Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/subgraph.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 import urllib
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2 from collections import namedtuple
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3 from typing import (
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4 Dict,
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5 List,
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6 MutableMapping,
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7 MutableSequence,
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8 Optional,
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9 Set,
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10 Tuple,
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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
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15
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16 from .utils import CWLObjectType, aslist
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17 from .workflow import Workflow, WorkflowStep
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18
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19 Node = namedtuple("Node", ("up", "down", "type"))
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20 UP = "up"
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21 DOWN = "down"
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22 INPUT = "input"
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23 OUTPUT = "output"
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24 STEP = "step"
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25
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26
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27 def subgraph_visit(
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28 current: str,
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29 nodes: MutableMapping[str, Node],
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30 visited: Set[str],
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31 direction: str,
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32 ) -> None:
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33
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34 if current in visited:
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35 return
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36 visited.add(current)
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37
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38 if direction == DOWN:
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39 d = nodes[current].down
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40 if direction == UP:
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41 d = nodes[current].up
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42 for c in d:
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43 subgraph_visit(c, nodes, visited, direction)
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44
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45
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46 def declare_node(nodes: Dict[str, Node], nodeid: str, tp: Optional[str]) -> Node:
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47 if nodeid in nodes:
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48 n = nodes[nodeid]
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49 if n.type is None:
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50 nodes[nodeid] = Node(n.up, n.down, tp)
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51 else:
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52 nodes[nodeid] = Node([], [], tp)
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53 return nodes[nodeid]
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54
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55
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56 def find_step(steps: List[WorkflowStep], stepid: str) -> Optional[CWLObjectType]:
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57 for st in steps:
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58 if st.tool["id"] == stepid:
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59 return st.tool
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60 return None
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61
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62
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63 def get_subgraph(roots: MutableSequence[str], tool: Workflow) -> CommentedMap:
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64 if tool.tool["class"] != "Workflow":
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65 raise Exception("Can only extract subgraph from workflow")
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66
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67 nodes: Dict[str, Node] = {}
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68
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69 for inp in tool.tool["inputs"]:
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70 declare_node(nodes, inp["id"], INPUT)
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71
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72 for out in tool.tool["outputs"]:
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73 declare_node(nodes, out["id"], OUTPUT)
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74 for i in aslist(out.get("outputSource", [])):
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75 # source is upstream from output (dependency)
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76 nodes[out["id"]].up.append(i)
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77 # output is downstream from source
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78 declare_node(nodes, i, None)
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79 nodes[i].down.append(out["id"])
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80
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81 for st in tool.tool["steps"]:
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82 step = declare_node(nodes, st["id"], STEP)
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83 for i in st["in"]:
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84 if "source" not in i:
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85 continue
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86 for src in aslist(i["source"]):
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87 # source is upstream from step (dependency)
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88 step.up.append(src)
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89 # step is downstream from source
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90 declare_node(nodes, src, None)
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91 nodes[src].down.append(st["id"])
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92 for out in st["out"]:
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93 # output is downstream from step
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94 step.down.append(out)
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95 # step is upstream from output
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96 declare_node(nodes, out, None)
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97 nodes[out].up.append(st["id"])
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98
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99 # Find all the downstream nodes from the starting points
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100 visited_down: Set[str] = set()
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101 for r in roots:
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102 if nodes[r].type == OUTPUT:
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103 subgraph_visit(r, nodes, visited_down, UP)
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104 else:
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105 subgraph_visit(r, nodes, visited_down, DOWN)
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106
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107 # Now make sure all the nodes are connected to upstream inputs
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108 visited: Set[str] = set()
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109 rewire: Dict[str, Tuple[str, CWLObjectType]] = {}
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110 for v in visited_down:
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111 visited.add(v)
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112 if nodes[v].type in (STEP, OUTPUT):
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113 for u in nodes[v].up:
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114 if u in visited_down:
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115 continue
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116 if nodes[u].type == INPUT:
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117 visited.add(u)
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118 else:
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119 # rewire
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120 df = urllib.parse.urldefrag(u)
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121 rn = str(df[0] + "#" + df[1].replace("/", "_"))
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122 if nodes[v].type == STEP:
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123 wfstep = find_step(tool.steps, v)
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124 if wfstep is not None:
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125 for inp in cast(
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126 MutableSequence[CWLObjectType], wfstep["inputs"]
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127 ):
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128 if "source" in inp and u in cast(
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129 CWLObjectType, inp["source"]
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130 ):
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131 rewire[u] = (rn, cast(CWLObjectType, inp["type"]))
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132 break
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133 else:
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134 raise Exception("Could not find step %s" % v)
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135
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136 extracted = CommentedMap()
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137 for f in tool.tool:
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138 if f in ("steps", "inputs", "outputs"):
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139 extracted[f] = []
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140 for i in tool.tool[f]:
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141 if i["id"] in visited:
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142 if f == "steps":
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143 for inport in i["in"]:
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144 if "source" not in inport:
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145 continue
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146 if isinstance(inport["source"], MutableSequence):
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147 inport["source"] = [
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148 rewire[s][0]
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149 for s in inport["source"]
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150 if s in rewire
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151 ]
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152 elif inport["source"] in rewire:
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153 inport["source"] = rewire[inport["source"]][0]
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154 extracted[f].append(i)
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155 else:
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156 extracted[f] = tool.tool[f]
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157
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158 for rv in rewire.values():
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159 extracted["inputs"].append({"id": rv[0], "type": rv[1]})
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160
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161 return extracted
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162
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163
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164 def get_step(tool: Workflow, step_id: str) -> CommentedMap:
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165
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166 extracted = CommentedMap()
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167
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168 step = find_step(tool.steps, step_id)
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169 if step is None:
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170 raise Exception(f"Step {step_id} was not found")
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171
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172 extracted["steps"] = [step]
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173 extracted["inputs"] = []
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174 extracted["outputs"] = []
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175
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176 for inport in cast(List[CWLObjectType], step["in"]):
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177 name = cast(str, inport["id"]).split("#")[-1].split("/")[-1]
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178 extracted["inputs"].append({"id": name, "type": "Any"})
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179 inport["source"] = name
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180 if "linkMerge" in inport:
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181 del inport["linkMerge"]
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182
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183 for outport in cast(List[str], step["out"]):
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184 name = outport.split("#")[-1].split("/")[-1]
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185 extracted["outputs"].append(
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186 {"id": name, "type": "Any", "outputSource": f"{step_id}/{name}"}
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187 )
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188
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189 for f in tool.tool:
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190 if f not in ("steps", "inputs", "outputs"):
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191 extracted[f] = tool.tool[f]
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192
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193 return extracted