Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/pack.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
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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
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3 import copy
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4 import urllib
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5 from typing import (
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6 Any,
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7 Callable,
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8 Dict,
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9 MutableMapping,
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10 MutableSequence,
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11 Optional,
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12 Set,
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13 Union,
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14 cast,
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15 )
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16
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17 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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18 from schema_salad.ref_resolver import Loader, SubLoader
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19 from schema_salad.utils import ResolveType
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20
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21 from .context import LoadingContext
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22 from .load_tool import fetch_document, resolve_and_validate_document
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23 from .process import shortname, uniquename
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24 from .update import ORDERED_VERSIONS, update
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25 from .utils import CWLObjectType, CWLOutputType
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26
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27 LoadRefType = Callable[[Optional[str], str], ResolveType]
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28
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29
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30 def find_run(
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31 d: Union[CWLObjectType, ResolveType],
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32 loadref: LoadRefType,
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33 runs: Set[str],
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34 ) -> None:
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35 if isinstance(d, MutableSequence):
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36 for s in d:
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37 find_run(s, loadref, runs)
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38 elif isinstance(d, MutableMapping):
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39 if "run" in d and isinstance(d["run"], str):
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40 if d["run"] not in runs:
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41 runs.add(d["run"])
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42 find_run(loadref(None, d["run"]), loadref, runs)
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43 for s in d.values():
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44 find_run(s, loadref, runs)
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45
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46
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47 def find_ids(
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48 d: Union[CWLObjectType, CWLOutputType, MutableSequence[CWLObjectType], None],
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49 ids: Set[str],
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50 ) -> None:
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51 if isinstance(d, MutableSequence):
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52 for s in d:
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53 find_ids(cast(CWLObjectType, s), ids)
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54 elif isinstance(d, MutableMapping):
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55 for i in ("id", "name"):
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56 if i in d and isinstance(d[i], str):
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57 ids.add(cast(str, d[i]))
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58 for s2 in d.values():
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59 find_ids(cast(CWLOutputType, s2), ids)
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60
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61
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62 def replace_refs(d: Any, rewrite: Dict[str, str], stem: str, newstem: str) -> None:
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63 if isinstance(d, MutableSequence):
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64 for s, v in enumerate(d):
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65 if isinstance(v, str):
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66 if v in rewrite:
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67 d[s] = rewrite[v]
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68 elif v.startswith(stem):
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69 d[s] = newstem + v[len(stem) :]
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70 rewrite[v] = d[s]
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71 else:
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72 replace_refs(v, rewrite, stem, newstem)
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73 elif isinstance(d, MutableMapping):
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74 for key, val in d.items():
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75 if isinstance(val, str):
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76 if val in rewrite:
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77 d[key] = rewrite[val]
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78 elif val.startswith(stem):
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79 id_ = val[len(stem) :]
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80 # prevent appending newstems if tool is already packed
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81 if id_.startswith(newstem.strip("#")):
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82 d[key] = "#" + id_
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83 else:
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84 d[key] = newstem + id_
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85 rewrite[val] = d[key]
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86 replace_refs(val, rewrite, stem, newstem)
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87
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88
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89 def import_embed(
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90 d: Union[MutableSequence[CWLObjectType], CWLObjectType, CWLOutputType],
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91 seen: Set[str],
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92 ) -> None:
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93 if isinstance(d, MutableSequence):
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94 for v in d:
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95 import_embed(cast(CWLOutputType, v), seen)
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96 elif isinstance(d, MutableMapping):
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97 for n in ("id", "name"):
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98 if n in d:
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99 if isinstance(d[n], str):
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100 ident = cast(str, d[n])
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101 if ident in seen:
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102 this = ident
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103 d.clear()
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104 d["$import"] = this
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105 else:
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106 this = ident
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107 seen.add(this)
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108 break
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109
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110 for k in sorted(d.keys()):
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111 import_embed(cast(CWLOutputType, d[k]), seen)
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112
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113
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114 def pack(
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115 loadingContext: LoadingContext,
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116 uri: str,
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117 rewrite_out: Optional[Dict[str, str]] = None,
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118 loader: Optional[Loader] = None,
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119 ) -> CWLObjectType:
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120
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121 # The workflow document we have in memory right now may have been
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122 # updated to the internal CWL version. We need to reload the
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123 # document to go back to its original version.
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124 #
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125 # What's going on here is that the updater replaces the
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126 # documents/fragments in the index with updated ones, the
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127 # index is also used as a cache, so we need to go through the
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128 # loading process with an empty index and updating turned off
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129 # so we have the original un-updated documents.
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130 #
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131 loadingContext = loadingContext.copy()
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132 document_loader = SubLoader(loader or loadingContext.loader or Loader({}))
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133 loadingContext.do_update = False
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134 loadingContext.loader = document_loader
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135 loadingContext.loader.idx = {}
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136 loadingContext.metadata = {}
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137 loadingContext, docobj, uri = fetch_document(uri, loadingContext)
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138 loadingContext, fileuri = resolve_and_validate_document(
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139 loadingContext, docobj, uri, preprocess_only=True
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140 )
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141 if loadingContext.loader is None:
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142 raise Exception("loadingContext.loader cannot be none")
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143 processobj, metadata = loadingContext.loader.resolve_ref(uri)
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144 document_loader = loadingContext.loader
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145
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146 if isinstance(processobj, MutableMapping):
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147 document_loader.idx[processobj["id"]] = CommentedMap(processobj.items())
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148 elif isinstance(processobj, MutableSequence):
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149 _, frag = urllib.parse.urldefrag(uri)
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150 for po in processobj:
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151 if not frag:
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152 if po["id"].endswith("#main"):
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153 uri = po["id"]
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154 document_loader.idx[po["id"]] = CommentedMap(po.items())
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155 document_loader.idx[metadata["id"]] = CommentedMap(metadata.items())
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156
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157 found_versions = {
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158 cast(str, loadingContext.metadata["cwlVersion"])
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159 } # type: Set[str]
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160
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161 def loadref(base: Optional[str], lr_uri: str) -> ResolveType:
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162 lr_loadingContext = loadingContext.copy()
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163 lr_loadingContext.metadata = {}
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164 lr_loadingContext, lr_workflowobj, lr_uri = fetch_document(
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165 lr_uri, lr_loadingContext
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166 )
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167 lr_loadingContext, lr_uri = resolve_and_validate_document(
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168 lr_loadingContext, lr_workflowobj, lr_uri
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169 )
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170 found_versions.add(cast(str, lr_loadingContext.metadata["cwlVersion"]))
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171 if lr_loadingContext.loader is None:
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172 raise Exception("loader should not be None")
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173 return lr_loadingContext.loader.resolve_ref(lr_uri, base_url=base)[0]
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174
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175 ids = set() # type: Set[str]
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176 find_ids(processobj, ids)
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177
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178 runs = {uri}
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179 find_run(processobj, loadref, runs)
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180
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181 # Figure out the highest version, everything needs to be updated
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182 # to it.
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183 m = 0
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184 for fv in found_versions:
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185 m = max(m, ORDERED_VERSIONS.index(fv))
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186 update_to_version = ORDERED_VERSIONS[m]
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187
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188 for f in runs:
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189 find_ids(document_loader.resolve_ref(f)[0], ids)
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190
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191 names = set() # type: Set[str]
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192 if rewrite_out is None:
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193 rewrite = {} # type: Dict[str, str]
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194 else:
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195 rewrite = rewrite_out
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196
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197 mainpath, _ = urllib.parse.urldefrag(uri)
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198
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199 def rewrite_id(r: str, mainuri: str) -> None:
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200 if r == mainuri:
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201 rewrite[r] = "#main"
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202 elif r.startswith(mainuri) and r[len(mainuri)] in ("#", "/"):
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203 if r[len(mainuri) :].startswith("#main/"):
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204 rewrite[r] = "#" + uniquename(r[len(mainuri) + 1 :], names)
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205 else:
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206 rewrite[r] = "#" + uniquename("main/" + r[len(mainuri) + 1 :], names)
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207 else:
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208 path, frag = urllib.parse.urldefrag(r)
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209 if path == mainpath:
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210 rewrite[r] = "#" + uniquename(frag, names)
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211 else:
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212 if path not in rewrite:
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213 rewrite[path] = "#" + uniquename(shortname(path), names)
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214
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215 sortedids = sorted(ids)
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216
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217 for r in sortedids:
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218 rewrite_id(r, uri)
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219
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220 packed = CommentedMap(
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221 (("$graph", CommentedSeq()), ("cwlVersion", update_to_version))
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222 )
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223 namespaces = metadata.get("$namespaces", None)
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224
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225 schemas = set() # type: Set[str]
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226 if "$schemas" in metadata:
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227 for each_schema in metadata["$schemas"]:
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228 schemas.add(each_schema)
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229 for r in sorted(runs):
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230 dcr, metadata = document_loader.resolve_ref(r)
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231 if isinstance(dcr, CommentedSeq):
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232 dcr = dcr[0]
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233 dcr = cast(CommentedMap, dcr)
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234 if not isinstance(dcr, MutableMapping):
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235 continue
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236
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237 dcr = update(
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238 dcr,
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239 document_loader,
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240 r,
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241 loadingContext.enable_dev,
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242 metadata,
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243 update_to_version,
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244 )
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245
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246 if "http://commonwl.org/cwltool#original_cwlVersion" in metadata:
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247 del metadata["http://commonwl.org/cwltool#original_cwlVersion"]
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248 if "http://commonwl.org/cwltool#original_cwlVersion" in dcr:
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249 del dcr["http://commonwl.org/cwltool#original_cwlVersion"]
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250
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251 if "$schemas" in metadata:
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252 for s in metadata["$schemas"]:
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253 schemas.add(s)
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254 if dcr.get("class") not in ("Workflow", "CommandLineTool", "ExpressionTool"):
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255 continue
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256 dc = cast(Dict[str, Any], copy.deepcopy(dcr))
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257 v = rewrite[r]
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258 dc["id"] = v
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259 for n in ("name", "cwlVersion", "$namespaces", "$schemas"):
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260 if n in dc:
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261 del dc[n]
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262 packed["$graph"].append(dc)
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263
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264 if schemas:
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265 packed["$schemas"] = list(schemas)
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266
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267 for r in list(rewrite.keys()):
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268 v = rewrite[r]
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269 replace_refs(packed, rewrite, r + "/" if "#" in r else r + "#", v + "/")
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270
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271 import_embed(packed, set())
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272
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273 if len(packed["$graph"]) == 1:
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274 # duplicate 'cwlVersion' and $schemas inside $graph when there is only
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275 # a single item because we will print the contents inside '$graph'
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276 # rather than whole dict
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277 packed["$graph"][0]["cwlVersion"] = packed["cwlVersion"]
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278 if schemas:
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279 packed["$graph"][0]["$schemas"] = list(schemas)
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280 # always include $namespaces in the #main
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281 if namespaces:
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282 packed["$graph"][0]["$namespaces"] = namespaces
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283
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284 return packed