diff env/lib/python3.9/site-packages/galaxy/util/simplegraph.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/util/simplegraph.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,130 @@
+"""
+Fencepost-simple graph structure implementation.
+"""
+# Currently (2013.7.12) only used in easing the parsing of graph datatype data.
+
+
+class SimpleGraphNode:
+    """
+    Node representation.
+    """
+
+    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
+
+
+class SimpleGraphEdge:
+    """
+    Edge representation.
+    """
+
+    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
+
+
+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.
+    """
+
+    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 {}
+        self.edges = edges or []
+
+    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
+
+    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
+
+    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}
+
+    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}
+
+    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())}