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Sigma knowledge engineering system is an system for developing, viewing and debugging theories in first
order logic. It works with Knowledge Interchange Format (KIF) and is optimized for the Suggested Upper Merged
Ontology (SUMO) www.ontologyportal.org.
The newest version!
/* This code is copyright Articulate Software (c) 2003.
This software is released under the GNU Public License .
Users of this code are also requested, to credit Articulate Software in any
writings, briefings, publications, presentations, or
other representations of any software which incorporates,
builds on, or uses this code. Please cite the following
article in any publication with references:
Pease, A., (2003). The Sigma Ontology Development Environment,
in Working Notes of the IJCAI-2003 Workshop on Ontology and Distributed Systems,
August 9, Acapulco, Mexico. See also http://sigmakee.sourceforge.net
*/
package com.articulate.sigma;
import TPTPWorld.TPTPFormula;
import TPTPWorld.TPTPParser;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class TPTP3ProofProcessor {
public String status;
public ArrayList bindings = new ArrayList();
public ArrayList proof = new ArrayList();
private HashMap idTable = new HashMap();
int idCounter = 0;
/** ***************************************************************
* Convert bindings in list to string
*/
public String toString () {
StringBuffer sb = new StringBuffer();
sb.append("Answers:");
for (int i = 0; i < bindings.size(); i++)
sb.append(bindings.get(i) + " ");
for (int i = 0; i < proof.size(); i++)
sb.append(proof.get(i));
return sb.toString();
}
/** ***************************************************************
* Remove brackets if it contains
*/
public static String trimBrackets (String line) {
if (line.startsWith("[") && line.endsWith("]"))
return line.substring(1,line.length()-1);
else {
System.out.println("Error in TPTP3ProofProcessor.trimBrackets() bad format: " + line);
return null;
}
}
/** ***************************************************************
* Remove parentheses if it contains
*/
public static String trimParens (String line) {
if (line.indexOf("(")!=-1 && line.indexOf(")")!=-1) {
return line.substring(line.indexOf("(")+1, line.lastIndexOf(")"));
}
else {
System.out.println("Error in TPTP3ProofProcessor.trimParens() bad format: " + line);
return null;
}
}
/** ***************************************************************
*/
public ArrayList parseInferenceObject(String supportId) {
ArrayList prems = new ArrayList();
int firstParen = supportId.indexOf("(");
int secondParen = StringUtil.findBalancedParen(firstParen, supportId);
int firstComma = supportId.indexOf(",");
int secondComma = supportId.indexOf(",",firstComma+1);
String supports = "";
if (secondComma+1 >= secondParen) // supportID = 10997,['proof']
supports = "[" + supportId + "]";
supports = supportId.substring(secondComma+1,secondParen);
if (supports.startsWith("inference"))
return parseInferenceObject(supports);
else
return parseSupports(supports.trim());
}
/** ***************************************************************
*/
public String getInferenceType(String supportId) {
String inferenceType = null;
if (supportId.startsWith("inference(")) {
int firstParen = supportId.indexOf("(");
int firstComma = supportId.indexOf(",");
inferenceType = supportId.substring(firstParen+1, firstComma);
}
return inferenceType;
}
/** ***************************************************************
* Parse support / proof statements in E's response
*/
public ArrayList parseSupports(String supportId) {
//System.out.println("Info in TPTP3ProofProcessor.parseSupports(): " + supportId);
ArrayList prems = new ArrayList();
if (supportId.startsWith("[")) {
supportId = trimBrackets(supportId).trim();
//System.out.println("Info in TPTP3ProofProcessor.parseSupports()2: " + supportId);
if (supportId.startsWith("inference("))
return parseInferenceObject(supportId);
String[] supportSet = supportId.split(",");
for (int i = 0; i < supportSet.length; i++) {
//System.out.println("Info in TPTP3ProofProcessor.parseSupports(): support element: " + supportSet[i]);
if (supportSet[i].indexOf("(") == -1) {
if (!supportSet[i].trim().startsWith("[symmetry]")) {
Integer stepnum = idTable.get(supportSet[i].trim());
if (stepnum == null)
System.out.println("Error in TPTP3ProofProcessor.parseSupports() no id: " + stepnum +
" for premises at step " + supportSet[i]);
else
prems.add(stepnum);
}
}
}
}
else if (supportId.startsWith("file(")) {
return prems;
}
else if (supportId.startsWith("inference(")) {
return parseInferenceObject(supportId);
}
else if (supportId.startsWith("introduced(")) {
return prems;
}
else {
Integer stepnum = idTable.get(supportId);
if (stepnum == null) {
return prems;
}
else {
prems.add(stepnum);
return prems;
}
}
return prems;
}
/** ***************************************************************
* Parse a step like the following into its constituents
* fof(c_0_5, axiom, (s__subclass(s__Artifact,s__Object)), c_0_3).
*
* fof(c_0_2,
* negated_conjecture,
* (~(?[X1]:(s__subclass(X1,s__Object)&~$answer(esk1_1(X1))))),
* inference(assume_negation,[status(cth)],[inference(add_answer_literal,[status(thm)],[c_0_0, theory(answers)])])).
*/
public ProofStep parseProofStep (String line) {
if (StringUtil.emptyString(line))
return null;
ProofStep ps = new ProofStep();
//System.out.println("Info in TPTP3ProofProcessor.parseProofStep(): " + line);
int paren = line.indexOf("(");
if (paren == -1) {
System.out.println("Error in TPTP3ProofProcessor.parseProofStep() bad format: " + line);
return null;
}
String type = line.substring(0,paren);
if (!line.endsWith(").")) {
System.out.println("Error in TPTP3ProofProcessor.parseProofStep() bad format: " + line);
return null;
}
String withoutWrapper = line.substring(paren + 1,line.length() - 2);
int comma1 = withoutWrapper.indexOf(",");
String id = withoutWrapper.substring(0,comma1).trim();
// System.out.println("ID : " + id);
Integer intID = new Integer(idCounter++);
idTable.put(id,intID);
ps.number = intID;
int comma2 = withoutWrapper.indexOf(",",comma1+1);
String formulaType = withoutWrapper.substring(comma1 + 1,comma2).trim();
ps.formulaType = formulaType;
// System.out.println("type : " + formulaType);
String rest = withoutWrapper.substring(comma2+1).trim();
int statementEnd = StringUtil.findBalancedParen(rest.indexOf("("), rest); // startIndex = index_of_first_"(", instead of 0;
// TODO: check if exists "="
if (statementEnd == rest.length()-1) // sepecial case: rest = "s__Class30_1=s__Reptile, file('/var/folders/s4/38700c8541z9h0t0sy_6lmk40000gn/T//epr_diiVH1', i_0_23)"
statementEnd = rest.indexOf(","); // expected: "foo(s__Class30_1,s__Reptile), file('/var/folders/s4/38700c8541z9h0t0sy_6lmk40000gn/T//epr_diiVH1', i_0_23)"
String stmnt = trimParens(rest.substring(0,statementEnd+1).trim());
// System.out.println("stmnt : " + stmnt);
// line = line.replaceAll("\\$answer\\(","answer(");
// System.out.println("after remove $answer: " + line);
StringReader reader = new StringReader(line);
// kif = TPTP2SUMO.convert(reader, false);
try {
TPTPParser tptpP = TPTPParser.parse(new BufferedReader(reader));
// System.out.println(tptpP.Items.get(0));
Iterator it = tptpP.ftable.keySet().iterator();
while (it.hasNext()) {
String tptpid = it.next();
TPTPFormula tptpF = tptpP.ftable.get(tptpid);
stmnt = TPTP2SUMO.convertType(tptpF,0,0,true).toString();
}
}
catch (Exception e) {
System.out.println("Error in TPTP3ProofProcessor.parseProofStep(): " + e.getMessage());
e.printStackTrace();
System.out.println("with input: " + line);
}
// System.out.println("KIF stmnt : " + stmnt);
ps.axiom = stmnt;
String supportId = rest.substring(statementEnd+2,rest.length()).trim();
// System.out.println("supportID: " + supportId);
// add an inference type
ps.inferenceType = getInferenceType(supportId.trim());
ps.premises.addAll(parseSupports(supportId.trim()));
return ps;
}
/** ***************************************************************
* Return bindings from E's answer tuples
*/
public void processAnswers (String line) {
String trimmed = trimBrackets(line);
if (trimmed == null) {
System.out.println("Error in TPTP3ProofProcessor.processAnswers() bad format: " + line);
return;
}
String[] answers = trimmed.split("\\|");
for (int i = 0; i < answers.length; i++) {
if (answers[i].equals("_"))
break;
String answer = trimBrackets(answers[i]);
if (answer != null) {
String[] esks = answer.split(", ");
for (String esk : esks) {
answer = removeEsk(esk);
bindings.add(answer);
}
}
}
}
/** ***************************************************************
* Return the most specific type for skolem variable.
*
* @param tpp The structure learned from E's response
* @param kb The knowledge base used to find skolem term's types
*
* For example,
* original binding = esk3_0
* set binding = "An instance of Human" (Human is the most specific
* type for esk3_0 in the given proof)
*
* original binding = esk3_1
* set binding = "An instance of Human, Agent" (If multiple types
* are found for esk3_1)
*/
public static void findTypesForSkolemTerms(TPTP3ProofProcessor tpp, KB kb) {
ArrayList bindings = tpp.bindings;
FormulaPreprocessor fp = new FormulaPreprocessor();
for (int i = 0; i < bindings.size(); i++) {
String binding = bindings.get(i);
if (binding.startsWith("esk")) {
ArrayList skolemStmts = ProofProcessor.returnSkolemStmt(binding, tpp.proof);
HashSet types = new HashSet<>();
for (String skolemStmt : skolemStmts) {
Pattern p = Pattern.compile("\\(names ([a-zA-Z0-9\\-_]+) ([a-zA-Z0-9\\-]+)");
Matcher m = p.matcher(skolemStmt);
while (m.find()) {
String cl = m.group(2);
types.add(cl);
}
// only find instance/subclass expression if no specific name is found
if (types.isEmpty()) {
p = Pattern.compile("\\(instance ([a-zA-Z0-9\\-_]+) ([a-zA-Z0-9\\-_]+)");
m = p.matcher(skolemStmt);
while (m.find()) {
String cl = m.group(2);
types.add(cl);
}
p = Pattern.compile("\\(subclass ([a-zA-Z0-9\\-_]+) ([a-zA-Z0-9\\-]+)");
m = p.matcher(skolemStmt);
while (m.find()) {
String cl = m.group(2);
types.add(cl);
}
}
}
if (kb.kbCache.checkDisjoint(kb, types) == true) {
// check if there are contradiction among the types returned from E
bindings.remove(binding);
binding = "Get type contradiction for " + binding + " in " + types;
bindings.add(binding);
}
else {
fp.winnowTypeList(types, kb);
if (types!=null && types.size()>0) {
if (types.size() == 1) {
binding = "an instance of " + types.toArray()[0];
}
else {
binding = "an instance of ";
boolean start = true;
for (String t : types) {
if (start) { binding += t; start = false; }
else { binding += ", " + t; }
}
}
bindings.set(i, binding);
}
}
}
else {
binding = TPTP2SUMO.transformTerm(binding);
bindings.set(i, binding);
}
}
}
/** ***************************************************************
* remove skolem symbol with arity n
*
* For example,
* Input: esk2_1(s__Arc13_1)
* Output: s__Arc13_1
*/
private String removeEsk(String line) {
if (line.startsWith("esk")) {
int leftParen = line.indexOf("(");
int rightParen = line.indexOf(")");
if (leftParen != -1 && rightParen != -1)
return line.substring(leftParen+1, rightParen);
}
return line;
}
/** ***************************************************************
* Print out E's bindings
*/
public void printAnswers () {
System.out.println("Answers:");
for (int i = 0; i < bindings.size(); i++)
System.out.println(bindings.get(i));
}
/** ***************************************************************
* Compute bindings and proof from E's response
*/
public static TPTP3ProofProcessor parseProofOutput (LineNumberReader lnr, KB kb) {
TPTP3ProofProcessor tpp = new TPTP3ProofProcessor();
try {
boolean inProof = false;
boolean finishAnswersTuple = false;
String line;
while ((line = lnr.readLine()) != null) {
if (line.indexOf("SZS output start") != -1) {
inProof = true;
line = lnr.readLine();
}
if (line.indexOf("SZS status") != -1) {
tpp.status = line.substring(15);
}
if (line.indexOf("SZS answers") != -1) {
if (!finishAnswersTuple) {
tpp.processAnswers(line.substring(20).trim());
finishAnswersTuple = true;
}
}
if (inProof) {
if (line.indexOf("SZS output end") != -1) {
inProof = false;
}
else {
ProofStep ps = tpp.parseProofStep(line);
if (ps != null) {
tpp.proof.add(ps);
}
}
}
}
}
catch (Exception ex) {
System.out.println(ex.getMessage());
}
// remove unnecessary steps, eg: conjectures, duplicate trues
tpp.proof = ProofStep.removeUnnecessary(tpp.proof);
tpp.proof = ProofStep.removeDuplicates(tpp.proof);
// find types for skolem terms
findTypesForSkolemTerms(tpp, kb);
return tpp;
}
/** ***************************************************************
* Compute binding and proof from E's response
*/
public static TPTP3ProofProcessor parseProofOutput (ArrayList lines, KB kb) {
TPTP3ProofProcessor tpp = new TPTP3ProofProcessor();
try {
boolean inProof = false;
boolean finishAnswersTuple = false;
String line;
Iterator it = lines.iterator();
while (it.hasNext()) {
line = it.next();
if (line.indexOf("SZS output start") != -1) {
inProof = true;
line = it.next();
}
if (line.indexOf("SZS status") != -1) {
tpp.status = line.substring(15);
}
if (line.indexOf("SZS answers") != -1) {
if (!finishAnswersTuple) {
tpp.processAnswers(line.substring(20).trim());
finishAnswersTuple = true;
}
}
if (inProof) {
if (line.indexOf("SZS output end") != -1) {
inProof = false;
}
else {
ProofStep ps = tpp.parseProofStep(line);
if (ps != null) {
tpp.proof.add(ps);
}
}
}
}
}
catch (Exception ex) {
System.out.println(ex.getMessage());
}
// remove unnecessary steps, eg: conjectures, duplicate trues
tpp.proof = ProofStep.removeUnnecessary(tpp.proof);
tpp.proof = ProofStep.removeDuplicates(tpp.proof);
// find types for skolem terms
findTypesForSkolemTerms(tpp, kb);
return tpp;
}
/** ***************************************************************
* Return a list of answers if E finds bindings for wh- queries.
* Return "Proof Found" if E finds contradiction for boolean queries.
*
* For example,
* tuple_list = [[esk3_1(s__Org1_1)]|_]
* Output = [Org1_1]
*
* tuple_list = [[esk3_0]|_]
* Output = [An instance of Human] (Human is the most specific type
* for esk3_0 in the given proof)
*/
public static ArrayList parseAnswerTuples(String st, KB kb, FormulaPreprocessor fp) {
ArrayList answers = new ArrayList<>();
TPTP3ProofProcessor tpp = TPTP3ProofProcessor.parseProofOutput(st, kb);
if (tpp.bindings == null || tpp.bindings.isEmpty()) {
if (tpp.proof != null && !tpp.proof.isEmpty()) {
answers.add("Proof Found"); // for boolean queries
}
return answers;
}
return tpp.bindings;
}
/** ***************************************************************
*/
public static TPTP3ProofProcessor parseProofOutput (String st, KB kb) {
StringReader sr = new StringReader(st);
LineNumberReader lnr = new LineNumberReader(sr);
return parseProofOutput(lnr, kb);
}
/** ***************************************************************
*/
public static void testParseProofFile () {
KB kb = null;
TPTP3ProofProcessor tpp = new TPTP3ProofProcessor();
try {
FileReader r = new FileReader("/home/apease/Programs/E/PROVER/eltb_out.txt");
LineNumberReader lnr = new LineNumberReader(r);
tpp = parseProofOutput(lnr, kb);
}
catch (Exception ex) {
System.out.println(ex.getMessage());
}
System.out.println("-------------------------------------------------");
System.out.println(tpp.proof);
}
/** ***************************************************************
*/
public static void testE () {
try {
System.out.println("INFO in EProver.main()");
//KBmanager.getMgr().initializeOnce();
//KB kb = KBmanager.getMgr().getKB("SUMO");
KB kb = null;
System.out.println("------------- INFO in EProver.main() completed initialization--------");
EProver eprover = new EProver("/home/apease/Programs/E/PROVER/e_ltb_runner",
"/home/apease/Sigma/KBs/SUMO.tptp");
String result = eprover.submitQuery("(subclass Patio Object)",kb);
StringReader sr = new StringReader(result);
LineNumberReader lnr = new LineNumberReader(sr);
TPTP3ProofProcessor tpp = parseProofOutput(lnr, kb);
System.out.println("-------------------------------------------------");
System.out.println(tpp.proof);
eprover.terminate();
}
catch (Exception e) {
System.out.println(e.getMessage());
}
}
/** ***************************************************************
*/
public static void testParseProofStep () {
String ps1 = "fof(c_0_5, axiom, (s__subclass(s__Artifact,s__Object)), c_0_3).";
String ps2 = "fof(c_0_2, negated_conjecture,(~(?[X1]:(s__subclass(X1,s__Object)&~$answer(esk1_1(X1)))))," +
"inference(assume_negation,[status(cth)],[inference(add_answer_literal,[status(thm)],[c_0_0, theory(answers)])])).";
String ps3 = "cnf(c_0_14,negated_conjecture,($false), " +
"inference(eval_answer_literal,[status(thm)], [inference(spm,[status(thm)],[c_0_12, c_0_13, theory(equality)]), theory(answers)]), ['proof']).";
TPTP3ProofProcessor tpp = new TPTP3ProofProcessor();
tpp.idTable.put("c_0_0", new Integer(0));
tpp.idTable.put("c_0_3", new Integer(1));
tpp.idTable.put("c_0_12", new Integer(2));
tpp.idTable.put("c_0_13", new Integer(3));
System.out.println(tpp.parseProofStep(ps1));
System.out.println();
System.out.println(tpp.parseProofStep(ps1));
System.out.println();
System.out.println(tpp.parseProofStep(ps3));
}
/** ***************************************************************
*/
public static void main (String[] args) {
//testParseProofStep();
//testParseProofFile();
testE();
}
}