GraphML Import

This is an example on how to import a graph from a string in GraphML format.

Start by importing the package.

import jgrapht
from jgrapht.io.importers import parse_graphml

Let us create a directed graph

g = jgrapht.create_graph(directed=True)

Let us assume that we are reading the following graph

graphml_input = r"""<?xml version="1.0" encoding="UTF-8"?><graphml xmlns="http://graphml.graphdrawing.org/xmlns"
             xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
                                 http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"
                                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <key id="edge_weight_key" for="edge" attr.name="weight" attr.type="double">
        <default>1.0</default>
    </key>
    <key id="key0" for="edge" attr.name="cost" attr.type="double"/>
    <key id="key1" for="node" attr.name="name" attr.type="string"/>
    <graph edgedefault="directed">
        <node id="0">
            <data key="key1">node 0</data>
        </node>
        <node id="1">
            <data key="key1">node 1</data>
        </node>
        <node id="2"/>
        <node id="3"/>
        <node id="4"/>
        <edge source="0" target="1">
            <data key="edge_weight_key">100.0</data>
            <data key="key0">20.3</data>
        </edge>
        <edge source="0" target="2"/>
        <edge source="0" target="3"/>
        <edge source="0" target="4"/>
        <edge source="1" target="2"/>
        <edge source="2" target="3"/>
        <edge source="3" target="4">
            <data key="edge_weight_key">33.3</data>
            <data key="key0">48.5</data>
        </edge>
    </graph>
</graphml>"""

We would also like to capture the vertex and edge attributes. The importer will inform us everytime that it reads a vertex or edge attribute. The edge attribute “weight” is considered special and is being read automatically if the provided graph object is weighted. Thus, we define the following callback functions.

v_attrs = {}
e_attrs = {}

def vertex_attribute_cb(vertex, attribute_name, attribute_value):
    if vertex not in v_attrs:
        v_attrs[vertex] = {}
    v_attrs[vertex][attribute_name] = attribute_value


def edge_attribute_cb(edge, attribute_name, attribute_value):
    if edge not in e_attrs:
        e_attrs[edge] = {}
    e_attrs[edge][attribute_name] = attribute_value

The importer needs a way to translate the vertex identifiers from the input to integer values. By default, if we do not provide a function, it will auto assign new integer values. If you want to control the actual vertices created, you can also provide a import_id_cb function like the following. Here we simply convert from a string to integer, since the actual input contains integer vertices.

def import_id_cb(vertex):
    return int(vertex)

Now we call the importer.

parse_graphml(
    g,
    graphml_input,
    import_id_cb=import_id_cb,
    vertex_attribute_cb=vertex_attribute_cb,
    edge_attribute_cb=edge_attribute_cb,
)

We print the graph for debugging purposes.

print(g)

Out:

({0, 1, 2, 3, 4}, {0=(0,1), 1=(0,2), 2=(0,3), 3=(0,4), 4=(1,2), 5=(2,3), 6=(3,4)})

The vertex attributes dictionary should contain all vertex attributes. The attribute with key ID contains the original identifier from the file. In our case it will be the same with the id.

print(v_attrs)

Out:

{0: {'ID': '0', 'id': '0', 'name': 'node 0'}, 1: {'ID': '1', 'id': '1', 'name': 'node 1'}, 2: {'ID': '2', 'id': '2'}, 3: {'ID': '3', 'id': '3'}, 4: {'ID': '4', 'id': '4'}}

The edge attributes dictionary should contain all edge attributes.

print(e_attrs)

Out:

{0: {'source': '0', 'target': '1', 'cost': '20.3', 'weight': '100.0'}, 1: {'source': '0', 'target': '2'}, 2: {'source': '0', 'target': '3'}, 3: {'source': '0', 'target': '4'}, 4: {'source': '1', 'target': '2'}, 5: {'source': '2', 'target': '3'}, 6: {'source': '3', 'target': '4', 'cost': '48.5', 'weight': '33.3'}}