Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/update.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 (2021-03-22)
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1 import copy
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2 from functools import partial
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3 from typing import (
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4 Callable,
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5 Dict,
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6 MutableMapping,
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7 MutableSequence,
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8 Optional,
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9 Tuple,
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10 Union,
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11 cast,
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12 )
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13
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14 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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15 from schema_salad.exceptions import ValidationException
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16 from schema_salad.ref_resolver import Loader
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17 from schema_salad.sourceline import SourceLine
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18
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19 from .loghandler import _logger
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20 from .utils import CWLObjectType, CWLOutputType, aslist, visit_class, visit_field
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21
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22
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23 def v1_1to1_2(
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24 doc: CommentedMap, loader: Loader, baseuri: str
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25 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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26 """Public updater for v1.1 to v1.2."""
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27 doc = copy.deepcopy(doc)
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28
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29 upd = doc
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30 if isinstance(upd, MutableMapping) and "$graph" in upd:
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31 upd = cast(CommentedMap, upd["$graph"])
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32 for proc in aslist(upd):
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33 if "cwlVersion" in proc:
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34 del proc["cwlVersion"]
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35
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36 return doc, "v1.2"
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37
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38
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39 def v1_0to1_1(
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40 doc: CommentedMap, loader: Loader, baseuri: str
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41 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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42 """Public updater for v1.0 to v1.1."""
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43 doc = copy.deepcopy(doc)
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44
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45 rewrite = {
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46 "http://commonwl.org/cwltool#WorkReuse": "WorkReuse",
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47 "http://arvados.org/cwl#ReuseRequirement": "WorkReuse",
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48 "http://commonwl.org/cwltool#TimeLimit": "ToolTimeLimit",
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49 "http://commonwl.org/cwltool#NetworkAccess": "NetworkAccess",
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50 "http://commonwl.org/cwltool#InplaceUpdateRequirement": "InplaceUpdateRequirement",
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51 "http://commonwl.org/cwltool#LoadListingRequirement": "LoadListingRequirement",
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52 }
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53
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54 def rewrite_requirements(t: CWLObjectType) -> None:
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55 if "requirements" in t:
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56 for r in cast(MutableSequence[CWLObjectType], t["requirements"]):
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57 if isinstance(r, MutableMapping):
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58 cls = cast(str, r["class"])
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59 if cls in rewrite:
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60 r["class"] = rewrite[cls]
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61 else:
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62 raise ValidationException(
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63 "requirements entries must be dictionaries: {} {}.".format(
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64 type(r), r
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65 )
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66 )
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67 if "hints" in t:
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68 for r in cast(MutableSequence[CWLObjectType], t["hints"]):
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69 if isinstance(r, MutableMapping):
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70 cls = cast(str, r["class"])
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71 if cls in rewrite:
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72 r["class"] = rewrite[cls]
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73 else:
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74 raise ValidationException(
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75 "hints entries must be dictionaries: {} {}.".format(type(r), r)
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76 )
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77 if "steps" in t:
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78 for s in cast(MutableSequence[CWLObjectType], t["steps"]):
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79 if isinstance(s, MutableMapping):
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80 rewrite_requirements(s)
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81 else:
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82 raise ValidationException(
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83 "steps entries must be dictionaries: {} {}.".format(type(s), s)
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84 )
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85
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86 def update_secondaryFiles(t, top=False):
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87 # type: (CWLOutputType, bool) -> Union[MutableSequence[MutableMapping[str, str]], MutableMapping[str, str]]
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88 if isinstance(t, CommentedSeq):
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89 new_seq = copy.deepcopy(t)
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90 for index, entry in enumerate(t):
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91 new_seq[index] = update_secondaryFiles(entry)
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92 return new_seq
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93 elif isinstance(t, MutableSequence):
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94 return CommentedSeq(
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95 [update_secondaryFiles(cast(CWLOutputType, p)) for p in t]
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96 )
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97 elif isinstance(t, MutableMapping):
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98 return cast(MutableMapping[str, str], t)
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99 elif top:
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100 return CommentedSeq([CommentedMap([("pattern", t)])])
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101 else:
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102 return CommentedMap([("pattern", t)])
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103
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104 def fix_inputBinding(t: CWLObjectType) -> None:
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105 for i in cast(MutableSequence[CWLObjectType], t["inputs"]):
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106 if "inputBinding" in i:
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107 ib = cast(CWLObjectType, i["inputBinding"])
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108 for k in list(ib.keys()):
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109 if k != "loadContents":
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110 _logger.warning(
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111 SourceLine(ib, k).makeError(
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112 "Will ignore field '{}' which is not valid in {} "
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113 "inputBinding".format(k, t["class"])
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114 )
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115 )
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116 del ib[k]
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117
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118 visit_class(doc, ("CommandLineTool", "Workflow"), rewrite_requirements)
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119 visit_class(doc, ("ExpressionTool", "Workflow"), fix_inputBinding)
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120 visit_field(doc, "secondaryFiles", partial(update_secondaryFiles, top=True))
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121
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122 upd = doc
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123 if isinstance(upd, MutableMapping) and "$graph" in upd:
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124 upd = cast(CommentedMap, upd["$graph"])
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125 for proc in aslist(upd):
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126 proc.setdefault("hints", CommentedSeq())
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127 proc["hints"].insert(
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128 0, CommentedMap([("class", "NetworkAccess"), ("networkAccess", True)])
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129 )
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130 proc["hints"].insert(
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131 0,
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132 CommentedMap(
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133 [("class", "LoadListingRequirement"), ("loadListing", "deep_listing")]
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134 ),
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135 )
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136 if "cwlVersion" in proc:
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137 del proc["cwlVersion"]
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138
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139 return (doc, "v1.1")
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140
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141
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142 def v1_1_0dev1to1_1(
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143 doc: CommentedMap, loader: Loader, baseuri: str
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144 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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145 """Public updater for v1.1.0-dev1 to v1.1."""
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146 return (doc, "v1.1")
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147
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148
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149 def v1_2_0dev1todev2(
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150 doc: CommentedMap, loader: Loader, baseuri: str
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151 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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152 """Public updater for v1.2.0-dev1 to v1.2.0-dev2."""
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153 return (doc, "v1.2.0-dev2")
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154
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155
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156 def v1_2_0dev2todev3(
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157 doc: CommentedMap, loader: Loader, baseuri: str
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158 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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159 """Public updater for v1.2.0-dev2 to v1.2.0-dev3."""
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160 doc = copy.deepcopy(doc)
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161
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162 def update_pickvalue(t: CWLObjectType) -> None:
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163 for step in cast(MutableSequence[CWLObjectType], t["steps"]):
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164 for inp in cast(MutableSequence[CWLObjectType], step["in"]):
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165 if "pickValue" in inp:
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166 if inp["pickValue"] == "only_non_null":
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167 inp["pickValue"] = "the_only_non_null"
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168
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169 visit_class(doc, "Workflow", update_pickvalue)
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170 upd = doc
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171 if isinstance(upd, MutableMapping) and "$graph" in upd:
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172 upd = cast(CommentedMap, upd["$graph"])
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173 for proc in aslist(upd):
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174 if "cwlVersion" in proc:
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175 del proc["cwlVersion"]
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176 return (doc, "v1.2.0-dev3")
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177
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178
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179 def v1_2_0dev3todev4(
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180 doc: CommentedMap, loader: Loader, baseuri: str
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181 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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182 """Public updater for v1.2.0-dev3 to v1.2.0-dev4."""
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183 return (doc, "v1.2.0-dev4")
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184
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185
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186 def v1_2_0dev4todev5(
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187 doc: CommentedMap, loader: Loader, baseuri: str
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188 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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189 """Public updater for v1.2.0-dev4 to v1.2.0-dev5."""
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190 return (doc, "v1.2.0-dev5")
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191
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192
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193 def v1_2_0dev5to1_2(
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194 doc: CommentedMap, loader: Loader, baseuri: str
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195 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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196 """Public updater for v1.2.0-dev5 to v1.2."""
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197 return (doc, "v1.2")
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198
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199
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200 ORDERED_VERSIONS = [
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201 "v1.0",
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202 "v1.1.0-dev1",
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203 "v1.1",
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204 "v1.2.0-dev1",
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205 "v1.2.0-dev2",
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206 "v1.2.0-dev3",
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207 "v1.2.0-dev4",
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208 "v1.2.0-dev5",
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209 "v1.2",
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210 ]
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211
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212 UPDATES = {
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213 "v1.0": v1_0to1_1,
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214 "v1.1": v1_1to1_2,
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215 "v1.2": None,
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216 } # type: Dict[str, Optional[Callable[[CommentedMap, Loader, str], Tuple[CommentedMap, str]]]]
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217
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218 DEVUPDATES = {
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219 "v1.1.0-dev1": v1_1_0dev1to1_1,
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220 "v1.2.0-dev1": v1_2_0dev1todev2,
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221 "v1.2.0-dev2": v1_2_0dev2todev3,
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222 "v1.2.0-dev3": v1_2_0dev3todev4,
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223 "v1.2.0-dev4": v1_2_0dev4todev5,
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224 "v1.2.0-dev5": v1_2_0dev5to1_2,
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225 } # type: Dict[str, Optional[Callable[[CommentedMap, Loader, str], Tuple[CommentedMap, str]]]]
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226
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227
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228 ALLUPDATES = UPDATES.copy()
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229 ALLUPDATES.update(DEVUPDATES)
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230
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231 INTERNAL_VERSION = "v1.2"
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232
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233 ORIGINAL_CWLVERSION = "http://commonwl.org/cwltool#original_cwlVersion"
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234
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235
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236 def identity(
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237 doc: CommentedMap, loader: Loader, baseuri: str
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238 ) -> Tuple[CommentedMap, str]: # pylint: disable=unused-argument
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239 """Do-nothing, CWL document upgrade function."""
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240 return (doc, cast(str, doc["cwlVersion"]))
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241
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242
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243 def checkversion(
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244 doc: Union[CommentedSeq, CommentedMap],
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245 metadata: CommentedMap,
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246 enable_dev: bool,
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247 ) -> Tuple[CommentedMap, str]:
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248 """Check the validity of the version of the give CWL document.
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249
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250 Returns the document and the validated version string.
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251 """
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252 cdoc = None # type: Optional[CommentedMap]
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253 if isinstance(doc, CommentedSeq):
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254 if not isinstance(metadata, CommentedMap):
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255 raise Exception("Expected metadata to be CommentedMap")
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256 lc = metadata.lc
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257 metadata = copy.deepcopy(metadata)
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258 metadata.lc.data = copy.copy(lc.data)
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259 metadata.lc.filename = lc.filename
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260 metadata["$graph"] = doc
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261 cdoc = metadata
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262 elif isinstance(doc, CommentedMap):
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263 cdoc = doc
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264 else:
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265 raise Exception("Expected CommentedMap or CommentedSeq")
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266
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267 version = metadata["cwlVersion"]
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268 cdoc["cwlVersion"] = version
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269
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270 updated_from = metadata.get(ORIGINAL_CWLVERSION) or cdoc.get(ORIGINAL_CWLVERSION)
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271
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272 if updated_from:
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273 if version != INTERNAL_VERSION:
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274 raise ValidationException(
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275 "original_cwlVersion is set (%s) but cwlVersion is '%s', expected '%s' "
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276 % (updated_from, version, INTERNAL_VERSION)
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277 )
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278 elif version not in UPDATES:
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279 if version in DEVUPDATES:
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280 if enable_dev:
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281 pass
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282 else:
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283 keys = list(UPDATES.keys())
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284 keys.sort()
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285 raise ValidationException(
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286 "Version '%s' is a development or deprecated version.\n "
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287 "Update your document to a stable version (%s) or use "
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288 "--enable-dev to enable support for development and "
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289 "deprecated versions." % (version, ", ".join(keys))
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290 )
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291 else:
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292 raise ValidationException("Unrecognized version %s" % version)
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293
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294 return (cdoc, version)
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295
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296
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297 def update(
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298 doc: Union[CommentedSeq, CommentedMap],
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299 loader: Loader,
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300 baseuri: str,
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301 enable_dev: bool,
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302 metadata: CommentedMap,
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303 update_to: Optional[str] = None,
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304 ) -> CommentedMap:
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305 """Update a CWL document to 'update_to' (if provided) or INTERNAL_VERSION."""
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306 if update_to is None:
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307 update_to = INTERNAL_VERSION
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308
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309 (cdoc, version) = checkversion(doc, metadata, enable_dev)
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310 originalversion = copy.copy(version)
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311
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312 nextupdate = (
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313 identity
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314 ) # type: Optional[Callable[[CommentedMap, Loader, str], Tuple[CommentedMap, str]]]
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315
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316 while version != update_to and nextupdate:
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317 (cdoc, version) = nextupdate(cdoc, loader, baseuri)
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318 nextupdate = ALLUPDATES[version]
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319
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320 cdoc["cwlVersion"] = version
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321 metadata["cwlVersion"] = version
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322 metadata["http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
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323 cdoc["http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
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324
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325 return cdoc