Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/util/simplegraph.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 """
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2 Fencepost-simple graph structure implementation.
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3 """
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4 # Currently (2013.7.12) only used in easing the parsing of graph datatype data.
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5
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6 from collections import OrderedDict
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7
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8
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9 class SimpleGraphNode(object):
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10 """
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11 Node representation.
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12 """
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13
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14 def __init__(self, index, **data):
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15 """
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16 :param index: index of this node in some parent list
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17 :type index: int
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18 :param data: any extra data that needs to be saved
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19 :type data: (variadic dictionary)
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20 """
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21 # a bit application specific (could be 'id')
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22 self.index = index
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23 self.data = data
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24
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25
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26 class SimpleGraphEdge(object):
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27 """
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28 Edge representation.
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29 """
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30
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31 def __init__(self, source_index, target_index, **data):
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32 """
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33 :param source_index: index of the edge's source node in some parent list
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34 :type source_index: int
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35 :param target_index: index of the edge's target node in some parent list
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36 :type target_index: int
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37 :param data: any extra data that needs to be saved
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38 :type data: (variadic dictionary)
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39 """
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40 self.source_index = source_index
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41 self.target_index = target_index
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42 self.data = data
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43
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44
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45 class SimpleGraph(object):
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46 """
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47 Each node is unique (by id) and stores its own index in the node list/odict.
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48 Each edge is represented as two indeces into the node list/odict.
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49 Both nodes and edges allow storing extra information if needed.
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50
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51 Allows:
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52 multiple edges between two nodes
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53 self referential edges (an edge from a node to itself)
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54
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55 These graphs are not specifically directed but since source and targets on the
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56 edges are listed - it could easily be used that way.
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57 """
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58
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59 def __init__(self, nodes=None, edges=None):
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60 # use an odict so that edge indeces actually match the final node list indeces
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61 self.nodes = nodes or OrderedDict()
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62 self.edges = edges or []
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63
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64 def add_node(self, node_id, **data):
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65 """
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66 Adds a new node only if it doesn't already exist.
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67 :param node_id: some unique identifier
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68 :type node_id: (hashable)
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69 :param data: any extra data that needs to be saved
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70 :type data: (variadic dictionary)
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71 :returns: the new node
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72 """
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73 if node_id in self.nodes:
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74 return self.nodes[node_id]
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75 node_index = len(self.nodes)
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76 new_node = SimpleGraphNode(node_index, **data)
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77 self.nodes[node_id] = new_node
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78 return new_node
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79
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80 def add_edge(self, source_id, target_id, **data):
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81 """
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82 Adds a new node only if it doesn't already exist.
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83 :param source_id: the id of the source node
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84 :type source_id: (hashable)
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85 :param target_id: the id of the target node
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86 :type target_id: (hashable)
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87 :param data: any extra data that needs to be saved for the edge
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88 :type data: (variadic dictionary)
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89 :returns: the new node
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90
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91 ..note: that, although this will create new nodes if necessary, there's
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92 no way to pass `data` to them - so if you need to assoc. more data with
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93 the nodes, use `add_node` first.
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94 """
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95 # adds target_id to source_id's edge list
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96 # adding source_id and/or target_id to nodes if not there already
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97 if source_id not in self.nodes:
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98 self.add_node(source_id)
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99 if target_id not in self.nodes:
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100 self.add_node(target_id)
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101 new_edge = SimpleGraphEdge(self.nodes[source_id].index, self.nodes[target_id].index, **data)
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102 self.edges.append(new_edge)
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103 return new_edge
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104
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105 def gen_node_dicts(self):
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106 """
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107 Returns a generator that yields node dictionaries in the form:
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108 { 'id': <the nodes unique id>, 'data': <any additional node data> }
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109 """
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110 for node_id, node in self.nodes.items():
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111 yield {'id': node_id, 'data': node.data}
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112
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113 def gen_edge_dicts(self):
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114 """
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115 Returns a generator that yields node dictionaries in the form::
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116
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117 {
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118 'source': <the index of the source node in the graph's node list>,
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119 'target': <the index of the target node in the graph's node list>,
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120 'data' : <any additional edge data>
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121 }
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122 """
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123 for edge in self.edges:
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124 yield {'source': edge.source_index, 'target': edge.target_index, 'data': edge.data}
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125
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126 def as_dict(self):
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127 """
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128 Returns a dictionary of the form::
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129
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130 { 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> }
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131 """
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132 return {'nodes': list(self.gen_node_dicts()), 'edges': list(self.gen_edge_dicts())}