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taxonomy.py
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# Copyright (c) 2014 University of California, Davis
#
#
# 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.
import re
import copy
import signal, time
from relations import *
from latent_tax_assumption import *
from reasoner import *
from utility import *
import pdb
# this module defines the classes: Authority, Taxon, Taxonomy
#
class Authority:
def __init__(self, fullName="", abbrev=""):
self.fullName = fullName
self.abbrev = abbrev
def __repr__(self):
return "Authority: " + self.abbrev + "\n"
class Taxon:
def __init__(self, level=0):
self.parent = ""
self.children = []
self.fullName = ""
self.abbrev = ""
self.level = level
self.taxonomy = Taxonomy()
def addChild(self, child):
self.children += [child]
def hasChildren(self):
result = False
if (len(self.children) > 0):
result = True
return result
def stringOfReasoner(self):
return self.taxonomy.authority.abbrev + "_" + self.abbrev
def stringOf(self):
return self.taxonomy.authority.abbrev + "." + self.abbrev
def depthFirstPrint(self):
result = self.abbrev + " "
for child in self.children:
result += child.depthFirstPrint()
return result
def depthFirstLTax(self):
result = ""
for child in self.children:
result += child.stringOfReasoner() + "(x) -> " + self.stringOfReasoner() + "(x).\n"
result += child.depthFirstLTax()
return result
class Taxonomy:
def __init__(self, initString=""):
self.authority = Authority()
if (initString != ""):
authInfo = re.match("(.*?)\s(.*)", initString)
self.authority.abbrev = authInfo.group(1)
if (len(authInfo.groups() > 1)):
self.authority.fullName = authInfo.group(2)
self.roots = []
self.taxa = {}
def isEmpty(self):
if len(self.taxa.keys) == 0:
return True
else:
return False
def hasTaxon(self, theTaxon):
return (self.taxa.has_key(theTaxon))
def getTaxon(self, theTaxon):
if (not(self.taxa.has_key(theTaxon))):
print "no taxon " + theTaxon + " in " + self.authority.abbrev
return None
else:
return (self.taxa[theTaxon]);
def addTaxon(self, parent):
if self.taxa.has_key(parent):
return None
else:
thisParent = Taxon()
thisParent.abbrev = parent
thisParent.taxonomy = self
self.taxa[parent] = thisParent
self.roots.append(thisParent)
def addDoubleTaxon(self, taxaMap, parent, child, onlyOne):
thisParent = self.taxa[parent]
if (child != ""):
if self.taxa.has_key(child):
thisChild = self.taxa[child]
else:
thisChild = Taxon(thisParent.level+1)
thisChild.abbrev = child
thisChild.taxonomy = self
self.taxa[child] = thisChild
thisChild.parent = thisParent
if(onlyOne):
taxaMap.addEMir(parent, child)
else:
taxaMap.addTMir(self.authority.abbrev, parent, child)
for sibling in thisParent.children:
taxaMap.addDMir(self.authority.abbrev, child, sibling.abbrev)
thisParent.addChild(thisChild)
def addTaxaWithList(self, taxaMap, theList):
noParens = re.match("\((.*)\)", theList).group(1)
if (noParens.find(" ") != -1):
elements = re.split("\s", noParens)
self.addTaxon(elements[0])
for index in range (1, len(elements)):
self.addDoubleTaxon(taxaMap, elements[0], elements[index], len(elements) == 2)
else:
self.addTaxon(noParens)
def toLTax(self):
result = ""
for root in self.roots:
result += root.depthFirstLTax()
return result
def __repr__(self):
result = "Taxonomy: " + self.authority.abbrev + "\n"
for root in self.roots:
result += root.depthFirstPrint()
return result + "\n"
class Articulation:
def __init__(self, initInput="", mapping=None):
self.string = initInput
self.numTaxon = 2
self.confidence = 2
if (initInput == ""):
self.taxon1 = Taxon()
self.taxon2 = Taxon()
self.taxon3 = Taxon()
self.taxon4 = Taxon()
self.relations = []
return None
if (initInput.find("confidence=") != -1):
elements = re.match("(.*) confidence=(.*)", initInput)
initInput = elements.group(1)
self.confidence = int(elements.group(2))
if (initInput.find("sum") != -1 or initInput.find("diff") != -1):
if (initInput.find("lsum") != -1):
self.relations = [relationDict["+="]]
elements = re.match("(.*)\.(.*) (.*)\.(.*) lsum (.*)\.(.*)", initInput)
elif (initInput.find("rsum") != -1):
self.relations = [relationDict["=+"]]
elements = re.match("(.*)\.(.*) rsum (.*)\.(.*) (.*)\.(.*)", initInput)
elif (initInput.find("ldiff") != -1):
self.relations = [relationDict["-="]]
elements = re.match("(.*)\.(.*) (.*)\.(.*) ldiff (.*)\.(.*)", initInput)
elif (initInput.find("rdiff") != -1):
self.relations = [relationDict["=-"]]
elements = re.match("(.*)\.(.*) rdiff (.*)\.(.*) (.*)\.(.*)", initInput)
elif (initInput.find("e4sum") != -1):
self.relations = [relationDict["+=+"]]
elements = re.match("(.*)_(.*) (.*)_(.*) e4sum (.*)_(.*) (.*)_(.*)", initInput)
elif (initInput.find("i4sum") != -1):
self.relations = [relationDict["+<=+"]]
elements = re.match("(.*)_(.*) (.*)_(.*) i4sum (.*)_(.*) (.*)_(.*)", initInput)
taxon1taxonomy = elements.group(1)
taxon1taxon = elements.group(2)
taxon2taxonomy = elements.group(3)
taxon2taxon = elements.group(4)
taxon3taxonomy = elements.group(5)
taxon3taxon = elements.group(6)
self.taxon1 = mapping.getTaxon(taxon1taxonomy, taxon1taxon)
self.taxon2 = mapping.getTaxon(taxon2taxonomy, taxon2taxon)
self.taxon3 = mapping.getTaxon(taxon3taxonomy, taxon3taxon)
self.numTaxon = 3
if(initInput.find("4sum") != -1):
taxon4taxonomy = elements.group(7)
taxon4taxon = elements.group(8)
self.taxon4 = mapping.getTaxon(taxon4taxonomy, taxon4taxon)
self.numTaxon = 4
else:
## initInput is of form b48.a equals k04.a
self.relations = []
if (initInput.find("{") != -1):
elements = re.match("(.*)\.(.*) {(.*)} (.*)\.(.*)", initInput)
else:
elements = re.match("(.*)\.(.*) (.*) (.*)\.(.*)", initInput)
taxon1taxonomy = elements.group(1)
taxon1taxon = elements.group(2)
relString = elements.group(3)
taxon2taxonomy = elements.group(4)
taxon2taxon = elements.group(5)
if (relString.find(" ") != -1):
if (relationDict.has_key(relString)):
self.relations = [relationDict[relString]]
else:
relElements = re.split("\s", relString)
for rel in relElements:
self.relations += [relationDict[rel]]
else:
self.relations = [relationDict[relString]]
self.taxon1 = mapping.getTaxon(taxon1taxonomy, taxon1taxon)
self.taxon2 = mapping.getTaxon(taxon2taxonomy, taxon2taxon)
def toString(self):
return self.string
def toLTax(self):
result = ""
if self.numTaxon > 2:
#self.relations == [relationDict["+="]] or self.relations == [relationDict["=+"]]:
result = self.sArticulationSubtitution(self.taxon1, self.taxon2, self.taxon3, self.relations[0])
elif len(self.relations) == 1:
result = self.articulationSubtitution(self.taxon1, self.taxon2, self.relations[0])
else:
for relation in self.relations:
result += "(" + self.articulationSubtitution(self.taxon1, self.taxon2, relation)+ ")"
if (relation != self.relations[-1:][0]):
result += " | "
return result
def articulationSubtitution(self, taxon1, taxon2, relation):
relString = relation.logicSymbol
relString = relString.replace("$x", taxon1.stringOfReasoner())
relString = relString.replace("$y", taxon2.stringOfReasoner())
return relString
def sArticulationSubtitution(self, taxon1, taxon2, taxon3, relation):
relString = relation.logicSymbol
relString = relString.replace("$x", taxon1.stringOfReasoner())
relString = relString.replace("$y", taxon2.stringOfReasoner())
relString = relString.replace("$z", taxon3.stringOfReasoner())
return relString
def __str__(self):
result = self.taxon1.stringOf() + " "
if len(self.relations) == 1:
result += self.relations[0].name
else:
result += "{"
for relation in self.relations:
if relation != self.relations[0]:
result += " "
result += relation.name
result += "}"
result += " " + self.taxon2.stringOf()
if self.numTaxon == 3:
result += " " + self.taxon3.stringOf()
return result
def __repr__(self):
return "<"+self.__str__()+">"
#result = "Articulation: " + self.taxon1.stringOf() + " "
#for relation in self.relations:
# result += relation.name + " "
#result += self.taxon2.stringOf() + " \n"
#return result
class ArticulationSet:
def __init__(self):
self.authority = Authority()
self.articulations = []
def addArticulationWithList(self, theList, taxonMapping):
articulation = Articulation(theList, taxonMapping)
self.articulations += [articulation]
def toLTax(self):
result = ""
for articulation in self.articulations:
result += articulation.toLTax() + ".\n"
return result
def __repr__(self):
result = "Articulation Set: " + self.authority.abbrev + "\n"
for articulation in self.articulations:
result += `articulation`
return result
class TaxonomyMapping:
#prover = Prover9()
#mace = Mace4()
def __init__(self):
self.articulationSet = ArticulationSet()
self.mir = {} # MIR
self.tr = [] # transitive reduction
self.eq = [] # euqlities
self.ltas = []
self.hypothesisType = ""
self.hypothesis = Articulation()
self.taxonomies = {}
def __repr__(self):
result = ""
for key in self.taxonomies.keys():
result += `self.taxonomies[key]`
result += `self.articulationSet`
return result
def createTMfromPW(self, pw, i):
newTM = TaxonomyMapping()
newTM.prover = self.prover
newTM.mace = self.mace
newTM.name = self.name+"_pw"+i.__str__()
newTM.taxonomies = copy.deepcopy(self.taxonomies)
newTM.ltas = self.ltas
newTM.mir = copy.deepcopy(self.mir)
newTM.tr = copy.deepcopy(self.tr)
newTM.eq = copy.deepcopy(self.eq)
for pair in pw.keys():
t=re.match("(.*),(.*)",pair)
tmpStr = pw[pair]
if(tmpStr == ""):
continue
if(tmpStr.find(",") != -1):
tmpStr = tmpStr.replace(","," ")
tmpStr = "{" + tmpStr + "}"
list = t.group(1)+" "+tmpStr+" "+t.group(2)
if(newTM.mir.has_key(pair) and newTM.mir[pair] != tmpStr):
newTM.mir[pair] = tmpStr
if(tmpStr == "is_included_in"):
newTM.tr.append([t.group(1), t.group(2), 1])
elif(tmpStr == "includes"):
newTM.tr.append([t.group(2), t.group(1), 1])
elif(tmpStr == "equals"):
newTM.eq.append([t.group(1), t.group(2)])
newTM.articulationSet.addArticulationWithList(list, newTM)
return newTM
def generatePW(self, outputDir, fileName):
tmpCnt = 1;
tmpBase = {};
PW = [];
for pair in self.mir.keys():
tmpList = self.mir[pair].replace("{", "").replace("}", "").split(",")
tmpBase[pair] = tmpCnt
tmpCnt = tmpCnt * len(tmpList)
for i in range(tmpCnt):
PW.append({})
for pair in self.mir.keys():
tmpList = self.mir[pair].replace("{", "").replace("}","").split(",")
for i in range(tmpCnt):
PW[i][pair]=tmpList[i / tmpBase[pair] % len(tmpList)]
consCnt = 0
for i in range(tmpCnt):
tm = self.createTMfromPW(PW[i], i)
consistencyCheck = tm.testConsistencyWithoutGoal(outputDir+"reasonerFiles/")
if consistencyCheck[0] == "true":
tm.outputPW(outputDir, fileName+"_pw_"+consCnt.__str__(), self)
consCnt = consCnt + 1
print "There is (are) " + consCnt.__str__() + " outof " + tmpCnt.__str__() + " possible world(s)."
def outputPW(self, outputDir, fileName, taxaMap):
fPW = open(outputDir+fileName+".csv", 'w')
for pair in self.mir.keys():
fPW.write(pair + "," + self.mir[pair] + "\n")
fPW.close()
# For testing purpose, disable provenance
#self.generateDot(outputDir,fileName, taxaMap)
def generateDot(self, outputDir, fileName, taxaMap):
fDot = open(outputDir+fileName+".dot", 'w')
fDot.write("digraph {\n\nrankdir = RL\n\n")
# Equalities
for [T1, T2] in self.eq:
T1s = T1.split(".")
T2s = T2.split(".")
if(T1s[1] == T2s[1]):
tmpStr = T1s[1]
fDot.write("\"" + tmpStr +"\" [color=blue];\n")
else:
tmpStr = T1+","+T2
tmpTr = list(self.tr)
for [T3, T4, P] in tmpTr:
if(T1 == T3 or T2 == T3):
self.tr.remove([T3, T4, P])
self.tr.append([tmpStr, T4, 0])
elif(T1 == T4 or T2 == T4):
self.tr.remove([T3, T4, P])
self.tr.append([T3, tmpStr, 0])
# Duplicates
tmpTr = list(self.tr)
for [T1, T2, P] in tmpTr:
if(self.tr.count([T1, T2, P]) > 1):
self.tr.remove([T1, T2, P])
tmpTr = list(self.tr)
for [T1, T2, P] in tmpTr:
if(P == 0):
if(self.tr.count([T1, T2, 1]) > 0):
self.tr.remove([T1, T2, 1])
# Reductions
tmpTr = list(self.tr)
for [T1, T2, P1] in tmpTr:
for [T3, T4, P2] in tmpTr:
if (T2 == T3):
if(self.tr.count([T1, T4, 0])>0):
self.tr.remove([T1, T4, 0])
self.tr.append([T1, T4, 2])
if(self.tr.count([T1, T4, 1])>0):
self.tr.remove([T1, T4, 1])
#self.tr.append([T1, T4, 3])
for [T1, T2, P] in self.tr:
if(P == 0):
fDot.write("\"" + T1 + "\" -> \"" + T2 + "\" [style=filled, color=black];\n")
elif(P == 1):
fDot.write("\"" + T1 + "\" -> \"" + T2 + "\" [style=filled, color=red];\n")
if(self == taxaMap):
self.traceDown(outputDir, T1, T2)
self.traceDown1(outputDir, T1, T2)
elif(P == 2):
fDot.write("\"" + T1 + "\" -> \"" + T2 + "\" [style=dashed, color=grey];\n")
fDot.write("}\n")
fDot.close()
def traceDown1(self, outputDir, T1, T2):
tmpStr = "Red edge " + T1 + "->"+ T2 + " is related to "
tmpTm = copy.deepcopy(self)
i = 0
while i < len(tmpTm.articulationSet.articulations):
a = tmpTm.articulationSet.articulations.pop(i)
tmpTm.hypothesisType = "implied"
tmpTm.hypothesis = Articulation(T1 + " is_included_in " + T2, tmpTm)
goal = tmpTm.testConsistencyWithGoal(outputDir, False, False)
#print tmpTm.articulationSet.articulations
if(goal[0].find("true") == -1):
tmpTm.articulationSet.articulations.insert(i, a)
i=i+1
tmpStr += tmpTm.articulationSet.articulations.__str__()
print tmpStr
def traceDown(self, outputDir, T1, T2):
tmpStr = "Red edge " + T1 + "->"+ T2 + " depends on ["
s = len(self.articulationSet.articulations)
for i in range(s):
a = self.articulationSet.articulations.pop(i)
self.hypothesisType = "implied"
self.hypothesis = Articulation(T1 + " is_included_in " + T2, self)
goal = self.testConsistencyWithGoal(outputDir + "reasonerFiles/", False, False)
if(goal[0].find("false") != -1):
tmpStr += `a`+" "
self.articulationSet.articulations.insert(i, a)
print tmpStr + "]"
def addTMir(self, tName, parent, child):
self.mir[tName + "." + parent +"," + tName + "." + child] = "{includes}"
self.tr.append([tName + "." + child, tName + "." + parent, 0])
self.addIMir(tName + "." + parent, tName + "." + child, 0)
def addDMir(self, tName, child, sibling):
self.mir[tName + "." + child +"," + tName + "." + sibling] ="{disjoint}"
self.mir[tName + "." + sibling +"," + tName + "." + child] ="{disjoint}"
def addPMir(self, t1, t2, r, provenance):
if(self.mir.has_key(t1 + "," + t2)):
return None
else:
r=r.rstrip()
#print t1+" "+r+" "+t2
#self.articulationSet.addArticulationWithList(t1+" "+r+" "+t2, self)
tmpStr=r.replace("{", "")
tmpStr=tmpStr.replace("}", "")
tmpStr=tmpStr.replace(" ", ",")
self.addAMir(t1+" "+tmpStr+" "+t2, provenance)
# articulation
def addAMir(self, astring, provenance):
r = astring.split(" ")
if (r[1] == "includes"):
self.addIMir(r[0], r[2], provenance)
self.tr.append([r[2], r[0], provenance])
elif (r[1] == "is_included_in"):
self.addIMir(r[2], r[0], provenance)
self.tr.append([r[0], r[2], provenance])
elif (r[1] == "equals"):
self.addEMir(r[0], r[2])
self.eq.append([r[0], r[2]])
elif (r[2] == "lsum"):
self.addIMir(r[3], r[0], provenance)
self.addIMir(r[3], r[1], provenance)
self.mir[r[0] + "," + r[3]] = "{is_included_in}"
self.mir[r[1] + "," + r[3]] = "{is_included_in}"
self.tr.append([r[0],r[3], provenance])
self.tr.append([r[1],r[3], provenance])
return None
elif (r[1] == "rsum"):
self.addIMir(r[0], r[2], provenance)
self.addIMir(r[0], r[3], provenance)
self.mir[r[0] + "," + r[2]] = "{includes}"
self.mir[r[0] + "," + r[3]] = "{includes}"
self.tr.append([r[2], r[0], provenance])
self.tr.append([r[3], r[0], provenance])
return None
elif (r[2] == "ldiff"):
self.addIMir(r[0], r[3], provenance)
self.mir[r[0] + "," + r[3]] = "{includes}"
self.tr.append([r[3], r[0], provenance])
return None
elif (r[1] == "rdiff"):
self.addIMir(r[3], r[0], provenance)
self.mir[r[3] + "," + r[0]] = "{is_included_in}"
self.tr.append([r[3], r[0], provenance])
return None
self.mir[r[0] + "," + r[2]] = "{"+r[1]+"}"
self.mir[r[0] + "," + r[2]] = "{"+r[1]+"}"
def removeMir(self, string):
r = string.split(" ")
self.mir[r[1] + "," + r[len(r)-1]] = ""
if(self.tr.count([r[1], r[len(r)-1]]) > 0):
self.tr.remove([r[1], r[len(r)-1]])
elif(self.tr.count([r[len(r)-1], r[1]]) > 0):
self.tr.remove([r[len(r)-1], r[1]])
if len(r) > 3:
if r[0] == "+=":
self.mir[r[2] + "," + r[3]] = ""
if(self.tr.count([r[2], r[3]]) > 0):
self.tr.remove([r[2], r[3]])
elif r[0] == "=+":
self.mir[r[1] + "," + r[2]] = ""
if(self.tr.count([r[2], r[1]]) > 0):
self.tr.remove([r[2], r[1]])
# isa
def addIMir(self, parent, child, provenance):
for pair in self.mir.keys():
if (self.mir[pair] == "{includes}"):
if (pair.find("," + parent) == len(pair) - len(parent) - 1):
newPair = pair.replace("," + parent, "," + child)
self.mir[newPair] = "{includes}"
elif (pair.find(child + ",") == 0):
newPair = pair.replace(child + ",", parent + ",")
self.mir[newPair] = "{includes}"
# Equality mir
def addEMir(self, parent, child):
for pair in self.mir.keys():
if (pair.find(parent+",") == 0):
newPair = pair.replace(parent+",", child+",")
self.mir[newPair] = self.mir[pair]
elif (pair.find(child+",") == 0):
newPair = pair.replace(child+",", parent+",")
self.mir[newPair] = self.mir[pair]
elif (pair.find(","+parent) == len(pair)-len(parent)-1):
newPair = pair.replace(","+parent, ","+child)
self.mir[newPair] = self.mir[pair]
elif (pair.find(","+child) == len(pair)-len(child)-1):
newPair = pair.replace(","+child, ","+parent)
self.mir[newPair] = self.mir[pair]
def setReasonerTimeout(self, timeout):
self.prover.setTimeout(timeout)
self.mace.setTimeout(timeout)
## this and the next
## method make it obvious
## that we need an ltaSet class
## which can print itself in various ways
##
def ltaString(self):
result = ""
if (len(self.ltas) == 0) :
result = "No LTAs"
else:
for lta in self.ltas:
result += lta.name + " "
return result
def ltaAbbrevString(self):
result = ""
for lta in self.ltas:
result += lta.abbrev + "_"
return result
def getTaxon(self, taxonomyName="", taxonName=""):
taxonomy = self.taxonomies[taxonomyName]
taxon = taxonomy.getTaxon(taxonName)
return taxon
def getAllArticulationPairs(self):
taxa = []
theseTaxonomies = self.taxonomies.keys()
for outerloop in range(len(theseTaxonomies)):
for innerloop in range(outerloop+1, len(theseTaxonomies)):
outerTaxa = self.taxonomies[theseTaxonomies[outerloop]].taxa.keys()
innerTaxa = self.taxonomies[theseTaxonomies[innerloop]].taxa.keys()
for outerTaxonLoop in range (len(outerTaxa)):
for innerTaxonLoop in range (len(innerTaxa)):
newTuple = (theseTaxonomies[outerloop] + "." + outerTaxa[outerTaxonLoop], theseTaxonomies[innerloop] + "." + innerTaxa[innerTaxonLoop])
taxa.append(newTuple)
return taxa
def getAllTaxonPairs(self):
taxa = self.getAllArticulationPairs()
theseTaxonomies = self.taxonomies.keys()
for taxonLoop in range(len(theseTaxonomies)):
thisTaxonomy = self.taxonomies[theseTaxonomies[taxonLoop]];
theseTaxa = thisTaxonomy.taxa.keys()
for outerloop in range(len(theseTaxa)):
for innerloop in range(outerloop+1, len(theseTaxa)):
newTuple = (theseTaxonomies[taxonLoop] + "." + theseTaxa[outerloop], theseTaxonomies[taxonLoop] + "." + theseTaxa[innerloop])
taxa.append(newTuple)
return taxa
def testConsistencyWithGoal(self,outputDir,compression, memory):
ltaxRules = ""
# write out taxonomies
for taxonomyName in self.taxonomies.keys():
ltaxRules += self.taxonomies[taxonomyName].toLTax()
# write out articulations
ltaxRules += self.articulationSet.toLTax()
#write out LTAs
for lta in self.ltas:
ltaxRules += lta.toLTax(self)
thisLTaxGoal = self.hypothesis.toLTax()
goalRel = str(self.hypothesis)
goalRel = goalRel.replace(" ","_")
goalRel = goalRel.replace("{","")
goalRel = goalRel.replace("}","")
thisGoal = goalRel + "_" + self.hypothesisType + "_"
#thisGoal = str(self.hypothesis).replace(" ", "_") + "_" + self.hypothesisType + "_"
# write out files for prover9 and mace4
# eventually this should be an option - it decides whether
# or not to test rules which have been given
#if (ltaxRules.find(thisLTaxGoal) == -1):
if (1 == 1):
if (memory == False):
proverOutputFile = outputDir + self.name + self.ltaAbbrevString() + thisGoal + "Prover.txt"
self.writeGoalFile(proverOutputFile, ltaxRules, self.prover, self.hypothesisType != "implied")
maceOutputFile = outputDir + self.name + self.ltaAbbrevString() + thisGoal + "Mace.txt"
self.writeGoalFile(maceOutputFile, ltaxRules, self.mace, False)
else:
proverOutputFile = self.makeGoalFile(ltaxRules, self.prover, True)
maceOutputFile = self.makeGoalFile(ltaxRules, self.mace, False)
if (self.hypothesisType == "implied"):
result = self.testConsistencyWithImpliedGoalNoMace(proverOutputFile, maceOutputFile, memory)
else:
result = self.testConsistencyWithPossibleGoal(proverOutputFile, maceOutputFile, memory)
if (ltaxRules.find(thisLTaxGoal) != -1):
result.append("given");
else:
result.append("inferred");
outputs = result[3]
if (compression):
compressFile(proverOutputFile)
compressFile(maceOutputFile)
for outputFile in outputs:
compressFile(outputFile)
else:
result = ["stated"]
#print "STATED!" + thisLTaxGoal
return result
def testConsistencyWithImpliedGoalNoMace(self, proverInput, maceInput, memory):
## this version does not do mace
reasoners = []
inputs = []
outputs = []
timeoutString = ""
proverOutput = self.prover.run(proverInput, memory)
reasoners.append(self.prover.name)
if (memory == False):
inputs.append(proverInput)
else:
inputs.append("memory");
outputs.append(proverOutput[1])
if (proverOutput[0] == "proved"):
result = "true"
else:
if (proverOutput[0].find("max_sec_no") != -1):
timeoutString += " prover9 timeout "
result = "false" + timeoutString
return [result, reasoners, inputs, outputs]
def testConsistencyWithImpliedGoal(self, proverInput, maceInput, memory):
reasoners = []
inputs = []
outputs = []
timeoutString = ""
proverOutput = self.prover.run(proverInput,memory)
reasoners.append(self.prover.name)
if (memory == False):
inputs.append(proverInput)
else:
inputs.append("memory");
outputs.append(proverOutput[1])
if (proverOutput[0] == "proved"):
result = "true"
self.prover.makeDot(proverOutput[1])
else:
if (proverOutput[0].find("max_sec_no") != -1):
timeoutString += " prover9 timeout "
maceOutput = self.mace.run(proverInput,memory)
reasoners.append(self.mace.name)
if (memory == False):
inputs.append(proverInput)
else:
inputs.append("memory");
outputs.append(maceOutput[1])
if (maceOutput[0] == "model found"):
result = "false" + timeoutString
else:
if (maceOutput[0].find("max_sec_no") != -1):
timeoutString += " mace4 timeout "
result = "unclear" + timeoutString
return [result, reasoners, inputs, outputs]
def testConsistencyWithPossibleGoal(self, proverInput, maceInput, memory):
reasoners = []
inputs = []
outputs = []
timeoutString = ""
# reasoners.append(self.mace.name)
# if (memory == False):
# inputs.append(maceInput)
# else:
# inputs.append("memory");
# maceOutput = self.mace.run(maceInput, False)
# outputs.append(maceOutput[1])
# if (maceOutput[0] == "model found"):
result = "true"
# else:
# if (maceOutput[0].find("max_sec_no") != -1):
# timeoutString += " mace4 timeout "
reasoners.append(self.prover.name)
if (memory == False):
inputs.append(proverInput)
else:
inputs.append("memory");
proverOutput = self.prover.run(proverInput, False)
outputs.append(proverOutput[1])
if (proverOutput[0] == "proved"):
result = "false" + timeoutString
else:
if (proverOutput[0].find("max_sec_no") != -1):
timeoutString += " prover9 timeout "
result = "unclear" + timeoutString
else:
result = "true" + timeoutString
return [result, reasoners, inputs, outputs]
#results are lists [result, [provers], [inputs], [outputs]]
def simpleRemedy(self, outputDir):
s = len(self.articulationSet.articulations)
for c in range(2):
for i in range(s):
a = self.articulationSet.articulations.pop(i)
if(a.confidence != 3-c):
self.articulationSet.articulations.insert(i, a)
continue
if(self.testConsistency(outputDir)):
self.removeMir(a.__str__())
fIE = open(outputDir + "../" + self.name + "_ie.txt", 'w')
print "Input is inconsistent!!"
print "Remedial measure: remove [" + a.toString() + "]"
fIE.write("Remedial measure: remove [" + a.toString() + "]\n")
self.traceOut1(outputDir, a, fIE)
fIE.close()
#self.traceOut(outputDir, a)
return True
self.articulationSet.articulations.insert(i, a)
return False
def nonrelatedArticulation(self, a, b):
A1 = Articulation(a.toString(), self)
A2 = Articulation(b.toString(), self)
if A1.taxon1.level > A2.taxon1.level+2 or\
A1.taxon1.level < A2.taxon1.level-2 or\
A1.taxon2.level > A2.taxon2.level+2 or\
A1.taxon2.level < A2.taxon2.level-2:
return True
return False
def traceOut1(self, outputDir, a, fIE):
tmpStr = "Articulation <" + a.__str__() + "> is inconsistent with "
tmpTm = copy.deepcopy(self)
i = 0
while i < len(tmpTm.articulationSet.articulations):
b = tmpTm.articulationSet.articulations.pop(i)
if(self.nonrelatedArticulation(a, b)):
tmpTm.articulationSet.articulations.insert(i, b)
i=i+1
continue
tmpTm.hypothesisType = "possible"
tmpTm.hypothesis = Articulation(b.toString(), self)
goal = tmpTm.testConsistencyWithGoal(outputDir, False, False)
#print tmpTm.articulationSet.articulations
if(goal[0].find("true") != -1):
tmpTm.articulationSet.articulations.insert(i, b)
i=i+1
tmpStr += tmpTm.articulationSet.articulations.__str__()
print tmpStr
fIE.write(tmpStr+"\n")
def traceOut(self, outputDir, a):
tmpStr = "Articulation " + a.__str__() + " is inconsistent with [ "
s = len(self.articulationSet.articulations)
for i in range(s):
a = self.articulationSet.articulations.pop(i)
self.hypothesisType = "possible"
self.hypothesis = Articulation(a.toString(), self)
goal = self.testConsistencyWithGoal(outputDir, False, False)
if(goal[0].find("false") != -1):
tmpStr += "<" + a.toString() + "> "
self.articulationSet.articulations.insert(i, a)
print tmpStr + "]"
def BCSremedy(self, outputDir):
testTaxMap = TaxonomyMapping()
testTaxMap = copy.deepcopy(self)
testTaxMap.articulationSet.articulations = []
consArti = self.BCS1(self.articulationSet.articulations, testTaxMap, outputDir)
print "BCS choose [" + ','.join(map(str,consArti)) + "] as the consistent articulation subset"
for a in self.articulationSet.articulations:
if not (a in consArti):
self.removeMir(a.__str__())
return True
def divideByTwo(self, articulations):
s = len(articulations)
arti1 = []
arti2 = []
for i in range(s/2):
arti1.append(articulations[i])
for i in range(s/2, s):
arti2.append(articulations[i])
return [arti1, arti2]
def BCS(self, articulations, inTaxMap, outputDir):
testTaxMap = copy.deepcopy(inTaxMap)
testTaxMap.articulationSet.articulations = testTaxMap.articulationSet.articulations + articulations
if(testTaxMap.testConsistency(outputDir)):
print ','.join(map(str,testTaxMap.articulationSet.articulations)) + " is consistent"
outArti = articulations
return outArti
if(len(articulations) <= 1):
return []
testTaxMap1 = copy.deepcopy(inTaxMap)
testTaxMap2 = copy.deepcopy(inTaxMap)
arti = self.divideByTwo(articulations)
testTaxMap1.articulationSet.articulations += arti[0]
testTaxMap2.articulationSet.articulations += arti[1]
flag1 = testTaxMap1.testConsistency(outputDir)
flag2 = testTaxMap2.testConsistency(outputDir)
if(flag1 and not flag2):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is consistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is inconsistent"
return arti[0]+self.BCS(arti[1],testTaxMap1, outputDir)
elif(flag2 and not flag1):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is inconsistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is consistent"
return arti[1]+self.BCS(arti[0],testTaxMap2, outputDir)
elif(flag1 and flag2):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is consistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is consistent"
arti1 = self.divideByTwo(arti[0])
testTaxMap11 = copy.deepcopy(testTaxMap2)
testTaxMap12 = copy.deepcopy(testTaxMap2)
testTaxMap11.articulationSet.articulations += arti1[0]
testTaxMap12.articulationSet.articulations += arti1[1]
flag11 = testTaxMap11.testConsistency(outputDir)
flag12 = testTaxMap12.testConsistency(outputDir)
if(not flag11 and not flag12):
return arti[0]+self.BCS(arti[1], testTaxMap1, outputDir)
elif(flag11 and not flag12):
return arti[1]+arti1[0]+self.BCS(arti1[1], testTaxMap11, outputDir)
return arti[1]+arti1[1]+self.BCS(arti1[0], testTaxMap12, outputDir)
else:
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is inconsistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is inconsistent"
return self.BCS(self.BCS(arti[0], inTaxMap, outputDir)+self.BCS(arti[1], inTaxMap, outputDir), inTaxMap, outputDir)
def BCS1(self, articulations, inTaxMap, outputDir):
testTaxMap = copy.deepcopy(inTaxMap)
testTaxMap.articulationSet.articulations = testTaxMap.articulationSet.articulations + articulations
if(testTaxMap.testConsistency(outputDir)):
print ','.join(map(str,testTaxMap.articulationSet.articulations)) + " is consistent"
outArti = articulations
return outArti
if(len(articulations) <= 1):
return []
testTaxMap1 = copy.deepcopy(inTaxMap)
testTaxMap2 = copy.deepcopy(inTaxMap)
arti = self.divideByTwo(articulations)
testTaxMap1.articulationSet.articulations += arti[0]
testTaxMap2.articulationSet.articulations += arti[1]
flag1 = testTaxMap1.testConsistency(outputDir)
flag2 = testTaxMap2.testConsistency(outputDir)
if(flag1 and not flag2):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is consistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is inconsistent"
return self.BCS1(arti[0]+self.BCS1(arti[1],inTaxMap, outputDir), inTaxMap, outputDir)
elif(flag2 and not flag1):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is inconsistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is consistent"
return self.BCS1(self.BCS1(arti[0],inTaxMap, outputDir)+arti[1], inTaxMap, outputDir)
elif(flag1 and flag2):
print ','.join(map(str,testTaxMap1.articulationSet.articulations)) + " is consistent"
print ','.join(map(str,testTaxMap2.articulationSet.articulations)) + " is consistent"
return self.BCS1_int(arti[0], arti[1], inTaxMap, outputDir)