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annotate planemo/lib/python3.7/site-packages/cwltool/executors.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 # -*- coding: utf-8 -*-
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2 """ Single and multi-threaded executors."""
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3 import datetime
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4 import os
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5 import tempfile
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6 import threading
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7 import logging
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8 from threading import Lock
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9 from abc import ABCMeta, abstractmethod
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10 from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
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11
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12 import psutil
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13 from six import string_types, with_metaclass
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14 from typing_extensions import Text # pylint: disable=unused-import
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15 from future.utils import raise_from
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16 from schema_salad.validate import ValidationException
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17
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18 from .builder import Builder # pylint: disable=unused-import
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19 from .context import (RuntimeContext, # pylint: disable=unused-import
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20 getdefault)
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21 from .errors import WorkflowException
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22 from .job import JobBase # pylint: disable=unused-import
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23 from .loghandler import _logger
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24 from .mutation import MutationManager
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25 from .process import Process # pylint: disable=unused-import
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26 from .process import cleanIntermediate, relocateOutputs
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27 from .provenance import ProvenanceProfile
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28 from .utils import DEFAULT_TMP_PREFIX
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29 from .workflow import Workflow, WorkflowJob, WorkflowJobStep
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30 from .command_line_tool import CallbackJob
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31
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32 TMPDIR_LOCK = Lock()
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33
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34
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35 class JobExecutor(with_metaclass(ABCMeta, object)):
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36 """Abstract base job executor."""
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37
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38 def __init__(self):
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39 # type: (...) -> None
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40 """Initialize."""
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41 self.final_output = [] # type: List[Union[Dict[Text, Any], List[Dict[Text, Any]]]]
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42 self.final_status = [] # type: List[Text]
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43 self.output_dirs = set() # type: Set[Text]
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44
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45 def __call__(self, *args, **kwargs): # type: (*Any, **Any) -> Any
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46 return self.execute(*args, **kwargs)
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47
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48 def output_callback(self, out, process_status): # type: (Dict[Text, Any], Text) -> None
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49 """Collect the final status and outputs."""
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50 self.final_status.append(process_status)
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51 self.final_output.append(out)
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52
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53 @abstractmethod
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54 def run_jobs(self,
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55 process, # type: Process
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56 job_order_object, # type: Dict[Text, Any]
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57 logger, # type: logging.Logger
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58 runtime_context # type: RuntimeContext
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59 ): # type: (...) -> None
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60 """Execute the jobs for the given Process."""
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61
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62 def execute(self,
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63 process, # type: Process
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64 job_order_object, # type: Dict[Text, Any]
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65 runtime_context, # type: RuntimeContext
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66 logger=_logger, # type: logging.Logger
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67 ): # type: (...) -> Tuple[Optional[Union[Dict[Text, Any], List[Dict[Text, Any]]]], Text]
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68 """Execute the process."""
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69 if not runtime_context.basedir:
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70 raise WorkflowException("Must provide 'basedir' in runtimeContext")
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71
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72 finaloutdir = None # Type: Optional[Text]
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73 original_outdir = runtime_context.outdir
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74 if isinstance(original_outdir, string_types):
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75 finaloutdir = os.path.abspath(original_outdir)
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76 runtime_context = runtime_context.copy()
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77 outdir = tempfile.mkdtemp(
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78 prefix=getdefault(runtime_context.tmp_outdir_prefix, DEFAULT_TMP_PREFIX))
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79 self.output_dirs.add(outdir)
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80 runtime_context.outdir = outdir
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81 runtime_context.mutation_manager = MutationManager()
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82 runtime_context.toplevel = True
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83 runtime_context.workflow_eval_lock = threading.Condition(threading.RLock())
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84
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85 job_reqs = None
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86 if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
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87 if process.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0':
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88 raise WorkflowException(
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89 "`cwl:requirements` in the input object is not part of CWL "
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90 "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
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91 "can set the cwlVersion to v1.1")
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92 job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
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93 elif ("cwl:defaults" in process.metadata
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94 and "https://w3id.org/cwl/cwl#requirements"
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95 in process.metadata["cwl:defaults"]):
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96 if process.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0':
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97 raise WorkflowException(
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98 "`cwl:requirements` in the input object is not part of CWL "
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99 "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
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100 "can set the cwlVersion to v1.1")
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101 job_reqs = process.metadata["cwl:defaults"]["https://w3id.org/cwl/cwl#requirements"]
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102 if job_reqs is not None:
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103 for req in job_reqs:
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104 process.requirements.append(req)
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105
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106 self.run_jobs(process, job_order_object, logger, runtime_context)
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107
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108 if self.final_output and self.final_output[0] is not None and finaloutdir is not None:
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109 self.final_output[0] = relocateOutputs(
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110 self.final_output[0], finaloutdir, self.output_dirs,
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111 runtime_context.move_outputs, runtime_context.make_fs_access(""),
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112 getdefault(runtime_context.compute_checksum, True),
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113 path_mapper=runtime_context.path_mapper)
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114
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115 if runtime_context.rm_tmpdir:
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116 if runtime_context.cachedir is None:
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117 output_dirs = self.output_dirs # type: Iterable[Any]
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118 else:
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119 output_dirs = filter(lambda x: not x.startswith(
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120 runtime_context.cachedir), self.output_dirs)
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121 cleanIntermediate(output_dirs)
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122
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123 if self.final_output and self.final_status:
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124
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125 if runtime_context.research_obj is not None and \
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126 isinstance(process, (JobBase, Process, WorkflowJobStep,
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127 WorkflowJob)) and process.parent_wf:
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128 process_run_id = None
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129 name = "primary"
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130 process.parent_wf.generate_output_prov(self.final_output[0],
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131 process_run_id, name)
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132 process.parent_wf.document.wasEndedBy(
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133 process.parent_wf.workflow_run_uri, None, process.parent_wf.engine_uuid,
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134 datetime.datetime.now())
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135 process.parent_wf.finalize_prov_profile(name=None)
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136 return (self.final_output[0], self.final_status[0])
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137 return (None, "permanentFail")
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138
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139
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140 class SingleJobExecutor(JobExecutor):
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141 """Default single-threaded CWL reference executor."""
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142
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143 def run_jobs(self,
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144 process, # type: Process
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145 job_order_object, # type: Dict[Text, Any]
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146 logger, # type: logging.Logger
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147 runtime_context # type: RuntimeContext
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148 ): # type: (...) -> None
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149
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150 process_run_id = None # type: Optional[str]
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151
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152 # define provenance profile for single commandline tool
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153 if not isinstance(process, Workflow) \
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154 and runtime_context.research_obj is not None:
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155 process.provenance_object = ProvenanceProfile(
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156 runtime_context.research_obj,
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157 full_name=runtime_context.cwl_full_name,
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158 host_provenance=False,
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159 user_provenance=False,
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160 orcid=runtime_context.orcid,
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161 # single tool execution, so RO UUID = wf UUID = tool UUID
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162 run_uuid=runtime_context.research_obj.ro_uuid,
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163 fsaccess=runtime_context.make_fs_access(''))
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164 process.parent_wf = process.provenance_object
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165 jobiter = process.job(job_order_object, self.output_callback,
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166 runtime_context)
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167
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168 try:
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169 for job in jobiter:
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170 if job is not None:
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171 if runtime_context.builder is not None:
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172 job.builder = runtime_context.builder
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173 if job.outdir is not None:
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174 self.output_dirs.add(job.outdir)
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175 if runtime_context.research_obj is not None:
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176 if not isinstance(process, Workflow):
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177 prov_obj = process.provenance_object
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178 else:
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179 prov_obj = job.prov_obj
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180 if prov_obj:
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181 runtime_context.prov_obj = prov_obj
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182 prov_obj.fsaccess = runtime_context.make_fs_access('')
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183 prov_obj.evaluate(
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184 process, job, job_order_object,
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185 runtime_context.research_obj)
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186 process_run_id =\
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187 prov_obj.record_process_start(process, job)
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188 runtime_context = runtime_context.copy()
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189 runtime_context.process_run_id = process_run_id
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190 job.run(runtime_context)
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191 else:
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192 logger.error("Workflow cannot make any more progress.")
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193 break
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194 except (ValidationException, WorkflowException): # pylint: disable=try-except-raise
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195 raise
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196 except Exception as err:
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197 logger.exception("Got workflow error")
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198 raise_from(WorkflowException(Text(err)), err)
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199
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200
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201 class MultithreadedJobExecutor(JobExecutor):
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202 """
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203 Experimental multi-threaded CWL executor.
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204
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205 Does simple resource accounting, will not start a job unless it
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206 has cores / ram available, but does not make any attempt to
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207 optimize usage.
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208 """
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209
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210 def __init__(self): # type: () -> None
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211 """Initialize."""
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212 super(MultithreadedJobExecutor, self).__init__()
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213 self.threads = set() # type: Set[threading.Thread]
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214 self.exceptions = [] # type: List[WorkflowException]
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215 self.pending_jobs = [] # type: List[Union[JobBase, WorkflowJob]]
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216 self.pending_jobs_lock = threading.Lock()
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217
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218 self.max_ram = int(psutil.virtual_memory().available / 2**20)
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219 self.max_cores = psutil.cpu_count()
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220 self.allocated_ram = 0
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221 self.allocated_cores = 0
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222
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223 def select_resources(self, request, runtime_context): # pylint: disable=unused-argument
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224 # type: (Dict[str, int], RuntimeContext) -> Dict[str, int]
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225 """Naïve check for available cpu cores and memory."""
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226 result = {} # type: Dict[str, int]
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227 maxrsc = {
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228 "cores": self.max_cores,
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229 "ram": self.max_ram
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230 }
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231 for rsc in ("cores", "ram"):
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232 if request[rsc+"Min"] > maxrsc[rsc]:
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233 raise WorkflowException(
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234 "Requested at least %d %s but only %d available" %
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235 (request[rsc+"Min"], rsc, maxrsc[rsc]))
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236 if request[rsc+"Max"] < maxrsc[rsc]:
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237 result[rsc] = request[rsc+"Max"]
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238 else:
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239 result[rsc] = maxrsc[rsc]
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240
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241 return result
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242
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243 def _runner(self, job, runtime_context, TMPDIR_LOCK):
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244 # type: (Union[JobBase, WorkflowJob, CallbackJob], RuntimeContext, threading.Lock) -> None
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245 """Job running thread."""
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246 try:
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247 _logger.debug("job: {}, runtime_context: {}, TMPDIR_LOCK: {}".format(job, runtime_context, TMPDIR_LOCK))
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248 job.run(runtime_context, TMPDIR_LOCK)
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249 except WorkflowException as err:
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250 _logger.exception("Got workflow error")
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251 self.exceptions.append(err)
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252 except Exception as err: # pylint: disable=broad-except
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253 _logger.exception("Got workflow error")
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254 self.exceptions.append(WorkflowException(Text(err)))
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255 finally:
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256 if runtime_context.workflow_eval_lock:
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257 with runtime_context.workflow_eval_lock:
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258 self.threads.remove(threading.current_thread())
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259 if isinstance(job, JobBase):
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260 self.allocated_ram -= job.builder.resources["ram"]
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261 self.allocated_cores -= job.builder.resources["cores"]
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262 runtime_context.workflow_eval_lock.notifyAll()
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263
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264 def run_job(self,
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265 job, # type: Union[JobBase, WorkflowJob, None]
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266 runtime_context # type: RuntimeContext
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267 ): # type: (...) -> None
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268 """Execute a single Job in a seperate thread."""
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269 if job is not None:
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270 with self.pending_jobs_lock:
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271 self.pending_jobs.append(job)
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272
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273 with self.pending_jobs_lock:
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274 n = 0
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275 while (n+1) <= len(self.pending_jobs):
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276 job = self.pending_jobs[n]
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277 if isinstance(job, JobBase):
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278 if ((job.builder.resources["ram"])
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279 > self.max_ram
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280 or (job.builder.resources["cores"])
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281 > self.max_cores):
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282 _logger.error(
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283 'Job "%s" cannot be run, requests more resources (%s) '
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284 'than available on this host (max ram %d, max cores %d',
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285 job.name, job.builder.resources,
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286 self.allocated_ram,
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287 self.allocated_cores,
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288 self.max_ram,
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289 self.max_cores)
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290 self.pending_jobs.remove(job)
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291 return
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292
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293 if ((self.allocated_ram + job.builder.resources["ram"])
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294 > self.max_ram
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295 or (self.allocated_cores + job.builder.resources["cores"])
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296 > self.max_cores):
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297 _logger.debug(
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298 'Job "%s" cannot run yet, resources (%s) are not '
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299 'available (already allocated ram is %d, allocated cores is %d, '
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300 'max ram %d, max cores %d',
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301 job.name, job.builder.resources,
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302 self.allocated_ram,
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303 self.allocated_cores,
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304 self.max_ram,
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305 self.max_cores)
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306 n += 1
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307 continue
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308
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309 thread = threading.Thread(target=self._runner, args=(job, runtime_context, TMPDIR_LOCK))
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310 thread.daemon = True
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311 self.threads.add(thread)
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312 if isinstance(job, JobBase):
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313 self.allocated_ram += job.builder.resources["ram"]
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314 self.allocated_cores += job.builder.resources["cores"]
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315 thread.start()
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316 self.pending_jobs.remove(job)
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317
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318 def wait_for_next_completion(self, runtime_context):
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319 # type: (RuntimeContext) -> None
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320 """Wait for jobs to finish."""
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321 if runtime_context.workflow_eval_lock is not None:
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322 runtime_context.workflow_eval_lock.wait()
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323 if self.exceptions:
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324 raise self.exceptions[0]
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325
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326 def run_jobs(self,
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327 process, # type: Process
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328 job_order_object, # type: Dict[Text, Any]
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329 logger, # type: logging.Logger
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330 runtime_context # type: RuntimeContext
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331 ): # type: (...) -> None
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332
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333 jobiter = process.job(job_order_object, self.output_callback,
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334 runtime_context)
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335
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336 if runtime_context.workflow_eval_lock is None:
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337 raise WorkflowException(
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338 "runtimeContext.workflow_eval_lock must not be None")
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339
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340 runtime_context.workflow_eval_lock.acquire()
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341 for job in jobiter:
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342 if job is not None:
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343 if isinstance(job, JobBase):
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344 job.builder = runtime_context.builder or job.builder
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345 if job.outdir is not None:
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346 self.output_dirs.add(job.outdir)
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347
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348 self.run_job(job, runtime_context)
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349
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350 if job is None:
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351 if self.threads:
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352 self.wait_for_next_completion(runtime_context)
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353 else:
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354 logger.error("Workflow cannot make any more progress.")
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355 break
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356
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357 self.run_job(None, runtime_context)
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358 while self.threads:
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359 self.wait_for_next_completion(runtime_context)
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360 self.run_job(None, runtime_context)
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361
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362 runtime_context.workflow_eval_lock.release()