annotate env/lib/python3.9/site-packages/pydot.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""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(
        "`pydot` could not import `dot_parser`, "
        "so `pydot` will be unable to parse DOT files. "
        "The error was:  {e}".format(e=e))


__author__ = 'Ero Carrera'
__version__ = '1.4.2'
__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_anaconda():
    # type: () -> bool
    import glob
    return glob.glob(os.path.join(sys.prefix, 'conda-meta\\graphviz*.json')) != []


def get_executable_extension():
    # type: () -> str
    if is_windows():
        return '.bat' if is_anaconda() 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', ''),
        'SYSTEMROOT': os.environ.get('SYSTEMROOT', ''),
    }

    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):
    """Enclose 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('%s%s' % (node_prefix, node_orig),
                         '%s%s' % (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('%s%s' % (node_prefix, abs(nodes[0])),
                     '%s%s' % (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 problem 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, subgraph or cluster
    dst: destination node, subgraph or cluster

    `src` and `dst` can be specified as a `Node`, `Subgraph` or
    `Cluster` object, or as the name string of such a component.

    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, Subgraph, Cluster)):
            src = src.get_name()
        if isinstance(dst, (Node, Subgraph, Cluster)):
            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

    if not PY3:
        def __ne__(self, other):
            result = self.__eq__(other)
            if result is NotImplemented:
                return NotImplemented
            return not result

    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):
        """Define default node attributes.

        These attributes only apply to nodes added to the graph after
        calling this method.
        """
        self.add_node( Node('node', **attrs) )


    def get_node_defaults(self, **attrs):


        graph_nodes = self.get_node('node')

        if isinstance( graph_nodes, (list, tuple)):
            return [ node.get_attributes() for node in graph_nodes ]

        return graph_nodes.get_attributes()


    def set_edge_defaults(self, **attrs):

        self.add_node( Node('edge', **attrs) )



    def get_edge_defaults(self, **attrs):

        graph_nodes = self.get_node('edge')

        if isinstance( graph_nodes, (list, tuple)):
            return [ node.get_attributes() for node in graph_nodes ]

        return graph_nodes.get_attributes()



    def set_simplify(self, simplify):
        """Set whether to simplify or not.

        If True it will avoid displaying equal edges, i.e.
        only one edge between two nodes. removing the
        duplicated ones.
        """

        self.obj_dict['simplify'] = simplify



    def get_simplify(self):
        """Get whether to simplify or not.

        Refer to set_simplify for more information.
        """

        return self.obj_dict['simplify']


    def set_type(self, graph_type):
        """Set the graph's type, 'graph' or 'digraph'."""

        self.obj_dict['type'] = graph_type



    def get_type(self):
        """Get the graph's type, 'graph' or 'digraph'."""

        return self.obj_dict['type']



    def set_name(self, graph_name):
        """Set the graph's name."""

        self.obj_dict['name'] = graph_name



    def get_name(self):
        """Get the graph's name."""

        return self.obj_dict['name']



    def set_strict(self, val):
        """Set graph to 'strict' mode.

        This option is only valid for top level graphs.
        """

        self.obj_dict['strict'] = val



    def get_strict(self, val):
        """Get graph's 'strict' mode (True, False).

        This option is only valid for top level graphs.
        """

        return self.obj_dict['strict']



    def set_suppress_disconnected(self, val):
        """Suppress disconnected nodes in the output graph.

        This option will skip nodes in
        the graph with no incoming or outgoing
        edges. This option works also
        for subgraphs and has effect only in the
        current graph/subgraph.
        """

        self.obj_dict['suppress_disconnected'] = val



    def get_suppress_disconnected(self, val):
        """Get if suppress disconnected is set.

        Refer to set_suppress_disconnected for more information.
        """

        return self.obj_dict['suppress_disconnected']


    def get_next_sequence_number(self):

        seq = self.obj_dict['current_child_sequence']

        self.obj_dict['current_child_sequence'] += 1

        return seq



    def add_node(self, graph_node):
        """Adds a node object to the graph.

        It takes a node object as its only argument and returns
        None.
        """

        if not isinstance(graph_node, Node):
            raise TypeError(
                'add_node() received ' +
                'a non node class object: ' + str(graph_node))


        node = self.get_node(graph_node.get_name())

        if not node:

            self.obj_dict['nodes'][graph_node.get_name()] = [
                graph_node.obj_dict ]

            #self.node_dict[graph_node.get_name()] = graph_node.attributes
            graph_node.set_parent_graph(self.get_parent_graph())

        else:

            self.obj_dict['nodes'][graph_node.get_name()].append(
                graph_node.obj_dict )

        graph_node.set_sequence(self.get_next_sequence_number())



    def del_node(self, name, index=None):
        """Delete a node from the graph.

        Given a node's name all node(s) with that same name
        will be deleted if 'index' is not specified or set
        to None.
        If there are several nodes with that same name and
        'index' is given, only the node in that position
        will be deleted.

        'index' should be an integer specifying the position
        of the node to delete. If index is larger than the
        number of nodes with that name, no action is taken.

        If nodes are deleted it returns True. If no action
        is taken it returns False.
        """

        if isinstance(name, Node):
            name = name.get_name()

        if name in self.obj_dict['nodes']:

            if (index is not None and
                index < len(self.obj_dict['nodes'][name])):
                del self.obj_dict['nodes'][name][index]
                return True
            else:
                del self.obj_dict['nodes'][name]
                return True

        return False


    def get_node(self, name):
        """Retrieve a node from the graph.

        Given a node's name the corresponding Node
        instance will be returned.

        If one or more nodes exist with that name a list of
        Node instances is returned.
        An empty list is returned otherwise.
        """

        match = list()

        if name in self.obj_dict['nodes']:

            match.extend(
                [Node(obj_dict=obj_dict)
                 for obj_dict in self.obj_dict['nodes'][name]])

        return match


    def get_nodes(self):
        """Get the list of Node instances."""

        return self.get_node_list()


    def get_node_list(self):
        """Get the list of Node instances.

        This method returns the list of Node instances
        composing the graph.
        """

        node_objs = list()

        for node in self.obj_dict['nodes']:
                obj_dict_list = self.obj_dict['nodes'][node]
                node_objs.extend( [ Node( obj_dict = obj_d )
                                   for obj_d in obj_dict_list ] )

        return node_objs



    def add_edge(self, graph_edge):
        """Adds an edge object to the graph.

        It takes a edge object as its only argument and returns
        None.
        """

        if not isinstance(graph_edge, Edge):
            raise TypeError(
                'add_edge() received a non edge class object: ' +
                str(graph_edge))

        edge_points = ( graph_edge.get_source(),
                       graph_edge.get_destination() )

        if edge_points in self.obj_dict['edges']:

            edge_list = self.obj_dict['edges'][edge_points]
            edge_list.append(graph_edge.obj_dict)

        else:

            self.obj_dict['edges'][edge_points] = [ graph_edge.obj_dict ]


        graph_edge.set_sequence( self.get_next_sequence_number() )

        graph_edge.set_parent_graph( self.get_parent_graph() )



    def del_edge(self, src_or_list, dst=None, index=None):
        """Delete an edge from the graph.

        Given an edge's (source, destination) node names all
        matching edges(s) will be deleted if 'index' is not
        specified or set to None.
        If there are several matching edges and 'index' is
        given, only the edge in that position will be deleted.

        'index' should be an integer specifying the position
        of the edge to delete. If index is larger than the
        number of matching edges, no action is taken.

        If edges are deleted it returns True. If no action
        is taken it returns False.
        """

        if isinstance( src_or_list, (list, tuple)):
            if dst is not None and isinstance(dst, int):
                index = dst
            src, dst = src_or_list
        else:
            src, dst = src_or_list, dst

        if isinstance(src, Node):
            src = src.get_name()

        if isinstance(dst, Node):
            dst = dst.get_name()

        if (src, dst) in self.obj_dict['edges']:

            if (index is not None and
                index < len(self.obj_dict['edges'][(src, dst)])):
                del self.obj_dict['edges'][(src, dst)][index]
                return True
            else:
                del self.obj_dict['edges'][(src, dst)]
                return True

        return False


    def get_edge(self, src_or_list, dst=None):
        """Retrieved an edge from the graph.

        Given an edge's source and destination the corresponding
        Edge instance(s) will be returned.

        If one or more edges exist with that source and destination
        a list of Edge instances is returned.
        An empty list is returned otherwise.
        """

        if isinstance( src_or_list, (list, tuple)) and dst is None:
            edge_points = tuple(src_or_list)
            edge_points_reverse = (edge_points[1], edge_points[0])
        else:
            edge_points = (src_or_list, dst)
            edge_points_reverse = (dst, src_or_list)

        match = list()

        if edge_points in self.obj_dict['edges'] or (
            self.get_top_graph_type() == 'graph' and
            edge_points_reverse in self.obj_dict['edges']):

            edges_obj_dict = self.obj_dict['edges'].get(
                edge_points,
                self.obj_dict['edges'].get( edge_points_reverse, None ))

            for edge_obj_dict in edges_obj_dict:
                match.append(
                    Edge(edge_points[0],
                         edge_points[1],
                         obj_dict=edge_obj_dict))

        return match


    def get_edges(self):
        return self.get_edge_list()


    def get_edge_list(self):
        """Get the list of Edge instances.

        This method returns the list of Edge instances
        composing the graph.
        """

        edge_objs = list()

        for edge in self.obj_dict['edges']:
                obj_dict_list = self.obj_dict['edges'][edge]
                edge_objs.extend(
                    [Edge(obj_dict=obj_d)
                     for obj_d in obj_dict_list])

        return edge_objs



    def add_subgraph(self, sgraph):
        """Adds an subgraph object to the graph.

        It takes a subgraph object as its only argument and returns
        None.
        """

        if (not isinstance(sgraph, Subgraph) and
            not isinstance(sgraph, Cluster)):
            raise TypeError(
                'add_subgraph() received a non subgraph class object:' +
                str(sgraph))

        if sgraph.get_name() in self.obj_dict['subgraphs']:

            sgraph_list = self.obj_dict['subgraphs'][ sgraph.get_name() ]
            sgraph_list.append( sgraph.obj_dict )

        else:
            self.obj_dict['subgraphs'][sgraph.get_name()] = [
                sgraph.obj_dict]

        sgraph.set_sequence( self.get_next_sequence_number() )

        sgraph.set_parent_graph( self.get_parent_graph() )




    def get_subgraph(self, name):
        """Retrieved a subgraph from the graph.

        Given a subgraph's name the corresponding
        Subgraph instance will be returned.

        If one or more subgraphs exist with the same name, a list of
        Subgraph instances is returned.
        An empty list is returned otherwise.
        """

        match = list()

        if name in self.obj_dict['subgraphs']:

            sgraphs_obj_dict = self.obj_dict['subgraphs'].get( name )

            for obj_dict_list in sgraphs_obj_dict:
                #match.extend( Subgraph( obj_dict = obj_d )
                #             for obj_d in obj_dict_list )
                match.append( Subgraph( obj_dict = obj_dict_list ) )

        return match


    def get_subgraphs(self):

        return self.get_subgraph_list()


    def get_subgraph_list(self):
        """Get the list of Subgraph instances.

        This method returns the list of Subgraph instances
        in the graph.
        """

        sgraph_objs = list()

        for sgraph in self.obj_dict['subgraphs']:
                obj_dict_list = self.obj_dict['subgraphs'][sgraph]
                sgraph_objs.extend(
                    [Subgraph(obj_dict=obj_d)
                     for obj_d in obj_dict_list])

        return sgraph_objs



    def set_parent_graph(self, parent_graph):

        self.obj_dict['parent_graph'] = parent_graph

        for k in self.obj_dict['nodes']:
            obj_list = self.obj_dict['nodes'][k]
            for obj in obj_list:
                obj['parent_graph'] = parent_graph

        for k in self.obj_dict['edges']:
            obj_list = self.obj_dict['edges'][k]
            for obj in obj_list:
                obj['parent_graph'] = parent_graph

        for k in self.obj_dict['subgraphs']:
            obj_list = self.obj_dict['subgraphs'][k]
            for obj in obj_list:
                Graph(obj_dict=obj).set_parent_graph(parent_graph)



    def to_string(self):
        """Return string representation of graph in DOT language.

        @return: graph and subelements
        @rtype: `str`
        """


        graph = list()

        if self.obj_dict.get('strict', None) is not None:

            if (self == self.get_parent_graph() and
                    self.obj_dict['strict']):

                graph.append('strict ')

        graph_type = self.obj_dict['type']
        if (graph_type == 'subgraph' and
                not self.obj_dict.get('show_keyword', True)):
            graph_type = ''
        s = '{type} {name} {{\n'.format(
            type=graph_type,
            name=self.obj_dict['name'])
        graph.append(s)

        for attr in sorted(self.obj_dict['attributes']):

            if self.obj_dict['attributes'].get(attr, None) is not None:

                val = self.obj_dict['attributes'].get(attr)
                if val == '':
                    val = '""'
                if val is not None:
                    graph.append('%s=%s' %
                                 (attr, quote_if_necessary(val)))
                else:
                    graph.append( attr )

                graph.append( ';\n' )


        edges_done = set()

        edge_obj_dicts = list()
        for k in self.obj_dict['edges']:
            edge_obj_dicts.extend(self.obj_dict['edges'][k])

        if edge_obj_dicts:
            edge_src_set, edge_dst_set = list(zip(
                *[obj['points'] for obj in edge_obj_dicts]))
            edge_src_set, edge_dst_set = set(edge_src_set), set(edge_dst_set)
        else:
            edge_src_set, edge_dst_set = set(), set()

        node_obj_dicts = list()
        for k in self.obj_dict['nodes']:
            node_obj_dicts.extend(self.obj_dict['nodes'][k])

        sgraph_obj_dicts = list()
        for k in self.obj_dict['subgraphs']:
            sgraph_obj_dicts.extend(self.obj_dict['subgraphs'][k])


        obj_list = [(obj['sequence'], obj)
                    for obj in (edge_obj_dicts +
                                node_obj_dicts + sgraph_obj_dicts) ]
        obj_list.sort(key=lambda x: x[0])

        for idx, obj in obj_list:

            if obj['type'] == 'node':

                node = Node(obj_dict=obj)

                if self.obj_dict.get('suppress_disconnected', False):

                    if (node.get_name() not in edge_src_set and
                        node.get_name() not in edge_dst_set):

                        continue

                graph.append( node.to_string()+'\n' )

            elif obj['type'] == 'edge':

                edge = Edge(obj_dict=obj)

                if (self.obj_dict.get('simplify', False) and
                        edge in edges_done):
                    continue

                graph.append( edge.to_string() + '\n' )
                edges_done.add(edge)

            else:

                sgraph = Subgraph(obj_dict=obj)

                graph.append( sgraph.to_string()+'\n' )

        graph.append( '}\n' )

        return ''.join(graph)



class Subgraph(Graph):

    """Class representing a subgraph in Graphviz's dot language.

    This class implements the methods to work on a representation
    of a subgraph in Graphviz's dot language.

    subgraph(graph_name='subG',
             suppress_disconnected=False,
             attribute=value,
             ...)

    graph_name:
        the subgraph's name
    suppress_disconnected:
        defaults to false, which will remove from the
        subgraph any disconnected nodes.
    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:

     Subgraph.obj_dict['attributes'][attribute name], i.e.

        subgraph_instance.obj_dict['attributes']['label']
        subgraph_instance.obj_dict['attributes']['fontname']
    """


    # RMF: subgraph should have all the
    # attributes of graph so it can be passed
    # as a graph to all methods
    #
    def __init__(self, graph_name='',
                 obj_dict=None, suppress_disconnected=False,
                 simplify=False, **attrs):


        Graph.__init__(
            self, graph_name=graph_name, obj_dict=obj_dict,
            suppress_disconnected=suppress_disconnected,
            simplify=simplify, **attrs)

        if obj_dict is None:

            self.obj_dict['type'] = 'subgraph'




class Cluster(Graph):

    """Class representing a cluster in Graphviz's dot language.

    This class implements the methods to work on a representation
    of a cluster in Graphviz's dot language.

    cluster(graph_name='subG',
            suppress_disconnected=False,
            attribute=value,
            ...)

    graph_name:
        the cluster's name
        (the string 'cluster' will be always prepended)
    suppress_disconnected:
        defaults to false, which will remove from the
        cluster any disconnected nodes.
    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_color, set_fontname

    or using the instance's attributes:

     Cluster.obj_dict['attributes'][attribute name], i.e.

        cluster_instance.obj_dict['attributes']['label']
        cluster_instance.obj_dict['attributes']['fontname']
    """


    def __init__(self, graph_name='subG',
                 obj_dict=None, suppress_disconnected=False,
                 simplify=False, **attrs):

        Graph.__init__(
            self, graph_name=graph_name, obj_dict=obj_dict,
            suppress_disconnected=suppress_disconnected,
            simplify=simplify, **attrs)

        if obj_dict is None:

            self.obj_dict['type'] = 'subgraph'
            self.obj_dict['name'] = quote_if_necessary('cluster_'+graph_name)

        self.create_attribute_methods(CLUSTER_ATTRIBUTES)






class Dot(Graph):
    """A container for handling a dot language file.

    This class implements methods to write and process
    a dot language file. It is a derived class of
    the base class 'Graph'.
    """



    def __init__(self, *argsl, **argsd):
        Graph.__init__(self, *argsl, **argsd)

        self.shape_files = list()
        self.formats = [
            'canon', 'cmap', 'cmapx',
            'cmapx_np', 'dia', 'dot',
            'fig', 'gd', 'gd2', 'gif',
            'hpgl', 'imap', 'imap_np', 'ismap',
            'jpe', 'jpeg', 'jpg', 'mif',
            'mp', 'pcl', 'pdf', 'pic', 'plain',
            'plain-ext', 'png', 'ps', 'ps2',
            'svg', 'svgz', 'vml', 'vmlz',
            'vrml', 'vtx', 'wbmp', 'xdot', 'xlib']

        self.prog = 'dot'

        # Automatically creates all
        # the methods enabling the creation
        # of output in any of the supported formats.
        for frmt in self.formats:
            def new_method(
                    f=frmt, prog=self.prog,
                    encoding=None):
                """Refer to docstring of method `create`."""
                return self.create(
                    format=f, prog=prog, encoding=encoding)
            name = 'create_{fmt}'.format(fmt=frmt)
            self.__setattr__(name, new_method)

        for frmt in self.formats+['raw']:
            def new_method(
                    path, f=frmt, prog=self.prog,
                    encoding=None):
                """Refer to docstring of method `write.`"""
                self.write(
                    path, format=f, prog=prog,
                    encoding=encoding)
            name = 'write_{fmt}'.format(fmt=frmt)
            self.__setattr__(name, new_method)

    def __getstate__(self):

        dict = copy.copy(self.obj_dict)

        return dict

    def __setstate__(self, state):

        self.obj_dict = state


    def set_shape_files(self, file_paths):
        """Add the paths of the required image files.

        If the graph needs graphic objects to
        be used as shapes or otherwise
        those need to be in the same folder as
        the graph is going to be rendered
        from. Alternatively the absolute path to
        the files can be specified when
        including the graphics in the graph.

        The files in the location pointed to by
        the path(s) specified as arguments
        to this method will be copied to
        the same temporary location where the
        graph is going to be rendered.
        """

        if isinstance( file_paths, str_type):
            self.shape_files.append( file_paths )

        if isinstance( file_paths, (list, tuple) ):
            self.shape_files.extend( file_paths )


    def set_prog(self, prog):
        """Sets the default program.

        Sets the default program in charge of processing
        the dot file into a graph.
        """
        self.prog = prog


    def write(self, path, prog=None, format='raw', encoding=None):
        """Writes a graph to a file.

        Given a filename 'path' it will open/create and truncate
        such file and write on it a representation of the graph
        defined by the dot object in the format specified by
        'format' and using the encoding specified by `encoding` for text.
        The format 'raw' is used to dump the string representation
        of the Dot object, without further processing.
        The output can be processed by any of graphviz tools, defined
        in 'prog', which defaults to 'dot'
        Returns True or False according to the success of the write
        operation.

        There's also the preferred possibility of using:

            write_'format'(path, prog='program')

        which are automatically defined for all the supported formats.
        [write_ps(), write_gif(), write_dia(), ...]

        The encoding is passed to `open` [1].

        [1] https://docs.python.org/3/library/functions.html#open
        """
        if prog is None:
            prog = self.prog
        if format == 'raw':
            s = self.to_string()
            if not PY3:
                s = unicode(s)
            with io.open(path, mode='wt', encoding=encoding) as f:
                f.write(s)
        else:
            s = self.create(prog, format, encoding=encoding)
            with io.open(path, mode='wb') as f:
                f.write(s)
        return True

    def create(self, prog=None, format='ps', encoding=None):
        """Creates and returns a binary image for the graph.

        create will write the graph to a temporary dot file in the
        encoding specified by `encoding` and process it with the
        program given by 'prog' (which defaults to 'twopi'), reading
        the binary image output and return it as:

        - `str` of bytes in Python 2
        - `bytes` in Python 3

        There's also the preferred possibility of using:

            create_'format'(prog='program')

        which are automatically defined for all the supported formats,
        for example:

          - `create_ps()`
          - `create_gif()`
          - `create_dia()`

        If 'prog' is a list, instead of a string,
        then the fist item is expected to be the program name,
        followed by any optional command-line arguments for it:

            [ 'twopi', '-Tdot', '-s10' ]


        @param prog: either:

          - name of GraphViz executable that
            can be found in the `$PATH`, or

          - absolute path to GraphViz executable.

          If you have added GraphViz to the `$PATH` and
          use its executables as installed
          (without renaming any of them)
          then their names are:

            - `'dot'`
            - `'twopi'`
            - `'neato'`
            - `'circo'`
            - `'fdp'`
            - `'sfdp'`

          On Windows, these have the notorious ".exe" extension that,
          only for the above strings, will be added automatically.

          The `$PATH` is inherited from `os.env['PATH']` and
          passed to `subprocess.Popen` using the `env` argument.

          If you haven't added GraphViz to your `$PATH` on Windows,
          then you may want to give the absolute path to the
          executable (for example, to `dot.exe`) in `prog`.
        """

        if prog is None:
            prog = self.prog

        assert prog is not None

        if isinstance(prog, (list, tuple)):
            prog, args = prog[0], prog[1:]
        else:
            args = []

        # temp file
        tmp_fd, tmp_name = tempfile.mkstemp()
        os.close(tmp_fd)
        self.write(tmp_name, encoding=encoding)
        tmp_dir = os.path.dirname(tmp_name)

        # For each of the image files...
        for img in self.shape_files:
            # Get its data
            f = open(img, 'rb')
            f_data = f.read()
            f.close()
            # And copy it under a file with the same name in
            # the temporary directory
            f = open(os.path.join(tmp_dir, os.path.basename(img)), 'wb')
            f.write(f_data)
            f.close()

        arguments = ['-T{}'.format(format), ] + args + [tmp_name]

        try:
            stdout_data, stderr_data, process = call_graphviz(
                program=prog,
                arguments=arguments,
                working_dir=tmp_dir,
            )
        except OSError as e:
            if e.errno == errno.ENOENT:
                args = list(e.args)
                args[1] = '"{prog}" not found in path.'.format(
                    prog=prog)
                raise OSError(*args)
            else:
                raise

        # clean file litter
        for img in self.shape_files:
            os.unlink(os.path.join(tmp_dir, os.path.basename(img)))

        os.unlink(tmp_name)

        if process.returncode != 0:
            message = (
                '"{prog}" with args {arguments} returned code: {code}\n\n'
                'stdout, stderr:\n {out}\n{err}\n'
            ).format(
                prog=prog,
                arguments=arguments,
                code=process.returncode,
                out=stdout_data,
                err=stderr_data,
            )
            print(message)

        assert process.returncode == 0, (
                '"{prog}" with args {arguments} returned code: {code}'.format(
                    prog=prog,
                    arguments=arguments,
                    code=process.returncode,
                )
            )

        return stdout_data