Source Code for Module TEES.Utils.InteractionXML.RemoveUnconnectedEntities

 1  import sys, os 
 2  thisPath = os.path.dirname(os.path.abspath(__file__)) 
 3  sys.path.append(os.path.abspath(os.path.join(thisPath,"../.."))) 
 4  import Utils.ElementTreeUtils as ETUtils 
 5   
 6 -def removeUnconnectedEntities(input, output=None): 
 7      input = ETUtils.ETFromObj(input) 
 8      root = input.getroot() 
 9      removed = 0 
10      preserved = 0 
11      for document in root.findall("document"): 
12          sentMap = {} # allow for intersentence interactions 
13          for sentence in document.findall("sentence"): 
14              sentMap[sentence.get("id")] = sentence 
15          connected = set() 
16          for interaction in document.getiterator("interaction"): 
17              connected.add(interaction.get("e1")) 
18              connected.add(interaction.get("e2")) 
19          entities = [] 
20          for entity in document.getiterator("entity"): 
21              entities.append(entity) 
22          for entity in entities: 
23              if entity.get("isName") == "True": # never remove named entities 
24                  continue 
25              eId = entity.get("id") 
26              if eId not in connected: 
27                  if eId.find(".s") != -1: # sentence level entity 
28                      sentMap[eId.rsplit(".", 1)[0]].remove(entity) 
29                  else: # document level entity 
30                      document.remove(entity) 
31                  removed += 1 
32              else: 
33                  preserved += 1 
34       
35      print >> sys.stderr, "Removed", removed, "entities, preserved", preserved, "entities" 
36       
37      if output != None: 
38          print >> sys.stderr, "Writing output to", output 
39          ETUtils.write(root, output) 
40      return input 
41   
42  if __name__=="__main__": 
43      import sys 
44       
45      from optparse import OptionParser 
46      # Import Psyco if available 
47      try: 
48          import psyco 
49          psyco.full() 
50          print >> sys.stderr, "Found Psyco, using" 
51      except ImportError: 
52          print >> sys.stderr, "Psyco not installed" 
53   
54      optparser = OptionParser(usage="%prog [options]\n") 
55      optparser.add_option("-i", "--input", default=None, dest="input", help="Corpus in interaction xml format", metavar="FILE") 
56      optparser.add_option("-o", "--output", default=None, dest="output", help="Output file in interaction xml format.") 
57      (options, args) = optparser.parse_args() 
58       
59      if options.input == None: 
60          print >> sys.stderr, "Error, first input file not defined." 
61          optparser.print_help() 
62          sys.exit(1) 
63      if options.output == None: 
64          print >> sys.stderr, "Error, output file not defined." 
65          optparser.print_help() 
66          sys.exit(1) 
67       
68      removeUnconnectedEntities(options.input, options.output) 
69