Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/context.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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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 threading # pylint: disable=unused-import
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4 from typing import (Any, Callable, Dict, Iterable, List, MutableMapping,
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5 Optional)
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6
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7 from schema_salad import schema
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8 from schema_salad.ref_resolver import (ContextType, # pylint: disable=unused-import
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9 Fetcher, Loader)
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10 from typing_extensions import (TYPE_CHECKING, # pylint: disable=unused-import
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11 Text)
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12 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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13 from .builder import Builder, HasReqsHints
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14 from .mutation import MutationManager
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15 from .pathmapper import PathMapper
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16 from .secrets import SecretStore
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17 from .software_requirements import DependenciesConfiguration
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18 from .stdfsaccess import StdFsAccess
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19 from .utils import DEFAULT_TMP_PREFIX
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20
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21 if TYPE_CHECKING:
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22 from .process import Process
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23 from .provenance import (ResearchObject, # pylint: disable=unused-import
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24 ProvenanceProfile)
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25
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26 class ContextBase(object):
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27 def __init__(self, kwargs=None): # type: (Optional[Dict[str, Any]]) -> None
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28 """Initialize."""
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29 if kwargs:
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30 for k, v in kwargs.items():
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31 if hasattr(self, k):
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32 setattr(self, k, v)
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33
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34 def make_tool_notimpl(toolpath_object, # type: MutableMapping[Text, Any]
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35 loadingContext # type: LoadingContext
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36 ): # type: (...) -> Process
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37 raise NotImplementedError()
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38
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39
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40 default_make_tool = make_tool_notimpl # type: Callable[[MutableMapping[Text, Any], LoadingContext], Process]
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41
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42 class LoadingContext(ContextBase):
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43
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44 def __init__(self, kwargs=None): # type: (Optional[Dict[str, Any]]) -> None
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45 """Initialize the LoadingContext from the kwargs."""
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46 self.debug = False # type: bool
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47 self.metadata = {} # type: Dict[Text, Any]
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48 self.requirements = None # type: Optional[List[Dict[Text, Any]]]
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49 self.hints = None # type: Optional[List[Dict[Text, Any]]]
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50 self.overrides_list = [] # type: List[Dict[Text, Any]]
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51 self.loader = None # type: Optional[Loader]
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52 self.avsc_names = None # type: Optional[schema.Names]
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53 self.disable_js_validation = False # type: bool
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54 self.js_hint_options_file = None
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55 self.do_validate = True # type: bool
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56 self.enable_dev = False # type: bool
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57 self.strict = True # type: bool
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58 self.resolver = None
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59 self.fetcher_constructor = None
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60 self.construct_tool_object = default_make_tool
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61 self.research_obj = None # type: Optional[ResearchObject]
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62 self.orcid = '' # type: str
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63 self.cwl_full_name = "" # type: str
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64 self.host_provenance = False # type: bool
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65 self.user_provenance = False # type: bool
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66 self.prov_obj = None # type: Optional[ProvenanceProfile]
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67 self.do_update = None # type: Optional[bool]
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68 self.jobdefaults = None # type: Optional[MutableMapping[Text, Any]]
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69
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70 super(LoadingContext, self).__init__(kwargs)
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71
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72 def copy(self):
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73 # type: () -> LoadingContext
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74 return copy.copy(self)
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75
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76 class RuntimeContext(ContextBase):
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77 def __init__(self, kwargs=None): # type: (Optional[Dict[str, Any]]) -> None
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78 """Initializet the RuntimeContext from the kwargs."""
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79 select_resources_callable = Callable[ # pylint: disable=unused-variable
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80 [Dict[str, int], RuntimeContext], Dict[str, int]]
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81 self.user_space_docker_cmd = "" # type: Text
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82 self.secret_store = None # type: Optional[SecretStore]
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83 self.no_read_only = False # type: bool
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84 self.custom_net = "" # type: Text
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85 self.no_match_user = False # type: bool
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86 self.preserve_environment = "" # type: Optional[Iterable[str]]
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87 self.preserve_entire_environment = False # type: bool
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88 self.use_container = True # type: bool
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89 self.force_docker_pull = False # type: bool
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90
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91 self.tmp_outdir_prefix = DEFAULT_TMP_PREFIX # type: Text
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92 self.tmpdir_prefix = DEFAULT_TMP_PREFIX # type: Text
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93 self.tmpdir = "" # type: Text
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94 self.rm_tmpdir = True # type: bool
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95 self.pull_image = True # type: bool
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96 self.rm_container = True # type: bool
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97 self.move_outputs = "move" # type: Text
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98
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99 self.singularity = False # type: bool
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100 self.disable_net = False # type: bool
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101 self.debug = False # type: bool
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102 self.compute_checksum = True # type: bool
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103 self.name = "" # type: Text
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104 self.default_container = "" # type: Text
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105 self.find_default_container = None # type: Optional[Callable[[HasReqsHints], Optional[Text]]]
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106 self.cachedir = None # type: Optional[Text]
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107 self.outdir = None # type: Optional[Text]
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108 self.stagedir = "" # type: Text
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109 self.part_of = "" # type: Text
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110 self.basedir = "" # type: Text
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111 self.toplevel = False # type: bool
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112 self.mutation_manager = None # type: Optional[MutationManager]
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113 self.make_fs_access = StdFsAccess # type: Callable[[Text], StdFsAccess]
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114 self.path_mapper = PathMapper
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115 self.builder = None # type: Optional[Builder]
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116 self.docker_outdir = "" # type: Text
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117 self.docker_tmpdir = "" # type: Text
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118 self.docker_stagedir = "" # type: Text
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119 self.js_console = False # type: bool
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120 self.job_script_provider = None # type: Optional[DependenciesConfiguration]
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121 self.select_resources = None # type: Optional[select_resources_callable]
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122 self.eval_timeout = 20 # type: float
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123 self.postScatterEval = None # type: Optional[Callable[[MutableMapping[Text, Any]], Dict[Text, Any]]]
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124 self.on_error = "stop" # type: Text
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125 self.strict_memory_limit = False # type: bool
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126
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127 self.cidfile_dir = None
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128 self.cidfile_prefix = None
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129
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130 self.workflow_eval_lock = None # type: Optional[threading.Condition]
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131 self.research_obj = None # type: Optional[ResearchObject]
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132 self.orcid = '' # type: str
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133 self.cwl_full_name = "" # type: str
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134 self.process_run_id = None # type: Optional[str]
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135 self.prov_obj = None # type: Optional[ProvenanceProfile]
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136 super(RuntimeContext, self).__init__(kwargs)
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137
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138
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139 def copy(self):
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140 # type: () -> RuntimeContext
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141 return copy.copy(self)
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142
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143 def getdefault(val, default):
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144 # type: (Any, Any) -> Any
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145 if val is None:
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146 return default
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147 else:
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148 return val