Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/subgraph.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import copy
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2 from .utils import aslist, json_dumps
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3 from collections import namedtuple
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4 from typing import (Dict, MutableMapping, MutableSequence, Set, Any, Text, Optional, Tuple)
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5 from .process import shortname
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6 from six import itervalues
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7 from six.moves import urllib
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8 from .workflow import Workflow
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9 from ruamel.yaml.comments import CommentedMap
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10
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11 Node = namedtuple('Node', ('up', 'down', 'type'))
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12 UP = "up"
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13 DOWN = "down"
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14 INPUT = "input"
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15 OUTPUT = "output"
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16 STEP = "step"
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17
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18 def subgraph_visit(current, # type: Text
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19 nodes, # type: MutableMapping[Text, Node]
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20 visited, # type: Set[Text]
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21 direction # type: Text
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22 ): # type: (...) -> None
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23
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24 if current in visited:
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25 return
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26 visited.add(current)
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27
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28 if direction == DOWN:
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29 d = nodes[current].down
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30 if direction == UP:
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31 d = nodes[current].up
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32 for c in d:
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33 subgraph_visit(c, nodes, visited, direction)
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34
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35 def declare_node(nodes, nodeid, tp):
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36 # type: (Dict[Text, Node], Text, Optional[Text]) -> Node
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37 if nodeid in nodes:
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38 n = nodes[nodeid]
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39 if n.type is None:
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40 nodes[nodeid] = Node(n.up, n.down, tp)
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41 else:
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42 nodes[nodeid] = Node([], [], tp)
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43 return nodes[nodeid]
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44
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45 def get_subgraph(roots, # type: MutableSequence[Text]
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46 tool # type: Workflow
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47 ): # type: (...) -> Optional[CommentedMap]
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48 if tool.tool["class"] != "Workflow":
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49 raise Exception("Can only extract subgraph from workflow")
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50
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51 nodes = {} # type: Dict[Text, Node]
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52
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53 for inp in tool.tool["inputs"]:
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54 declare_node(nodes, inp["id"], INPUT)
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55
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56 for out in tool.tool["outputs"]:
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57 declare_node(nodes, out["id"], OUTPUT)
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58 for i in aslist(out.get("outputSource", [])):
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59 # source is upstream from output (dependency)
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60 nodes[out["id"]].up.append(i)
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61 # output is downstream from source
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62 declare_node(nodes, i, None)
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63 nodes[i].down.append(out["id"])
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64
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65 for st in tool.tool["steps"]:
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66 step = declare_node(nodes, st["id"], STEP)
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67 for i in st["in"]:
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68 if "source" not in i:
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69 continue
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70 for src in aslist(i["source"]):
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71 # source is upstream from step (dependency)
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72 step.up.append(src)
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73 # step is downstream from source
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74 declare_node(nodes, src, None)
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75 nodes[src].down.append(st["id"])
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76 for out in st["out"]:
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77 # output is downstream from step
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78 step.down.append(out)
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79 # step is upstream from output
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80 declare_node(nodes, out, None)
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81 nodes[out].up.append(st["id"])
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82
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83
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84 # Find all the downstream nodes from the starting points
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85 visited_down = set() # type: Set[Text]
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86 for r in roots:
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87 if nodes[r].type == OUTPUT:
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88 subgraph_visit(r, nodes, visited_down, UP)
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89 else:
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90 subgraph_visit(r, nodes, visited_down, DOWN)
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91
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92 def find_step(stepid): # type: (Text) -> Optional[MutableMapping[Text, Any]]
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93 for st in tool.steps:
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94 if st.tool["id"] == stepid:
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95 return st.tool
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96 return None
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97
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98 # Now make sure all the nodes are connected to upstream inputs
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99 visited = set() # type: Set[Text]
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100 rewire = {} # type: Dict[Text, Tuple[Text, Text]]
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101 for v in visited_down:
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102 visited.add(v)
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103 if nodes[v].type in (STEP, OUTPUT):
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104 for u in nodes[v].up:
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105 if u in visited_down:
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106 continue
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107 if nodes[u].type == INPUT:
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108 visited.add(u)
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109 else:
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110 # rewire
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111 df = urllib.parse.urldefrag(u)
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112 rn = df[0] + "#" + df[1].replace("/", "_")
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113 if nodes[v].type == STEP:
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114 wfstep = find_step(v)
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115 if wfstep is not None:
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116 for inp in wfstep["inputs"]:
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117 if u in inp["source"]:
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118 rewire[u] = (rn, inp["type"])
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119 break
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120 else:
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121 raise Exception("Could not find step %s" % v)
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122
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123
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124 extracted = CommentedMap()
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125 for f in tool.tool:
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126 if f in ("steps", "inputs", "outputs"):
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127 extracted[f] = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
128 for i in tool.tool[f]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
129 if i["id"] in visited:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
130 if f == "steps":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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131 for inport in i["in"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
132 if "source" not in inport:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
133 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
134 if isinstance(inport["source"], MutableSequence):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
135 inport["source"] = [rewire[s][0] for s in inport["source"] if s in rewire]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
136 elif inport["source"] in rewire:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
137 inport["source"] = rewire[inport["source"]][0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
138 extracted[f].append(i)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
139 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
140 extracted[f] = tool.tool[f]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
141
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
142 for rv in itervalues(rewire):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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143 extracted["inputs"].append({
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
144 "id": rv[0],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
145 "type": rv[1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
146 })
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
147
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
148 return extracted