def read_gml(gml, graph=None):
"""
Read graph in GML format
:param gml: GML graph data.
:type gml: File, string, stream or URL
:param graph: Graph object to import GML data in
:type graph: :graphit:Graph
:return: Graph object
:rtype: :graphit:Graph
"""
# User defined or default Graph object
if graph is None:
graph = Graph()
elif not isinstance(graph, Graph):
raise GraphitException('Unsupported graph type {0}'.format(type(graph)))
# Parse GML into nested structure of Record class instances
gml_stream = StreamReader(open_anything(gml))
records = Record(gml_stream, name='root')
gml_graphs = [g for g in records if g.name == 'graph']
if len(gml_graphs) > 1:
logging.warning("GML file contains {0} 'graph' objects. Only parse first".format(len(gml_graphs)))
gml_graph_record = gml_graphs[0]
# GML node and edge labels are unique, turn off auto_nid
graph.data['auto_nid'] = False
# Set graph meta-data and attributes
graph_attr = gml_graph_record.to_dict({})
graph.directed = True
if 'directed' in graph_attr:
directed = graph_attr.pop('directed')
graph.directed = True if directed == 1 else False
graph.data['directed'] = graph.directed
graph.data.update(graph_attr)
# Build graph from records
build_nodes(graph, gml_graph_record)
build_edges(graph, gml_graph_record)
return graph
def read_tgf(tgf, graph=None, key_tag=None):
"""
Read graph in Trivial Graph Format
TGF format dictates that nodes to be listed in the file first with each
node on a new line. A '#' character signals the end of the node list and
the start of the edge list.
Node and edge ID's can be integers, float or strings. They are parsed
automatically to their most likely format.
Simple node and edge labels are supported in TGF as all characters that
follow the node or edge ID's. They are parsed and stored in the Graph
node and edge data stores using the graphs default or custom 'key_tag'.
TGF data is imported into a default Graph object if no custom Graph
instance is provided. The graph behaviour and the data import process is
influenced and can be controlled using a (custom) Graph class.
.. note:: TGF format always defines edges in a directed fashion.
This is enforced even for custom graphs.
:param tgf: TGF graph data.
:type tgf: File, string, stream or URL
:param graph: Graph object to import TGF data in
:type graph: :graphit:Graph
:param key_tag: Data key to use for parsed node/edge labels.
:type key_tag: :py:str
:return: Graph object
:rtype: :graphit:Graph
"""
tgf_file = open_anything(tgf)
if not isinstance(graph, Graph):
graph = Graph()
# Define node/edge data labels
if key_tag:
graph.key_tag = key_tag
# TGF defines edges in a directed fashion. Enforce but restore later
default_directionality = graph.directed
graph.directed = True
# TGF node and edge labels are unique, turn off auto_nid
graph.auto_nid = False
# Start parsing. First extract nodes
nodes = True
node_dict = {}
for line in tgf_file.readlines():
line = line.strip()
if len(line):
# Reading '#' character means switching from node
# definition to edges
if line.startswith('#'):
nodes = False
continue
# Coarse string to types
line = [coarse_type(n) for n in line.split()]
# Parse nodes
if nodes:
attr = {}
# Has node data
if len(line) > 1:
attr = {graph.key_tag: ' '.join(line[1:])}
nid = graph.add_node(line[0], **attr)
node_dict[line[0]] = nid
# Parse edges
else:
e1 = node_dict[line[0]]
e2 = node_dict[line[1]]
attr = {}
# Has edge data
if len(line) > 2:
attr = {graph.key_tag: ' '.join(line[2:])}
graph.add_edge(e1, e2, **attr)
tgf_file.close()
# Restore directionality
graph.directed = default_directionality
return graph
def read_lgf(lgf, graph=None):
"""
Read graph in LEMON Graph Format (LGF)
:param lgf: LGF graph data.
:type lgf: File, string, stream or URL
:param graph: Graph object to import LGF data in
:type graph: :graphit:Graph
:return: Graph object
:rtype: :graphit:Graph
"""
lgf_file = open_anything(lgf)
# User defined or default Graph object
if graph is None:
graph = Graph()
elif not isinstance(graph, Graph):
raise GraphitException('Unsupported graph type {0}'.format(
type(graph)))
# LGF node and edge labels are unique, turn off auto_nid
graph.data['auto_nid'] = False
parser = None
header = None
did_parse_nodes = False
is_directed = False
for line in lgf_file.readlines():
line = line.strip()
# Skip empty lines and comment lines
if not len(line) or line.startswith('#'):
parser = None
continue
# Define parser
if line.startswith('@') or parser is None:
if 'nodes' in line:
parser = parse_nodes
did_parse_nodes = True
elif line.startswith('@edges'):
parser = parse_edges
elif line.startswith('@arcs'):
parser = parse_arcs
is_directed = True
elif line.startswith('@attributes'):
logging.warning(
'Not importing LGF @attributes. Graph attributes not supported by graphit'
)
header = None
continue
# Immediately after parser definition, parse table column headers
if header is None:
header = split_line(line)
continue
parser(line, header, graph, did_parse_nodes=did_parse_nodes)
# Set graph to 'directed' if arcs where parsed
if is_directed:
graph.directed = True
return graph
def read_p2g(p2g_file, graph=None):
"""
Read graph in P2G format
:param p2g_file: P2G data to parse
:type p2g_file: File, string, stream or URL
:param graph: Graph object to import to or Graph by default
:type graph: :graphit:Graph
:return: Graph instance
:rtype: :graphit:Graph
"""
p2g_file = open_anything(p2g_file)
if graph is None:
graph = Graph()
elif not isinstance(graph, Graph):
raise GraphitException('Unsupported graph type {0}'.format(
type(graph)))
# P2G graphs are directed
graph.directed = True
graph_name = None
graph_layout = None
curr_node = None
nodes = {}
for i, line in enumerate(p2g_file.readlines()):
line = line.strip()
if line:
# Parse p2g graph name (first line)
sline = line.split()
if not graph_name:
graph_name = line
continue
# Parse number of nodes and edges (second line)
elif not graph_layout:
try:
graph_layout = map(int, sline)
except ValueError:
raise GraphitException(
'P2G import error: line {0} - {1}'.format(i, line))
continue
# Parse nodes and edges
if len(sline) == 1:
nodes[line] = []
curr_node = line
elif len(sline) == 2:
try:
nodes[curr_node] = map(int, sline)
except ValueError:
raise GraphitException(
'P2G import error: malformed edge on line {0} - {1}'.
format(i, line))
else:
raise GraphitException(
'P2G import error: line {0} - {1}'.format(i, line))
graph.data['name'] = graph_name
# Add nodes
mapped_nodes = graph.add_nodes(nodes.keys())
# Add edges
for i, nid in enumerate(nodes.keys()):
for e in nodes[nid]:
if e < len(mapped_nodes):
graph.add_edge(mapped_nodes[i], mapped_nodes[e])
else:
raise GraphitException(
'P2G import error: edge node index {0} not in graph'.
format(e))
if len(nodes) != graph_layout[0] or (len(graph.edges)) != graph_layout[1]:
logging.warning(
'P2G import warning: declared number of nodes and edges {0}-{1} does not match {2}-{3}'
.format(graph_layout[0], graph_layout[1], len(nodes),
len(graph.edges)))
return graph
def read_lgr(lgr, graph=None, edge_label='label'):
"""
Read graph in LEDA format
Nodes are added to the graph using a unique ID or with the node data
as label depending if the graph.data.auto_nid is True or False.
Edge data is added to the edge attributes using `edge_label` as key.
The data types for both nodes and edges is set according to the
specifications in the LEDA header as either string, int, float or bool.
:param lgr: LEDA graph data.
:type lgr: File, string, stream or URL
:param graph: Graph object to import LEDA data in
:type graph: :graphit:Graph
:param edge_label: edge data label name
:type edge_label: :py:str
:return: Graph object
:rtype: :graphit:Graph
:raises: TypeError if node/edge type conversion failed
GraphitException in case of malformed LEDA file
"""
# User defined or default Graph object
if graph is None:
graph = Graph()
elif not isinstance(graph, Graph):
raise GraphitException('Unsupported graph type {0}'.format(
type(graph)))
# Parse LEDA file
lgr_file = open_anything(lgr)
header = []
nodes = []
edges = []
container = header
for line in lgr_file.readlines():
line = line.strip()
if line:
if line.startswith('#header'):
container = header
continue
if line.startswith('#nodes'):
container = nodes
continue
if line.startswith('#edges'):
container = edges
continue
container.append(line)
# Parse LEDA header
if not header[0] == 'LEDA.GRAPH':
raise GraphitException('File is not a valid LEDA graph format')
# Node and edge data types and graph directionality
node_type = data_types.get(header[1])
edge_type = data_types.get(header[2])
graph.directed = int(header[3]) == -1
# Parse LEDA nodes
node_mapping = {}
for i, node in enumerate(nodes[1:], start=1):
data = node.strip('|{}|') or None
if node_type and data:
data = node_type(data)
nid = graph.add_node(data)
node_mapping[i] = nid
# Parse LEDA edges
for edge in edges[1:]:
try:
source, target, reversal, label = edge.split()
except ValueError:
raise GraphitException(
'Too few fields in LEDA edge {0}'.format(edge))
attr = {edge_label: label.strip('|{}|') or None}
if edge_type and attr[edge_label]:
attr[edge_label] = edge_type(attr[edge_label])
graph.add_edge(node_mapping[int(source)], node_mapping[int(target)],
**attr)
return graph
def read_gexf(gexf_file, graph=None):
"""
Read graphs in GEXF format
Uses the Python build-in etree cElementTree parser to parse the XML
document and convert the elements into nodes.
The XML element tag becomes the node key, XML text becomes the node
value and XML attributes are added to the node as additional attributes.
:param gexf_file: XML data to parse
:type gexf_file: File, string, stream or URL
:param graph: Graph object to import dictionary data in
:type graph: :graphit:Graph
:return: GraphAxis object
:rtype: :graphit:GraphAxis
"""
gexf_file = open_anything(gexf_file)
# User defined or default Graph object
if graph is None:
graph = Graph()
elif not isinstance(graph, Graph):
raise GraphitException('Unsupported graph type {0}'.format(
type(graph)))
# Try parsing the string using default Python cElementTree parser
try:
tree = et.fromstring(gexf_file.read())
except et.ParseError as error:
logging.error(
'Unable to parse GEXF file. cElementTree error: {0}'.format(error))
return
# Get XMLNS namespace from root
xmlns = None
for elem in tree.iter():
if elem.tag.endswith('gexf'):
xmlns = elem.tag.split('}')[0] + '}'
break
if xmlns is None:
raise GraphitException(
'Invalid GEXF file format, "gexf" tag not found')
# Add graph meta-data and XMLNS namespace
for meta in tree.iter('{0}meta'.format(xmlns)):
graph.data.update(meta.attrib)
for meta_data in meta:
tag = meta_data.tag.split('}')[1]
graph.data[tag] = meta_data.text
# GEXF node and edge labels are unique, turn off auto_nid
graph.data['auto_nid'] = False
graph_tag = tree.find('{0}graph'.format(xmlns))
graph.directed = graph_tag.get('defaultedgetype', 'directed') == 'directed'
graph.data.update(graph_tag.attrib)
# Parse all nodes
nodes = tree.findall('.//{0}node'.format(xmlns))
if not len(nodes):
raise GraphitException('GEXF file containes no "node" elements')
for node in nodes:
attr = node.attrib
attr = parse_attvalue_elements(node, attr, xmlns=xmlns)
graph.add_node(attr['id'],
**dict([n for n in attr.items() if n[0] != 'id']))
# Parse all edges
edges = tree.findall('.//{0}edge'.format(xmlns))
for edge in edges:
attr = edge.attrib
# Edge direction differs from global graph directionality
edge_directed = graph.directed
if 'type' in attr:
edge_directed = attr['type'] == 'directed'
attr = parse_attvalue_elements(edge, attr, xmlns=xmlns)
graph.add_edge(attr['source'],
attr['target'],
directed=edge_directed,
**dict([
n for n in attr.items()
if n[0] not in ('source', 'target')
]))
logger.info('Import graph in GEXF format. XMLNS: {0}'.format(xmlns))
return graph
