target.startswith(container_outdir + "/"):
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462 host_outdir_tgt = os.path.join(
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parents:
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463 host_outdir, p.target[len(container_outdir) + 1 :]
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diff changeset
464 )
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diff changeset
465 os.remove(host_outdir_tgt)
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466
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467 if runtimeContext.workflow_eval_lock is None:
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parents:
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468 raise WorkflowException(
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diff changeset
469 "runtimeContext.workflow_eval_lock must not be None"
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470 )
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471
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diff changeset
472 if self.output_callback:
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diff changeset
473 with runtimeContext.workflow_eval_lock:
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diff changeset
474 self.output_callback(outputs, processStatus)
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475
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diff changeset
476 if self.stagedir is not None and os.path.exists(self.stagedir):
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parents:
diff changeset
477 _logger.debug(
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478 "[job %s] Removing input staging directory %s",
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diff changeset
479 self.name,
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parents:
diff changeset
480 self.stagedir,
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diff changeset
481 )
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diff changeset
482 shutil.rmtree(self.stagedir, True)
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483
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parents:
diff changeset
484 if runtimeContext.rm_tmpdir:
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parents:
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485 _logger.debug(
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486 "[job %s] Removing temporary directory %s", self.name, self.tmpdir
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487 )
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488 shutil.rmtree(self.tmpdir, True)
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489
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490 def process_monitor(self, sproc): # type: (subprocess.Popen[str]) -> None
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491 monitor = psutil.Process(sproc.pid)
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492 # Value must be list rather than integer to utilise pass-by-reference in python
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diff changeset
493 memory_usage = [None] # type: MutableSequence[Optional[int]]
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494
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495 def get_tree_mem_usage(memory_usage: MutableSequence[Optional[int]]) -> None:
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496 children = monitor.children()
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497 rss = monitor.memory_info().rss
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498 while len(children):
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499 rss += sum([process.memory_info().rss for process in children])
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500 children = list(
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501 itertools.chain(*[process.children() for process in children])
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502 )
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503 if memory_usage[0] is None or rss > memory_usage[0]:
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504 memory_usage[0] = rss
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505
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diff changeset
506 mem_tm = Timer(interval=1, function=get_tree_mem_usage, args=(memory_usage,))
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507 mem_tm.daemon = True
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diff changeset
508 mem_tm.start()
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parents:
diff changeset
509 sproc.wait()
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diff changeset
510 mem_tm.cancel()
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diff changeset
511 if memory_usage[0] is not None:
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512 _logger.info(
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parents:
diff changeset
513 "[job %s] Max memory used: %iMiB",
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parents:
diff changeset
514 self.name,
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parents:
diff changeset
515 round(memory_usage[0] / (2 ** 20)),
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parents:
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516 )
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517 else:
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518 _logger.debug(
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diff changeset
519 "Could not collect memory usage, job ended before monitoring began."
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parents:
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520 )
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521
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522
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523 class CommandLineJob(JobBase):
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parents:
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524 def run(
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525 self,
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526 runtimeContext: RuntimeContext,
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527 tmpdir_lock: Optional[threading.Lock] = None,
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parents:
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528 ) -> None:
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529
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530 if tmpdir_lock:
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parents:
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531 with tmpdir_lock:
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parents:
diff changeset
532 if not os.path.exists(self.tmpdir):
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parents:
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533 os.makedirs(self.tmpdir)
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534 else:
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parents:
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535 if not os.path.exists(self.tmpdir):
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parents:
diff changeset
536 os.makedirs(self.tmpdir)
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537
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538 self._setup(runtimeContext)
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539
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540 env = self.environment
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diff changeset
541 vars_to_preserve = runtimeContext.preserve_environment
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parents:
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542 if runtimeContext.preserve_entire_environment is not False:
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parents:
diff changeset
543 vars_to_preserve = os.environ
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parents:
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544 if vars_to_preserve:
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parents:
diff changeset
545 for key, value in os.environ.items():
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parents:
diff changeset
546 if key in vars_to_preserve and key not in env:
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parents:
diff changeset
547 # On Windows, subprocess env can't handle unicode.
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parents:
diff changeset
548 env[key] = str(value) if onWindows() else value
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parents:
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549 env["HOME"] = str(self.outdir) if onWindows() else self.outdir
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parents:
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550 env["TMPDIR"] = str(self.tmpdir) if onWindows() else self.tmpdir
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parents:
diff changeset
551 if "PATH" not in env:
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parents:
diff changeset
552 env["PATH"] = str(os.environ["PATH"]) if onWindows() else os.environ["PATH"]
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parents:
diff changeset
553 if "SYSTEMROOT" not in env and "SYSTEMROOT" in os.environ:
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parents:
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554 env["SYSTEMROOT"] = (
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parents:
diff changeset
555 str(os.environ["SYSTEMROOT"])
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parents:
diff changeset
556 if onWindows()
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parents:
diff changeset
557 else os.environ["SYSTEMROOT"]
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parents:
diff changeset
558 )
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diff changeset
559
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parents:
diff changeset
560 stage_files(
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parents:
diff changeset
561 self.pathmapper,
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parents:
diff changeset
562 ignore_writable=True,
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parents:
diff changeset
563 symlink=True,
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parents:
diff changeset
564 secret_store=runtimeContext.secret_store,
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parents:
diff changeset
565 )
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parents:
diff changeset
566 if self.generatemapper is not None:
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parents:
diff changeset
567 stage_files(
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parents:
diff changeset
568 self.generatemapper,
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parents:
diff changeset
569 ignore_writable=self.inplace_update,
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parents:
diff changeset
570 symlink=True,
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parents:
diff changeset
571 secret_store=runtimeContext.secret_store,
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parents:
diff changeset
572 )
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parents:
diff changeset
573 relink_initialworkdir(
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parents:
diff changeset
574 self.generatemapper,
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parents:
diff changeset
575 self.outdir,
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parents:
diff changeset
576 self.builder.outdir,
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parents:
diff changeset
577 inplace_update=self.inplace_update,
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parents:
diff changeset
578 )
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parents:
diff changeset
579
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parents:
diff changeset
580 monitor_function = functools.partial(self.process_monitor)
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parents:
diff changeset
581
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parents:
diff changeset
582 self._execute([], env, runtimeContext, monitor_function)
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parents:
diff changeset
583
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diff changeset
584
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parents:
diff changeset
585 CONTROL_CODE_RE = r"\x1b\[[0-9;]*[a-zA-Z]"
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diff changeset
586
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diff changeset
587
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parents:
diff changeset
588 class ContainerCommandLineJob(JobBase, metaclass=ABCMeta):
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parents:
diff changeset
589 """Commandline job using containers."""
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parents:
diff changeset
590
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diff changeset
591 @abstractmethod
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parents:
diff changeset
592 def get_from_requirements(
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parents:
diff changeset
593 self,
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parents:
diff changeset
594 r: CWLObjectType,
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parents:
diff changeset
595 pull_image: bool,
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parents:
diff changeset
596 force_pull: bool,
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parents:
diff changeset
597 tmp_outdir_prefix: str,
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parents:
diff changeset
598 ) -> Optional[str]:
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shellac
parents:
diff changeset
599 pass
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parents:
diff changeset
600
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shellac
parents:
diff changeset
601 @abstractmethod
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parents:
diff changeset
602 def create_runtime(
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parents:
diff changeset
603 self,
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parents:
diff changeset
604 env: MutableMapping[str, str],
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shellac
parents:
diff changeset
605 runtime_context: RuntimeContext,
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shellac
parents:
diff changeset
606 ) -> Tuple[List[str], Optional[str]]:
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shellac
parents:
diff changeset
607 """Return the list of commands to run the selected container engine."""
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parents:
diff changeset
608
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parents:
diff changeset
609 @staticmethod
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parents:
diff changeset
610 @abstractmethod
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parents:
diff changeset
611 def append_volume(
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parents:
diff changeset
612 runtime: List[str], source: str, target: str, writable: bool = False
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parents:
diff changeset
613 ) -> None:
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shellac
parents:
diff changeset
614 """Add binding arguments to the runtime list."""
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parents:
diff changeset
615
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shellac
parents:
diff changeset
616 @abstractmethod
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parents:
diff changeset
617 def add_file_or_directory_volume(
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parents:
diff changeset
618 self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]
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parents:
diff changeset
619 ) -> None:
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parents:
diff changeset
620 """Append volume a file/dir mapping to the runtime option list."""
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parents:
diff changeset
621
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parents:
diff changeset
622 @abstractmethod
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parents:
diff changeset
623 def add_writable_file_volume(
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parents:
diff changeset
624 self,
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parents:
diff changeset
625 runtime: List[str],
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parents:
diff changeset
626 volume: MapperEnt,
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parents:
diff changeset
627 host_outdir_tgt: Optional[str],
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parents:
diff changeset
628 tmpdir_prefix: str,
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parents:
diff changeset
629 ) -> None:
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parents:
diff changeset
630 """Append a writable file mapping to the runtime option list."""
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parents:
diff changeset
631
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parents:
diff changeset
632 @abstractmethod
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parents:
diff changeset
633 def add_writable_directory_volume(
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parents:
diff changeset
634 self,
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parents:
diff changeset
635 runtime: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
636 volume: MapperEnt,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
637 host_outdir_tgt: Optional[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 tmpdir_prefix: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 """Append a writable directory mapping to the runtime option list."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
641
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642 def create_file_and_add_volume(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
643 self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
644 runtime: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
645 volume: MapperEnt,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
646 host_outdir_tgt: Optional[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
647 secret_store: Optional[SecretStore],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
648 tmpdir_prefix: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
649 ) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
650 """Create the file and add a mapping."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
651 if not host_outdir_tgt:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
652 new_file = os.path.join(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
653 create_tmp_dir(tmpdir_prefix),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
654 os.path.basename(volume.target),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
655 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
656 writable = True if volume.type == "CreateWritableFile" else False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
657 contents = volume.resolved
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
658 if secret_store:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
659 contents = cast(str, secret_store.retrieve(volume.resolved))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
660 dirname = os.path.dirname(host_outdir_tgt or new_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
661 if not os.path.exists(dirname):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
662 os.makedirs(dirname)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
663 with open(host_outdir_tgt or new_file, "wb") as file_literal:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
664 file_literal.write(contents.encode("utf-8"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
665 if not host_outdir_tgt:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
666 self.append_volume(runtime, new_file, volume.target, writable=writable)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
667 if writable:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
668 ensure_writable(host_outdir_tgt or new_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
669 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
670 ensure_non_writable(host_outdir_tgt or new_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
671 return host_outdir_tgt or new_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
672
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
673 def add_volumes(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
674 self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
675 pathmapper: PathMapper,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676 runtime: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
677 tmpdir_prefix: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678 secret_store: Optional[SecretStore] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
679 any_path_okay: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
680 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
681 """Append volume mappings to the runtime option list."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
682 container_outdir = self.builder.outdir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 for key, vol in (itm for itm in pathmapper.items() if itm[1].staged):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
684 host_outdir_tgt = None # type: Optional[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 if vol.target.startswith(container_outdir + "/"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
686 host_outdir_tgt = os.path.join(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
687 self.outdir, vol.target[len(container_outdir) + 1 :]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
688 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
689 if not host_outdir_tgt and not any_path_okay:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
690 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
691 "No mandatory DockerRequirement, yet path is outside "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
692 "the designated output directory, also know as "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
693 "$(runtime.outdir): {}".format(vol)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
694 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 if vol.type in ("File", "Directory"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
696 self.add_file_or_directory_volume(runtime, vol, host_outdir_tgt)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697 elif vol.type == "WritableFile":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
698 self.add_writable_file_volume(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 runtime, vol, host_outdir_tgt, tmpdir_prefix
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701 elif vol.type == "WritableDirectory":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702 self.add_writable_directory_volume(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703 runtime, vol, host_outdir_tgt, tmpdir_prefix
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705 elif vol.type in ["CreateFile", "CreateWritableFile"]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 new_path = self.create_file_and_add_volume(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 runtime, vol, host_outdir_tgt, secret_store, tmpdir_prefix
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
708 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
709 pathmapper.update(key, new_path, vol.target, vol.type, vol.staged)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711 def run(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 runtimeContext: RuntimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 tmpdir_lock: Optional[threading.Lock] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716 if tmpdir_lock:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 with tmpdir_lock:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718 if not os.path.exists(self.tmpdir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 os.makedirs(self.tmpdir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 if not os.path.exists(self.tmpdir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 os.makedirs(self.tmpdir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 self.prov_obj = runtimeContext.prov_obj
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 img_id = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727 env = cast(MutableMapping[str, str], os.environ)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 user_space_docker_cmd = runtimeContext.user_space_docker_cmd
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 if docker_req is not None and user_space_docker_cmd:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 # For user-space docker implementations, a local image name or ID
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 # takes precedence over a network pull
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 if "dockerImageId" in docker_req:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 img_id = str(docker_req["dockerImageId"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 elif "dockerPull" in docker_req:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 img_id = str(docker_req["dockerPull"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 cmd = [user_space_docker_cmd, "pull", img_id]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 _logger.info(str(cmd))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 subprocess.check_call(cmd, stdout=sys.stderr) # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740 except OSError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 SourceLine(docker_req).makeError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 "Either Docker container {} is not available with "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 "user space docker implementation {} or {} is missing "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745 "or broken.".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 img_id, user_space_docker_cmd, user_space_docker_cmd
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 SourceLine(docker_req).makeError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753 "Docker image must be specified as 'dockerImageId' or "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 "'dockerPull' when using user space implementations of "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 "Docker"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 if docker_req is not None and runtimeContext.use_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 img_id = str(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762 self.get_from_requirements(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 docker_req,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 runtimeContext.pull_image,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 runtimeContext.force_docker_pull,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766 runtimeContext.tmp_outdir_prefix,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769 if img_id is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
770 if self.builder.find_default_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
771 default_container = self.builder.find_default_container()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
772 if default_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
773 img_id = str(default_container)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
774
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
775 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
776 docker_req is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777 and img_id is None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
778 and runtimeContext.use_container
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
779 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
780 raise Exception("Docker image not available")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
781
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
782 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
783 self.prov_obj is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 and img_id is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 and runtimeContext.process_run_id is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
786 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
787 container_agent = self.prov_obj.document.agent(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 uuid.uuid4().urn,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789 {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
790 "prov:type": PROV["SoftwareAgent"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
791 "cwlprov:image": img_id,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
792 "prov:label": "Container execution of image %s" % img_id,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
793 },
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
794 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
795 # FIXME: img_id is not a sha256 id, it might just be "debian:8"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
796 # img_entity = document.entity("nih:sha-256;%s" % img_id,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
797 # {"prov:label": "Container image %s" % img_id} )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
798 # The image is the plan for this activity-agent association
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
799 # document.wasAssociatedWith(process_run_ID, container_agent, img_entity)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
800 self.prov_obj.document.wasAssociatedWith(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
801 runtimeContext.process_run_id, container_agent
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
802 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
803 except Exception as err:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
804 container = "Singularity" if runtimeContext.singularity else "Docker"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
805 _logger.debug("%s error", container, exc_info=True)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
806 if docker_is_req:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
807 raise UnsupportedRequirement(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
808 "{} is required to run this tool: {}".format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
809 container, str(err)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
810 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
811 ) from err
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
812 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
813 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
814 "{0} is not available for this tool, try "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
815 "--no-container to disable {0}, or install "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
816 "a user space Docker replacement like uDocker with "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
817 "--user-space-docker-cmd.: {1}".format(container, err)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
818 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
819
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
820 self._setup(runtimeContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
821 (runtime, cidfile) = self.create_runtime(env, runtimeContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
822 runtime.append(str(img_id))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823 monitor_function = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
824 if cidfile:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
825 monitor_function = functools.partial(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
826 self.docker_monitor,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
827 cidfile,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
828 runtimeContext.tmpdir_prefix,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
829 not bool(runtimeContext.cidfile_dir),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
830 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
831 elif runtimeContext.user_space_docker_cmd:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
832 monitor_function = functools.partial(self.process_monitor)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
833 self._execute(runtime, env, runtimeContext, monitor_function)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
834
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
835 def docker_monitor(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
836 self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
837 cidfile: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
838 tmpdir_prefix: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
839 cleanup_cidfile: bool,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
840 process, # type: subprocess.Popen[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 """Record memory usage of the running Docker container."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
843 # Todo: consider switching to `docker create` / `docker start`
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
844 # instead of `docker run` as `docker create` outputs the container ID
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
845 # to stdout, but the container is frozen, thus allowing us to start the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
846 # monitoring process without dealing with the cidfile or too-fast
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
847 # container execution
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 cid = None # type: Optional[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 while cid is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850 time.sleep(1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 if process.returncode is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852 if cleanup_cidfile:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 os.remove(cidfile)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855 except OSError as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856 _logger.warn(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857 "Ignored error cleaning up Docker cidfile: %s", exc
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 with open(cidfile) as cidhandle:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862 cid = cidhandle.readline().strip()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863 except (OSError):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864 cid = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865 max_mem = psutil.virtual_memory().total
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
866 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 stats_file = tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 stats_file_name = stats_file.name
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870 with open(stats_file_name, mode="w") as stats_file_handle:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
871 stats_proc = subprocess.Popen( # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 ["docker", "stats", "--no-trunc", "--format", "{{.MemPerc}}", cid],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 stdout=stats_file_handle,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
874 stderr=subprocess.DEVNULL,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 process.wait()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
877 stats_proc.kill()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 except OSError as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
879 _logger.warn("Ignored error with docker stats: %s", exc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 max_mem_percent = 0 # type: float
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882 mem_percent = 0 # type: float
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883 with open(stats_file_name, mode="r") as stats:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884 while True:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885 line = stats.readline()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886 if not line:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 break
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889 mem_percent = float(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 re.sub(CONTROL_CODE_RE, "", line).replace("%", "")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892 if mem_percent > max_mem_percent:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 max_mem_percent = mem_percent
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894 except ValueError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895 break
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 _logger.info(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 "[job %s] Max memory used: %iMiB",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 self.name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 int((max_mem_percent / 100 * max_mem) / (2 ** 20)),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 if cleanup_cidfile:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 os.remove(cidfile)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 def _job_popen(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 commands: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
907 stdin_path: Optional[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
908 stdout_path: Optional[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
909 stderr_path: Optional[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
910 env: MutableMapping[str, str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
911 cwd: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
912 make_job_dir: Callable[[], str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 job_script_contents: Optional[str] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
914 timelimit: Optional[int] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
915 name: Optional[str] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
916 monitor_function=None, # type: Optional[Callable[[subprocess.Popen[str]], None]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
917 default_stdout=None, # type: Optional[Union[IO[bytes], TextIO]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
918 default_stderr=None, # type: Optional[Union[IO[bytes], TextIO]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
919 ) -> int:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
920
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
921 if job_script_contents is None and not FORCE_SHELLED_POPEN:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
922
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
923 stdin = subprocess.PIPE # type: Union[IO[bytes], int]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
924 if stdin_path is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
925 stdin = open(stdin_path, "rb")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
926
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
927 stdout = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
928 default_stdout if default_stdout is not None else sys.stderr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
929 ) # type: Union[IO[bytes], TextIO]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
930 if stdout_path is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 stdout = open(stdout_path, "wb")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
933 stderr = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 default_stderr if default_stderr is not None else sys.stderr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 ) # type: Union[IO[bytes], TextIO]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
936 if stderr_path is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
937 stderr = open(stderr_path, "wb")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939 sproc = subprocess.Popen(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
940 commands,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941 shell=False, # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 close_fds=not onWindows(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
943 stdin=stdin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944 stdout=stdout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
945 stderr=stderr,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
946 env=env,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
947 cwd=cwd,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
948 universal_newlines=True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
950 processes_to_kill.append(sproc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
951
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
952 if sproc.stdin is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
953 sproc.stdin.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
954
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
955 tm = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
956 if timelimit is not None and timelimit > 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
957
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
958 def terminate(): # type: () -> None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
959 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
960 _logger.warning(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
961 "[job %s] exceeded time limit of %d seconds and will be terminated",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
962 name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
963 timelimit,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
964 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
965 sproc.terminate()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
966 except OSError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
967 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
968
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
969 tm = Timer(timelimit, terminate)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
970 tm.daemon = True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
971 tm.start()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972 if monitor_function:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
973 monitor_function(sproc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
974 rcode = sproc.wait()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
975
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
976 if tm is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
977 tm.cancel()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
978
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
979 if isinstance(stdin, IOBase) and hasattr(stdin, "close"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
980 stdin.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
981
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
982 if stdout is not sys.stderr and hasattr(stdout, "close"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
983 stdout.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
984
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
985 if stderr is not sys.stderr and hasattr(stderr, "close"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
986 stderr.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
987
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
988 return rcode
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
989 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
990 if job_script_contents is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
991 job_script_contents = SHELL_COMMAND_TEMPLATE
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
992
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
993 env_copy = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
994 key = None # type: Optional[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
995 for key in env:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
996 env_copy[key] = env[key]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
997
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
998 job_description = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
999 "commands": commands,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1000 "cwd": cwd,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1001 "env": env_copy,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1002 "stdout_path": stdout_path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1003 "stderr_path": stderr_path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1004 "stdin_path": stdin_path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1005 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1006
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1007 job_dir = make_job_dir()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1008 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1009 with open(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1010 os.path.join(job_dir, "job.json"), mode="w", encoding="utf-8"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1011 ) as job_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1012 json_dump(job_description, job_file, ensure_ascii=False)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1013 job_script = os.path.join(job_dir, "run_job.bash")
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1014 with open(job_script, "wb") as _:
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1015 _.write(job_script_contents.encode("utf-8"))
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1016 job_run = os.path.join(job_dir, "run_job.py")
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1017 with open(job_run, "wb") as _:
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1018 _.write(PYTHON_RUN_SCRIPT.encode("utf-8"))
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1019 sproc = subprocess.Popen( # nosec
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1020 ["bash", job_script.encode("utf-8")],
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1021 shell=False, # nosec
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1022 cwd=job_dir,
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1023 # The nested script will output the paths to the correct files if they need
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1024 # to be captured. Else just write everything to stderr (same as above).
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1025 stdout=sys.stderr,
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1026 stderr=sys.stderr,
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1027 stdin=subprocess.PIPE,
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1028 universal_newlines=True,
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1029 )
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1030 processes_to_kill.append(sproc)
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1031 if sproc.stdin is not None:
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1032 sproc.stdin.close()
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1033
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1034 rcode = sproc.wait()
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1035
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1036 return rcode
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1037 finally:
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1038 shutil.rmtree(job_dir)