Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/pack.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """Reformat a CWL document and all its references to be a single stream."""
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2 from __future__ import absolute_import
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3
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4 import copy
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5 from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
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6 Optional, Set, Union, cast)
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7
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8 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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9 from schema_salad.ref_resolver import Loader # pylint: disable=unused-import
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10 from schema_salad.ref_resolver import SubLoader
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11 from schema_salad.sourceline import cmap
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12 from six import iteritems, string_types
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13 from six.moves import urllib
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14 from typing_extensions import Text # pylint: disable=unused-import
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15 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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16
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17 from .process import shortname, uniquename
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18
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19
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20 def flatten_deps(d, files): # type: (Any, Set[Text]) -> None
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21 if isinstance(d, MutableSequence):
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22 for s in d:
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23 flatten_deps(s, files)
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24 elif isinstance(d, MutableMapping):
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25 if d["class"] == "File":
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26 files.add(d["location"])
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27 if "secondaryFiles" in d:
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28 flatten_deps(d["secondaryFiles"], files)
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29 if "listing" in d:
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30 flatten_deps(d["listing"], files)
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31
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32 LoadRefType = Callable[[Optional[Text], Text], Union[Dict[Text, Any], List[Dict[Text, Any]], Text, None]]
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33
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34
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35 def find_run(d, # type: Any
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36 loadref, # type: LoadRefType
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37 runs # type: Set[Text]
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38 ): # type: (...) -> None
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39 if isinstance(d, MutableSequence):
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40 for s in d:
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41 find_run(s, loadref, runs)
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42 elif isinstance(d, MutableMapping):
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43 if "run" in d and isinstance(d["run"], string_types):
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44 if d["run"] not in runs:
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45 runs.add(d["run"])
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46 find_run(loadref(None, d["run"]), loadref, runs)
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47 for s in d.values():
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48 find_run(s, loadref, runs)
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49
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50
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51 def find_ids(d, ids): # type: (Any, Set[Text]) -> None
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52 if isinstance(d, MutableSequence):
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53 for s in d:
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54 find_ids(s, ids)
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55 elif isinstance(d, MutableMapping):
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56 for i in ("id", "name"):
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57 if i in d and isinstance(d[i], string_types):
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58 ids.add(d[i])
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59 for s in d.values():
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60 find_ids(s, ids)
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61
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62
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63 def replace_refs(d, rewrite, stem, newstem):
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64 # type: (Any, Dict[Text, Text], Text, Text) -> None
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65 if isinstance(d, MutableSequence):
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66 for s, v in enumerate(d):
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67 if isinstance(v, string_types):
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68 if v in rewrite:
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69 d[s] = rewrite[v]
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70 elif v.startswith(stem):
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71 d[s] = newstem + v[len(stem):]
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72 rewrite[v] = d[s]
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73 else:
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74 replace_refs(v, rewrite, stem, newstem)
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75 elif isinstance(d, MutableMapping):
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76 for s, v in d.items():
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77 if isinstance(v, string_types):
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78 if v in rewrite:
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79 d[s] = rewrite[v]
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80 elif v.startswith(stem):
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81 id_ = v[len(stem):]
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82 # prevent appending newstems if tool is already packed
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83 if id_.startswith(newstem.strip("#")):
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84 d[s] = "#" + id_
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85 else:
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86 d[s] = newstem + id_
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87 rewrite[v] = d[s]
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88 replace_refs(v, rewrite, stem, newstem)
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89
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90 def import_embed(d, seen):
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91 # type: (Any, Set[Text]) -> None
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92 if isinstance(d, MutableSequence):
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93 for v in d:
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94 import_embed(v, seen)
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95 elif isinstance(d, MutableMapping):
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96 for n in ("id", "name"):
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97 if n in d:
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98 if d[n] in seen:
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99 this = d[n]
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100 d.clear()
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101 d["$import"] = this
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102 else:
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103 this = d[n]
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104 seen.add(this)
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105 break
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106
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107 for k in sorted(d.keys()):
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108 import_embed(d[k], seen)
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109
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110
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111 def pack(document_loader, # type: Loader
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112 processobj, # type: Union[Dict[Text, Any], List[Dict[Text, Any]]]
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113 uri, # type: Text
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114 metadata, # type: Dict[Text, Text]
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115 rewrite_out=None # type: Optional[Dict[Text, Text]]
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116 ): # type: (...) -> Dict[Text, Any]
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117
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118 document_loader = SubLoader(document_loader)
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119 document_loader.idx = {}
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120 if isinstance(processobj, MutableMapping):
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121 document_loader.idx[processobj["id"]] = CommentedMap(iteritems(processobj))
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122 elif isinstance(processobj, MutableSequence):
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123 _, frag = urllib.parse.urldefrag(uri)
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124 for po in processobj:
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125 if not frag:
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126 if po["id"].endswith("#main"):
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127 uri = po["id"]
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128 document_loader.idx[po["id"]] = CommentedMap(iteritems(po))
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129 document_loader.idx[metadata["id"]] = CommentedMap(iteritems(metadata))
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130
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131 def loadref(base, uri):
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132 # type: (Optional[Text], Text) -> Union[Dict[Text, Any], List[Dict[Text, Any]], Text, None]
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133 return document_loader.resolve_ref(uri, base_url=base)[0]
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134
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135 ids = set() # type: Set[Text]
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136 find_ids(processobj, ids)
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137
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138 runs = {uri}
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139 find_run(processobj, loadref, runs)
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140
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141 for f in runs:
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142 find_ids(document_loader.resolve_ref(f)[0], ids)
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143
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144 names = set() # type: Set[Text]
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145 if rewrite_out is None:
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146 rewrite = {} # type: Dict[Text, Text]
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147 else:
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148 rewrite = rewrite_out
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149
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150 mainpath, _ = urllib.parse.urldefrag(uri)
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151
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152 def rewrite_id(r, mainuri):
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153 # type: (Text, Text) -> None
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154 if r == mainuri:
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155 rewrite[r] = "#main"
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156 elif r.startswith(mainuri) and r[len(mainuri)] in ("#", "/"):
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157 if r[len(mainuri):].startswith("#main/"):
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158 rewrite[r] = "#" + uniquename(r[len(mainuri)+1:], names)
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159 else:
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160 rewrite[r] = "#" + uniquename("main/"+r[len(mainuri)+1:], names)
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161 else:
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162 path, frag = urllib.parse.urldefrag(r)
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163 if path == mainpath:
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164 rewrite[r] = "#" + uniquename(frag, names)
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165 else:
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166 if path not in rewrite:
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167 rewrite[path] = "#" + uniquename(shortname(path), names)
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168
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169 sortedids = sorted(ids)
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170
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171 for r in sortedids:
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172 rewrite_id(r, uri)
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173
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174 packed = CommentedMap((("$graph", CommentedSeq()),
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175 ("cwlVersion", metadata["cwlVersion"])))
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176 namespaces = metadata.get('$namespaces', None)
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177
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178 schemas = set() # type: Set[Text]
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179 if '$schemas' in metadata:
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180 for each_schema in metadata["$schemas"]:
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181 schemas.add(each_schema)
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182 for r in sorted(runs):
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183 dcr, metadata = document_loader.resolve_ref(r)
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184 if isinstance(dcr, CommentedSeq):
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185 dcr = dcr[0]
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186 dcr = cast(CommentedMap, dcr)
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187 if not isinstance(dcr, MutableMapping):
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188 continue
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189 metadata = cast(Dict[Text, Any], metadata)
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190 if "$schemas" in metadata:
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191 for s in metadata["$schemas"]:
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192 schemas.add(s)
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193 if dcr.get("class") not in ("Workflow", "CommandLineTool", "ExpressionTool"):
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194 continue
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195 dc = cast(Dict[Text, Any], copy.deepcopy(dcr))
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196 v = rewrite[r]
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197 dc["id"] = v
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198 for n in ("name", "cwlVersion", "$namespaces", "$schemas"):
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199 if n in dc:
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200 del dc[n]
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201 packed["$graph"].append(dc)
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202
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203 if schemas:
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204 packed["$schemas"] = list(schemas)
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205
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206 for r in list(rewrite.keys()):
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207 v = rewrite[r]
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208 replace_refs(packed, rewrite, r + "/" if "#" in r else r + "#", v + "/")
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209
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210 import_embed(packed, set())
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211
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212 if len(packed["$graph"]) == 1:
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213 # duplicate 'cwlVersion' and $schemas inside $graph when there is only
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214 # a single item because we will print the contents inside '$graph'
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215 # rather than whole dict
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216 packed["$graph"][0]["cwlVersion"] = packed["cwlVersion"]
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217 if schemas:
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218 packed["$graph"][0]["$schemas"] = list(schemas)
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219 # always include $namespaces in the #main
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220 if namespaces:
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221 packed["$graph"][0]["$namespaces"] = namespaces
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222
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223 return packed