Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/cwlrdf.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 urllib
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2 from codecs import StreamWriter
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3 from typing import Any, Dict, Optional, TextIO, Union, cast
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4
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5 from rdflib import Graph
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6 from ruamel.yaml.comments import CommentedMap
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7 from schema_salad.jsonld_context import makerdf
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8 from schema_salad.utils import ContextType
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9
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10 from .cwlviewer import CWLViewer
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11 from .process import Process
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12
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13
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14 def gather(tool: Process, ctx: ContextType) -> Graph:
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15 g = Graph()
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16
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17 def visitor(t: CommentedMap) -> None:
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18 makerdf(t["id"], t, ctx, graph=g)
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19
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20 tool.visit(visitor)
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21 return g
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22
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23
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24 def printrdf(wflow: Process, ctx: ContextType, style: str) -> str:
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25 """Serialize the CWL document into a string, ready for printing."""
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26 rdf = gather(wflow, ctx).serialize(format=style, encoding="utf-8")
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27 if not rdf:
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28 return ""
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29 return cast(str, rdf.decode("utf-8"))
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30
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31
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32 def lastpart(uri: Any) -> str:
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33 uri2 = str(uri)
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34 if "/" in uri2:
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35 return uri2[uri2.rindex("/") + 1 :]
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36 return uri2
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37
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38
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39 def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None:
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40 qres = g.query(
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41 """SELECT ?step ?run ?runtype
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42 WHERE {
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43 ?step cwl:run ?run .
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44 ?run rdf:type ?runtype .
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45 }"""
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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(
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50 '"%s" [label="%s"]\n'
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51 % (lastpart(step), "{} ({})".format(lastpart(step), lastpart(run)))
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52 )
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53
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54 qres = g.query(
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55 """SELECT ?step ?inp ?source
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56 WHERE {
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57 ?wf Workflow:steps ?step .
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58 ?step cwl:inputs ?inp .
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59 ?inp cwl:source ?source .
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60 }"""
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61 )
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62
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63 for step, inp, source in qres:
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64 stdout.write('"%s" [shape=box]\n' % (lastpart(inp)))
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65 stdout.write(
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66 '"{}" -> "{}" [label="{}"]\n'.format(lastpart(source), lastpart(inp), "")
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67 )
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68 stdout.write(
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69 '"{}" -> "{}" [label="{}"]\n'.format(lastpart(inp), lastpart(step), "")
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70 )
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71
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72 qres = g.query(
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73 """SELECT ?step ?out
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74 WHERE {
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75 ?wf Workflow:steps ?step .
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76 ?step cwl:outputs ?out .
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77 }"""
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78 )
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79
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80 for step, out in qres:
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81 stdout.write('"%s" [shape=box]\n' % (lastpart(out)))
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82 stdout.write(
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83 '"{}" -> "{}" [label="{}"]\n'.format(lastpart(step), lastpart(out), "")
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84 )
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85
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86 qres = g.query(
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87 """SELECT ?out ?source
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88 WHERE {
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89 ?wf cwl:outputs ?out .
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90 ?out cwl:source ?source .
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91 }"""
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92 )
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93
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94 for out, source in qres:
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95 stdout.write('"%s" [shape=octagon]\n' % (lastpart(out)))
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96 stdout.write(
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97 '"{}" -> "{}" [label="{}"]\n'.format(lastpart(source), lastpart(out), "")
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98 )
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99
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100 qres = g.query(
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101 """SELECT ?inp
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102 WHERE {
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103 ?wf rdf:type cwl:Workflow .
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104 ?wf cwl:inputs ?inp .
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105 }"""
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106 )
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107
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108 for (inp,) in qres:
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109 stdout.write('"%s" [shape=octagon]\n' % (lastpart(inp)))
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110
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111
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112 def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None:
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113 dotname = {} # type: Dict[str,str]
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114 clusternode = {}
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115
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116 stdout.write("compound=true\n")
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117
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118 subworkflows = set()
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119 qres = g.query(
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120 """SELECT ?run
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121 WHERE {
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122 ?wf rdf:type cwl:Workflow .
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123 ?wf Workflow:steps ?step .
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124 ?step cwl:run ?run .
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125 ?run rdf:type cwl:Workflow .
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126 } ORDER BY ?wf"""
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127 )
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128 for (run,) in qres:
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129 subworkflows.add(run)
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130
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131 qres = g.query(
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132 """SELECT ?wf ?step ?run ?runtype
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133 WHERE {
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134 ?wf rdf:type cwl:Workflow .
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135 ?wf Workflow:steps ?step .
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136 ?step cwl:run ?run .
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137 ?run rdf:type ?runtype .
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138 } ORDER BY ?wf"""
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139 )
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140
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141 currentwf = None # type: Optional[str]
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142 for wf, step, _run, runtype in qres:
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143 if step not in dotname:
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144 dotname[step] = lastpart(step)
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145
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146 if wf != currentwf:
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147 if currentwf is not None:
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148 stdout.write("}\n")
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149 if wf in subworkflows:
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150 if wf not in dotname:
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151 dotname[wf] = "cluster_" + lastpart(wf)
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152 stdout.write(
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153 'subgraph "{}" {{ label="{}"\n'.format(dotname[wf], lastpart(wf))
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154 )
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155 currentwf = wf
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156 clusternode[wf] = step
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157 else:
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158 currentwf = None
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159
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160 if str(runtype) != "https://w3id.org/cwl/cwl#Workflow":
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161 stdout.write(
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162 '"%s" [label="%s"]\n'
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163 % (dotname[step], urllib.parse.urldefrag(str(step))[1])
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164 )
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165
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166 if currentwf is not None:
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167 stdout.write("}\n")
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168
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169 qres = g.query(
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170 """SELECT DISTINCT ?src ?sink ?srcrun ?sinkrun
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171 WHERE {
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172 ?wf1 Workflow:steps ?src .
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173 ?wf2 Workflow:steps ?sink .
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174 ?src cwl:out ?out .
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175 ?inp cwl:source ?out .
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176 ?sink cwl:in ?inp .
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177 ?src cwl:run ?srcrun .
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178 ?sink cwl:run ?sinkrun .
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179 }"""
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180 )
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181
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182 for src, sink, srcrun, sinkrun in qres:
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183 attr = ""
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184 if srcrun in clusternode:
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185 attr += 'ltail="%s"' % dotname[srcrun]
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186 src = clusternode[srcrun]
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187 if sinkrun in clusternode:
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188 attr += ' lhead="%s"' % dotname[sinkrun]
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189 sink = clusternode[sinkrun]
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190 stdout.write('"{}" -> "{}" [{}]\n'.format(dotname[src], dotname[sink], attr))
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191
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192
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193 def printdot(
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194 wf: Process,
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195 ctx: ContextType,
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196 stdout: Union[TextIO, StreamWriter],
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197 ) -> None:
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198 cwl_viewer = CWLViewer(printrdf(wf, ctx, "n3")) # type: CWLViewer
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199 stdout.write(cwl_viewer.dot())