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pydot.py
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pydot.py
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"""An interface to GraphViz."""
from __future__ import division
from __future__ import print_function
import copy
import io
import errno
import os
import re
import subprocess
import sys
import tempfile
import warnings
try:
import dot_parser
except Exception as e:
warnings.warn(
"Couldn't import dot_parser, "
"loading of dot files will not be possible.")
__author__ = 'Ero Carrera'
__version__ = '1.4.1'
__license__ = 'MIT'
PY3 = sys.version_info >= (3, 0, 0)
if PY3:
str_type = str
else:
str_type = basestring
GRAPH_ATTRIBUTES = { 'Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',
'center', 'charset', 'clusterrank', 'colorscheme', 'comment', 'compound',
'concentrate', 'defaultdist', 'dim', 'dimen', 'diredgeconstraints',
'dpi', 'epsilon', 'esep', 'fontcolor', 'fontname', 'fontnames',
'fontpath', 'fontsize', 'id', 'label', 'labeljust', 'labelloc',
'landscape', 'layers', 'layersep', 'layout', 'levels', 'levelsgap',
'lheight', 'lp', 'lwidth', 'margin', 'maxiter', 'mclimit', 'mindist',
'mode', 'model', 'mosek', 'nodesep', 'nojustify', 'normalize', 'nslimit',
'nslimit1', 'ordering', 'orientation', 'outputorder', 'overlap',
'overlap_scaling', 'pack', 'packmode', 'pad', 'page', 'pagedir',
'quadtree', 'quantum', 'rankdir', 'ranksep', 'ratio', 'remincross',
'repulsiveforce', 'resolution', 'root', 'rotate', 'searchsize', 'sep',
'showboxes', 'size', 'smoothing', 'sortv', 'splines', 'start',
'stylesheet', 'target', 'truecolor', 'viewport', 'voro_margin',
# for subgraphs
'rank' }
EDGE_ATTRIBUTES = { 'URL', 'arrowhead', 'arrowsize', 'arrowtail',
'color', 'colorscheme', 'comment', 'constraint', 'decorate', 'dir',
'edgeURL', 'edgehref', 'edgetarget', 'edgetooltip', 'fontcolor',
'fontname', 'fontsize', 'headURL', 'headclip', 'headhref', 'headlabel',
'headport', 'headtarget', 'headtooltip', 'href', 'id', 'label',
'labelURL', 'labelangle', 'labeldistance', 'labelfloat', 'labelfontcolor',
'labelfontname', 'labelfontsize', 'labelhref', 'labeltarget',
'labeltooltip', 'layer', 'len', 'lhead', 'lp', 'ltail', 'minlen',
'nojustify', 'penwidth', 'pos', 'samehead', 'sametail', 'showboxes',
'style', 'tailURL', 'tailclip', 'tailhref', 'taillabel', 'tailport',
'tailtarget', 'tailtooltip', 'target', 'tooltip', 'weight',
'rank' }
NODE_ATTRIBUTES = { 'URL', 'color', 'colorscheme', 'comment',
'distortion', 'fillcolor', 'fixedsize', 'fontcolor', 'fontname',
'fontsize', 'group', 'height', 'id', 'image', 'imagescale', 'label',
'labelloc', 'layer', 'margin', 'nojustify', 'orientation', 'penwidth',
'peripheries', 'pin', 'pos', 'rects', 'regular', 'root', 'samplepoints',
'shape', 'shapefile', 'showboxes', 'sides', 'skew', 'sortv', 'style',
'target', 'tooltip', 'vertices', 'width', 'z',
# The following are attributes dot2tex
'texlbl', 'texmode' }
CLUSTER_ATTRIBUTES = { 'K', 'URL', 'bgcolor', 'color', 'colorscheme',
'fillcolor', 'fontcolor', 'fontname', 'fontsize', 'label', 'labeljust',
'labelloc', 'lheight', 'lp', 'lwidth', 'nojustify', 'pencolor',
'penwidth', 'peripheries', 'sortv', 'style', 'target', 'tooltip' }
DEFAULT_PROGRAMS = {
'dot',
'twopi',
'neato',
'circo',
'fdp',
'sfdp',
}
def is_windows():
# type: () -> bool
return os.name == 'nt'
def is_anacoda():
# type: () -> bool
return os.path.exists(os.path.join(sys.prefix, 'conda-meta'))
def get_executable_extension():
# type: () -> str
if is_windows():
return '.bat' if is_anacoda() else '.exe'
else:
return ''
def call_graphviz(program, arguments, working_dir, **kwargs):
# explicitly inherit `$PATH`, on Windows too,
# with `shell=False`
if program in DEFAULT_PROGRAMS:
extension = get_executable_extension()
program += extension
if arguments is None:
arguments = []
env = {
'PATH': os.environ.get('PATH', ''),
'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''),
}
program_with_args = [program, ] + arguments
process = subprocess.Popen(
program_with_args,
env=env,
cwd=working_dir,
shell=False,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
**kwargs
)
stdout_data, stderr_data = process.communicate()
return stdout_data, stderr_data, process
#
# Extended version of ASPN's Python Cookbook Recipe:
# Frozen dictionaries.
# https://code.activestate.com/recipes/414283/
#
# This version freezes dictionaries used as values within dictionaries.
#
class frozendict(dict):
def _blocked_attribute(obj):
raise AttributeError('A frozendict cannot be modified.')
_blocked_attribute = property(_blocked_attribute)
__delitem__ = __setitem__ = clear = _blocked_attribute
pop = popitem = setdefault = update = _blocked_attribute
def __new__(cls, *args, **kw):
new = dict.__new__(cls)
args_ = []
for arg in args:
if isinstance(arg, dict):
arg = copy.copy(arg)
for k in arg:
v = arg[k]
if isinstance(v, frozendict):
arg[k] = v
elif isinstance(v, dict):
arg[k] = frozendict(v)
elif isinstance(v, list):
v_ = list()
for elm in v:
if isinstance(elm, dict):
v_.append( frozendict(elm) )
else:
v_.append( elm )
arg[k] = tuple(v_)
args_.append( arg )
else:
args_.append( arg )
dict.__init__(new, *args_, **kw)
return new
def __init__(self, *args, **kw):
pass
def __hash__(self):
try:
return self._cached_hash
except AttributeError:
h = self._cached_hash = hash(tuple(sorted(self.items())))
return h
def __repr__(self):
return "frozendict(%s)" % dict.__repr__(self)
dot_keywords = ['graph', 'subgraph', 'digraph', 'node', 'edge', 'strict']
id_re_alpha_nums = re.compile('^[_a-zA-Z][a-zA-Z0-9_,]*$', re.UNICODE)
id_re_alpha_nums_with_ports = re.compile(
'^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$', re.UNICODE)
id_re_num = re.compile('^[0-9,]+$', re.UNICODE)
id_re_with_port = re.compile('^([^:]*):([^:]*)$', re.UNICODE)
id_re_dbl_quoted = re.compile('^\".*\"$', re.S|re.UNICODE)
id_re_html = re.compile('^<.*>$', re.S|re.UNICODE)
def needs_quotes( s ):
"""Checks whether a string is a dot language ID.
It will check whether the string is solely composed
by the characters allowed in an ID or not.
If the string is one of the reserved keywords it will
need quotes too but the user will need to add them
manually.
"""
# If the name is a reserved keyword it will need quotes but pydot
# can't tell when it's being used as a keyword or when it's simply
# a name. Hence the user needs to supply the quotes when an element
# would use a reserved keyword as name. This function will return
# false indicating that a keyword string, if provided as-is, won't
# need quotes.
if s in dot_keywords:
return False
chars = [ord(c) for c in s if ord(c)>0x7f or ord(c)==0]
if chars and not id_re_dbl_quoted.match(s) and not id_re_html.match(s):
return True
for test_re in [id_re_alpha_nums, id_re_num,
id_re_dbl_quoted, id_re_html,
id_re_alpha_nums_with_ports]:
if test_re.match(s):
return False
m = id_re_with_port.match(s)
if m:
return needs_quotes(m.group(1)) or needs_quotes(m.group(2))
return True
def quote_if_necessary(s):
"""Enclode attribute value in quotes, if needed."""
if isinstance(s, bool):
if s is True:
return 'True'
return 'False'
if not isinstance( s, str_type):
return s
if not s:
return s
if needs_quotes(s):
replace = {'"' : r'\"',
"\n" : r'\n',
"\r" : r'\r'}
for (a,b) in replace.items():
s = s.replace(a, b)
return '"' + s + '"'
return s
def graph_from_dot_data(s):
"""Load graphs from DOT description in string `s`.
@param s: string in [DOT language](
https://en.wikipedia.org/wiki/DOT_(graph_description_language))
@return: Graphs that result from parsing.
@rtype: `list` of `pydot.Dot`
"""
return dot_parser.parse_dot_data(s)
def graph_from_dot_file(path, encoding=None):
"""Load graphs from DOT file at `path`.
@param path: to DOT file
@param encoding: as passed to `io.open`.
For example, `'utf-8'`.
@return: Graphs that result from parsing.
@rtype: `list` of `pydot.Dot`
"""
with io.open(path, 'rt', encoding=encoding) as f:
s = f.read()
if not PY3:
s = unicode(s)
graphs = graph_from_dot_data(s)
return graphs
def graph_from_edges(edge_list, node_prefix='', directed=False):
"""Creates a basic graph out of an edge list.
The edge list has to be a list of tuples representing
the nodes connected by the edge.
The values can be anything: bool, int, float, str.
If the graph is undirected by default, it is only
calculated from one of the symmetric halves of the matrix.
"""
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for edge in edge_list:
if isinstance(edge[0], str):
src = node_prefix + edge[0]
else:
src = node_prefix + str(edge[0])
if isinstance(edge[1], str):
dst = node_prefix + edge[1]
else:
dst = node_prefix + str(edge[1])
e = Edge( src, dst )
graph.add_edge(e)
return graph
def graph_from_adjacency_matrix(matrix, node_prefix= u'', directed=False):
"""Creates a basic graph out of an adjacency matrix.
The matrix has to be a list of rows of values
representing an adjacency matrix.
The values can be anything: bool, int, float, as long
as they can evaluate to True or False.
"""
node_orig = 1
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for row in matrix:
if not directed:
skip = matrix.index(row)
r = row[skip:]
else:
skip = 0
r = row
node_dest = skip+1
for e in r:
if e:
graph.add_edge(
Edge( node_prefix + node_orig,
node_prefix + node_dest) )
node_dest += 1
node_orig += 1
return graph
def graph_from_incidence_matrix(matrix, node_prefix='', directed=False):
"""Creates a basic graph out of an incidence matrix.
The matrix has to be a list of rows of values
representing an incidence matrix.
The values can be anything: bool, int, float, as long
as they can evaluate to True or False.
"""
node_orig = 1
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for row in matrix:
nodes = []
c = 1
for node in row:
if node:
nodes.append(c*node)
c += 1
nodes.sort()
if len(nodes) == 2:
graph.add_edge(
Edge( node_prefix + abs(nodes[0]),
node_prefix + nodes[1] ))
if not directed:
graph.set_simplify(True)
return graph
class Common(object):
"""Common information to several classes.
Should not be directly used, several classes are derived from
this one.
"""
def __getstate__(self):
dict = copy.copy(self.obj_dict)
return dict
def __setstate__(self, state):
self.obj_dict = state
def __get_attribute__(self, attr):
"""Look for default attributes for this node"""
attr_val = self.obj_dict['attributes'].get(attr, None)
if attr_val is None:
# get the defaults for nodes/edges
default_node_name = self.obj_dict['type']
# The defaults for graphs are set on a node named 'graph'
if default_node_name in ('subgraph', 'digraph', 'cluster'):
default_node_name = 'graph'
g = self.get_parent_graph()
if g is not None:
defaults = g.get_node( default_node_name )
else:
return None
# Multiple defaults could be set by having repeated 'graph [...]'
# 'node [...]', 'edge [...]' statements. In such case, if the
# same attribute is set in different statements, only the first
# will be returned. In order to get all, one would call the
# get_*_defaults() methods and handle those. Or go node by node
# (of the ones specifying defaults) and modify the attributes
# individually.
#
if not isinstance(defaults, (list, tuple)):
defaults = [defaults]
for default in defaults:
attr_val = default.obj_dict['attributes'].get(attr, None)
if attr_val:
return attr_val
else:
return attr_val
return None
def set_parent_graph(self, parent_graph):
self.obj_dict['parent_graph'] = parent_graph
def get_parent_graph(self):
return self.obj_dict.get('parent_graph', None)
def set(self, name, value):
"""Set an attribute value by name.
Given an attribute 'name' it will set its value to 'value'.
There's always the possibility of using the methods:
set_'name'(value)
which are defined for all the existing attributes.
"""
self.obj_dict['attributes'][name] = value
def get(self, name):
"""Get an attribute value by name.
Given an attribute 'name' it will get its value.
There's always the possibility of using the methods:
get_'name'()
which are defined for all the existing attributes.
"""
return self.obj_dict['attributes'].get(name, None)
def get_attributes(self):
""""""
return self.obj_dict['attributes']
def set_sequence(self, seq):
self.obj_dict['sequence'] = seq
def get_sequence(self):
return self.obj_dict['sequence']
def create_attribute_methods(self, obj_attributes):
#for attr in self.obj_dict['attributes']:
for attr in obj_attributes:
# Generate all the Setter methods.
#
self.__setattr__(
'set_'+attr,
lambda x, a=attr :
self.obj_dict['attributes'].__setitem__(a, x) )
# Generate all the Getter methods.
#
self.__setattr__(
'get_'+attr, lambda a=attr : self.__get_attribute__(a))
class Error(Exception):
"""General error handling class.
"""
def __init__(self, value):
self.value = value
def __str__(self):
return self.value
class InvocationException(Exception):
"""Indicate ploblem while running any GraphViz executable.
"""
def __init__(self, value):
self.value = value
def __str__(self):
return self.value
class Node(Common):
"""A graph node.
This class represents a graph's node with all its attributes.
node(name, attribute=value, ...)
name: node's name
All the attributes defined in the Graphviz dot language should
be supported.
"""
def __init__(self, name = '', obj_dict = None, **attrs):
#
# Nodes will take attributes of
# all other types because the defaults
# for any GraphViz object are dealt with
# as if they were Node definitions
#
if obj_dict is not None:
self.obj_dict = obj_dict
else:
self.obj_dict = dict()
# Copy the attributes
#
self.obj_dict[ 'attributes' ] = dict( attrs )
self.obj_dict[ 'type' ] = 'node'
self.obj_dict[ 'parent_graph' ] = None
self.obj_dict[ 'parent_node_list' ] = None
self.obj_dict[ 'sequence' ] = None
# Remove the compass point
#
port = None
if isinstance(name, str_type) and not name.startswith('"'):
idx = name.find(':')
if idx > 0 and idx+1 < len(name):
name, port = name[:idx], name[idx:]
if isinstance(name, int):
name = str(name)
self.obj_dict['name'] = quote_if_necessary(name)
self.obj_dict['port'] = port
self.create_attribute_methods(NODE_ATTRIBUTES)
def __str__(self):
return self.to_string()
def set_name(self, node_name):
"""Set the node's name."""
self.obj_dict['name'] = node_name
def get_name(self):
"""Get the node's name."""
return self.obj_dict['name']
def get_port(self):
"""Get the node's port."""
return self.obj_dict['port']
def add_style(self, style):
styles = self.obj_dict['attributes'].get('style', None)
if not styles and style:
styles = [ style ]
else:
styles = styles.split(',')
styles.append( style )
self.obj_dict['attributes']['style'] = ','.join( styles )
def to_string(self):
"""Return string representation of node in DOT language."""
# RMF: special case defaults for node, edge and graph properties.
#
node = quote_if_necessary(self.obj_dict['name'])
node_attr = list()
for attr in sorted(self.obj_dict['attributes']):
value = self.obj_dict['attributes'][attr]
if value == '':
value = '""'
if value is not None:
node_attr.append(
'%s=%s' % (attr, quote_if_necessary(value) ) )
else:
node_attr.append( attr )
# No point in having nodes setting any defaults if the don't set
# any attributes...
#
if node in ('graph', 'node', 'edge') and len(node_attr) == 0:
return ''
node_attr = ', '.join(node_attr)
if node_attr:
node += ' [' + node_attr + ']'
return node + ';'
class Edge(Common):
"""A graph edge.
This class represents a graph's edge with all its attributes.
edge(src, dst, attribute=value, ...)
src: source node
dst: destination node
`src` and `dst` can be specified as a `Node` object,
or as the node's name string.
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_label, set_fontname
or directly by using the instance's special dictionary:
Edge.obj_dict['attributes'][attribute name], i.e.
edge_instance.obj_dict['attributes']['label']
edge_instance.obj_dict['attributes']['fontname']
"""
def __init__(self, src='', dst='', obj_dict=None, **attrs):
self.obj_dict = dict()
if isinstance(src, Node):
src = src.get_name()
if isinstance(dst, Node):
dst = dst.get_name()
points = (quote_if_necessary(src),
quote_if_necessary(dst))
self.obj_dict['points'] = points
if obj_dict is None:
# Copy the attributes
self.obj_dict[ 'attributes' ] = dict( attrs )
self.obj_dict[ 'type' ] = 'edge'
self.obj_dict[ 'parent_graph' ] = None
self.obj_dict[ 'parent_edge_list' ] = None
self.obj_dict[ 'sequence' ] = None
else:
self.obj_dict = obj_dict
self.create_attribute_methods(EDGE_ATTRIBUTES)
def __str__(self):
return self.to_string()
def get_source(self):
"""Get the edges source node name."""
return self.obj_dict['points'][0]
def get_destination(self):
"""Get the edge's destination node name."""
return self.obj_dict['points'][1]
def __hash__(self):
return hash( hash(self.get_source()) +
hash(self.get_destination()) )
def __eq__(self, edge):
"""Compare two edges.
If the parent graph is directed, arcs linking
node A to B are considered equal and A->B != B->A
If the parent graph is undirected, any edge
connecting two nodes is equal to any other
edge connecting the same nodes, A->B == B->A
"""
if not isinstance(edge, Edge):
raise Error('Can not compare and '
'edge to a non-edge object.')
if self.get_parent_graph().get_top_graph_type() == 'graph':
# If the graph is undirected, the edge has neither
# source nor destination.
#
if ( ( self.get_source() == edge.get_source() and
self.get_destination() == edge.get_destination() ) or
( edge.get_source() == self.get_destination() and
edge.get_destination() == self.get_source() ) ):
return True
else:
if (self.get_source()==edge.get_source() and
self.get_destination()==edge.get_destination()):
return True
return False
def parse_node_ref(self, node_str):
if not isinstance(node_str, str):
return node_str
if node_str.startswith('"') and node_str.endswith('"'):
return node_str
node_port_idx = node_str.rfind(':')
if (node_port_idx>0 and node_str[0]=='"' and
node_str[node_port_idx-1]=='"'):
return node_str
if node_port_idx>0:
a = node_str[:node_port_idx]
b = node_str[node_port_idx+1:]
node = quote_if_necessary(a)
node += ':'+quote_if_necessary(b)
return node
return node_str
def to_string(self):
"""Return string representation of edge in DOT language."""
src = self.parse_node_ref( self.get_source() )
dst = self.parse_node_ref( self.get_destination() )
if isinstance(src, frozendict):
edge = [ Subgraph(obj_dict=src).to_string() ]
elif isinstance(src, int):
edge = [ str(src) ]
else:
edge = [ src ]
if (self.get_parent_graph() and
self.get_parent_graph().get_top_graph_type() and
self.get_parent_graph().get_top_graph_type() == 'digraph' ):
edge.append( '->' )
else:
edge.append( '--' )
if isinstance(dst, frozendict):
edge.append( Subgraph(obj_dict=dst).to_string() )
elif isinstance(dst, int):
edge.append( str(dst) )
else:
edge.append( dst )
edge_attr = list()
for attr in sorted(self.obj_dict['attributes']):
value = self.obj_dict['attributes'][attr]
if value == '':
value = '""'
if value is not None:
edge_attr.append(
'%s=%s' % (attr, quote_if_necessary(value) ) )
else:
edge_attr.append( attr )
edge_attr = ', '.join(edge_attr)
if edge_attr:
edge.append( ' [' + edge_attr + ']' )
return ' '.join(edge) + ';'
class Graph(Common):
"""Class representing a graph in Graphviz's dot language.
This class implements the methods to work on a representation
of a graph in Graphviz's dot language.
graph( graph_name='G', graph_type='digraph',
strict=False, suppress_disconnected=False, attribute=value, ...)
graph_name:
the graph's name
graph_type:
can be 'graph' or 'digraph'
suppress_disconnected:
defaults to False, which will remove from the
graph any disconnected nodes.
simplify:
if True it will avoid displaying equal edges, i.e.
only one edge between two nodes. removing the
duplicated ones.
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_size, set_fontname
or using the instance's attributes:
Graph.obj_dict['attributes'][attribute name], i.e.
graph_instance.obj_dict['attributes']['label']
graph_instance.obj_dict['attributes']['fontname']
"""
def __init__(self, graph_name='G', obj_dict=None,
graph_type='digraph', strict=False,
suppress_disconnected=False, simplify=False, **attrs):
if obj_dict is not None:
self.obj_dict = obj_dict
else:
self.obj_dict = dict()
self.obj_dict['attributes'] = dict(attrs)
if graph_type not in ['graph', 'digraph']:
raise Error((
'Invalid type "{t}". '
'Accepted graph types are: '
'graph, digraph').format(t=graph_type))
self.obj_dict['name'] = quote_if_necessary(graph_name)
self.obj_dict['type'] = graph_type
self.obj_dict['strict'] = strict
self.obj_dict['suppress_disconnected'] = suppress_disconnected
self.obj_dict['simplify'] = simplify
self.obj_dict['current_child_sequence'] = 1
self.obj_dict['nodes'] = dict()
self.obj_dict['edges'] = dict()
self.obj_dict['subgraphs'] = dict()
self.set_parent_graph(self)
self.create_attribute_methods(GRAPH_ATTRIBUTES)
def __str__(self):
return self.to_string()
def get_graph_type(self):
return self.obj_dict['type']
def get_top_graph_type(self):
parent = self
while True:
parent_ = parent.get_parent_graph()
if parent_ == parent:
break
parent = parent_
return parent.obj_dict['type']
def set_graph_defaults(self, **attrs):
self.add_node( Node('graph', **attrs) )
def get_graph_defaults(self, **attrs):
graph_nodes = self.get_node('graph')
if isinstance( graph_nodes, (list, tuple)):
return [ node.get_attributes() for node in graph_nodes ]
return graph_nodes.get_attributes()
def set_node_defaults(self, **attrs):
self.add_node( Node('node', **attrs) )
def get_node_defaults(self, **attrs):
graph_nodes = self.get_node('node')