#! /usr/bin/python """CAnonicalize N-Triples Options: --verbose -v Print what you are doing as you go --help -h Print this message and exit --from=uri -f uri Specify an input file (or web resource) --diff=uri -d uri Specify a difference file Can have any number of --from parameters, in which case files are merged. If none are given, /dev/stdin is used. If any diff files are given then the diff files are read merged separately and compared with the input files. the result is a list of differences instead of the canonicalizd graph. This is NOT a minimal diff. Exits with nonzero system status if graphs do not match. This is an independent n-triples cannonicalizer. It uses heuristics, and will not terminate on all graphs. It is designed for testing: the output and the reference output are both canonicalized and compared. It uses the very simple NTriples format. It is designed to be independent of the SWAP code so that it can be used to test the SWAP code. It doesn't boast any fancy algorithms - just tries to get the job done for the small files in the test datasets. The algorithm to generate a "signature" for each bnode. This is just found by looking in its immediate viscinity, treating any local bnode as a blank. Bnodes which have signatures unique within the graph can be allocated cannonical identifiers as a function of the ordering of the signatures. These are then treated as fixed nodes. If another pass is done of the new graph, the signatures are more distinct. This works for well-labelled graphs, and graphs which don't have large areas of interconnected bnodes or large duplicate areas. A particular failing is complete lack of treatment of symmetry between bnodes. References: .google graph isomorphism See also eg http://www.w3.org/2000/10/rdf-tests/rdfcore/utils/ntc/compare.cc NTriples: see http://www.w3.org/TR/rdf-testcases/#ntriples Not to mention, published this month by coincidence: Kelly, Brian, [Whitehead Institute] "Graph cannonicalization", Dr Dobb's Journal, May 2003. $Id: cant.py,v 1.13 2004/11/09 01:08:28 syosi Exp $ This is or was http://www.w3.org/2000/10/swap/cant.py W3C open source licence . 2004-02-31 Serious bug fixed. This is a test program, shoul dbe itself tested. Quis custodiet ipsos custodes? """ # canticle - Canonicalizer of NTriples Independent of Cwm , Llyn, Etc. ? import os import sys import urllib try: from swap import uripath # http://www.w3.org/2000/10/swap/ except ImportError: import uripath from sys import stderr, exit import uripath import getopt import re import types name = "[A-Za-z][A-Za-z0-9]*" #http://www.w3.org/TR/rdf-testcases/#ntriples nodeID = '_:' + name uriref = r'<[^>]*>' language = r'[a-z0-9]+(?:-[a-z0-9]+)?' string_pattern = r'".*"' # We know in ntriples that there can only be one string on the line langString = string_pattern + r'(?:@' + language + r')?' datatypeString = langString + '(?:\^\^' + uriref + r')?' #literal = langString + "|" + datatypeString object = r'(' + nodeID + "|" + datatypeString + "|" + uriref + r')' ws = r'[ \t]*' com = ws + r'(#.*)?[\r\n]*' comment = re.compile("^"+com+"$") statement = re.compile( ws + object + ws + object + ws + object + com) # #" def usage(): print __doc__ def loadFiles(testFiles): graph = [] WD = "file://" + os.getcwd() + "/" for fn in testFiles: if verbose: stderr.write("Loading data from %s\n" % fn) uri = uripath.join(WD, fn) inStream = urllib.urlopen(uri) while 1: line = inStream.readline() if line == "" : break # if verbose: stderr.write("%s\n" % line) m = comment.match(line) if m != None: continue m = statement.match(line) if m == None: stderr.write("Syntax error: "+line+"\n") if verbose: [stderr.write('%2x ' % ord(c)) for c in line] stderr.write('\n') exit(-1) triple = m.group(1), m.group(2), m.group(3) if verbose: stderr.write( "Triple: %s %s %s.\n" % (triple[0], triple[1], triple[2])) graph.append(triple) if verbose: stderr.write("\nThere are %i statements in graph\n" % (len(graph))) return graph def main(): testFiles = [] diffFiles = [] global ploughOn # even if error ploughOn = 0 global verbose verbose = 0 try: opts, args = getopt.getopt(sys.argv[1:], "hf:d:iv", ["help", "from=", "diff=" "ignoreErrors", "verbose"]) except getopt.GetoptError: # print help information and exit: usage() sys.exit(2) output = None for o, a in opts: if o in ("-h", "--help"): usage() sys.exit() if o in ("-v", "--verbose"): verbose = 1 if o in ("-i", "--ignoreErrors"): ploughOn = 1 if o in ("-f", "--from"): testFiles.append(a) if o in ("-d", "--diff"): diffFiles.append(a) if testFiles == []: testFiles = [ "/dev/stdin" ] graph = loadFiles(testFiles) graph = canonicalize(graph) if diffFiles != []: graph2 = loadFiles(diffFiles) graph2 = canonicalize(graph2) d = compareCanonicalGraphs(graph, graph2) if d != 0: sys.exit(d) else: serialize(graph) def compareCanonicalGraphs(g1, g2): inserted, deleted = [], [] g1.sort() g2.sort() i1, i2 = 0,0 while 1: if i1 == len(g1): inserted = inserted + g2[i2:] if verbose: stderr.write("All other %i triples were inserted.\n" % (len(g2)-i2)) break if i2 == len(g2): deleted = deleted + g1[i1:] if verbose: stderr.write("All other %i triples were deleted.\n" % (len(g1)-i1)) break d = cmp(g1[i1], g2[i2]) # 1-2 if d==0: if verbose: stderr.write("Common: %s %s %s.\n" % g2[i2]) i1 += 1 i2 += 1 elif d<0: if verbose: stderr.write("Deleted: %s %s %s.\n" % g1[i1]) deleted.append(g1[i1]) i1 += 1 else: if verbose: stderr.write("Inserted: %s %s %s.\n" % g2[i2]) inserted.append(g2[i2]) i2 += 1 for triple in deleted: print "- %s %s %s." % triple for triple in inserted: print "+ %s %s %s." % triple number = len(deleted) + len(inserted) if verbose: if number == 0: stderr.write("FILES MATCH.\n") else: stderr.write("FILES DIFFER. (%i statements by our count)\n"% number) return number def canonicalize(g): "Do our best with this algo" dups, graph, c = canon(g) while dups != 0: newDups, graph, c = canon(graph, c) if newDups == dups: exit(-2) # give up dups = newDups return graph def serialize(graph): graph.sort() if verbose: print "# Canonicalized:" for t in graph: for x in t: if x.startswith("__"): x = x[1:] print x, print "." def compareFirst(a,b): "Compare consistently nested lists of strings" d = cmp(`a[0]`, `b[0]`) if verbose: if d<0: stderr.write("Comparing: %s]\n LESS THAN %s\n" % (`a`,`b`)) elif d>0: stderr.write("Comparing: %s]\n LESS THAN %s\n" % (`b`,`a`)) else: stderr.write("Comparing: %s]\n EQUALS %s\n" % (`b`,`a`)) return d #@@@@@@@@@@@@ if a==None and b == None: return 0 if a == None: return -1 if b == None: return 1 if isinstance(a, types.IntType): if isinstance (b,types.IntType): return a-b else: return -1 # Ints are less than strings or lists if isinstance(a, types.StringTypes): if isinstance (b, types.IntType): return 1 if isinstance (b,types.StringTypes): if a < b: return -1 if a > b: return 1 return 0 else: return -1 # Strings are less than lists else: # a is list if isinstance (b,types.StringTypes): return 1 else: # list vs list # assert isinstance(a, types.ListType) or isinstance(a, TupleType) if len(a) < len(b): return -1 if len(a) > len(b): return 1 for i in range(len(a)): d = compare(a[i], b[i], level+1) if d != 0: return d return 0 def canon(graph, c0=0): """Try one pass at canonicalizing this using 1 step sigs. Return as a triple: - The new graph - The number of duplicate signatures in the bnodes - The index number for th enext constant to be generated.""" nextBnode = 0 bnodes = {} pattern = [] signature = [] canonical = {} for j in range(len(graph)): triple = graph[j] pat = [] for i in range(3): if triple[i].startswith("_:"): b = bnodes.get(triple[i], None) if b == None: b = nextBnode nextBnode = nextBnode + 1 bnodes[triple[i]] = b signature.append([]) pat.append(None) else: pat.append(triple[i]) pattern.append(pat) for i in range(3): if triple[i].startswith("_:"): b = bnodes[triple[i]] signature[b].append((i, pat)) if verbose: stderr.write("\n") n = nextBnode s = [] for i in range(n): signature[i].sort() # Signature is now intrinsic to the local environment of that bnode. if verbose: stderr.write( "Bnode %3i) %s\n\n" % (i, signature[i])) s.append((signature[i], i)) s.sort(compareFirst) dups = 0 c = c0 if verbose: stderr.write("\nIn order\n") for i in range(n): sig, original = s[i] if verbose: stderr.write("%3i) Orig: %i Sig:%s\n" %(i, original, sig)) if i != n-1 and s[i][0] == s[i+1][0]: if verbose: stderr.write( "@@@ %3i] %i and %i have same signature: \n\t%s\nand\t%s\n" % ( i, s[i][1], s[i+1][1], s[i][0], s[i+1][0])) dups = dups + 1 elif i != 0 and s[i][0] == s[i-1][0]: if verbose: stderr.write( "@@@ %3i] %i and %i have same signature: \n\t%s\nand\t%s\n" % ( i, s[i][1], s[i-1][1], s[i][0], s[i-1][0])) else: canonical[original] = c if verbose: stderr.write( "\tBnode#%i canonicalized to new fixed C%i\n" %(s[i][1], c)) c = c + 1 newGraph = [] for j in range(len(graph)): triple = graph[j] newTriple = [] for i in range(3): x = triple[i] if x.startswith("_:"): b = bnodes[x] c1 = canonical.get(b, None) if c1 != None: x = "__:c" + str(c1) # New name newTriple.append(x) newGraph.append((newTriple[0], newTriple[1], newTriple[2])) if verbose: stderr.write("Iteration complete with %i duplicate signatures\n\n" %dups) return dups, newGraph, c if __name__ == "__main__": main() # ends