Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/load_tool.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 """Loads a CWL document."""
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2 from __future__ import absolute_import
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3
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4 import hashlib
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5 import logging
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6 import os
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7 import re
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8 import uuid
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9 from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
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10 Optional, Tuple, Union, cast)
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11
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12 import requests.sessions
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13 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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14 from schema_salad import schema
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15 from schema_salad.ref_resolver import (ContextType, # pylint: disable=unused-import
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16 Fetcher, Loader, file_uri, SubLoader)
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17 from schema_salad.sourceline import SourceLine, cmap
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18 from schema_salad.validate import ValidationException
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19 from six import itervalues, string_types
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20 from six.moves import urllib
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21 from typing_extensions import Text # pylint: disable=unused-import
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22 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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23
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24 from . import process, update
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25 from .context import LoadingContext # pylint: disable=unused-import
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26 from .errors import WorkflowException
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27 from .loghandler import _logger
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28 from .process import (Process, get_schema, # pylint: disable=unused-import
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29 shortname)
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30 from .software_requirements import ( # pylint: disable=unused-import
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31 DependenciesConfiguration)
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32 from .update import ALLUPDATES
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33 from .utils import json_dumps
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34
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37
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38 jobloaderctx = {
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39 u"cwl": "https://w3id.org/cwl/cwl#",
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40 u"cwltool": "http://commonwl.org/cwltool#",
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41 u"path": {u"@type": u"@id"},
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42 u"location": {u"@type": u"@id"},
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43 u"id": u"@id"
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44 } # type: ContextType
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45
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46
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47 overrides_ctx = {
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48 u"overrideTarget": {u"@type": u"@id"},
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49 u"cwltool": "http://commonwl.org/cwltool#",
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50 u"http://commonwl.org/cwltool#overrides": {
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51 "@id": "cwltool:overrides",
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52 "mapSubject": "overrideTarget",
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53 },
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54 "requirements": {
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55 "@id": "https://w3id.org/cwl/cwl#requirements",
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56 "mapSubject": "class"
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57 }
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58 } # type: ContextType
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59
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60
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61 FetcherConstructorType = Callable[
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62 [Dict[Text, Union[Text, bool]], requests.sessions.Session], Fetcher]
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63 ResolverType = Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
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64
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65 def default_loader(fetcher_constructor=None, enable_dev=False):
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66 # type: (Optional[FetcherConstructorType], bool) -> Loader
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67 return Loader(jobloaderctx, fetcher_constructor=fetcher_constructor,
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68 allow_attachments=lambda r: enable_dev)
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69
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70 def resolve_tool_uri(argsworkflow, # type: Text
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71 resolver=None, # type: Optional[ResolverType]
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72 fetcher_constructor=None, # type: Optional[FetcherConstructorType]
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73 document_loader=None # type: Optional[Loader]
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74 ): # type: (...) -> Tuple[Text, Text]
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75
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76 uri = None # type: Optional[Text]
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77 split = urllib.parse.urlsplit(argsworkflow)
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78 # In case of Windows path, urlsplit misjudge Drive letters as scheme, here we are skipping that
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79 if split.scheme and split.scheme in [u'http', u'https', u'file']:
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80 uri = argsworkflow
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81 elif os.path.exists(os.path.abspath(argsworkflow)):
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82 uri = file_uri(str(os.path.abspath(argsworkflow)))
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83 elif resolver is not None:
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84 if document_loader is None:
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85 document_loader = default_loader(fetcher_constructor)
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86 uri = resolver(document_loader, argsworkflow)
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87
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88 if uri is None:
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89 raise ValidationException("Not found: '%s'" % argsworkflow)
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90
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91 if argsworkflow != uri:
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92 _logger.info("Resolved '%s' to '%s'", argsworkflow, uri)
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93
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94 fileuri = urllib.parse.urldefrag(uri)[0]
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95 return uri, fileuri
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96
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97
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98 def fetch_document(argsworkflow, # type: Union[Text, Dict[Text, Any]]
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99 loadingContext=None # type: Optional[LoadingContext]
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100 ): # type: (...) -> Tuple[LoadingContext, CommentedMap, Text]
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101 """Retrieve a CWL document."""
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102 if loadingContext is None:
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103 loadingContext = LoadingContext()
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104 loadingContext.loader = default_loader()
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105 else:
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106 loadingContext = loadingContext.copy()
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107 if loadingContext.loader is None:
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108 loadingContext.loader = default_loader(loadingContext.fetcher_constructor)
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109
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110 if isinstance(argsworkflow, string_types):
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111 uri, fileuri = resolve_tool_uri(argsworkflow,
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112 resolver=loadingContext.resolver,
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113 document_loader=loadingContext.loader)
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114 workflowobj = loadingContext.loader.fetch(fileuri)
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115 return loadingContext, workflowobj, uri
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116 if isinstance(argsworkflow, dict):
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117 uri = argsworkflow["id"] if argsworkflow.get("id") else "_:" + Text(uuid.uuid4())
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118 workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
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119 loadingContext.loader.idx[uri] = workflowobj
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120 return loadingContext, workflowobj, uri
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121 raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
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122
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123
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124 def _convert_stdstreams_to_files(workflowobj):
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125 # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]]) -> None
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126
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127 if isinstance(workflowobj, MutableMapping):
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128 if workflowobj.get('class') == 'CommandLineTool':
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129 with SourceLine(workflowobj, "outputs", ValidationException,
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130 _logger.isEnabledFor(logging.DEBUG)):
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131 outputs = workflowobj.get('outputs', [])
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132 if not isinstance(outputs, CommentedSeq):
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133 raise ValidationException('"outputs" section is not '
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134 'valid.')
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135 for out in workflowobj.get('outputs', []):
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136 if not isinstance(out, CommentedMap):
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137 raise ValidationException(
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138 "Output '{}' is not a valid "
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139 "OutputParameter.".format(out))
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140 for streamtype in ['stdout', 'stderr']:
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141 if out.get('type') == streamtype:
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142 if 'outputBinding' in out:
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143 raise ValidationException(
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144 "Not allowed to specify outputBinding when"
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145 " using %s shortcut." % streamtype)
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146 if streamtype in workflowobj:
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147 filename = workflowobj[streamtype]
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148 else:
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149 filename = Text(
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150 hashlib.sha1( # nosec
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151 json_dumps(workflowobj, sort_keys=True
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152 ).encode('utf-8')).hexdigest())
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153 workflowobj[streamtype] = filename
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154 out['type'] = 'File'
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155 out['outputBinding'] = cmap({'glob': filename})
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156 for inp in workflowobj.get('inputs', []):
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157 if inp.get('type') == 'stdin':
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158 if 'inputBinding' in inp:
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159 raise ValidationException(
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160 "Not allowed to specify inputBinding when"
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161 " using stdin shortcut.")
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162 if 'stdin' in workflowobj:
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163 raise ValidationException(
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164 "Not allowed to specify stdin path when"
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165 " using stdin type shortcut.")
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166 else:
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167 workflowobj['stdin'] = \
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168 "$(inputs.%s.path)" % \
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169 inp['id'].rpartition('#')[2]
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170 inp['type'] = 'File'
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171 else:
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172 for entry in itervalues(workflowobj):
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173 _convert_stdstreams_to_files(entry)
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174 if isinstance(workflowobj, MutableSequence):
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175 for entry in workflowobj:
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176 _convert_stdstreams_to_files(entry)
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177
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178 def _add_blank_ids(workflowobj):
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179 # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]]) -> None
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180
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181 if isinstance(workflowobj, MutableMapping):
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182 if ("run" in workflowobj and
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183 isinstance(workflowobj["run"], MutableMapping) and
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184 "id" not in workflowobj["run"] and
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185 "$import" not in workflowobj["run"]):
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186 workflowobj["run"]["id"] = Text(uuid.uuid4())
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187 for entry in itervalues(workflowobj):
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188 _add_blank_ids(entry)
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189 if isinstance(workflowobj, MutableSequence):
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190 for entry in workflowobj:
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191 _add_blank_ids(entry)
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192
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193 def resolve_and_validate_document(
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194 loadingContext, # type: LoadingContext
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195 workflowobj, # type: Union[CommentedMap, CommentedSeq]
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196 uri, # type: Text
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197 preprocess_only=False, # type: bool
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198 skip_schemas=None, # type: Optional[bool]
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199 ):
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200 # type: (...) -> Tuple[LoadingContext, Text]
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201 """Validate a CWL document."""
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202 if not loadingContext.loader:
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203 raise ValueError("loadingContext must have a loader.")
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204 else:
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205 loader = loadingContext.loader
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206 loadingContext = loadingContext.copy()
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207
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208 if not isinstance(workflowobj, MutableMapping):
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209 raise ValueError("workflowjobj must be a dict, got '{}': {}".format(
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210 type(workflowobj), workflowobj))
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211
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212 jobobj = None
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213 if "cwl:tool" in workflowobj:
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214 jobobj, _ = loader.resolve_all(workflowobj, uri)
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215 uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
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216 del cast(Dict[Text, Any], jobobj)["https://w3id.org/cwl/cwl#tool"]
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217
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218 workflowobj = fetch_document(uri, loadingContext)[1]
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219
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220 fileuri = urllib.parse.urldefrag(uri)[0]
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221
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222 cwlVersion = loadingContext.metadata.get("cwlVersion")
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223 if not cwlVersion:
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224 cwlVersion = workflowobj.get("cwlVersion")
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225 if not cwlVersion and fileuri != uri:
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226 # The tool we're loading is a fragment of a bigger file. Get
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227 # the document root element and look for cwlVersion there.
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228 metadata = fetch_document(fileuri, loadingContext)[1] # type: Dict[Text, Any]
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229 cwlVersion = metadata.get("cwlVersion")
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230 if not cwlVersion:
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231 raise ValidationException(
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232 "No cwlVersion found. "
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233 "Use the following syntax in your CWL document to declare "
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234 "the version: cwlVersion: <version>.\n"
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235 "Note: if this is a CWL draft-2 (pre v1.0) document then it "
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236 "will need to be upgraded first.")
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237
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238 if not isinstance(cwlVersion, string_types):
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239 with SourceLine(workflowobj, "cwlVersion", ValidationException):
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240 raise ValidationException("'cwlVersion' must be a string, "
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241 "got {}".format(
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242 type(cwlVersion)))
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243 # strip out version
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244 cwlVersion = re.sub(
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245 r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
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246 cwlVersion)
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247 if cwlVersion not in list(ALLUPDATES):
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248 # print out all the Supported Versions of cwlVersion
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249 versions = []
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250 for version in list(ALLUPDATES):
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251 if "dev" in version:
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252 version += " (with --enable-dev flag only)"
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253 versions.append(version)
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254 versions.sort()
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255 raise ValidationException(
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256 "The CWL reference runner no longer supports pre CWL v1.0 "
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257 "documents. Supported versions are: "
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258 "\n{}".format("\n".join(versions)))
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259
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260 if isinstance(jobobj, CommentedMap) and "http://commonwl.org/cwltool#overrides" in jobobj:
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261 loadingContext.overrides_list.extend(resolve_overrides(jobobj, uri, uri))
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262 del jobobj["http://commonwl.org/cwltool#overrides"]
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263
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264 if isinstance(jobobj, CommentedMap) and "https://w3id.org/cwl/cwl#requirements" in jobobj:
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265 if cwlVersion not in ("v1.1.0-dev1","v1.1"):
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266 raise ValidationException(
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267 "`cwl:requirements` in the input object is not part of CWL "
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268 "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
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269 "can set the cwlVersion to v1.1 or greater.")
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270 loadingContext.overrides_list.append({"overrideTarget": uri,
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271 "requirements": jobobj["https://w3id.org/cwl/cwl#requirements"]})
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272 del jobobj["https://w3id.org/cwl/cwl#requirements"]
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273
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274 (sch_document_loader, avsc_names) = \
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275 process.get_schema(cwlVersion)[:2]
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276
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277 if isinstance(avsc_names, Exception):
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278 raise avsc_names
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279
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280 processobj = None # type: Union[CommentedMap, CommentedSeq, Text, None]
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281 document_loader = Loader(sch_document_loader.ctx,
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282 schemagraph=sch_document_loader.graph,
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283 idx=loader.idx,
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284 cache=sch_document_loader.cache,
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285 fetcher_constructor=loadingContext.fetcher_constructor,
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286 skip_schemas=skip_schemas)
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287
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288 if cwlVersion == "v1.0":
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289 _add_blank_ids(workflowobj)
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290
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291 processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
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292 if loadingContext.metadata:
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293 metadata = loadingContext.metadata
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294 if not isinstance(processobj, (CommentedMap, CommentedSeq)):
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295 raise ValidationException("Workflow must be a CommentedMap or CommentedSeq.")
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296 if not isinstance(metadata, CommentedMap):
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297 raise ValidationException("metadata must be a CommentedMap, was %s" % type(metadata))
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298
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299 if isinstance(processobj, CommentedMap):
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300 uri = processobj["id"]
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301
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302 _convert_stdstreams_to_files(workflowobj)
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303
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304 if preprocess_only:
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305 return loadingContext, uri
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306
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307 if loadingContext.do_validate:
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308 schema.validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)
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309
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310 # None means default behavior (do update)
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311 if loadingContext.do_update in (True, None):
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312 if "cwlVersion" not in metadata:
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313 metadata["cwlVersion"] = cwlVersion
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314 processobj = update.update(
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315 processobj, document_loader, fileuri, loadingContext.enable_dev, metadata)
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316 document_loader.idx[processobj["id"]] = processobj
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317
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318 if jobobj is not None:
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319 loadingContext.jobdefaults = jobobj
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320
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321 loadingContext.loader = document_loader
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322 loadingContext.avsc_names = avsc_names
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323 loadingContext.metadata = metadata
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324
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325 return loadingContext, uri
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326
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327
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328 def make_tool(uri, # type: Union[Text, CommentedMap, CommentedSeq]
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329 loadingContext # type: LoadingContext
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330 ): # type: (...) -> Process
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331 """Make a Python CWL object."""
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332 if loadingContext.loader is None:
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333 raise ValueError("loadingContext must have a loader")
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334 resolveduri, metadata = loadingContext.loader.resolve_ref(uri)
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335
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336 processobj = None
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337 if isinstance(resolveduri, MutableSequence):
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338 for obj in resolveduri:
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339 if obj['id'].endswith('#main'):
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340 processobj = obj
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341 break
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342 if not processobj:
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343 raise WorkflowException(
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344 u"Tool file contains graph of multiple objects, must specify "
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345 "one of #%s" % ", #".join(
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346 urllib.parse.urldefrag(i["id"])[1] for i in resolveduri
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347 if "id" in i))
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348 elif isinstance(resolveduri, MutableMapping):
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349 processobj = resolveduri
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350 else:
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351 raise Exception("Must resolve to list or dict")
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352
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353 tool = loadingContext.construct_tool_object(processobj, loadingContext)
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354
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355 if loadingContext.jobdefaults:
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356 jobobj = loadingContext.jobdefaults
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357 for inp in tool.tool["inputs"]:
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358 if shortname(inp["id"]) in jobobj:
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359 inp["default"] = jobobj[shortname(inp["id"])]
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360
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361 return tool
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362
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363
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364 def load_tool(argsworkflow, # type: Union[Text, Dict[Text, Any]]
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365 loadingContext=None # type: Optional[LoadingContext]
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366 ): # type: (...) -> Process
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367
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368 loadingContext, workflowobj, uri = fetch_document(
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369 argsworkflow, loadingContext)
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370
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371 loadingContext, uri = resolve_and_validate_document(
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372 loadingContext, workflowobj, uri)
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373
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374 return make_tool(uri,
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375 loadingContext)
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376
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377 def resolve_overrides(ov, # type: CommentedMap
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378 ov_uri, # type: Text
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379 baseurl # type: Text
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380 ): # type: (...) -> List[Dict[Text, Any]]
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381 ovloader = Loader(overrides_ctx)
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382 ret, _ = ovloader.resolve_all(ov, baseurl)
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383 if not isinstance(ret, CommentedMap):
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384 raise Exception("Expected CommentedMap, got %s" % type(ret))
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385 cwl_docloader = get_schema("v1.0")[0]
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386 cwl_docloader.resolve_all(ret, ov_uri)
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387 return cast(List[Dict[Text, Any]],
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388 ret["http://commonwl.org/cwltool#overrides"])
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389
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390 def load_overrides(ov, base_url): # type: (Text, Text) -> List[Dict[Text, Any]]
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391 ovloader = Loader(overrides_ctx)
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392 return resolve_overrides(ovloader.fetch(ov), ov, base_url)