Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.util.simplegraph

"""
Fencepost-simple graph structure implementation.
"""
# Currently (2013.7.12) only used in easing the parsing of graph datatype data.

from collections import OrderedDict


[docs]class SimpleGraphNode: """ Node representation. """
[docs] def __init__(self, index, **data): """ :param index: index of this node in some parent list :type index: int :param data: any extra data that needs to be saved :type data: (variadic dictionary) """ # a bit application specific (could be 'id') self.index = index self.data = data
[docs]class SimpleGraphEdge: """ Edge representation. """
[docs] def __init__(self, source_index, target_index, **data): """ :param source_index: index of the edge's source node in some parent list :type source_index: int :param target_index: index of the edge's target node in some parent list :type target_index: int :param data: any extra data that needs to be saved :type data: (variadic dictionary) """ self.source_index = source_index self.target_index = target_index self.data = data
[docs]class SimpleGraph: """ Each node is unique (by id) and stores its own index in the node list/odict. Each edge is represented as two indeces into the node list/odict. Both nodes and edges allow storing extra information if needed. Allows: multiple edges between two nodes self referential edges (an edge from a node to itself) These graphs are not specifically directed but since source and targets on the edges are listed - it could easily be used that way. """
[docs] def __init__(self, nodes=None, edges=None): # use an odict so that edge indeces actually match the final node list indeces self.nodes = nodes or OrderedDict() self.edges = edges or []
[docs] def add_node(self, node_id, **data): """ Adds a new node only if it doesn't already exist. :param node_id: some unique identifier :type node_id: (hashable) :param data: any extra data that needs to be saved :type data: (variadic dictionary) :returns: the new node """ if node_id in self.nodes: return self.nodes[node_id] node_index = len(self.nodes) new_node = SimpleGraphNode(node_index, **data) self.nodes[node_id] = new_node return new_node
[docs] def add_edge(self, source_id, target_id, **data): """ Adds a new node only if it doesn't already exist. :param source_id: the id of the source node :type source_id: (hashable) :param target_id: the id of the target node :type target_id: (hashable) :param data: any extra data that needs to be saved for the edge :type data: (variadic dictionary) :returns: the new node ..note: that, although this will create new nodes if necessary, there's no way to pass `data` to them - so if you need to assoc. more data with the nodes, use `add_node` first. """ # adds target_id to source_id's edge list # adding source_id and/or target_id to nodes if not there already if source_id not in self.nodes: self.add_node(source_id) if target_id not in self.nodes: self.add_node(target_id) new_edge = SimpleGraphEdge(self.nodes[source_id].index, self.nodes[target_id].index, **data) self.edges.append(new_edge) return new_edge
[docs] def gen_node_dicts(self): """ Returns a generator that yields node dictionaries in the form: { 'id': <the nodes unique id>, 'data': <any additional node data> } """ for node_id, node in self.nodes.items(): yield {'id': node_id, 'data': node.data}
[docs] def gen_edge_dicts(self): """ Returns a generator that yields node dictionaries in the form:: { 'source': <the index of the source node in the graph's node list>, 'target': <the index of the target node in the graph's node list>, 'data' : <any additional edge data> } """ for edge in self.edges: yield {'source': edge.source_index, 'target': edge.target_index, 'data': edge.data}
[docs] def as_dict(self): """ Returns a dictionary of the form:: { 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> } """ return {'nodes': list(self.gen_node_dicts()), 'edges': list(self.gen_edge_dicts())}