Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/context.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
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1 """Shared context objects that replace use of kwargs."""
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2 import copy
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3 import os
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4 import tempfile
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5 import threading
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6 from typing import IO, Any, Callable, Dict, Iterable, List, Optional, TextIO, Union
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7
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8 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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9 from ruamel.yaml.comments import CommentedMap
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10 from schema_salad.avro.schema import Names
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11 from schema_salad.ref_resolver import Loader
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12 from schema_salad.utils import FetcherCallableType
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13 from typing_extensions import TYPE_CHECKING
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14
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15 from .builder import Builder, HasReqsHints
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16 from .mpi import MpiConfig
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17 from .mutation import MutationManager
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18 from .pathmapper import PathMapper
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19 from .secrets import SecretStore
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20 from .software_requirements import DependenciesConfiguration
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21 from .stdfsaccess import StdFsAccess
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22 from .utils import DEFAULT_TMP_PREFIX, CWLObjectType, ResolverType
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23
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24 if TYPE_CHECKING:
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25 from .process import Process
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26 from .provenance import ResearchObject # pylint: disable=unused-import
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27 from .provenance_profile import ProvenanceProfile
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28
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29
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30 class ContextBase:
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31 """Shared kwargs based initilizer for {Runtime,Loading}Context."""
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32
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33 def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
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34 """Initialize."""
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35 if kwargs:
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36 for k, v in kwargs.items():
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37 if hasattr(self, k):
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38 setattr(self, k, v)
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39
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40
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41 def make_tool_notimpl(
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42 toolpath_object: CommentedMap, loadingContext: "LoadingContext"
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43 ) -> "Process":
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44 raise NotImplementedError()
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45
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46
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47 default_make_tool = make_tool_notimpl
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48
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49
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50 class LoadingContext(ContextBase):
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51 def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
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52 """Initialize the LoadingContext from the kwargs."""
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53 self.debug = False # type: bool
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54 self.metadata = {} # type: CWLObjectType
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55 self.requirements = None # type: Optional[List[CWLObjectType]]
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56 self.hints = None # type: Optional[List[CWLObjectType]]
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57 self.overrides_list = [] # type: List[CWLObjectType]
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58 self.loader = None # type: Optional[Loader]
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59 self.avsc_names = None # type: Optional[Names]
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60 self.disable_js_validation = False # type: bool
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61 self.js_hint_options_file = None
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62 self.do_validate = True # type: bool
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63 self.enable_dev = False # type: bool
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64 self.strict = True # type: bool
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65 self.resolver = None # type: Optional[ResolverType]
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66 self.fetcher_constructor = None # type: Optional[FetcherCallableType]
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67 self.construct_tool_object = default_make_tool
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68 self.research_obj = None # type: Optional[ResearchObject]
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69 self.orcid = "" # type: str
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70 self.cwl_full_name = "" # type: str
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71 self.host_provenance = False # type: bool
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72 self.user_provenance = False # type: bool
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73 self.prov_obj = None # type: Optional[ProvenanceProfile]
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74 self.do_update = None # type: Optional[bool]
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75 self.jobdefaults = None # type: Optional[CommentedMap]
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76 self.doc_cache = True # type: bool
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77 self.relax_path_checks = False # type: bool
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78
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79 super().__init__(kwargs)
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80
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81 def copy(self):
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82 # type: () -> LoadingContext
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83 return copy.copy(self)
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84
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85
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86 class RuntimeContext(ContextBase):
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87 def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
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88 """Initialize the RuntimeContext from the kwargs."""
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89 select_resources_callable = Callable[ # pylint: disable=unused-variable
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90 [Dict[str, Union[int, float, str]], RuntimeContext],
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91 Dict[str, Union[int, float, str]],
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92 ]
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93 self.user_space_docker_cmd = "" # type: Optional[str]
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94 self.secret_store = None # type: Optional[SecretStore]
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95 self.no_read_only = False # type: bool
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96 self.custom_net = "" # type: Optional[str]
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97 self.no_match_user = False # type: bool
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98 self.preserve_environment = "" # type: Optional[Iterable[str]]
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99 self.preserve_entire_environment = False # type: bool
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100 self.use_container = True # type: bool
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101 self.force_docker_pull = False # type: bool
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102
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103 self.tmp_outdir_prefix = "" # type: str
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104 self.tmpdir_prefix = DEFAULT_TMP_PREFIX # type: str
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105 self.tmpdir = "" # type: str
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106 self.rm_tmpdir = True # type: bool
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107 self.pull_image = True # type: bool
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108 self.rm_container = True # type: bool
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109 self.move_outputs = "move" # type: str
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110
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111 self.singularity = False # type: bool
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112 self.disable_net = False # type: bool
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113 self.debug = False # type: bool
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114 self.compute_checksum = True # type: bool
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115 self.name = "" # type: str
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116 self.default_container = "" # type: Optional[str]
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117 self.find_default_container = (
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118 None
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119 ) # type: Optional[Callable[[HasReqsHints], Optional[str]]]
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120 self.cachedir = None # type: Optional[str]
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121 self.outdir = None # type: Optional[str]
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122 self.stagedir = "" # type: str
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123 self.part_of = "" # type: str
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124 self.basedir = "" # type: str
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125 self.toplevel = False # type: bool
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126 self.mutation_manager = None # type: Optional[MutationManager]
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127 self.make_fs_access = StdFsAccess # type: Callable[[str], StdFsAccess]
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128 self.path_mapper = PathMapper
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129 self.builder = None # type: Optional[Builder]
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130 self.docker_outdir = "" # type: str
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131 self.docker_tmpdir = "" # type: str
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132 self.docker_stagedir = "" # type: str
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133 self.js_console = False # type: bool
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134 self.job_script_provider = None # type: Optional[DependenciesConfiguration]
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135 self.select_resources = None # type: Optional[select_resources_callable]
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136 self.eval_timeout = 20 # type: float
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137 self.postScatterEval = (
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138 None
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139 ) # type: Optional[Callable[[CWLObjectType], Optional[CWLObjectType]]]
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140 self.on_error = "stop" # type: str
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141 self.strict_memory_limit = False # type: bool
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142
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143 self.cidfile_dir = None # type: Optional[str]
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144 self.cidfile_prefix = None # type: Optional[str]
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145
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146 self.workflow_eval_lock = None # type: Optional[threading.Condition]
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147 self.research_obj = None # type: Optional[ResearchObject]
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148 self.orcid = "" # type: str
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149 self.cwl_full_name = "" # type: str
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150 self.process_run_id = None # type: Optional[str]
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151 self.prov_obj = None # type: Optional[ProvenanceProfile]
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152 self.mpi_config = MpiConfig() # type: MpiConfig
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153 self.default_stdout = None # type: Optional[Union[IO[bytes], TextIO]]
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154 self.default_stderr = None # type: Optional[Union[IO[bytes], TextIO]]
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155 super().__init__(kwargs)
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156 if self.tmp_outdir_prefix == "":
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157 self.tmp_outdir_prefix = self.tmpdir_prefix
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158
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159 def get_outdir(self) -> str:
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160 """Return self.outdir or create one with self.tmp_outdir_prefix."""
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161 if self.outdir:
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162 return self.outdir
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163 return self.create_outdir()
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164
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165 def get_tmpdir(self) -> str:
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166 """Return self.tmpdir or create one with self.tmpdir_prefix."""
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167 if self.tmpdir:
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168 return self.tmpdir
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169 return self.create_tmpdir()
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170
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171 def get_stagedir(self) -> str:
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172 """Return self.stagedir or create one with self.tmpdir_prefix."""
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173 if self.stagedir:
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174 return self.stagedir
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175 tmp_dir, tmp_prefix = os.path.split(self.tmpdir_prefix)
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176 return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
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177
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178 def create_tmpdir(self) -> str:
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179 """Create a temporary directory that respects self.tmpdir_prefix."""
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180 tmp_dir, tmp_prefix = os.path.split(self.tmpdir_prefix)
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181 return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
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182
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183 def create_outdir(self) -> str:
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184 """Create a temporary directory that respects self.tmp_outdir_prefix."""
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185 out_dir, out_prefix = os.path.split(self.tmp_outdir_prefix)
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186 return tempfile.mkdtemp(prefix=out_prefix, dir=out_dir)
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187
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188 def copy(self):
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189 # type: () -> RuntimeContext
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190 return copy.copy(self)
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191
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192
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193 def getdefault(val, default):
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194 # type: (Any, Any) -> Any
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195 if val is None:
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196 return default
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197 else:
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198 return val