This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.util.topsort
""" Topological sort. From Tim Peters, see: http://mail.python.org/pipermail/python-list/1999-July/006660.html topsort takes a list of pairs, where each pair (x, y) is taken to mean that x <= y wrt some abstract partial ordering. The return value is a list, representing a total ordering that respects all the input constraints. E.g., topsort( [(1,2), (3,3)] ) Valid topological sorts would be any of (but nothing other than) [3, 1, 2] [1, 3, 2] [1, 2, 3] ... however this variant ensures that 'key' order (first element of tuple) is preserved so the following will be result returned: [1, 3, 2] because those are the permutations of the input elements that respect the "1 precedes 2" and "3 precedes 3" input constraints. Note that a constraint of the form (x, x) is really just a trick to make sure x appears *somewhere* in the output list. If there's a cycle in the constraints, say topsort( [(1,2), (2,1)] ) then CycleError is raised, and the exception object supports many methods to help analyze and break the cycles. This requires a good deal more code than topsort itself! """ from galaxy.util.odict import odict as OrderedDict[docs]class CycleError(Exception):def _numpreds_and_successors_from_pairlist(pairlist): numpreds = OrderedDict() # elt -> # of predecessors successors = OrderedDict() # elt -> list of successors for first, second in pairlist: # make sure every elt is a key in numpreds if first not in numpreds: numpreds[first] = 0 if second not in numpreds: numpreds[second] = 0 # if they're the same, there's no real dependence if first == second: continue # since first < second, second gains a pred ... numpreds[second] = numpreds[second] + 1 # ... and first gains a succ if first in successors: successors[first].append(second) else: successors[first] = [second] return numpreds, successors[docs] def __init__(self, sofar, numpreds, succs): Exception.__init__(self, "cycle in constraints", sofar, numpreds, succs) self.preds = None# return as much of the total ordering as topsort was able to # find before it hit a cycle[docs] def get_partial(self): return self# return remaining elt -> count of predecessors map[docs] def get_pred_counts(self): return self# return remaining elt -> list of successors map[docs] def get_succs(self): return self# return remaining elements (== those that don't appear in # get_partial())[docs] def get_elements(self): return self.get_pred_counts().keys()# Return a list of pairs representing the full state of what's # remaining (if you pass this list back to topsort, it will raise # CycleError again, and if you invoke get_pairlist on *that* # exception object, the result will be isomorphic to *this* # invocation of get_pairlist). # The idea is that you can use pick_a_cycle to find a cycle, # through some means or another pick an (x,y) pair in the cycle # you no longer want to respect, then remove that pair from the # output of get_pairlist and try topsort again.[docs] def get_pairlist(self): succs = self.get_succs() answer =  for x in self.get_elements(): if x in succs: for y in succs[x]: answer.append((x, y)) else: # make sure x appears in topsort's output! answer.append((x, x)) return answer# return remaining elt -> list of predecessors map[docs] def get_preds(self): if self.preds is not None: return self.preds self.preds = preds = OrderedDict() remaining_elts = self.get_elements() for x in remaining_elts: preds[x] =  succs = self.get_succs() for x in remaining_elts: if x in succs: for y in succs[x]: preds[y].append(x) if __debug__: for x in remaining_elts: assert len(preds[x]) > 0 return preds# return a cycle [x, ..., x] at random[docs] def pick_a_cycle(self): remaining_elts = self.get_elements() # We know that everything in remaining_elts has a predecessor, # but don't know that everything in it has a successor. So # crawling forward over succs may hit a dead end. Instead we # crawl backward over the preds until we hit a duplicate, then # reverse the path. preds = self.get_preds() from random import choice x = choice(remaining_elts) answer =  index = OrderedDict() in_answer = index.has_key while not in_answer(x): index[x] = len(answer) # index of x in answer answer.append(x) x = choice(preds[x]) answer.append(x) answer = answer[index[x]:] answer.reverse() return answer[docs]def topsort(pairlist): numpreds, successors = _numpreds_and_successors_from_pairlist(pairlist) # suck up everything without a predecessor answer = [x for x in numpreds.keys() if numpreds[x] == 0] # for everything in answer, knock down the pred count on # its successors; note that answer grows *in* the loop for x in answer: assert numpreds[x] == 0 del numpreds[x] if x in successors: for y in successors[x]: numpreds[y] = numpreds[y] - 1 if numpreds[y] == 0: answer.append(y) # following "del" isn't needed; just makes # CycleError details easier to grasp del successors[x] if numpreds: # everything in numpreds has at least one predecessor -> # there's a cycle if __debug__: for x in numpreds.keys(): assert numpreds[x] > 0 raise CycleError(answer, numpreds, successors) return answer[docs]def topsort_levels(pairlist): numpreds, successors = _numpreds_and_successors_from_pairlist(pairlist) answer =  while 1: # Suck up everything without a predecessor. levparents = [x for x in numpreds.keys() if numpreds[x] == 0] if not levparents: break answer.append(levparents) for levparent in levparents: del numpreds[levparent] if levparent in successors: for levparentsucc in successors[levparent]: numpreds[levparentsucc] -= 1 del successors[levparent] if numpreds: # Everything in num_parents has at least one child -> # there's a cycle. raise CycleError(answer, numpreds, successors) return answer