#!/usr/bin/env python
################################################################################
#
#   graph.py
#
#
#   Copyright (c) 10/9/2009 Leo Goodstadt
#
#   Permission is hereby granted, free of charge, to any person obtaining a copy
#   of this software and associated documentation files (the "Software"), to deal
#   in the Software without restriction, including without limitation the rights
#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#   copies of the Software, and to permit persons to whom the Software is
#   furnished to do so, subject to the following conditions:
#
#   The above copyright notice and this permission notice shall be included in
#   all copies or substantial portions of the Software.
#
#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
#   THE SOFTWARE.
#################################################################################
"""
    graph.py

        provides support for diacyclic graph
        with topological_sort

"""
import sys, re, os

# use simplejson in place of json for python < 2.6
try:
    import json
except ImportError:
    import simplejson
    json = simplejson

from collections import defaultdict
from itertools import chain
from print_dependencies import *
import tempfile
import subprocess
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   class node

#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
class graph_error(Exception):
    def __init__(self, message):
        self.message = message
    def __str__ (self):
        return self.message

class error_duplicate_node_name(graph_error):
    pass

class node (object):
    """
    node
        designed for diacyclic graphs but can hold anything
        contains lists of nodes and
        dictionary to look up node name from node
    """

    _all_nodes         = list()
    _name_to_node      = dict()
    _global_node_index = 0

    one_to_one              = 0
    many_to_many            = 1
    one_to_many             = 2
    many_to_one             = 3

    @staticmethod
    def get_leaves ():
        for n in node._all_nodes:
            if len(n._inward) == 0:
                yield n

    @staticmethod
    def get_roots ():
        for n in node._all_nodes:
            if len(n._outward) == 0:
                yield n


    @staticmethod
    def count_nodes ():
        return len(_all_nodes)

    @staticmethod
    def dump_tree_as_str ():
        """
        dumps entire tree
        """
        return ("%d nodes " % node.count_nodes()) + "\n" + \
            "\n".join(map(lambda x: x.fullstr(), node._all_nodes))


    @staticmethod
    def lookup_node_from_name (name):
        return node._name_to_node[name]

    @staticmethod
    def is_node (name):
        return name in node._name_to_node


    #_____________________________________________________________________________________

    #   init

    #_____________________________________________________________________________________
    def __init__ (self, name, **args):
        """
        each node has
            _name
            _inward :   lists of incoming edges
            _outward:   lists of outgoing edges
        """
        #
        #   make sure node name is unique
        #
        if name in node._name_to_node:
            raise error_duplicate_node_name("[%s] has already been added" % name)

        self.__dict__.update(args)
        self._inward = list()
        self._outward= list()
        self.args = args
        self._name = name
        self._signal = False
        self._node_index = node._global_node_index
        node._global_node_index += 1

        #
        #   for looking up node for name
        #
        node._all_nodes.append(self)
        node._name_to_node[name] = self

    #_____________________________________________________________________________________

    #   add_child

    #_____________________________________________________________________________________
    def add_child(self, child, no_duplicates = True):
        """
        connect edges
        """
        # do not add duplicates
        if no_duplicates and child in self._outward:
            return child

        self._outward.append(child)
        child._inward.append(self)
        return child

    #_____________________________________________________________________________________

    #   inward/outward

    #_____________________________________________________________________________________
    def outward (self):
        """
        just in case we need to return inward when we mean outward!
            (for reversed graphs)
        """
        return self._outward

    def inward (self):
        """
        just in case we need to return inward when we mean outward!
            (for reversed graphs)
        """
        return self._inward


    #_____________________________________________________________________________________

    #   fullstr

    #_____________________________________________________________________________________
    def fullstr(self):
        """
        Full dump. Normally edges are not printed out
        Everything is indented except name
        """
        self_desc = list()
        for k,v in sorted(self.__dict__.iteritems(), key = lambda (x,v): (0,x,v) if x == "_name" else (1,x,v)):
            indent = "    " if k != "_name" else ""
            if k in ("_inward", "_outward"):
                v = ",".join(map(lambda x: x._name, v))
                self_desc.append(indent + str(k) + "=" + str(v))
            else:
                self_desc.append(indent + str(k) + "=" + str(v))
        return "\n".join(self_desc)

    #_____________________________________________________________________________________

    #   __str__

    #_____________________________________________________________________________________
    def __str__ (self):
        """
        Dump.
        Print everything except lists of edges
        Everything is indented except name
        """
        self_desc = list()
        for k,v in sorted(self.__dict__.iteritems(), reverse=True):
            indent = "    " if k != "_name" else ""
            if k[0] == '_':
                continue
            else:
                self_desc.append(indent + str(k) + "=" + str(v))
        return "\n".join(self_desc)



    #_____________________________________________________________________________________

    #   signal
    #
    #_____________________________________________________________________________________
    def signal (self, extra_data_for_signal = None):
        """
        Signals whether depth first search ends without this node
        """
        return self._signal






#_____________________________________________________________________________________

#   node_to_json
#
#
#_____________________________________________________________________________________
class node_to_json(json.JSONEncoder):
    """
    output node using json
    """
    def default(self, obj):
        print str(obj)
        if isinstance(obj, node):
            return obj._name, {
                    "index": obj._node_index,
                    "signal": obj._signal,
                    "inward": [n._name for n in obj._inward],
                    "outward": [n._name for n in obj._outward],
                    }
        return json.JSONEncoder.default(self, obj)








#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   topological_sort_visitor

#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888


class topological_sort_visitor (object):
    """
    topological sort
        used with DFS to find all nodes in topologically sorted order
        All finds all DAG breaking cycles

    """

    IGNORE_NODE_SIGNAL = 0
    NOTE_NODE_SIGNAL   = 1
    END_ON_SIGNAL      = 2

    #_____________________________________________________________________________________

    #   init

    #_____________________________________________________________________________________
    def __init__ (self, forced_dfs_nodes,
                    node_termination = END_ON_SIGNAL,
                    extra_data_for_signal = None):
        """
        list of saved results
        """
        self._forced_dfs_nodes         = set(forced_dfs_nodes)
        self._node_termination         = node_termination

        self._start_nodes              = set()
        self._back_edges               = set()
        self._back_nodes               = set()
        self._signalling_nodes         = set()

        # keep order for tree traversal later
        self._examined_edges           = list()
        # keep order for topological sorted results
        self._finished_nodes           = list()

        self._extra_data_for_signal    = extra_data_for_signal


    def combine_with (self, other):
        """
        combine the results of two visitors
            (add other to self)
        """
        self._back_edges              .update(other._back_edges)
        self._back_nodes              .update(other._back_nodes)
        extra_finished_nodes          = set(other._finished_nodes) - set(self._finished_nodes)
        self._finished_nodes          .extend(extra_finished_nodes)



    #_____________________________________________________________________________________

    #   __str__

    #_____________________________________________________________________________________
    def __str__ (self):
        """
        for diagnostics
        """
        signalling_str    = get_nodes_str ("Signalling", self._signalling_nodes)
        finished_str      = get_nodes_str ("Finished", self._finished_nodes)
        forced_str        = get_nodes_str ("Forced to run", self._forced_dfs_nodes)
        start_str         = get_nodes_str ("Start", self._start_nodes)
        back_edges_str    = get_edges_str ("back", self._back_edges)
        return (""
                        + finished_str
                        + start_str
                        + back_edges_str
                        + signalling_str
                        + finished_str
                )

    #_____________________________________________________________________________________

    #   not_dag

    #_____________________________________________________________________________________
    def not_dag (self):
        """
        back edges add circularity
        """
        return len(self._back_edges)

    #_____________________________________________________________________________________

    #   dag_violating_edges

    #_____________________________________________________________________________________
    def dag_violating_edges (self):
        """
        back edges add circularity
        """
        return self._back_edges



    #_____________________________________________________________________________________

    #   dag_violating_nodes

    #_____________________________________________________________________________________
    def dag_violating_nodes (self):
        """
        all nodes involved in cycless
        """
        return self._back_nodes

    #_____________________________________________________________________________________

    #   identify_dag_violating_nodes_and_edges
    #
    #_____________________________________________________________________________________
    def identify_dag_violating_nodes_and_edges (self):
        """
        find all nodes and edges in any cycles

        All dag violating cycles are defined by the back edge identified in DFS.
        All paths which go the other way: start at the to_node and end up at the from_node
            are therefore also part of the cycle

        """
        if not len(self._back_edges):
            return
        cnt_examined_edges = len(self._examined_edges)

        # add this to _back_edges at the end
        cycle_edges = set()

        #
        #   each cycle
        #       starts from the to_node   of each back_edge and
        #       ends   with the from_node of each back_edge
        #
        for cycle_to_node, cycle_from_node in self._back_edges:
            start_search_from = 0
            while 1:
                #
                # find start of cycle
                for i, (f,t,n) in enumerate(self._examined_edges[start_search_from:]):
                    if f == cycle_from_node:
                        break

                # no more cycles for this cycle_from_node/cycle_to_node pair
                else:
                    break


                #
                # cycle end might be within the same pair
                #   if so, don't search the current (not the next) edge for the cycle end
                #
                #   Otherwise incrementing search position avoids infinite loop
                #
                start_search_from = cycle_start = start_search_from + i
                if self._examined_edges[cycle_start][1] != cycle_to_node:
                    start_search_from += 1

                for i, (f,t,n) in enumerate(self._examined_edges[start_search_from:]):

                    #
                    #   found end of cycle
                    #
                    if t == cycle_to_node:
                        cycle_end = start_search_from + i + 1
                        #
                        #   ignore backtracked nodes which will not be part of the cycle
                        #       we are essentially doing tree traversal here
                        #
                        backtracked_nodes = set()
                        for f,t,n in self._examined_edges[cycle_start:cycle_end]:
                            if t == None:
                                backtracked_nodes.add(n)
                        for f,t,n in self._examined_edges[cycle_start:cycle_end]:
                            if f == None or f in backtracked_nodes or t in  backtracked_nodes:
                                continue
                            cycle_edges.add((f,t))
                            self._back_nodes.add(f)
                            self._back_nodes.add(t)
                        start_search_from = cycle_end
                        break

                    # if cycle_from_node comes around again, this is not a cycle
                    if cycle_from_node == f:
                        if not i:
                            i += 1
                        start_search_from = start_search_from + i
                        break


                    continue

                # no more cycles for this cycle_from_node/cycle_to_node pair
                else:
                    break

        self._back_edges.update(cycle_edges)


    #_____________________________________________________________________________________

    #   not_dag

    #_____________________________________________________________________________________
    def topological_sorted (self):
        """
        _finished_nodes
        """
        return self._finished_nodes




    #_____________________________________________________________________________________

    #   terminate_before

    #_____________________________________________________________________________________
    def terminate_before(self, node):
        """
        Allow node to terminate this path in DFS without including itself
            (see terminate_at)

        If node in _forced_dfs_nodes that overrides what the node wants
        """

        #
        #   If _node_termination = IGNORE_NODE_TERMINATION
        #       always go through whole tree
        #
        if self._node_termination == self.IGNORE_NODE_SIGNAL:
            return False

        #
        #   If _node_termination = NOTE_NODE_TERMINATION
        #       always go through whole tree but remember
        #       which nodes want to terminate
        #
        #   Note that _forced_dfs_nodes is ignored
        #
        if self._node_termination == self.NOTE_NODE_SIGNAL:
            if node.signal(self._extra_data_for_signal):
                self._signalling_nodes.add(node)
            return False

        #
        #   _forced_dfs_nodes always overrides node preferences
        #       but let us save what the node says anyway for posterity
        #
        if node in self._forced_dfs_nodes:
            ##   Commented out code lets us save self_terminating_nodes even when
            ##       they have been overridden by _forced_dfs_nodes
            #if node.signal():
            #    self._signalling_nodes.add(node)
            return False

        #
        #   OK. Go by what the node wants then
        #
        if node.signal(self._extra_data_for_signal):
            self._signalling_nodes.add(node)
            return True
        return False




    #_____________________________________________________________________________________

    #   call_backs

    #_____________________________________________________________________________________
    def discover_vertex(self, node):
        pass
    def start_vertex(self, node):
        self._start_nodes.add(node)
    def finish_vertex(self, node):
        """
        Save
            1) topologically sorted nodes
            2) as "None" (back) edges which allows _examined_edges to be traversed
               like a tree

        """
        self._examined_edges.append((None, None, node))
        self._finished_nodes.append(node)

    def examine_edge(self, node_from, node_to):
        """
        Save edges as we encounter then so we can look for loops

        """
        self._examined_edges.append((node_from, node_to, None))
    def back_edge(self, node_from, node_to):
        self._back_edges.add((node_from, node_to))
    def tree_edge(self, node_from, node_to):
        pass
    def forward_or_cross_edge(self, node_from, node_to):
        pass
    def terminate_at (self, node):
        """
        Terminate this line of DFS but include myself
        """
        return False

#
#_________________________________________________________________________________________

#   debug_print_visitor

#_________________________________________________________________________________________
class debug_print_visitor (object):
    """
    log progress through DFS: for debugging

    """
    def terminate_before(self, node):
        return False
    def terminate_at (self, node):
        return False
    def start_vertex(self, node):
        print "s  start vertex %s" % (node._name)
    def finish_vertex(self, node):
        print "  v  finish vertex %s" % (node._name)
    def discover_vertex(self, node):
        print "  |  discover vertex %s" % (node._name)
    def examine_edge(self, node_from, node_to):
        print "  -- examine edge %s -> %s" % (node_from._name, node_to._name)
    def back_edge(self, node_from, node_to):
        print "    back edge %s -> %s" % (node_from._name, node_to._name)
    def tree_edge(self, node_from, node_to):
        print "   - tree edge %s -> %s" % (node_from._name, node_to._name)
    def forward_or_cross_edge(self, node_from, node_to):
        print "   - forward/cross edge %s -> %s" % (node_from._name, node_to._name)













#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   Functions


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888


#_________________________________________________________________________________________

#   depth first search

#_________________________________________________________________________________________
#
#
#
WHITE = 0       # virgin
GRAY  = 1       # processing
BLACK = 2       # finished

def depth_first_visit(u, visitor, colours, outedges_func):
    """
    depth_first_visit
        unused callbacks are commented out
    """
    # start processing this node: so gray
    colours[u] = GRAY

    stack = list()

    #
    # unused callback
    #
    #visitor.discover_vertex(u)

    curr_edges = outedges_func(u)


    if visitor.terminate_before(u):
        colours[u] = BLACK
        return
    # If this vertex terminates the search, we push empty range
    if visitor.terminate_at(u):
        stack.append((u, curr_edges, len(curr_edges)))
    else:
        stack.append((u, curr_edges, 0))


    while len(stack):
        u, curr_edges, curr_edge_pos = stack.pop()
        while curr_edge_pos < len(curr_edges):
            v = curr_edges[curr_edge_pos]
            visitor.examine_edge(u, v)
            v_colour = colours[v]

            if visitor.terminate_before(v):
                colours[v] = BLACK
                curr_edge_pos += 1
                continue

            if v_colour == WHITE:
                #
                # unused callback
                #
                #visitor.tree_edge(u, v)
                curr_edge_pos += 1
                stack.append((u, curr_edges, curr_edge_pos))
                u = v
                colours[u] = GRAY
                #
                # unused callback
                #
                #visitor.discover_vertex(u)
                curr_edges = outedges_func(u)
                curr_edge_pos = 0


                if visitor.terminate_at(u):
                    break
            elif v_colour == GRAY:
                visitor.back_edge(u, v)
                curr_edge_pos += 1
            else:
                #
                # unused callback
                #
                #visitor.forward_or_cross_edge(u, v)
                curr_edge_pos += 1
        colours[u] = BLACK
        visitor.finish_vertex(u)


def depth_first_search(starting_nodes, visitor, outedges_func = node.outward):
    """
    depth_first_search
        go through all starting points and DFV on each of them
        if they haven't been seen before
    """
    colours = defaultdict(int)  # defaults to WHITE
    if len(starting_nodes):
        for start in starting_nodes:
            if colours[start] == WHITE:
                visitor.start_vertex(start)
                depth_first_visit(start, visitor, colours, outedges_func)
    else:

        #
        #   go through all nodes, maintaining order
        #
        for start in node._all_nodes:
            if colours[start] == WHITE:
                visitor.start_vertex(start)
                depth_first_visit(start, visitor, colours, outedges_func)



#_________________________________________________________________________________________

#   topologically_sorted_nodes



#_________________________________________________________________________________________
def topologically_sorted_nodes( to_leaves,
                                force_start_from = [],
                                gather_all_non_signalled = True,
                                test_all_signals = False,
                                extra_data_for_signal = None):
    """
    Get all nodes which are children of to_leaves
        in topological sorted order

    Defaults to including all nodes which are non-signalled
        i.e. includes the *last* non-signalling node on each branch


    Otherwise stops at each branch just before signalling node
        i.e. includes the last non-signalling *run* on each branch


    force_start_from
    Optionally specify all the child nodes which *have* to
        be included in the list at least
        This will override any node signals

    force_start_from = True to get the whole tree irrespective of signalling


    Rewritten to minimise calls to node.signal()

    """

    #
    #   got through entire tree, looking for signalling nodes,
    #       usually for debugging or for printing
    #
    if test_all_signals:
        v = topological_sort_visitor([],
                                    topological_sort_visitor.NOTE_NODE_SIGNAL,
                                    extra_data_for_signal)
        depth_first_search(to_leaves, v, node.outward)
        signalling_nodes = v._signalling_nodes
    else:
        signalling_nodes = set()

    if gather_all_non_signalled:
        #
        #   get whole tree, ignoring signalling
        #
        v = topological_sort_visitor([],
                                     topological_sort_visitor.IGNORE_NODE_SIGNAL,
                                    None)
        depth_first_search(to_leaves, v, node.outward)

        #
        #   not dag: no further processing
        #
        if v.not_dag():
            v.identify_dag_violating_nodes_and_edges ()
            return (v.topological_sorted(), v._signalling_nodes, v.dag_violating_edges(),
                    v.dag_violating_nodes())


        #
        #   return entire tree
        #
        if force_start_from == True:
            return (v.topological_sorted(), v._signalling_nodes, v.dag_violating_edges(),
                    v.dag_violating_nodes())



        #
        #   If we include these nodes anyway,
        #       why bother to check if they do not signal?
        #   Expensive signal checking should  be minimised
        #
        nodes_to_include = set()
        for n in force_start_from:
            if n in nodes_to_include:
                continue
            nodes_to_include.add(n)
            nodes_to_include.update(get_parent_nodes([n]))


        reversed_nodes = v.topological_sorted()
        for n in reversed_nodes:
            if n in nodes_to_include:
                continue

            if not n.signal(extra_data_for_signal):
                nodes_to_include.add(n)
                nodes_to_include.update(get_parent_nodes([n]))
            else:
                signalling_nodes.add(n)
                #sys.stderr.write(json.dumps(n, cls=node_to_json, sort_keys=1) + "\n")


        return ([n for n in v.topological_sorted() if n in nodes_to_include],
                signalling_nodes,
                [],[])

    else:

        if force_start_from == True:
            #
            #   get whole tree, ignoring signalling
            #
            v = topological_sort_visitor([],
                                         topological_sort_visitor.IGNORE_NODE_SIGNAL,
                                         extra_data_for_signal)
        else:
            #
            #   End at each branch without including signalling node
            #       but ignore signalling for forced_nodes_and_dependencies
            #

            #   Get all parents of forced nodes if necessary
            forced_nodes_and_dependencies = []
            if len(force_start_from):
                forced_nodes_and_dependencies = get_parent_nodes(force_start_from)

            v = topological_sort_visitor(   forced_nodes_and_dependencies,
                                            topological_sort_visitor.END_ON_SIGNAL,
                                            extra_data_for_signal)


        #
        #   Forward graph iteration
        #
        depth_first_search(to_leaves, v, node.outward)

        if v.not_dag():
            v.identify_dag_violating_nodes_and_edges ()

        signalling_nodes.update(v._signalling_nodes)
        return (v.topological_sorted(), signalling_nodes, v.dag_violating_edges(), v.dag_violating_nodes())


#
def debug_print_nodes(to_leaves):
    v = debug_print_visitor()
    depth_first_search(to_leaves, v, node.outward)



#_________________________________________________________________________________________

#   graph_printout

#_________________________________________________________________________________________
def graph_colour_demo_printout (stream,
                                output_format,
                                size                      = '11,8',
                                dpi                       = '120'):
    """
    Demo of the different colour schemes
    """

    if output_format == 'dot':
        write_colour_scheme_demo_in_dot_format(stream)
        return

    # print to dot file
    #temp_dot_file = tempfile.NamedTemporaryFile(suffix='.dot', delete=False)
    fh, temp_dot_file_name = tempfile.mkstemp(suffix='.dot')
    temp_dot_file = os.fdopen(fh, "w")

    write_colour_scheme_demo_in_dot_format(temp_dot_file)
    temp_dot_file.close()

    print_dpi = ("-Gdpi='%s'" % dpi) if output_format != "svg" else ""
    run_dot = os.popen("dot -Gsize='%s' %s -T%s < %s" % (size, print_dpi, output_format, temp_dot_file_name))

    #
    #   wierd bug fix for firefox and svg
    #
    result_str = run_dot.read()
    err = run_dot.close()
    if err:
        raise RuntimeError("dot failed to run with exit code %d" % err)
    if output_format == "svg":
        result_str = result_str.replace("0.12", "0.0px")
    stream.write(result_str)
#_________________________________________________________________________________________

#   graph_printout_in_dot_format

#_________________________________________________________________________________________
def graph_printout_in_dot_format (  stream,
                                    to_leaves,
                                    force_start_from          = [],
                                    draw_vertically           = True,
                                    ignore_upstream_of_target = False,
                                    skip_signalling_nodes     = False,
                                    gather_all_non_signalled  = True,
                                    test_all_signals          = True,
                                    no_key_legend             = False,
                                    minimal_key_legend        = True,
                                    user_colour_scheme        = None,
                                    pipeline_name             = "Pipeline:",
                                    extra_data_for_signal     = None):
    """
    print out pipeline dependencies in dot formatting
    """

    (topological_sorted,
    signalling_nodes,
    dag_violating_edges,
    dag_violating_nodes) = topologically_sorted_nodes(to_leaves, force_start_from,
                                                        gather_all_non_signalled,
                                                        test_all_signals,
                                                        extra_data_for_signal)

    #
    #   N.B. For graph:
    #           upstream   = parent
    #           dependents/downstream
    #                      = children
    #
    #
    nodes_to_display = get_reachable_nodes(to_leaves, not ignore_upstream_of_target)

    #
    #   print out dependencies in dot format
    #
    write_flowchart_in_dot_format(topological_sorted,
                                  signalling_nodes,
                                  dag_violating_edges,
                                  dag_violating_nodes,
                                  stream,
                                  to_leaves,
                                  force_start_from,
                                  nodes_to_display,
                                  draw_vertically,
                                  skip_signalling_nodes,
                                  no_key_legend,
                                  minimal_key_legend,
                                  user_colour_scheme,
                                  pipeline_name)

#_________________________________________________________________________________________

#   graph_printout

#_________________________________________________________________________________________
def graph_printout (stream,
                    output_format,
                    to_leaves,
                    force_start_from          = [],
                    draw_vertically           = True,
                    ignore_upstream_of_target = False,
                    skip_signalling_nodes     = False,
                    gather_all_non_signalled  = True,
                    test_all_signals          = True,
                    no_key_legend             = False,
                    minimal_key_legend        = True,
                    user_colour_scheme        = None,
                    pipeline_name             = "Pipeline:",
                    size                      = (11,8),
                    dpi                       = 120,
                    extra_data_for_signal     = None):
    """
    print out pipeline dependencies in a variety of formats, using the programme "dot"
        an intermediary
    """

    if output_format == 'dot':
        graph_printout_in_dot_format (  stream,
                                        to_leaves,
                                        force_start_from,
                                        draw_vertically,
                                        ignore_upstream_of_target,
                                        skip_signalling_nodes,
                                        gather_all_non_signalled,
                                        test_all_signals,
                                        no_key_legend,
                                        minimal_key_legend,
                                        user_colour_scheme,
                                        pipeline_name,
                                        extra_data_for_signal)
        return

    # print to dot file
    #temp_dot_file = tempfile.NamedTemporaryFile(suffix='.dot', delete=False)
    fh, temp_dot_file_name = tempfile.mkstemp(suffix='.dot')
    temp_dot_file = os.fdopen(fh, "w")

    graph_printout_in_dot_format (  temp_dot_file,
                                    to_leaves,
                                    force_start_from,
                                    draw_vertically,
                                    ignore_upstream_of_target,
                                    skip_signalling_nodes,
                                    gather_all_non_signalled,
                                    test_all_signals,
                                    no_key_legend,
                                    minimal_key_legend,
                                    user_colour_scheme,
                                    pipeline_name,
                                    extra_data_for_signal)
    temp_dot_file.close()

    if isinstance(size, tuple):
        print_size = "(%d,%d)" % size
    elif isinstance(size, basestring):
        print_size = size
    else:
        raise Exception("Flowchart print size [%s] should be specified as a tuple of X,Y in inches" % str(size))

    #
    #   N.B. Resolution doesn't seem to play nice with SVG and is ignored
    #
    print_dpi = ("-Gdpi='%s'" % dpi) if output_format != "svg" else ""
    cmd = "dot -Gsize='%s' %s -T%s < %s" % (print_size, print_dpi, output_format, temp_dot_file_name)


    proc = subprocess.Popen(cmd, shell = True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    result_str, error_str = proc.communicate()
    retcode = proc.returncode
    if retcode:
        raise subprocess.CalledProcessError(retcode, cmd + "\n" + "\n".join([result_str, error_str]))



    #run_dot = os.popen(cmd)
    #result_str = run_dot.read()
    #err = run_dot.close()
    #
    #if err:
    #    raise RuntimeError("dot failed to run with exit code %d" % err)


    #
    #   wierd workaround for bug / bad interaction between firefox and svg:
    #           Font sizes have "px" appended.
    #


    if output_format == "svg":
        result_str = result_str.replace("0.12", "0.0px")
    stream.write(result_str)



#_________________________________________________________________________________________

#   get_parent_nodes

#_________________________________________________________________________________________
def get_parent_nodes (nodes):
    """
    Get all parent nodes by DFS in the inward direction,
    Ignores signals
    """
    parent_visitor = topological_sort_visitor([],
                                            topological_sort_visitor.IGNORE_NODE_SIGNAL)
    depth_first_search(nodes, parent_visitor, node.inward)
    return parent_visitor.topological_sorted()


#_________________________________________________________________________________________

#   get_reachable_nodes

#_________________________________________________________________________________________
def get_reachable_nodes(nodes, parents_as_well = True):
    """
    Get all nodes which are parents and children of nodes
        recursing through the entire tree

    1) specify parents_as_well = False
        to only get children and not parents of nodes
        """

    # look for parents of nodes and start there instead
    if parents_as_well:
        nodes = get_parent_nodes (nodes)

    child_visitor = topological_sort_visitor([],
                                                topological_sort_visitor.IGNORE_NODE_SIGNAL)
    depth_first_search(nodes, child_visitor, node.outward)
    return child_visitor.topological_sorted()


#_________________________________________________________________________________________

#   Helper functions to dump edges and nodes

#_________________________________________________________________________________________
def get_edges_str (name, edges):
    """
    helper function to dump edges as a list of names
    """
    edges_str = "  %d %s edges\n" % (len(edges), name)
    edges_str += "    " + ", ".join(map(lambda (x, y): x._name + "->" + y._name, edges)) + "\n"
    return edges_str
def get_nodes_str (name, nodes):
    """
    helper function to dump nodes as a list of names
    """
    nodes_str = "  %s nodes = %d\n" % (name, len(nodes))
    nodes_str += "    " + ", ".join(map(lambda x: x._name, nodes)) + "\n"
    return nodes_str


