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[DL-Learner SVN] SF.net SVN: dl-learner: [174] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2007-10-07 18:00:23
|
Revision: 174
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=174&view=rev
Author: jenslehmann
Date: 2007-10-07 11:00:21 -0700 (Sun, 07 Oct 2007)
Log Message:
-----------
transition from old command line interface completed
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/gp/GPUtilities.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/modules/TestModule.java
trunk/src/dl-learner/org/dllearner/modules/sparql/SparqlModule.java
trunk/src/dl-learner/org/dllearner/parser/ConfParser.java
trunk/src/dl-learner/org/dllearner/parser/ConfParserTokenManager.java
trunk/src/dl-learner/org/dllearner/parser/conf.jj
trunk/src/dl-learner/org/dllearner/reasoning/DIGReasonerNew.java
trunk/src/dl-learner/org/dllearner/server/ClientState.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWSoriginal.java
trunk/src/dl-learner/org/dllearner/server/LearnMonitor.java
trunk/src/dl-learner/org/dllearner/utilities/Helper.java
trunk/src/dl-learner/org/dllearner/utilities/PaperStatistics.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/Main.java
Deleted: trunk/src/dl-learner/org/dllearner/Main.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/Main.java 2007-10-07 16:35:12 UTC (rev 173)
+++ trunk/src/dl-learner/org/dllearner/Main.java 2007-10-07 18:00:21 UTC (rev 174)
@@ -1,1379 +0,0 @@
-/**
- * Copyright (C) 2007, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-package org.dllearner;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.text.DecimalFormat;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.dllearner.Config.Algorithm;
-import org.dllearner.algorithms.BruteForceLearner;
-import org.dllearner.algorithms.LearningAlgorithm;
-import org.dllearner.algorithms.gp.GP;
-import org.dllearner.algorithms.refinement.ROLearner;
-import org.dllearner.cli.ConfFileOption;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.core.LearningAlgorithmNew;
-import org.dllearner.core.LearningProblem;
-import org.dllearner.core.Reasoner;
-import org.dllearner.core.ReasoningMethodUnsupportedException;
-import org.dllearner.core.ReasoningService;
-import org.dllearner.core.Score;
-import org.dllearner.core.dl.AssertionalAxiom;
-import org.dllearner.core.dl.AtomicConcept;
-import org.dllearner.core.dl.AtomicRole;
-import org.dllearner.core.dl.Concept;
-import org.dllearner.core.dl.ConceptAssertion;
-import org.dllearner.core.dl.FlatABox;
-import org.dllearner.core.dl.Individual;
-import org.dllearner.core.dl.KB;
-import org.dllearner.core.dl.Negation;
-import org.dllearner.core.dl.RoleAssertion;
-import org.dllearner.kb.OntologyFileFormat;
-import org.dllearner.learningproblems.DefinitionLP;
-import org.dllearner.learningproblems.PosNegDefinitionLP;
-import org.dllearner.learningproblems.PosNegLP;
-import org.dllearner.modules.ModuleInvocator;
-import org.dllearner.parser.KBParser;
-import org.dllearner.parser.ParseException;
-import org.dllearner.parser.TokenMgrError;
-import org.dllearner.reasoning.DIGReasoner;
-import org.dllearner.reasoning.FastRetrievalReasoner;
-import org.dllearner.reasoning.KAON2Reasoner;
-import org.dllearner.reasoning.ReasonerType;
-import org.dllearner.utilities.ConceptComparator;
-import org.dllearner.utilities.ConceptTransformation;
-import org.dllearner.utilities.Files;
-import org.dllearner.utilities.Helper;
-import org.dllearner.utilities.RoleComparator;
-import org.dllearner.utilities.Stat;
-
-/**
- * Stellt die Verbindung zwischen Parser und den anderen Programmteilen her.
- * Startet den Algorithmus.
- *
- * TODO: Die Hauptmethode sollte noch in kleinere Einheiten zerlegt werden zur
- * besseren Lesbarkeit.
- *
- * TODO: einige Errors können durch RuntimeException ersetzt werden (kein throws
- * und Exception-Handling notwendig)
- *
- * @author Jens Lehmann
- *
- */
-public class Main {
-
- private static FlatABox abox;
-
- private static ConfigurationManager confMgr;
-
- private Reasoner reasoner;
- private ReasoningService rs;
- private PosNegLP learningProblem;
- // es werden jeweils die Dateien mit dem zugehörigen Format abgelegt
- Map<URL, OntologyFileFormat> importedFiles;
- Map<File, OntologyFileFormat> exportedFiles;
- KB kb;
- SortedSet<Individual> posExamples;
- SortedSet<Individual> negExamples;
- List<File> loadedJars;
- List<String> preprocessingModules;
-
- private static long algorithmStartTime = 0;
-
- private String baseDir;
-
- // neuer Hauptkonstruktor
- public Main(KB kb, Map<AtomicConcept, SortedSet<Individual>> positiveExamples,
- Map<AtomicConcept, SortedSet<Individual>> negativeExamples,
- List<ConfFileOption> confOptions, List<List<String>> functionCalls,
- String baseDir, boolean useQueryMode) {
-
- this.kb = kb;
- this.baseDir = baseDir;
-
- // Konfigurationsmanager erstellen
- confMgr = new ConfigurationManager(confOptions);
- if (!confMgr.checkConsistency()) {
- throw new Error(
- "inconsistent/unsupported combination of configuration options");
- }
-
- // Funktionsaufrufe in Klassenvariablen laden
- parseFunctionCalls(functionCalls);
-
-
-
- // verwandte Individuen entfernen
- /*
- * removeIndividualSubtree(kb, new
- * Individual("http://localhost/foo#nonnie"));
- * removeIndividualSubtree(kb, new
- * Individual("http://localhost/foo#beatrice"));
- * removeIndividualSubtree(kb, new
- * Individual("http://localhost/foo#ann"));
- */
-
- // momentan keine Unterst�tzung f�r das gleichzeitige Lernen mehrerer
- // Konzepte
- // TODO: irgendwann lernen mehrerer Konzepte eventuell unterst�tzen
- // (momentan keine hohe Priorit�t)
- if (positiveExamples.size() > 1 || negativeExamples.size() > 1) {
- throw new Error("Currently only one target concept is supported.");
- }
-
- // Jar-Dateien laden
- List<URL> urls = new LinkedList<URL>();
- // for (List<String> call : functionCalls) {
- // if (call.get(0).equals("loadJarFile")) {
- for(File f : loadedJars) {
- // base dir wird hier nicht verwendet, da die Module eher
- // relativ zum DL-Learner als zu den Beispielen liegen
- // File f = new File(baseDir,call.get(1));
- // File f = new File(call.get(1));
- System.out.println("Loading jar file \"" + f.getAbsolutePath() + "\".");
- try {
- urls.add(new URL("file", "localhost", f.getAbsolutePath()));
- } catch (MalformedURLException e) {
- e.printStackTrace();
- }
- // }
- //}
- }
-
- URLClassLoader loader = new URLClassLoader(urls.toArray(new URL[] {}));
-
- // confMgr.applyOptions();
-
- // Preprocessing-Modul aufrufen, falls notwendig
- for (String module : preprocessingModules) {
- //if (!Config.preprocessingModule.equals("")) {
- System.out.println("Invoking preprocessing module main class " + module + ".");
- ModuleInvocator mi = new ModuleInvocator(loader, module);
- mi.invokePreprocessingModule(kb, positiveExamples, negativeExamples, confOptions, functionCalls, baseDir, useQueryMode);
- //}
- }
-
- // Funktionsaufrufe nochmal in Klassenvariablen laden, falls sie sich
- // geändert haben
- parseFunctionCalls(functionCalls);
-
- // Konfigurationsoptionen anwenden (könnten auch von einem Modul
- // gesetzt werden)
- confMgr.applyOptions();
-
- // Beispiele werden in eine Menge gebracht
- posExamples = new TreeSet<Individual>();
- negExamples = new TreeSet<Individual>();
-
- for (AtomicConcept target : positiveExamples.keySet())
- posExamples = positiveExamples.get(target);
-
- for (AtomicConcept target : negativeExamples.keySet())
- negExamples = negativeExamples.get(target);
-
- // File-Objekte an function calls binden
- /*
- * boolean importKB = functionCalls.containsKey("import"); importedFiles =
- * new LinkedList<File>(); if (importKB) { Set<String>
- * importedFilesStr = functionCalls.get("import"); for (String
- * importFileStr : importedFilesStr) { importedFiles.add(new
- * File(baseDir, importFileStr)); } }
- */
- /*
- importedFiles = new HashMap<File, OntologyFileFormat>();
- for (List<String> call : functionCalls) {
- if (call.get(0).equals("import")) {
- File f = new File(baseDir, call.get(1));
- if (call.size() == 2)
- // falls nichts angegeben, dann wird RDF/XML gewählt
- importedFiles.put(f, OntologyFileFormat.RDF_XML);
- else {
- String formatString = call.get(2);
- OntologyFileFormat format;
- if (formatString.equals("RDF/XML"))
- format = OntologyFileFormat.RDF_XML;
- else
- format = OntologyFileFormat.N_TRIPLES;
- importedFiles.put(f, format);
- }
- }
- }
- */
-
- // DIG-Reasoner testen
- // new DIGReasonerTest(kb);
- // System.exit(0);
-
- reasoner = createReasoner(kb, importedFiles);
- ReasoningService rs = new ReasoningService(reasoner);
- // commented out during changes
- // learningProblem = new LearningProblem(rs, posExamples, negExamples);
-
- // export function
- /*
- * if (functionCalls.containsKey("export")) { for (String export :
- * functionCalls.get("export")) { rs.saveOntology(export, baseDir); } }
- */
- /*
- for (List<String> call : functionCalls) {
- if (call.get(0).equals("export")) {
- File f = new File(baseDir, call.get(1));
- if (call.size() == 2)
- // falls nichts angegeben, dann wird RDF/XML gewählt
- rs.saveOntology(f, OntologyFileFormat.RDF_XML);
- else {
- String formatString = call.get(2);
- OntologyFileFormat format;
- if (formatString.equals("RDF/XML"))
- format = OntologyFileFormat.RDF_XML;
- else
- format = OntologyFileFormat.N_TRIPLES;
- rs.saveOntology(f, format);
- }
- }
- }
- */
- for(File f : exportedFiles.keySet()) {
- rs.saveOntology(f, exportedFiles.get(f));
- }
-
- // Satisfiability Check
- if (Config.reasonerType != ReasonerType.FAST_RETRIEVAL) {
- System.out.print("Satisfiability Check ... ");
- long satStartTime = System.nanoTime();
- boolean satisfiable = rs.isSatisfiable();
- long satDuration = System.nanoTime() - satStartTime;
-
- String result = satisfiable ? "OK" : "not satisfiable!";
- System.out.println(result + " ("
- + Helper.prettyPrintNanoSeconds(satDuration, true, false) + ")");
- if (!satisfiable)
- System.exit(0);
- }
-
- autoDetectConceptsAndRoles(rs);
-
- // Subsumptionhierarchie vorbereiten
- System.out.print("Preparing Subsumption Hierarchy ... ");
- long subHierTimeStart = System.nanoTime();
- reasoner.prepareSubsumptionHierarchy();
- long subHierTime = System.nanoTime() - subHierTimeStart;
- System.out.println("OK ("
- + Helper.prettyPrintNanoSeconds(subHierTime, true, false) + ")");
-
- // prepare role hierarchy
- System.out.print("Preparing Role Hierarchy ... ");
- long roleHierTimeStart = System.nanoTime();
- try {
- reasoner.prepareRoleHierarchy();
- // System.out.println();
- // System.out.println(reasoner.getRoleHierarchy());
- } catch (ReasoningMethodUnsupportedException e1) {
- System.out.println("Tried to construct the role hierarchy, but the reasoner "
- + "does not support it. Currently only DIG reasoners support this feature.");
- }
- long roleHierTime = System.nanoTime() - roleHierTimeStart;
- System.out.println("OK ("
- + Helper.prettyPrintNanoSeconds(roleHierTime, true, false) + ")");
-
- // Beispiele anzeigen
- boolean oneLineExampleInfo = true;
- int maxExampleStringLength = posExamples.toString().length();
- maxExampleStringLength = Math.max(maxExampleStringLength, negExamples.toString()
- .length());
- if (maxExampleStringLength > 100)
- oneLineExampleInfo = false;
-
- if (oneLineExampleInfo) {
- System.out.println("positive examples[" + posExamples.size() + "]: "
- + posExamples);
- System.out.println("negative examples[" + negExamples.size() + "]: "
- + negExamples);
- } else {
- System.out.println("positive examples[" + posExamples.size() + "]: ");
- for (Individual ex : posExamples)
- System.out.println(" " + ex);
- System.out.println("negative examples[" + negExamples.size() + "]: ");
- for (Individual ex : negExamples)
- System.out.println(" " + ex);
- }
-
- // Individuals
- if (Config.showIndividuals) {
- int stringLength = reasoner.getIndividuals().toString().length();
- if (stringLength > Config.maxLineLength) {
- System.out.println("individuals[" + reasoner.getIndividuals().size()
- + "]: ");
- for (Individual ind : reasoner.getIndividuals())
- System.out.println(" " + ind);
- } else
- System.out.println("individuals[" + reasoner.getIndividuals().size()
- + "]: " + reasoner.getIndividuals());
- }
-
- // Konzepte
- if (Config.showConcepts) {
- int stringLength = reasoner.getAtomicConcepts().toString().length();
- if (stringLength > Config.maxLineLength) {
- System.out.println("concepts[" + reasoner.getAtomicConcepts().size()
- + "]: ");
- for (AtomicConcept ac : reasoner.getAtomicConcepts())
- System.out.println(" " + ac);
- } else
- System.out.println("concepts[" + reasoner.getAtomicConcepts().size()
- + "]: " + reasoner.getAtomicConcepts());
- }
-
- // Rollen
- if (Config.showRoles) {
- int stringLength = reasoner.getAtomicRoles().toString().length();
- if (stringLength > Config.maxLineLength) {
- System.out.println("roles[" + reasoner.getAtomicRoles().size() + "]: ");
- for (AtomicRole r : reasoner.getAtomicRoles())
- System.out.println(" " + r);
- } else
- System.out.println("roles[" + reasoner.getAtomicRoles().size() + "]: "
- + reasoner.getAtomicRoles());
- }
-
- // Anzeige der Subsumptionhierarchie
- if (Config.showSubsumptionHierarchy) {
- System.out.println("Subsumption Hierarchy:");
- try {
- System.out.println(reasoner.getSubsumptionHierarchy());
- } catch (ReasoningMethodUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- // Anzeige der Wissensbasis
- if (Config.showInternalKB) {
- System.out.println(kb);
- }
-
-
- // Vergleichsreasoner erstellen zum Testen
- // Reasoner reasoner2 = null;
- // try {
- // URL dig2URL = new URL("http://localhost:8081");
- // reasoner2 = new DIGReasoner(kb, dig2URL);
- // reasoner2 = new KAON2Reasoner(kb, importedFiles);
- // } catch (MalformedURLException e) {
- // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
- // ReasoningService rs2 = new ReasoningService(reasoner2);
- // LearningProblem learningProblem2 = new LearningProblem(rs2,
- // posExamples, negExamples);
-
- // test(learningProblem);
- // test2(learningProblem);
-
- // createStatisticsMLDMPaper(learningProblem, baseDir);
- // System.exit(0);
-
- if (useQueryMode) {
- processQueryMode(reasoner);
- } else {
- if (Config.statisticMode)
- ; // createStatistics(learningProblem, baseDir);
- else {
-
- rs.resetStatistics();
- algorithmStartTime = System.nanoTime();
-
- if (Config.algorithm == Algorithm.BRUTE_FORCE) {
- LearningAlgorithmNew la = new BruteForceLearner(learningProblem, null);
- la.start();
- } else if (Config.algorithm == Algorithm.RANDOM_GUESSER) {
- // new RandomGuesser(learningProblem, 10000, 10);
- } else if (Config.algorithm == Algorithm.GP
- || Config.algorithm == Algorithm.HYBRID_GP) {
- //LearningAlgorithm la = new GP(learningProblem);
- //la.start();
- } else {
- if (Config.Refinement.improveSubsumptionHierarchy) {
- // if(Config.reasonerType == ReasonerType.DIG) {
- System.out
- .println("Subsumption Hierarchy is improved for Refinement Operator Based Algorithm");
-
-
- try {
- reasoner.getSubsumptionHierarchy()
- .improveSubsumptionHierarchy();
- // System.out.println(reasoner.getSubsumptionHierarchy());
- } catch (ReasoningMethodUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- // ((DIGReasoner)reasoner).improveSubsumptionHierarchy();
- // ((DIGReasoner)reasoner).printSubsumptionHierarchies();
- // } else {
- // System.out.println("Subsumption Hierarchy not
- // improved (support for selected reasoner not
- // implemented)");
- // }
- }
- LearningAlgorithmNew la = new ROLearner(learningProblem, null);
- la.start();
- // new ROLearner(learningProblem, learningProblem2);
- }
-
- long algorithmDuration = System.nanoTime() - algorithmStartTime;
-
- if (rs.getNrOfRetrievals() > 0) {
- System.out.println("number of retrievals: " + rs.getNrOfRetrievals());
- System.out.println("retrieval reasoning time: "
- + Helper.prettyPrintNanoSeconds(rs
- .getRetrievalReasoningTimeNs()) + " ( "
- + Helper.prettyPrintNanoSeconds(rs.getTimePerRetrievalNs())
- + " per retrieval)");
- }
- if (rs.getNrOfInstanceChecks() > 0) {
- System.out.println("number of instance checks: "
- + rs.getNrOfInstanceChecks() + " ("
- + rs.getNrOfMultiInstanceChecks() + " multiple)");
- System.out.println("instance check reasoning time: "
- + Helper.prettyPrintNanoSeconds(rs
- .getInstanceCheckReasoningTimeNs())
- + " ( "
- + Helper.prettyPrintNanoSeconds(rs
- .getTimePerInstanceCheckNs())
- + " per instance check)");
- }
- if (rs.getNrOfSubsumptionHierarchyQueries() > 0) {
- System.out.println("subsumption hierarchy queries: "
- + rs.getNrOfSubsumptionHierarchyQueries());
- /*
- * System.out.println("subsumption hierarchy reasoning time: " +
- * Helper.prettyPrintNanoSeconds(rs
- * .getSubsumptionHierarchyTimeNs()) + " ( " +
- * Helper.prettyPrintNanoSeconds(rs
- * .getTimePerSubsumptionHierarchyQueryNs()) + " per
- * subsumption hierachy query)");
- */
- }
- if (rs.getNrOfSubsumptionChecks() > 0) {
- System.out.println("(complex) subsumption checks: "
- + rs.getNrOfSubsumptionChecks() + " ("
- + rs.getNrOfMultiSubsumptionChecks() + " multiple)");
- System.out.println("subsumption reasoning time: "
- + Helper.prettyPrintNanoSeconds(rs
- .getSubsumptionReasoningTimeNs())
- + " ( "
- + Helper.prettyPrintNanoSeconds(rs
- .getTimePerSubsumptionCheckNs())
- + " per subsumption check)");
- }
- DecimalFormat df = new DecimalFormat();
- double reasoningPercentage = 100 * rs.getOverallReasoningTimeNs()
- / (double) algorithmDuration;
- System.out
- .println("overall reasoning time: "
- + Helper.prettyPrintNanoSeconds(rs
- .getOverallReasoningTimeNs()) + " ("
- + df.format(reasoningPercentage)
- + "% of overall runtime)");
- System.out.println("overall algorithm runtime: "
- + Helper.prettyPrintNanoSeconds(algorithmDuration));
- }
- }
-
- // Aufräumarbeiten (TODO: das fehlt für KAON2 noch)
- if (reasoner instanceof DIGReasoner)
- ((DIGReasoner) reasoner).releaseKB();
- }
-
- // parst Funktionsaufrufe in Klassenvariablen
- private void parseFunctionCalls(List<List<String>> functionCalls) {
- // Funktionsaufrufe parsen
- importedFiles = new HashMap<URL, OntologyFileFormat>();
- exportedFiles = new HashMap<File, OntologyFileFormat>();
- loadedJars = new LinkedList<File>();
- preprocessingModules = new LinkedList<String>();
- for (List<String> call : functionCalls) {
- if(call.get(0).equals("import")) {
- // alte Methode mit file statt URI
- // File f = new File(baseDir, call.get(1));
-
- URL url = null;
- try {
- String fileString = call.get(1);
- if(fileString.startsWith("http:")) {
- url = new URL(fileString);
- } else {
- File f = new File(baseDir, call.get(1));
- url = f.toURI().toURL();
- }
- } catch (MalformedURLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- if (call.size() == 2)
- // falls nichts angegeben, dann wird RDF/XML gewählt
- importedFiles.put(url, OntologyFileFormat.RDF_XML);
- else {
- String formatString = call.get(2);
- OntologyFileFormat format;
- if (formatString.equals("RDF/XML"))
- format = OntologyFileFormat.RDF_XML;
- else
- format = OntologyFileFormat.N_TRIPLES;
- importedFiles.put(url, format);
- }
- } else if(call.get(0).equals("export")) {
- File f = new File(baseDir, call.get(1));
- if (call.size() == 2)
- // falls nichts angegeben, dann wird RDF/XML gewählt
- exportedFiles.put(f, OntologyFileFormat.RDF_XML);
- else {
- String formatString = call.get(2);
- OntologyFileFormat format;
- if (formatString.equals("RDF/XML"))
- format = OntologyFileFormat.RDF_XML;
- else
- format = OntologyFileFormat.N_TRIPLES;
- exportedFiles.put(f, format);
- }
- } else if(call.get(0).equals("loadJarFile")) {
- loadedJars.add(new File(call.get(1)));
- } else if(call.get(0).equals("runPreprocessingModule")) {
- preprocessingModules.add(call.get(1));
- } else {
- System.out.println("Unknown function \"" + call.get(0) + "\". Exiting.");
- System.exit(0);
- }
- }
- }
-
- // Reasoning-Service erstellen
- // TODO: überlegen, ob man die Methode nicht ev. auslagert, da sich Klassenvariablen
- // mit Parametern überlappen
- public static Reasoner createReasoner(KB kb, Map<URL, OntologyFileFormat> importedFiles) {
- Reasoner reasoner = null;
- if (Config.reasonerType == ReasonerType.KAON2) {
- reasoner = new KAON2Reasoner(kb, importedFiles);
- System.out.println("Reasoner: KAON2 (over Java API)");
- } else if (Config.reasonerType == ReasonerType.DIG) {
- reasoner = new DIGReasoner(kb, Config.digReasonerURL, importedFiles);
- System.out.println("Reasoner: " + ((DIGReasoner) reasoner).getIdentifier()
- + " - connected via DIG 1.1 at " + Config.digReasonerURL);
- } else if (Config.reasonerType == ReasonerType.FAST_RETRIEVAL) {
- // erst KAON2-Reasoner erstellen um FlatABox zu erzeugen
- if (Config.startUpReasoningType == ReasonerType.KAON2) {
- Reasoner startUpReasoner = new KAON2Reasoner(kb, importedFiles);
- // FlatABox abox;
- try {
- abox = createFlatABox(startUpReasoner);
- } catch (ReasoningMethodUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- throw new Error(
- "StartUpReasoner does not support all necessary reasoning methods.");
- }
- reasoner = new FastRetrievalReasoner(abox);
- } else
- throw new Error("Unsupported startup reasoner.");
- } else {
- throw new Error("Unsupported Reasoner");
- }
-
- // Reasoner.initializeReasoner(ReasonerType.KAON2,kb,importedFiles);
- // ReasoningService reasoner = new ReasoningService(Config.reasonerType,
- // Config.startUpReasoningType, kb, importedFiles);
- // ReasoningService
- // return new ReasoningService(reasoner);
- return reasoner;
- }
-
- /**
- * Computes the set of allowed concepts based on configuration settings (also
- * ignores anonymous and standard RDF, RDFS, OWL concept produces by Jena).
- *
- */
- public static void autoDetectConceptsAndRoles(ReasoningService rs) {
- // einige Sachen, die momentan nur vom Refinement-Algorithmus
- // unterstützt werden (später ev. auch von anderen Algorithmen)
- //if (Config.algorithm == Algorithm.REFINEMENT) {
-
- // berechnen der verwendbaren Konzepte
- if (Config.Refinement.allowedConceptsAutoDetect) {
- // TODO: Code aus DIG-Reasoner-Klasse einfügen
-
- Set<AtomicConcept> allowedConceptsTmp = new TreeSet<AtomicConcept>(
- new ConceptComparator());
- allowedConceptsTmp.addAll(rs.getAtomicConcepts());
- Iterator<AtomicConcept> it = allowedConceptsTmp.iterator();
- while (it.hasNext()) {
- String conceptName = it.next().getName();
- // System.out.println(conceptName);
- // seltsame anon-Konzepte, die von Jena erzeugt werden
- // löschen
- if (conceptName.startsWith("anon")) {
- System.out
- .println(" Ignoring concept "
- + conceptName
- + " (probably an anonymous concept produced by Jena when reading in OWL file).");
- it.remove();
- } else if (conceptName
- .startsWith("http://www.w3.org/1999/02/22-rdf-syntax-ns#")) {
- System.out
- .println(" Ignoring concept "
- + conceptName
- + " (RDF construct produced by Jena when reading in OWL file).");
- it.remove();
- } else if (conceptName
- .startsWith("http://www.w3.org/2000/01/rdf-schema#")) {
- System.out
- .println(" Ignoring concept "
- + conceptName
- + " (RDF Schema construct produced by Jena when reading in OWL file).");
- it.remove();
- } else if (conceptName.startsWith("http://www.w3.org/2002/07/owl#")) {
- System.out
- .println(" Ignoring concept "
- + conceptName
- + " (OWL construct produced by Jena when reading in OWL file).");
- it.remove();
- }
- }
-
- // hier werden jetzt noch die zu ignorierenden Konzepte entfernt
- if(Config.Refinement.ignoredConcepts != null) {
-
-
- for(AtomicConcept ac : Config.Refinement.ignoredConcepts) {
- boolean success = allowedConceptsTmp.remove(ac);
- if(!success) {
- System.out.println("Ignored concept " + ac + " does not exist in knowledge base.");
- System.exit(0);
- }
-
- }
- }
-
-
- Config.Refinement.allowedConcepts = allowedConceptsTmp;
- } else {
- // prüfen, ob nur verfügbare Konzepte vom Nutzer gewählt worden
- Set<AtomicConcept> allowed = new HashSet<AtomicConcept>();
- allowed.addAll(Config.Refinement.allowedConcepts);
- allowed.removeAll(rs.getAtomicConcepts());
- if (allowed.size() > 0) {
- System.out
- .println("Some of the concepts you told the learner to use in the definition, "
- + "do not exist in the background knowledge: "
- + allowed);
- System.out.println("Please correct this problem and restart.");
- System.exit(0);
- }
- }
-
- if (Config.Refinement.allowedRolesAutoDetect) {
- Set<AtomicRole> allowedRolesTmp = rs.getAtomicRoles();
-
- // hier werden jetzt noch die zu ignorierenden Rollen entfernt
- if(Config.Refinement.ignoredRoles != null) {
-
-
- for(AtomicRole ar : Config.Refinement.ignoredRoles) {
- boolean success = allowedRolesTmp.remove(ar);
- if(!success) {
- System.out.println("Ignored role " + ar + " does not exist in knowledge base.");
- System.exit(0);
- }
-
- }
- }
-
- Config.Refinement.allowedRoles = allowedRolesTmp;
-
- } else {
- Set<AtomicRole> allowedR = new HashSet<AtomicRole>();
- allowedR.addAll(Config.Refinement.allowedRoles);
-
- Set<AtomicRole> existingR = new TreeSet<AtomicRole>(new RoleComparator());
- existingR.addAll(rs.getAtomicRoles());
-
- // allowedR.removeAll(rs.getAtomicRoles());
- allowedR.removeAll(existingR);
-
- if (allowedR.size() > 0) {
- System.out
- .println("Some of the roles you told the learner to use in the definition, "
- + "do not exist in the background knowledge: "
- + allowedR);
- System.out.println("Please correct this problem and restart.");
- System.out.println(rs.getAtomicRoles());
- System.out.println(Config.Refinement.allowedRoles);
- System.exit(0);
- }
-
- }
- }
-
- // Statistikerzeugung wird ausgelagert, damit im "normalen" Programm
- // nichts ge�ndert werden muss
-// private void createStatistics(LearningProblemNew learningProblem, String baseDir) {
-//
-// int runs = 20;
-// LearningAlgorithm alg;
-//
-// Stat stat1 = new Stat();
-// Stat stat2 = new Stat();
-// Stat stat3 = new Stat();
-// // Stat stat4 = new Stat();
-// File exportFile1 = new File(baseDir, "../../stats/guesser.data");
-// File exportFile2 = new File(baseDir, "../../stats/gp1.data");
-// File exportFile3 = new File(baseDir, "../../stats/gp2.data");
-// // File exportFile4 = new File(baseDir, "../../stats/gp3.data");
-// StringBuilder exportString1 = new StringBuilder();
-// StringBuilder exportString2 = new StringBuilder();
-// StringBuilder exportString3 = new StringBuilder();
-// // StringBuilder exportString4 = new StringBuilder();
-//
-// for (int i = 1000; i <= 30000; i += 2000) {
-// stat1 = new Stat();
-// stat2 = new Stat();
-// stat3 = new Stat();
-// // stat4 = new Stat();
-// for (int run = 0; run < runs; run++) {
-// System.out.println("=============");
-// System.out.println("i " + i + " run " + run);
-// System.out.println("=============");
-// alg = new RandomGuesser(learningProblem, i, 6);
-// stat1.addNumber(alg.getSolutionScore().getScore() - 0.1
-// * alg.getBestSolution().getLength());
-//
-// Config.GP.numberOfIndividuals = i / 10;
-// Config.GP.mutationProbability = 0.03f;
-// Config.GP.crossoverProbability = 0.9f;
-// Config.GP.hillClimbingProbability = 0.0f;
-// alg = new GP(learningProblem);
-// stat2.addNumber(alg.getSolutionScore().getScore() - 0.1
-// * alg.getBestSolution().getLength());
-//
-// // wie GP 1, aber mit Hill Climbing
-// Config.GP.crossoverProbability = 0.8f;
-// Config.GP.hillClimbingProbability = 0.15f;
-// alg = new GP(learningProblem);
-// stat3.addNumber(alg.getSolutionScore().getScore() - 0.1
-// * alg.getBestSolution().getLength());
-// // stat.addNumber(((GP)alg).fittestIndividualGeneration);
-//
-// // wie GP 1, aber mit festem return type
-// /*
-// * Config.GP.crossoverProbability = 0.85f;
-// * Config.GP.hillClimbingProbability = 0.0f; Config.returnType =
-// * "male"; alg = new GP();
-// * stat4.addNumber(alg.getSolutionScore().getScore()-0.1*alg.getBestSolution().getConceptLength());
-// * Config.returnType = "";
-// */
-//
-// }
-// exportString1.append(i + " " + stat1.getMean() + " "
-// + stat1.getStandardDeviation() + "\n");
-// exportString2.append(i + " " + stat2.getMean() + " "
-// + stat2.getStandardDeviation() + "\n");
-// exportString3.append(i + " " + stat3.getMean() + " "
-// + stat3.getStandardDeviation() + "\n");
-// // exportString4.append(i + " " + stat4.getMean() + " " +
-// // stat4.getStandardDeviation() + "\n");
-// }
-//
-// createFile(exportFile1, exportString1.toString());
-// createFile(exportFile2, exportString2.toString());
-// createFile(exportFile3, exportString3.toString());
-// // createFile(exportFile4, exportString4.toString());
-// }
-
- // erzeugt Statistiken für MLDM-Paper zur Verarbeitung mit GnuPlot
- // Vorsicht: Laufzeit von mehreren Stunden
- @SuppressWarnings("unused")
- private void createStatisticsMLDMPaper(PosNegDefinitionLP learningProblem, String baseDir) {
- // Algorithmus 1: hybrid GP (100% refinement)
- // Algorithmus 2: 50% refinement, 40% crossover, 1% mutation
- // Algorithmus 3: 80% crossover, 2% mutation
-
- // Diagramm 1: Prozentzahl richtig klassifiziert
- // Diagramm 2: Konzeptlänge
- // Diagramm 3: Laufzeit
-
- int runs = 9;
- GP gp;
- int nrOfExamples = learningProblem.getPositiveExamples().size()
- + learningProblem.getNegativeExamples().size();
-
- Stat[][] statAr = new Stat[4][3];
- File[][] fileAr = new File[4][3];
- StringBuilder[][] exportString = new StringBuilder[4][3];
- // initialise export strings
- for (int j = 0; j < 4; j++) {
- for (int k = 0; k < 3; k++) {
- exportString[j][k] = new StringBuilder();
- }
- }
-
- fileAr[0][0] = new File(baseDir, "gnuplot/hybrid100classification.data");
- fileAr[0][1] = new File(baseDir, "gnuplot/hybrid100length.data");
- fileAr[0][2] = new File(baseDir, "gnuplot/hybrid100runtime.data");
- fileAr[1][0] = new File(baseDir, "gnuplot/hybrid50classification.data");
- fileAr[1][1] = new File(baseDir, "gnuplot/hybrid50length.data");
- fileAr[1][2] = new File(baseDir, "gnuplot/hybrid50runtime.data");
- fileAr[2][0] = new File(baseDir, "gnuplot/gpclassification.data");
- fileAr[2][1] = new File(baseDir, "gnuplot/gplength.data");
- fileAr[2][2] = new File(baseDir, "gnuplot/gpruntime.data");
-
- // Extra-Test
- fileAr[3][0] = new File(baseDir, "gnuplot/extraclassification.data");
- fileAr[3][1] = new File(baseDir, "gnuplot/extralength.data");
- fileAr[3][2] = new File(baseDir, "gnuplot/extraruntime.data");
-
- ComponentManager cm = ComponentManager.getInstance();
-
- long overallTimeStart = System.nanoTime();
-
- // allgemeine Einstellungen
- // Config.GP.elitism = true;
-
- for (int i = 700; i <= 700; i += 100) {
- // initialise statistics array
- for (int j = 0; j < 4; j++) {
- for (int k = 0; k < 3; k++) {
- statAr[j][k] = new Stat();
- }
- }
-
- for (int run = 0; run < runs; run++) {
- System.out.println("=============");
- System.out.println("i " + i + " run " + run);
- System.out.println("=============");
-
- // nur ein Test durchlaufen
- for (int j = 0; j < 3; j++) {
-
- // Reasoner neu erstellen um Speicherprobleme zu vermeiden
- reasoner = new DIGReasoner(kb, Config.digReasonerURL, importedFiles);
- reasoner.prepareSubsumptionHierarchy();
- rs = new ReasoningService(reasoner);
- // learningProblem = new LearningProblem(rs, posExamples, negExamples);
- learningProblem = cm.learningProblem(PosNegDefinitionLP.class, rs);
- cm.applyConfigEntry(learningProblem, "positiveExamples", posExamples);
- cm.applyConfigEntry(learningProblem, "negativeExamples", negExamples);
-
- if (j == 0) {
- Config.algorithm = Algorithm.HYBRID_GP;
- Config.GP.numberOfIndividuals = i + 1;
- Config.GP.refinementProbability = 0.85;
- Config.GP.mutationProbability = 0.02;
- Config.GP.crossoverProbability = 0.05;
- Config.GP.hillClimbingProbability = 0;
- } else if (j == 1) {
- Config.algorithm = Algorithm.HYBRID_GP;
- Config.GP.numberOfIndividuals = i + 1;
- Config.GP.refinementProbability = 0.4;
- Config.GP.mutationProbability = 0.02;
- Config.GP.crossoverProbability = 0.4;
- Config.GP.hillClimbingProbability = 0;
- } else if (j == 2) {
- Config.algorithm = Algorithm.GP;
- Config.GP.numberOfIndividuals = i + 1;
- Config.GP.refinementProbability = 0;
- Config.GP.mutationProbability = 0.02;
- Config.GP.crossoverProbability = 0.8;
- Config.GP.hillClimbingProbability = 0;
- } else if (j == 3) {
- Config.algorithm = Algorithm.HYBRID_GP;
- Config.GP.numberOfIndividuals = i + 1;
- Config.GP.refinementProbability = 0.7;
- Config.GP.mutationProbability = 0.02;
- Config.GP.crossoverProbability = 0.1;
- Config.GP.hillClimbingProbability = 0;
- }
-
- algorithmStartTime = System.nanoTime();
- gp = new GP(learningProblem);
- long algorithmTime = System.nanoTime() - algorithmStartTime;
- long algorithmTimeSeconds = algorithmTime / 1000000000;
-
- // Release, damit Pellet (hoffentlich) Speicher wieder
- // freigibt
- ((DIGReasoner) reasoner).releaseKB();
-
- int conceptLength = gp.getBestSolution().getLength();
- Score bestScore = gp.getSolutionScore();
- int misClassifications = bestScore.getCoveredNegatives().size()
- + bestScore.getNotCoveredPositives().size();
- double classificationRatePercent = 100 * ((nrOfExamples - misClassifications) / (double) nrOfExamples);
-
- statAr[j][0].addNumber(classificationRatePercent);
- statAr[j][1].addNumber(conceptLength);
- statAr[j][2].addNumber(algorithmTimeSeconds);
-
- }
- }
-
- for (int j = 0; j < 3; j++) {
- for (int k = 0; k < 3; k++) {
- exportString[j][k].append(i + " " + statAr[j][k].getMean() + " "
- + statAr[j][k].getStandardDeviation() + "\n");
- }
- }
-
- // Daten werden nach jeder Populationserhöhung geschrieben, nicht
- // nur
- // am Ende => man kann den Test also auch zwischendurch abbrechen
- for (int j = 0; j < 3; j++) {
- for (int k = 0; k < 3; k++) {
- Files.createFile(fileAr[j][k], exportString[j][k].toString());
- }
- }
- }
-
- long overallTime = System.nanoTime() - overallTimeStart;
- System.out.println("\noverall time: "
- + Helper.prettyPrintNanoSeconds(overallTime));
- }
-
- // TODO: query mode umschreiben
- private void processQueryMode(Reasoner reasoner) {
-
- System.out
- .println("Entering query mode. Enter a concept for performing retrieval or q to quit.");
- String queryStr = "";
- do {
-
- System.out.print("enter query: "); // String einlesen
- BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-
- // Eingabestring einlesen
- try {
- queryStr = input.readLine();
- } catch (IOException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
-
- if (!queryStr.equals("q")) {
-
- // Konzept parsen
- Concept concept = null;
- boolean parsedCorrectly = true;
-
- try {
- concept = KBParser.parseConcept(queryStr);
- } catch (ParseException e1) {
- e1.printStackTrace();
- System.err
- .println("The concept you entered could not be parsed. Please try again.");
- parsedCorrectly = false;
- } catch (TokenMgrError e) {
- e.printStackTrace();
- System.err
- .println("An error occured during parsing. Please enter a syntactically valid concept.");
- parsedCorrectly = false;
- }
-
- if (parsedCorrectly) {
- // berechne im Konzept vorkommende atomare Rollen und
- // Konzepte
- SortedSet<AtomicConcept> occurringConcepts = new TreeSet<AtomicConcept>(
- new ConceptComparator());
- occurringConcepts.addAll(Helper.getAtomicConcepts(concept));
- SortedSet<AtomicRole> occurringRoles = new TreeSet<AtomicRole>(
- new RoleComparator());
- occurringRoles.addAll(Helper.getAtomicRoles(concept));
-
- // ziehe davon die existierenden ab => die resultierenden
- // Mengen
- // sollten leer sein, ansonsten Fehler (der DIG-Reasoner
- // fängt das
- // leider nicht selbst ab)
- // => momentan etwas umständlich gelöst, da es in Java bei
- // removeAll darauf
- // ankommt, dass die Argumentmenge den Comparator
- // implementiert hat, was hier
- // (noch) nicht der Fall ist
- for (AtomicConcept ac : rs.getAtomicConcepts())
- occurringConcepts.remove(ac);
- for (AtomicRole ar : rs.getAtomicRoles())
- occurringRoles.remove(ar);
-
- boolean nonExistingConstructs = false;
- if (occurringConcepts.size() != 0 || occurringRoles.size() != 0) {
- System.out
- .println("You used non-existing atomic concepts or roles. Please correct your query.");
- if (occurringConcepts.size() > 0)
- System.out.println("non-existing concepts: "
- + occurringConcepts);
- if (occurringRoles.size() > 0)
- System.out.println("non-existing roles: " + occurringRoles);
- nonExistingConstructs = true;
- }
-
- if (!nonExistingConstructs) {
- // Retrieval stellen
- Set<Individual> result = null;
- try {
- result = reasoner.retrieval(concept);
- } catch (ReasoningMethodUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- System.out.println(result);
-
- Score score = learningProblem.computeScore(concept);
- System.out.println(score);
-
- // feststellen, was zur Lösung noch fehlt
- // Set<String> notCoveredPositives
- }
- }
- }
-
- } while (!queryStr.equals("q"));
-
- /*
- * String queryStr = "";
- *
- * do {
- *
- * System.out.print("enter query: "); // String einlesen BufferedReader
- * input = new BufferedReader(new InputStreamReader(System.in));
- *
- * try { queryStr = input.readLine(); // queryStr.trim(); } catch
- * (IOException e) { e.printStackTrace(); }
- *
- * if (!queryStr.equals("q")) {
- *
- * Predicate queryPredicate = null; boolean parseError = false; boolean
- * showRole = false; ASTConcept conceptNode = null; // testen, ob es
- * einem Rollennamen entspricht if (roles.containsKey(queryStr)) {
- * queryPredicate = roles.get(queryStr); showRole = true; } else { // zu
- * einer Konzeptbeschreibung vervollst�ndigen queryStr = "query = " +
- * queryStr + "."; // String parsen SimpleNode queryNode = null; try {
- * queryNode = DLLearner.parseString(queryStr); conceptNode =
- * (ASTConcept) queryNode.jjtGetChild(0).jjtGetChild(1); queryPredicate =
- * parseConcept(conceptNode); } catch (ParseException e) {
- * System.out.println(e); // e.printStackTrace(); System.out
- * .println("Exception encountered. Please enter a valid concept
- * description or a role name."); parseError = true; } catch
- * (TokenMgrError e2) { System.out.println(e2); System.out
- * .println("Error encountered. Please enter a valid concept description
- * or a role name."); parseError = true; } }
- *
- * if (!parseError) { // Kind ermitteln (Kind 0 ist "query", Kind 1 //
- * "=", Kind // 2 Konzept) // Node conceptNode = //
- * queryNode.jjtGetChild(0).jjtGetChild(1); // if (conceptNode
- * instanceof ASTConcept) { // Description d = parseConcept((ASTConcept) // //
- * conceptNode); // Query stellen List<String> results = new //
- * LinkedList<String>(); Map<String, List<String>> resultMap = new
- * HashMap<String, List<String>>(); try { query =
- * reasoner.createQuery(queryPredicate); Object[] tupleBuffer = null;
- *
- * query.open(); while (!query.afterLast()) { tupleBuffer =
- * query.tupleBuffer(); // .toString(); if (tupleBuffer.length == 1)
- * results.add(tupleBuffer[0].toString()); else { String ind1 =
- * tupleBuffer[0].toString(); String ind2 = tupleBuffer[1].toString();
- * List<String> l; if (!resultMap.containsKey(ind1)) l = new LinkedList<String>();
- * else l = resultMap.get(ind1);
- *
- * l.add(ind2); resultMap.put(ind1, l); } query.next(); } // Query an
- * eigenen Algorithmus stellen if(!showRole) { org.dllearner.dl.Concept
- * conceptOwn = parseConceptOwn(conceptNode); // Score score =
- * conceptOwn.computeScore(); Score score = new Score(conceptOwn);
- * System.out.println(score); System.out.println("positive (own
- * algorithm): " + score.getDefPosSet()); System.out.println("negative
- * (own algorithm): " + score.getDefNegSet()); }
- *
- * if (tupleBuffer == null || tupleBuffer.length <= 1) {
- * System.out.println("KAON2: " + results); } else
- * System.out.println(resultMap); query.close(); query.dispose(); }
- * catch (KAON2Exception e) { e.printStackTrace(); } catch
- * (InterruptedException e) { e.printStackTrace(); } // } else { //
- * System.out.println("Please enter a concept."); // } } // String
- * einlesen, String parsen => SimpleNode, falls // einzigstes Kind //
- * kein Konzept ist, dann Abbruch; falls doch dann parsen // und // //
- * zur�ckerhaltene // Description an Reasoner geben } } while
- * (!queryStr.equals("q"));
- */
-
- /*
- * String queryStr = ""; Query query;
- *
- * do {
- *
- * System.out.print("enter query: "); // String einlesen BufferedReader
- * input = new BufferedReader(new InputStreamReader(System.in));
- *
- * try { queryStr = input.readLine(); // queryStr.trim(); } catch
- * (IOException e) { e.printStackTrace(); }
- *
- * if (!queryStr.equals("q")) {
- *
- * Predicate queryPredicate = null; boolean parseError = false; boolean
- * showRole = false; ASTConcept conceptNode = null; // testen, ob es
- * einem Rollennamen entspricht if (roles.containsKey(queryStr)) {
- * queryPredicate = roles.get(queryStr); showRole = true; } else { // zu
- * einer Konzeptbeschreibung vervollst�ndigen queryStr = "query = " +
- * queryStr + "."; // String parsen SimpleNode queryNode = null; try {
- * queryNode = DLLearner.parseString(queryStr); conceptNode =
- * (ASTConcept) queryNode.jjtGetChild(0).jjtGetChild(1); queryPredicate =
- * parseConcept(conceptNode); } catch (ParseException e) {
- * System.out.println(e); // e.printStackTrace(); System.out
- * .println("Exception encountered. Please enter a valid concept
- * description or a role name."); parseError = true; } catch
- * (TokenMgrError e2) { System.out.println(e2); System.out
- * .println("Error encountered. Please enter a valid concept description
- * or a role name."); parseError = true; } }
- *
- * if (!parseError) { // Kind ermitteln (Kind 0 ist "query", Kind 1 "=",
- * Kind // 2 Konzept) // Node conceptNode = //
- * queryNode.jjtGetChild(0).jjtGetChild(1); // if (conceptNode
- * instanceof ASTConcept) { // Description d = parseConcept((ASTConcept) //
- * conceptNode); // Query stellen List<String> results = new LinkedList<String>();
- * Map<String, List<String>> resultMap = new HashMap<String, List<String>>();
- * try { query = reasoner.createQuery(queryPredicate); Object[]
- * tupleBuffer = null;
- *
- * query.open(); while (!query.afterLast()) { tupleBuffer =
- * query.tupleBuffer(); // .toString(); if (tupleBuffer.length == 1)
- * results.add(tupleBuffer[0].toString()); else { String ind1 =
- * tupleBuffer[0].toString(); String ind2 = tupleBuffer[1].toString();
- * List<String> l; if (!resultMap.containsKey(ind1)) l = new LinkedList<String>();
- * else l = resultMap.get(ind1);
- *
- * l.add(ind2); resultMap.put(ind1, l); } query.next(); } // Query an
- * eigenen Algorithmus stellen if(!showRole) { org.dllearner.dl.Concept
- * conceptOwn = parseConceptOwn(conceptNode); // Score score =
- * conceptOwn.computeScore(); Score score = new Score(conceptOwn);
- * System.out.println(score); System.out.println("positive (own
- * algorithm): " + score.getDefPosSet()); System.out.println("negative
- * (own algorithm): " + score.getDefNegSet()); }
- *
- * if (tupleBuffer == null || tupleBuffer.length <= 1) {
- * System.out.println("KAON2: " + results); } else
- * System.out.println(resultMap); query.close(); query.dispose(); }
- * catch (KAON2Exception e) { e.printStackTrace(); } catch
- * (InterruptedException e) { e.printStackTrace(); } // } else { //
- * System.out.println("Please enter a concept."); // } } // String
- * einlesen, String parsen => SimpleNode, falls // einzigstes Kind //
- * kein Konzept ist, dann Abbruch; falls doch dann parsen // und //
- * zur�ckerhaltene // Description an Reasoner geben } } while
- * (!queryStr.equals("q"));
- */
- }
-
- // Funktion wird nicht mehr ben�tigt
- /*
- * private File searchImports(Node rootNode, String baseDir) { // es wird
- * zuerst nach einer import-Anweisung gesucht // boolean importKB = false;
- * File importedFile = null; for (int i = 0; i <
- * rootNode.jjtGetNumChildren(); i++) { if (rootNode.jjtGetChild(i)
- * instanceof ASTFunctionCall) { Node functionCall = (ASTFunctionCall)
- * rootNode.jjtGetChild(i); String function = ((ASTId)
- * functionCall.jjtGetChild(0)).getId(); if (function.equals("import")) {
- * String importFile = ""; importFile = ((ASTString)
- * functionCall.jjtGetChild(1)).getId(); // Anf�hrungszeichen im String
- * wegschneiden importFile = importFile.substring(1, importFile.length() -
- * 1); importedFile = new File(baseDir, importFile); // importKB = true; } } }
- * return importedFile; }
- */
-
- // VERALTET
- /*
- * private void handleReturnType(Ontology ontology) { // es wird eine Regel:
- * "zielkonzept SUBCLASS r�ckgabetyp" zur Ontologie // hinzugef�gt // TODO:
- * es muss noch gepr�ft werden was bei Inkosistenz mit pos. bzw. //
- * negativen Beispiel passiert // Problem: diese Implementierungsvariante
- * bringt leider nichts, da der // einfache DL-Algorithmus daraus keinen
- * Nutzen zieht (au�erdem kann ein // Nutzer falls er m�chte einfach so eine
- * Regel in die Konf.datei // schreiben) FlatABox abox =
- * FlatABox.getInstance(); String subClass = abox.getTargetConcept() + "
- * SUBCLASS " + Config.returnType; Description d2 = null; try { d2 =
- * parseConcept((ASTConcept)
- * DLLearner.parseString(subClass).jjtGetChild(1)); } catch (ParseException
- * e) { System.err.println("Cannot parse return type.");
- * e.printStackTrace(); System.exit(0); } Description d1 =
- * getConcept(abox.getTargetConcept());
- *
- * List<OntologyChangeEvent> changes = new ArrayList<OntologyChangeEvent>();
- * changes.add(new OntologyChangeEvent(KAON2Manager.factory().subClassOf(d1,
- * d2), OntologyChangeEvent.ChangeType.ADD));
- *
- * try { ontology.applyChanges(changes); } catch (KAON2Exception e) {
- * System.err.println("Error in handling return type " + Config.returnType +
- * "."); e.printStackTrace(); System.exit(0); } }
- */
-
- /*
- * private static OWLClass getConcept(String name) { if
- * (!concepts.containsKey(name)) { concepts.put(name,
- * KAON2Manager.factory().owlClass(name)); } return concepts.get(name); }
- *
- * private static ObjectProperty getRole(String name) { if
- * (!roles.containsKey(name)) { roles.put(name,
- * KAON2Manager.factory().objectProperty(name)); } return roles.get(name); }
- *
- * public static Individual getIndividual(String name) { if
- * (!individuals.containsKey(name)) { individuals.put(name,
- * KAON2Manager.factory().individual(name)); } return individuals.get(name); }
- */
-
- // die Methode muss private bleiben
- private static FlatABox createFlatABox(Reasoner reasoner)
- throws ReasoningMethodUnsupportedException {
- long dematStartTime = System.currentTimeMillis();
-
- FlatABox aBox = new FlatABox(); // FlatABox.getInstance();
- for (AtomicConcept atomicConcept : reasoner.getAtomicConcepts()) {
- aBox.atomicConceptsPos.put(atomicConcept.getName(), Helper
- .getStringSet(reasoner.retrieval(atomicConcept)));
- Negation negatedAtomicConcept = new Negation(atomicConcept);
- aBox.atomicConceptsNeg.put(atomicConcept.getName(), Helper
- .getStringSet(reasoner.retrieval(negatedAtomicConcept)));
- aBox.concepts.add(atomicConcept.getName());
- }
-
- for (AtomicRole atomicRole : reasoner.getAtomicRoles()) {
- aBox.rolesPos.put(atomicRole.getName(), Helper.getStringMap(reasoner
- .getRoleMembers(atomicRole)));
- aBox.roles.add(atomicRole.getName());
- }
-
- aBox.domain = Helper.getStringSet(reasoner.getIndividuals());
- aBox.top = aBox.domain;
- // ab hier keine �nderungen mehr an FlatABox
- aBox.prepare();
-
- // System.out.println(aBox);
-
- long dematDuration = System.currentTimeMillis() - dematStartTime;
- System.out.println("OK (" + dematDuration + " ms)");
- return aBox;
- }
-
- // gibt M�glickeit flat Abox zu bekommen, falls eine erzeugt wurde
- // (wird momentan nur f�r hill climbing ben�tigt und es ist sauberer diese
- // hier
- // zu erzeugen und bekommen als die ReasoningService-Klasse zu hacken)
- public static FlatABox getFlatAbox() {
- return abox;
- }
-
- // generiert sibling aus Forte-Daten
- @SuppressWarnings("unused")
- private void test2(PosNegLP learningProblem) {
- // Set<AtomicRole> roles = reasoner.getAtomicRoles();
- // for(AtomicRole role : roles) {
- // System.out.println(rs.getRoleMembers(role));
- // }
- /*
- * AtomicRole sibling = new AtomicRole("sibling"); Map<String,SortedSet<String>>
- * members = rs.getRoleMembers(sibling); for(String name :
- * members.keySet()) { SortedSet<String> fillers = members.get(name);
- * for(String filler : fillers) {
- * System.out.println("sibling("+name+","+filler+")."); } }
- */
- Concept c = null;
- try {
- c = KBParser.parseConcept("EXISTS uncle.TOP");
- } catch (ParseException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- Set<Individual> uncles = rs.retrieval(c);
- Set<Individual> inds = rs.getIndividuals();
- for (Individual ind : uncles)
- System.out.println("+isUncle(" + ind + ").");
- inds.removeAll(uncles);
- for (Individual ind : inds)
- System.out.println("-isUncle(" + ind + ").");
-
- System.exit(0);
- }
-
- public static long getAlgorithmStartTime() {
- return algorithmStartTime;
- }
-
- // die Methode soll alle Konzeptzusicherungen und Rollenzusicherungen von
- // Individuen entfernen, die mit diesem Individuum verbunden sind
- @SuppressWarnings("unused")
- private void removeIndividualSubtree(KB kb, Individual individual) {
- System.out.println();
- // erster Schritt: alle verbundenen Individuen finden
- Set<Individual> connectedIndividuals = kb.findRelatedIndividuals(individual);
- System.out.println("connected individuals: " + connectedIndividuals);
- // Individual selbst auch entfernen
- connectedIndividuals.add(individual);
-
- // zweiter Schritt: entfernen von Rollen- und Konzeptzusicherungen
- Set<AssertionalAxiom> abox = kb.getAbox();
- Iterator<AssertionalAxiom> it = abox.iterator();
- while (it.hasNext()) {
- AssertionalAxiom a = it.next();
- if (a instanceof RoleAssertion) {
- RoleAssertion ra = (RoleAssertion) a;
- if (connectedIndividuals.contains(ra.getIndividual1())
- || connectedIndividuals.contains(ra.getIndividual2())) {
- System.out.println("remove " + ra);
- it.remove();
- }
- } else if (a instanceof ConceptAssertion) {
- if (connectedIndividuals.contains(((ConceptAssertion) a).getIndividual())) {
- System.out.println("remove " + a);
- it.remove();
- }
- } else
- throw new RuntimeException();
- }
-
- Set<Individual> inds = kb.findAllIndividuals();
- System.out.println("remaining individuals: " + inds);
- System.out.println();
- }
-
- public static ConfigurationManager getConfMgr() {
- return confMgr;
- }
-
-}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GPUtilities.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GPUtilities.java 2007-10-07 16:35:12 UTC (rev 173)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GPUtilities.java 2007-10-07 18:00:21 UTC (rev 174)
@@ -8,8 +8,8 @@
import java.util.TreeMap;
import org.dllearner.Config;
-import org.dllearner.Main;
import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.Score;
import org.dllearner.core.dl.All;
import org.dllearner.core.dl.AtomicConcept;
@@ -340,7 +340,14 @@
Score tmpScore;
SortedSetTuple<String> tmp, tmp2;
// FlatABox abox = ((FastRetrievalReasoner)learningProblem.getReasoner().getFastRetrieval().getAbox();
- FlatABox abox = Main.getFlatAbox();
+ // FlatABox abox = Main.getFlatAbox();
+ FlatABox abox = null;
+ try {
+ abox = Helper.createFlatABox(learningProblem.getReasoningService());
+ } catch (ReasoningMethodUnsupportedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
// TODO: testen, ob aktuelles Konzept zu speziell bzw. allgemein ist;
// dann kann man das effizienter implementieren
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2007-10-07 16:35:12 UTC (rev 173)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2007-10-07 18:00:21 UTC (rev 174)
@@ -11,7 +11,6 @@
import java.util.TreeSet;
import org.dllearner.Config;
-import org.dllearner.Main;
import org.dllearner.core.ConfigEntry;
import org.dllearner.core.ConfigOption;
import org.dllearner.core.InvalidConfigOptionValueException;
@@ -243,7 +242,7 @@
@Override
public void init() {
// TODO: this needs to be changed
- Main.autoDetectConceptsAndRoles(rs);
+ Helper.autoDetectConceptsAndRoles(rs);
// prepare subsumption and role hierarchies, because they are needed
// during the run of the algorithm
rs.prepareSubsumptionHierarchy();
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2007-10-07 16:35:12 UTC (rev 173)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2007-10-07 18:00:21 UTC (rev 174)
@@ -19,15 +19,20 @@
*/
package org.dllearner.cli;
+import java.io.BufferedReader;
import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
import java.net.MalformedURLException;
import java.net.URL;
+import java.text.DecimalFormat;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.algorithms.gp.GP;
import org.dllearner.algorithms.refinement.ROLearner;
@@ -42,22 +47,31 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.LearningAlgorithmNew;
import org.dllearner.core.LearningProblem;
+import org.dllearner.core.Reasoner;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.ReasoningService;
+import org.dllearner.core.Score;
import org.dllearner.core.StringConfigOption;
import org.dllearner.core.StringSetConfigOption;
import org.dllearner.core.dl.AtomicConcept;
import org.dllearner.core.dl.AtomicRole;
+import org.dllearner.core.dl.Concept;
import org.dllearner.core.dl.Individual;
import org.dllearner.kb.KBFile;
import org.dllearner.kb.OWLFile;
+import org.dllearner.kb.OntologyFileFormat;
import org.dllearner.kb.SparqlEndpoint;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.parser.ConfParser;
+import org.dllearner.parser.KBParser;
+import org.dllearner.parser.ParseException;
+import org.dllearner.parser.TokenMgrError;
import org.dllearner.reasoning.DIGReasonerNew;
+import org.dllearner.utilities.ConceptComparator;
import org.dllearner.utilities.Datastructures;
import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.RoleComparator;
/**
* Startup file for Command Line Interface.
@@ -140,6 +154,9 @@
initComponent(cm, lp);
initComponent(cm, la);
+ // perform file exports
+ performExports(parser, baseDir, rs);
+
// show examples (display each one if they do not take up much space,
// otherwise just show the number of examples)
boolean oneLineExampleInfo = true;
@@ -163,7 +180,11 @@
processCLIOptions(cm, parser, rs);
// start algorithm
+ long algStartTime = System.nanoTime();
la.start();
+ long algDuration = System.nanoTime() - algStartTime;
+
+ printConclusions(rs, algDuration);
}
// creates a mapping from components to option prefix strings
@@ -180,6 +201,10 @@
return componentPrefixMapping;
}
+ // convenience method
+ // basically every prefix (e.g. "refinement" in "refinement.horizontalExpFactor)
+ // corresponds to a specific component - this way the CLI will automatically
+ // support any configuration options supported by the component
private static void configureComponent(ComponentManager cm, Component component,
Map<Class<? extends Component>, String> componentPrefixMapping, ConfParser parser) {
String prefix = componentPrefixMapping.get(component.getClass());
@@ -187,6 +212,7 @@
configureComponent(cm, component, parser.getConfOptionsByPrefix(prefix));
}
+ // convenience method - see above method
private static void configureComponent(ComponentManager cm, Component component,
List<ConfFileOption> options) {
if (options != null)
@@ -19...
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