Mercurial > repos > shellac > guppy_basecaller

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 from __future__ import absolute_import
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2
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3 import copy
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4 import re
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5 from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
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6 Optional, Tuple, Union)
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7
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8 from functools import partial
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9
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10 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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11 from schema_salad import validate
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12 from schema_salad.ref_resolver import Loader # pylint: disable=unused-import
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13 from six import string_types
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14 from six.moves import urllib
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15 from typing_extensions import Text
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16 from schema_salad.sourceline import SourceLine
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17 from .loghandler import _logger
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18
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19 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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20
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21 from .utils import visit_class, visit_field, aslist
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22
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23
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24 def v1_0to1_1(doc, loader, baseuri): # pylint: disable=unused-argument
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25 # type: (Any, Loader, Text) -> Tuple[Any, Text]
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26 """Public updater for v1.0 to v1.1."""
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27 doc = copy.deepcopy(doc)
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28
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29 rewrite = {
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30 "http://commonwl.org/cwltool#WorkReuse": "WorkReuse",
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31 "http://arvados.org/cwl#ReuseRequirement": "WorkReuse",
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32 "http://commonwl.org/cwltool#TimeLimit": "ToolTimeLimit",
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33 "http://commonwl.org/cwltool#NetworkAccess": "NetworkAccess",
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34 "http://commonwl.org/cwltool#InplaceUpdateRequirement": "InplaceUpdateRequirement",
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35 "http://commonwl.org/cwltool#LoadListingRequirement": "LoadListingRequirement"
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36 }
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37 def rewrite_requirements(t): # type: (MutableMapping[Text, Union[Text, Dict[Text, Any]]]) -> None
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38 if "requirements" in t:
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39 for r in t["requirements"]:
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40 if isinstance(r, MutableMapping):
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41 if r["class"] in rewrite:
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42 r["class"] = rewrite[r["class"]]
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43 else:
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44 raise validate.ValidationException(
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45 "requirements entries must be dictionaries: {} {}.".format(
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46 type(r), r))
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47 if "hints" in t:
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48 for r in t["hints"]:
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49 if isinstance(r, MutableMapping):
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50 if r["class"] in rewrite:
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51 r["class"] = rewrite[r["class"]]
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52 else:
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53 raise validate.ValidationException(
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54 "hints entries must be dictionaries: {} {}.".format(
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55 type(r), r))
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56 if "steps" in t:
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57 for s in t["steps"]:
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58 if isinstance(s, MutableMapping):
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59 rewrite_requirements(s)
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60 else:
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61 raise validate.ValidationException(
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62 "steps entries must be dictionaries: {} {}.".format(
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63 type(s), s))
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64
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65
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66 def update_secondaryFiles(t, top=False):
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67 # type: (Any, bool) -> Union[MutableSequence[MutableMapping[Text, Text]], MutableMapping[Text, Text]]
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68 if isinstance(t, CommentedSeq):
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69 new_seq = copy.deepcopy(t)
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70 for index, entry in enumerate(t):
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71 new_seq[index] = update_secondaryFiles(entry)
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72 return new_seq
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73 elif isinstance(t, MutableSequence):
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74 return CommentedSeq([update_secondaryFiles(p) for p in t])
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75 elif isinstance(t, MutableMapping):
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76 return t
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77 elif top:
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78 return CommentedSeq([CommentedMap([("pattern", t)])])
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79 else:
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80 return CommentedMap([("pattern", t)])
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81
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82 def fix_inputBinding(t): # type: (Dict[Text, Any]) -> None
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83 for i in t["inputs"]:
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84 if "inputBinding" in i:
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85 ib = i["inputBinding"]
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86 for k in list(ib.keys()):
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87 if k != "loadContents":
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88 _logger.warning(SourceLine(ib, k).makeError(
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89 "Will ignore field '{}' which is not valid in {} "
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90 "inputBinding".format(k, t["class"])))
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91 del ib[k]
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92
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93 visit_class(doc, ("CommandLineTool","Workflow"), rewrite_requirements)
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94 visit_class(doc, ("ExpressionTool","Workflow"), fix_inputBinding)
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95 visit_field(doc, "secondaryFiles", partial(update_secondaryFiles, top=True))
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96
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97 upd = doc
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98 if isinstance(upd, MutableMapping) and "$graph" in upd:
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99 upd = upd["$graph"]
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100 for proc in aslist(upd):
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101 proc.setdefault("hints", CommentedSeq())
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102 proc["hints"].insert(0, CommentedMap([("class", "NetworkAccess"),( "networkAccess", True)]))
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103 proc["hints"].insert(0, CommentedMap([("class", "LoadListingRequirement"),("loadListing", "deep_listing")]))
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104 if "cwlVersion" in proc:
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105 del proc["cwlVersion"]
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106
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107 return (doc, "v1.1")
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108
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109 def v1_1_0dev1to1_1(doc, loader, baseuri): # pylint: disable=unused-argument
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110 # type: (Any, Loader, Text) -> Tuple[Any, Text]
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111 return (doc, "v1.1")
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112
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113 UPDATES = {
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114 u"v1.0": v1_0to1_1,
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115 u"v1.1": None
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116 } # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]]
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117
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118 DEVUPDATES = {
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119 u"v1.0": v1_0to1_1,
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120 u"v1.1.0-dev1": v1_1_0dev1to1_1,
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121 u"v1.1": None
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122 } # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]]
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123
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124 ALLUPDATES = UPDATES.copy()
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125 ALLUPDATES.update(DEVUPDATES)
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126
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127 INTERNAL_VERSION = u"v1.1"
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128
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129 def identity(doc, loader, baseuri): # pylint: disable=unused-argument
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130 # type: (Any, Loader, Text) -> Tuple[Any, Union[Text, Text]]
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131 """Default, do-nothing, CWL document upgrade function."""
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132 return (doc, doc["cwlVersion"])
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133
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134
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135 def checkversion(doc, # type: Union[CommentedSeq, CommentedMap]
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136 metadata, # type: CommentedMap
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137 enable_dev # type: bool
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138 ):
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139 # type: (...) -> Tuple[CommentedMap, Text]
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140 """Check the validity of the version of the give CWL document.
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141
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142 Returns the document and the validated version string.
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143 """
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144 cdoc = None # type: Optional[CommentedMap]
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145 if isinstance(doc, CommentedSeq):
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146 if not isinstance(metadata, CommentedMap):
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147 raise Exception("Expected metadata to be CommentedMap")
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148 lc = metadata.lc
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149 metadata = copy.deepcopy(metadata)
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150 metadata.lc.data = copy.copy(lc.data)
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151 metadata.lc.filename = lc.filename
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152 metadata[u"$graph"] = doc
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153 cdoc = metadata
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154 elif isinstance(doc, CommentedMap):
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155 cdoc = doc
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156 else:
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157 raise Exception("Expected CommentedMap or CommentedSeq")
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158
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159 version = metadata[u"cwlVersion"]
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160 cdoc["cwlVersion"] = version
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161
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162 if version not in UPDATES:
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163 if version in DEVUPDATES:
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164 if enable_dev:
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165 pass
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166 else:
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167 keys = list(UPDATES.keys())
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168 keys.sort()
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169 raise validate.ValidationException(
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170 u"Version '%s' is a development or deprecated version.\n "
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171 "Update your document to a stable version (%s) or use "
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172 "--enable-dev to enable support for development and "
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173 "deprecated versions." % (version, ", ".join(keys)))
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174 else:
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175 raise validate.ValidationException(
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176 u"Unrecognized version %s" % version)
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177
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178 return (cdoc, version)
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179
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180
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181 def update(doc, loader, baseuri, enable_dev, metadata):
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182 # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> CommentedMap
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183
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184 if isinstance(doc, CommentedMap):
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185 if metadata.get("http://commonwl.org/cwltool#original_cwlVersion") \
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186 or doc.get("http://commonwl.org/cwltool#original_cwlVersion"):
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187 return doc
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188
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189 (cdoc, version) = checkversion(doc, metadata, enable_dev)
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190 originalversion = copy.copy(version)
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191
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192 nextupdate = identity # type: Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]
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193
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194 while nextupdate:
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195 (cdoc, version) = nextupdate(cdoc, loader, baseuri)
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196 nextupdate = ALLUPDATES[version]
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197
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198 cdoc[u"cwlVersion"] = version
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199 metadata[u"cwlVersion"] = version
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200 metadata[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
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201 cdoc[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
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202
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203 return cdoc