Mercurial > repos > shellac > guppy_basecaller

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 from __future__ import absolute_import
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2
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3 from typing import cast, IO, Any, Dict, MutableMapping
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4
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5 from rdflib import Graph
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6 from schema_salad.jsonld_context import makerdf
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7 from schema_salad.ref_resolver import ContextType
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8 from six.moves import urllib
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9 from typing_extensions import Text # pylint: disable=unused-import
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10 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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11
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12 from .process import Process
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13
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14
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15 def gather(tool, ctx): # type: (Process, ContextType) -> Graph
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16 g = Graph()
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17
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18 def visitor(t): # type: (MutableMapping[Text, Any]) -> None
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19 makerdf(t["id"], t, ctx, graph=g)
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20
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21 tool.visit(visitor)
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22 return g
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23
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24
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25 def printrdf(wflow, ctx, style): # type: (Process, ContextType, str) -> Text
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26 """Serialize the CWL document into a string, ready for printing."""
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27 rdf = gather(wflow, ctx).serialize(format=style, encoding='utf-8')
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28 if not rdf:
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29 return u""
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30 return cast(Text, rdf.decode('utf-8'))
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31
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32
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33 def lastpart(uri): # type: (Any) -> Text
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34 uri2 = Text(uri)
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35 if "/" in uri2:
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36 return uri2[uri2.rindex("/") + 1:]
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37 return uri2
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38
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39
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40 def dot_with_parameters(g, stdout): # type: (Graph, IO[Any]) -> None
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41 qres = g.query(
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42 """SELECT ?step ?run ?runtype
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43 WHERE {
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44 ?step cwl:run ?run .
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45 ?run rdf:type ?runtype .
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46 }""")
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47
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48 for step, run, _ in qres:
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49 stdout.write(u'"%s" [label="%s"]\n' % (lastpart(step), "%s (%s)" % (lastpart(step), lastpart(run))))
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50
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51 qres = g.query(
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52 """SELECT ?step ?inp ?source
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53 WHERE {
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54 ?wf Workflow:steps ?step .
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55 ?step cwl:inputs ?inp .
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56 ?inp cwl:source ?source .
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57 }""")
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58
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59 for step, inp, source in qres:
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60 stdout.write(u'"%s" [shape=box]\n' % (lastpart(inp)))
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61 stdout.write(u'"%s" -> "%s" [label="%s"]\n' % (lastpart(source), lastpart(inp), ""))
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62 stdout.write(u'"%s" -> "%s" [label="%s"]\n' % (lastpart(inp), lastpart(step), ""))
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63
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64 qres = g.query(
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65 """SELECT ?step ?out
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66 WHERE {
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67 ?wf Workflow:steps ?step .
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68 ?step cwl:outputs ?out .
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69 }""")
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70
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71 for step, out in qres:
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72 stdout.write(u'"%s" [shape=box]\n' % (lastpart(out)))
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73 stdout.write(u'"%s" -> "%s" [label="%s"]\n' % (lastpart(step), lastpart(out), ""))
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74
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75 qres = g.query(
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76 """SELECT ?out ?source
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77 WHERE {
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78 ?wf cwl:outputs ?out .
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79 ?out cwl:source ?source .
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80 }""")
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81
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82 for out, source in qres:
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83 stdout.write(u'"%s" [shape=octagon]\n' % (lastpart(out)))
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84 stdout.write(u'"%s" -> "%s" [label="%s"]\n' % (lastpart(source), lastpart(out), ""))
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85
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86 qres = g.query(
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87 """SELECT ?inp
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88 WHERE {
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89 ?wf rdf:type cwl:Workflow .
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90 ?wf cwl:inputs ?inp .
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91 }""")
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92
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93 for (inp,) in qres:
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94 stdout.write(u'"%s" [shape=octagon]\n' % (lastpart(inp)))
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95
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96
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97 def dot_without_parameters(g, stdout): # type: (Graph, IO[Any]) -> None
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98 dotname = {} # type: Dict[Text,Text]
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99 clusternode = {}
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100
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101 stdout.write("compound=true\n")
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102
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103 subworkflows = set()
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104 qres = g.query(
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105 """SELECT ?run
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106 WHERE {
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107 ?wf rdf:type cwl:Workflow .
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108 ?wf Workflow:steps ?step .
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109 ?step cwl:run ?run .
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110 ?run rdf:type cwl:Workflow .
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111 } ORDER BY ?wf""")
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112 for (run,) in qres:
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113 subworkflows.add(run)
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114
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115 qres = g.query(
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116 """SELECT ?wf ?step ?run ?runtype
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117 WHERE {
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118 ?wf rdf:type cwl:Workflow .
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119 ?wf Workflow:steps ?step .
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120 ?step cwl:run ?run .
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121 ?run rdf:type ?runtype .
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122 } ORDER BY ?wf""")
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123
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124 currentwf = None
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125 for wf, step, run, runtype in qres:
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126 if step not in dotname:
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127 dotname[step] = lastpart(step)
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128
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129 if wf != currentwf:
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130 if currentwf is not None:
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131 stdout.write("}\n")
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132 if wf in subworkflows:
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133 if wf not in dotname:
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134 dotname[wf] = "cluster_" + lastpart(wf)
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135 stdout.write(u'subgraph "%s" { label="%s"\n' % (dotname[wf], lastpart(wf)))
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136 currentwf = wf
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137 clusternode[wf] = step
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138 else:
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139 currentwf = None
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140
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141 if Text(runtype) != "https://w3id.org/cwl/cwl#Workflow":
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142 stdout.write(u'"%s" [label="%s"]\n' % (dotname[step], urllib.parse.urldefrag(Text(step))[1]))
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143
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144 if currentwf is not None:
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145 stdout.write("}\n")
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146
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147 qres = g.query(
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148 """SELECT DISTINCT ?src ?sink ?srcrun ?sinkrun
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149 WHERE {
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150 ?wf1 Workflow:steps ?src .
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151 ?wf2 Workflow:steps ?sink .
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152 ?src cwl:out ?out .
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153 ?inp cwl:source ?out .
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154 ?sink cwl:in ?inp .
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155 ?src cwl:run ?srcrun .
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156 ?sink cwl:run ?sinkrun .
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157 }""")
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158
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159 for src, sink, srcrun, sinkrun in qres:
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160 attr = u""
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161 if srcrun in clusternode:
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162 attr += u'ltail="%s"' % dotname[srcrun]
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163 src = clusternode[srcrun]
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164 if sinkrun in clusternode:
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165 attr += u' lhead="%s"' % dotname[sinkrun]
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166 sink = clusternode[sinkrun]
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167 stdout.write(u'"%s" -> "%s" [%s]\n' % (dotname[src], dotname[sink], attr))
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168
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169
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170 def printdot(wf, ctx, stdout, include_parameters=False):
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171 # type: (Process, ContextType, Any, bool) -> None
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172 g = gather(wf, ctx)
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173
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174 stdout.write("digraph {")
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175
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176 # g.namespace_manager.qname(predicate)
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177
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178 if include_parameters:
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179 dot_with_parameters(g, stdout)
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180 else:
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181 dot_without_parameters(g, stdout)
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182
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183 stdout.write("}")