Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/cwlviewer.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Visualize a CWL workflow.""" |
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2 import os |
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3 from urllib.parse import urlparse |
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4 |
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5 import pydot # type: ignore |
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6 import rdflib |
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7 |
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8 |
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9 class CWLViewer: |
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10 """Produce similar images with the https://github.com/common-workflow-language/cwlviewer.""" |
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11 |
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12 _queries_dir = os.path.join( |
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13 os.path.abspath(os.path.dirname(__file__)), "rdfqueries" |
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14 ) |
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15 _get_inner_edges_query_path = os.path.join(_queries_dir, "get_inner_edges.sparql") |
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16 _get_input_edges_query_path = os.path.join(_queries_dir, "get_input_edges.sparql") |
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17 _get_output_edges_query_path = os.path.join(_queries_dir, "get_output_edges.sparql") |
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18 _get_root_query_path = os.path.join(_queries_dir, "get_root.sparql") |
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19 |
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20 def __init__( |
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21 self, rdf_description # type: str |
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22 ): |
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23 """Create a viewer object based on the rdf description of the workflow.""" |
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24 self._dot_graph = CWLViewer._init_dot_graph() # type: pydot.Graph |
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25 self._rdf_graph = self._load_cwl_graph( |
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26 rdf_description |
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27 ) # type: rdflib.graph.Graph |
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28 self._root_graph_uri = self._get_root_graph_uri() # type: str |
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29 self._set_inner_edges() |
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30 self._set_input_edges() |
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31 self._set_output_edges() |
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32 |
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33 def _load_cwl_graph( |
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34 self, rdf_description # type: str |
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35 ) -> rdflib.graph.Graph: |
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36 rdf_graph = rdflib.Graph() |
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37 rdf_graph.parse(data=rdf_description, format="n3") |
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38 return rdf_graph |
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39 |
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40 def _set_inner_edges(self) -> None: |
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41 with open(self._get_inner_edges_query_path) as f: |
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42 get_inner_edges_query = f.read() |
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43 inner_edges = self._rdf_graph.query( |
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44 get_inner_edges_query, initBindings={"root_graph": self._root_graph_uri} |
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45 ) |
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46 for inner_edge_row in inner_edges: |
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47 source_label = ( |
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48 inner_edge_row["source_label"] |
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49 if inner_edge_row["source_label"] is not None |
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50 else urlparse(inner_edge_row["source_step"]).fragment |
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51 ) |
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52 n = pydot.Node( |
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53 "", |
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54 fillcolor="lightgoldenrodyellow", |
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55 style="filled", |
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56 label=source_label, |
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57 shape="record", |
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58 ) |
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59 n.set_name(str(inner_edge_row["source_step"])) |
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60 self._dot_graph.add_node(n) |
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61 target_label = ( |
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62 inner_edge_row["target_label"] |
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63 if inner_edge_row["target_label"] is not None |
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64 else urlparse(inner_edge_row["target_step"]).fragment |
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65 ) |
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66 n = pydot.Node( |
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67 "", |
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68 fillcolor="lightgoldenrodyellow", |
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69 style="filled", |
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70 label=target_label, |
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71 shape="record", |
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72 ) |
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73 n.set_name(str(inner_edge_row["target_step"])) |
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74 self._dot_graph.add_node(n) |
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75 self._dot_graph.add_edge( |
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76 pydot.Edge( |
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77 str(inner_edge_row["source_step"]), |
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78 str(inner_edge_row["target_step"]), |
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79 ) |
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80 ) |
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81 |
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82 def _set_input_edges(self) -> None: |
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83 with open(self._get_input_edges_query_path) as f: |
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84 get_input_edges_query = f.read() |
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85 inputs_subgraph = pydot.Subgraph(graph_name="cluster_inputs") |
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86 self._dot_graph.add_subgraph(inputs_subgraph) |
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87 inputs_subgraph.set_rank("same") |
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88 inputs_subgraph.create_attribute_methods(["style"]) |
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89 inputs_subgraph.set_style("dashed") |
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90 inputs_subgraph.set_label("Workflow Inputs") |
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91 |
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92 input_edges = self._rdf_graph.query( |
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93 get_input_edges_query, initBindings={"root_graph": self._root_graph_uri} |
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94 ) |
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95 for input_row in input_edges: |
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96 n = pydot.Node( |
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97 "", |
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98 fillcolor="#94DDF4", |
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99 style="filled", |
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100 label=urlparse(input_row["input"]).fragment, |
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101 shape="record", |
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102 ) |
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103 n.set_name(str(input_row["input"])) |
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104 inputs_subgraph.add_node(n) |
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105 self._dot_graph.add_edge( |
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106 pydot.Edge(str(input_row["input"]), str(input_row["step"])) |
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107 ) |
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108 |
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109 def _set_output_edges(self) -> None: |
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110 with open(self._get_output_edges_query_path) as f: |
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111 get_output_edges = f.read() |
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112 outputs_graph = pydot.Subgraph(graph_name="cluster_outputs") |
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113 self._dot_graph.add_subgraph(outputs_graph) |
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114 outputs_graph.set_rank("same") |
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115 outputs_graph.create_attribute_methods(["style"]) |
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116 outputs_graph.set_style("dashed") |
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117 outputs_graph.set_label("Workflow Outputs") |
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118 outputs_graph.set_labelloc("b") |
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119 output_edges = self._rdf_graph.query( |
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120 get_output_edges, initBindings={"root_graph": self._root_graph_uri} |
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121 ) |
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122 for output_edge_row in output_edges: |
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123 n = pydot.Node( |
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124 "", |
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125 fillcolor="#94DDF4", |
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126 style="filled", |
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127 label=urlparse(output_edge_row["output"]).fragment, |
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128 shape="record", |
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129 ) |
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130 n.set_name(str(output_edge_row["output"])) |
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131 outputs_graph.add_node(n) |
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132 self._dot_graph.add_edge( |
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133 pydot.Edge(output_edge_row["step"], output_edge_row["output"]) |
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134 ) |
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135 |
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136 def _get_root_graph_uri(self) -> rdflib.URIRef: |
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137 with open(self._get_root_query_path) as f: |
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138 get_root_query = f.read() |
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139 root = list( |
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140 self._rdf_graph.query( |
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141 get_root_query, |
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142 ) |
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143 ) |
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144 if len(root) != 1: |
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145 raise RuntimeError( |
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146 "Cannot identify root workflow! Notice that only Workflows can be visualized" |
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147 ) |
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148 |
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149 workflow = root[0]["workflow"] # type: rdflib.URIRef |
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150 return workflow |
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151 |
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152 @classmethod |
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153 def _init_dot_graph(cls) -> pydot.Graph: |
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154 graph = pydot.Graph(graph_type="digraph", simplify=False) |
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155 graph.set_bgcolor("#eeeeee") |
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156 graph.set_clusterrank("local") |
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157 graph.set_labelloc("bottom") |
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158 graph.set_labelloc("bottom") |
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159 graph.set_labeljust("right") |
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160 |
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161 return graph |
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162 |
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163 def get_dot_graph(self) -> pydot.Graph: |
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164 """Get the dot graph object.""" |
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165 return self._dot_graph |
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166 |
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167 def dot(self) -> str: |
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168 """Get the graph as graphviz.""" |
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169 return str(self._dot_graph.to_string()) |