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From: <jen...@us...> - 2008-05-19 13:11:36
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Revision: 901
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=901&view=rev
Author: jenslehmann
Date: 2008-05-19 06:11:24 -0700 (Mon, 19 May 2008)
Log Message:
-----------
small fixes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/package.html
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/statistics/PaperStatistics.java
Modified: trunk/src/dl-learner/org/dllearner/core/owl/package.html
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/package.html 2008-05-19 12:57:31 UTC (rev 900)
+++ trunk/src/dl-learner/org/dllearner/core/owl/package.html 2008-05-19 13:11:24 UTC (rev 901)
@@ -3,7 +3,7 @@
<head></head>
<body bgcolor="white">
<p>Classes/Interfaces for representing OWL constructs - see
-the <a href="http://www.w3.org/TR/owl11-syntax">OWL 1.1 Structural
+the <a href="http://www.w3.org/TR/owl2-syntax/">OWL 2 Structural
Specification</a> for details.</p>
</body>
</html>
\ No newline at end of file
Copied: trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java (from rev 899, trunk/src/dl-learner/org/dllearner/utilities/statistics/PaperStatistics.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-05-19 13:11:24 UTC (rev 901)
@@ -0,0 +1,525 @@
+/**
+ * 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.scripts;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedSet;
+
+import org.dllearner.algorithms.gp.GP;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.OntologyFormat;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.Score;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.parser.ConfParser;
+import org.dllearner.reasoning.DIGReasoner;
+import org.dllearner.utilities.Files;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.statistics.Stat;
+
+/**
+ * Utility script for creating statistics for publications.
+ * (Warning: Scripts may run for several hours. Results may change
+ * when core algorithms are modified.)
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class PaperStatistics {
+
+ /**
+ * Points to the current statistic generation function.
+ *
+ * @param args None.
+ */
+ public static void main(String[] args) {
+ createStatistics();
+ }
+
+ @SuppressWarnings("unused")
+ private static void createStatistics() {
+
+ // experimental setup:
+
+ // algorithms: refinement, GP, hybrid GP (YinYang)
+ // settings GP:
+ // - average over 10 runs
+ // ...
+ // settings Hybrid GP:
+ // - average over 10 runs
+ // ...
+ // settings refinement:
+ // - single run
+ // ...
+
+ // observations:
+ // - correctness
+ // - concept length
+ // - runtime
+
+ // learning examples:
+ // - trains
+ // - arches
+ // - moral (simple)
+ // - moral (complex)
+ // - poker (pair)
+ // - poker (straight)
+ // - uncle (FORTE)
+ // - more?
+
+ String exampleBaseDir = "examples/";
+ String gnuplotBaseDir = "log/gnuplot/";
+ String statBaseDir = "log/stat/";
+
+ File[] confFiles = new File[7];
+ confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl.conf");
+ confFiles[1] = new File(exampleBaseDir + "arch", "arch_owl.conf");
+ confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl.conf");
+ confFiles[3] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl.conf");
+ confFiles[4] = new File(exampleBaseDir + "poker", "pair_owl.conf");
+ confFiles[5] = new File(exampleBaseDir + "poker", "straight_owl.conf");
+ confFiles[6] = new File(exampleBaseDir + "forte", "forte_uncle_owl.conf");
+
+ String[] examples = new String[7];
+ examples[0] = "trains";
+ examples[1] = "arches";
+ examples[2] = "moral reasoner (43 examples, simple)";
+ examples[3] = "moral reasoner (43 examples, complex)";
+ examples[4] = "poker (49 examples, pair)";
+ examples[5] = "poker (55 examples, straight)";
+ examples[6] = "uncle (FORTE data set)";
+ int startExampleNr = 0;
+
+ String[] algorithms = new String[3];
+ algorithms[0] = "refinement";
+ algorithms[1] = "gp";
+ algorithms[2] = "hybrid";
+
+ int[] algorithmRuns = {1,10,10};
+ int startAlgorithmNr = 0;
+
+ // Config.GP.maxConceptLength = 30;
+ // Config.writeDIGProtocol = true;
+ // Config.digProtocolFile = new File(statBaseDir, "dig.log");
+
+ // do not plot anything
+ // File[][][] gnuplotFiles = new File[examples.length][algorithms.length][3];
+ // for(int i=0; i<examples.length; i++) {
+ // for(int j=0; j<algorithms.length; j++) {
+ // gnuplotFiles[i][j][0] = new File(gnuplotBaseDir, examples[i] + "_classification_" + algorithms[j] + ".data");
+ // gnuplotFiles[i][j][1] = new File(gnuplotBaseDir, examples[i] + "_length_" + algorithms[j] + ".data");
+ // gnuplotFiles[i][j][2] = new File(gnuplotBaseDir, examples[i] + "_runtime_" + algorithms[j] + ".data");
+ // }
+ //}
+
+ File statFile = new File(statBaseDir, "statistics.txt");
+ File statDetailsFile = new File(statBaseDir, "statistics_details.txt");
+ String statString = "**automatically generated statistics**\n\n";
+ String statDetailsString = statString;
+
+ ComponentManager cm = ComponentManager.getInstance();
+
+ // just set default options
+// ConfigurationManager confMgr = new ConfigurationManager();
+// confMgr.applyOptions();
+
+ for(int exampleNr=startExampleNr; exampleNr < examples.length; exampleNr++) {
+
+ // parse current conf file
+ ConfParser learner = ConfParser.parseFile(confFiles[exampleNr]);
+
+ String baseDir = confFiles[exampleNr].getParent();
+
+ // read which files were imported (internal KB is ignored) and initialise reasoner
+ Map<URL, OntologyFormat> imports = getImports(learner.getFunctionCalls(), confFiles[exampleNr]);
+ //Map<URL, Class<? extends KnowledgeSource>> imports = Start.getImportedFiles(learner, baseDir);
+
+ // detect specified positive and negative examples
+ SortedSet<String> positiveExamples = learner.getPositiveExamples();
+ SortedSet<String> negativeExamples = learner.getNegativeExamples();
+ int nrOfExamples = positiveExamples.size() + negativeExamples.size();
+
+ statString += "example: " + examples[exampleNr] + "\n\n";
+
+ for(int algorithmNr=startAlgorithmNr; algorithmNr < algorithms.length; algorithmNr++) {
+ // reset algorithm number (next example starts with first algorithm)
+ startAlgorithmNr = 0;
+
+ Stat classification = new Stat();
+ Stat length = new Stat();
+ Stat runtime = new Stat();
+
+ for(int runNr=0; runNr < algorithmRuns[algorithmNr]; runNr++) {
+
+ // create reasoner (this has to be done in this inner loop to
+ // ensure that none of the algorithm benefits from e.g. caching
+ // of previous reasoning requests
+ // Reasoner reasoner = Main.createReasoner(new KB(), imports);
+ // TODO: needs fixing
+ KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
+ ReasonerComponent reasoner = cm.reasoner(DIGReasoner.class, ks);
+ ReasoningService rs = new ReasoningService(reasoner);
+
+ // System.out.println(positiveExamples);
+ // System.out.println(negativeExamples);
+ // System.exit(0);
+
+ // create learning problem
+ // LearningProblem learningProblem = new LearningProblem(rs, positiveExamples, negativeExamples);
+ LearningProblem learningProblem = cm.learningProblem(PosNegDefinitionLP.class, rs);
+
+ // prepare reasoner for using subsumption and role hierarchy
+ // TODO: currently, it is a small unfairness that each algorithm
+ // uses the same reasoning object (e.g. the second algorithm may
+ // have a small advantage if the reasoner cached reasoning requests
+ // of the first algorithm)
+// Helper.autoDetectConceptsAndRoles(rs);
+// try {
+// reasoner.prepareSubsumptionHierarchy();
+// reasoner.prepareRoleHierarchy();
+// // improving the subsumption hierarchy makes only sense
+// // for the refinement based algorithm
+// if(algorithmNr==0)
+// reasoner.getSubsumptionHierarchy().improveSubsumptionHierarchy();
+// } catch (ReasoningMethodUnsupportedException e) {
+// e.printStackTrace();
+// }
+
+ LearningAlgorithm learningAlgorithm = null;
+ if(algorithmNr==0) {
+ // Config.algorithm = Algorithm.REFINEMENT;
+ // Config.Refinement.heuristic = Config.Refinement.Heuristic.FLEXIBLE;
+// Config.Refinement.horizontalExpansionFactor = 0.6;
+// Config.Refinement.quiet = true;
+ // Config.percentPerLengthUnit = 0.05;
+ // learningAlgorithm = new ROLearner(learningProblem);
+ // learningAlgorithm = cm.learningAlgorithm(ROLearner.class, learningProblem);
+ } else if(algorithmNr==1) {
+ // Config.algorithm = Algorithm.GP;
+// Config.GP.algorithmType = GP.AlgorithmType.GENERATIONAL;
+//// Config.GP.selectionType = GP.SelectionType.RANK_SELECTION;
+// Config.GP.generations = 50;
+// Config.GP.useFixedNumberOfGenerations = true;
+// Config.GP.numberOfIndividuals = 201;
+ // if(exampleNr == 3 || exampleNr == 4)
+ // Config.GP.numberOfIndividuals = 51;
+// Config.GP.refinementProbability = 0;
+// Config.GP.mutationProbability = 0.02;
+// Config.GP.crossoverProbability = 0.8;
+// Config.GP.hillClimbingProbability = 0;
+ // Config.percentPerLengthUnit = 0.005;
+ // give GP a chance to find the long solution of the
+ // uncle problem
+ // if(exampleNr==3 || exampleNr==5 || exampleNr == 6)
+ // Config.percentPerLengthUnit = 0.002;
+ // learningAlgorithm = new GP(learningProblem);
+ try {
+ learningAlgorithm = cm.learningAlgorithm(GP.class, learningProblem, rs);
+ } catch (LearningProblemUnsupportedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ } else if(algorithmNr==2) {
+ // Config.algorithm = Algorithm.HYBRID_GP;
+// Config.GP.algorithmType = GP.AlgorithmType.GENERATIONAL;
+// Config.GP.selectionType = GP.SelectionType.RANK_SELECTION;
+// Config.GP.generations = 50;
+// Config.GP.useFixedNumberOfGenerations = true;
+// Config.GP.numberOfIndividuals = 201;
+ //if(exampleNr == 3 || exampleNr == 4)
+ // Config.GP.numberOfIndividuals = 51;
+// Config.GP.refinementProbability = 0.65;
+// Config.GP.mutationProbability = 0.02;
+// Config.GP.crossoverProbability = 0.2;
+// Config.GP.hillClimbingProbability = 0;
+ // Config.percentPerLengthUnit = 0.005;
+ // if(exampleNr == 3 || exampleNr==5 || exampleNr==6)
+// Config.percentPerLengthUnit = 0.002;
+ // learningAlgorithm = new GP(learningProblem);
+ try {
+ learningAlgorithm = cm.learningAlgorithm(GP.class, learningProblem, rs);
+ } catch (LearningProblemUnsupportedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ // rs.resetStatistics();
+
+ long algorithmStartTime = System.nanoTime();
+ learningAlgorithm.start();
+ long algorithmTime = System.nanoTime() - algorithmStartTime;
+ // long algorithmTimeSeconds = algorithmTime / 1000000000;
+
+ int conceptLength = learningAlgorithm.getBestSolution().getLength();
+ Score bestScore = learningAlgorithm.getSolutionScore();
+ int misClassifications = bestScore.getCoveredNegatives().size()
+ + bestScore.getNotCoveredPositives().size();
+ double classificationRatePercent = 100 * ((nrOfExamples - misClassifications) / (double) nrOfExamples);
+
+ classification.addNumber(classificationRatePercent);
+ length.addNumber(conceptLength);
+ runtime.addNumber(algorithmTime);
+
+ // free knowledge base to avoid memory leaks
+ ((DIGReasoner) reasoner).releaseKB();
+
+ statDetailsString += "example: " + examples[exampleNr] + "\n";
+ statDetailsString += "algorithm: " + algorithms[algorithmNr] + "\n";
+ statDetailsString += "learned concept: " + learningAlgorithm.getBestSolution() + "\n";
+ statDetailsString += "classification: " + classificationRatePercent + "%\n";
+ statDetailsString += "concept length: " + conceptLength + "\n";
+ statDetailsString += "runtime: " + Helper.prettyPrintNanoSeconds(algorithmTime) + "\n\n";
+
+ Files.createFile(statDetailsFile, statDetailsString);
+
+ } // end run loop
+
+ statString += "algorithm: " + algorithms[algorithmNr] + " (runs: " + algorithmRuns[algorithmNr] + ")\n";
+ statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
+ statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
+ statString += "runtime: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getMean())) + " (standard deviation: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getStandardDeviation())) + ")\n\n";
+
+ Files.createFile(statFile, statString);
+
+ } // end algorithm loop
+
+ } // end example loop
+
+ }
+
+ private static Map<URL, OntologyFormat> getImports(Map<String,List<List<String>>> functionCalls, File confFile) {
+ Map<URL, OntologyFormat> importedFiles = new HashMap<URL, OntologyFormat>();
+
+ OntologyFormat format = null;
+ URL url = null;
+
+ List<List<String>> imports = functionCalls.get("import");
+
+ for (List<String> call : imports) {
+
+ //if(call.get(0).equals("import")) {
+
+ try {
+ String fileString = call.get(1);
+ if(fileString.startsWith("http:")) {
+ url = new URL(fileString);
+ } else {
+ File f = new File(confFile.getParent(), 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, OntologyFormat.RDF_XML);
+ else {
+ String formatString = call.get(2);
+ if (formatString.equals("RDF/XML"))
+ format = OntologyFormat.RDF_XML;
+ else
+ format = OntologyFormat.N_TRIPLES;
+ importedFiles.put(url, format);
+ }
+ // }
+ }
+
+ return importedFiles;
+ }
+
+ // erzeugt Statistiken für MLDM-Paper zur Verarbeitung mit GnuPlot
+ // Vorsicht: Laufzeit von mehreren Stunden
+
+ /**
+ * Has been used to create the statistics for the MLDM 2007 paper.
+ * Warning: this method runs for several hours
+ *
+ * @todo: This method has not been fully adapted to the base structure
+ * changes. To reproduce the results, the method has to be implemented
+ * properly.
+ */
+ @SuppressWarnings("unused")
+ public static 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;
+ long algorithmStartTime;
+ 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);
+ // TODO: set up knowledge source
+ KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
+ ReasonerComponent reasoner = cm.reasoner(DIGReasoner.class, ks);
+ // reasoner.prepareSubsumptionHierarchy();
+ // rs = new ReasoningService(reasoner);
+ ReasoningService rs = cm.reasoningService(reasoner);
+ // learningProblem = new LearningProblem(rs, posExamples, negExamples);
+ learningProblem = cm.learningProblem(PosNegDefinitionLP.class, rs);
+
+ // TODO: set up pos/neg examples
+ cm.applyConfigEntry(learningProblem, "positiveExamples", null);
+ cm.applyConfigEntry(learningProblem, "negativeExamples", null);
+
+ 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));
+ }
+
+}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/statistics/PaperStatistics.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/PaperStatistics.java 2008-05-19 12:57:31 UTC (rev 900)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/PaperStatistics.java 2008-05-19 13:11:24 UTC (rev 901)
@@ -1,524 +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.utilities.statistics;
-
-import java.io.File;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedSet;
-
-import org.dllearner.algorithms.gp.GP;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.core.KnowledgeSource;
-import org.dllearner.core.LearningAlgorithm;
-import org.dllearner.core.LearningProblem;
-import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.OntologyFormat;
-import org.dllearner.core.ReasonerComponent;
-import org.dllearner.core.ReasoningService;
-import org.dllearner.core.Score;
-import org.dllearner.kb.OWLFile;
-import org.dllearner.learningproblems.PosNegDefinitionLP;
-import org.dllearner.parser.ConfParser;
-import org.dllearner.reasoning.DIGReasoner;
-import org.dllearner.utilities.Files;
-import org.dllearner.utilities.Helper;
-
-/**
- * Utility script for creating statistics for publications.
- * (Warning: Scripts may run for several hours. Results may change
- * when core algorithms are modified.)
- *
- * @author Jens Lehmann
- *
- */
-public class PaperStatistics {
-
- /**
- * Points to the current statistic generation function.
- *
- * @param args None.
- */
- public static void main(String[] args) {
- createStatistics();
- }
-
- @SuppressWarnings("unused")
- private static void createStatistics() {
-
- // experimental setup:
-
- // algorithms: refinement, GP, hybrid GP (YinYang)
- // settings GP:
- // - average over 10 runs
- // ...
- // settings Hybrid GP:
- // - average over 10 runs
- // ...
- // settings refinement:
- // - single run
- // ...
-
- // observations:
- // - correctness
- // - concept length
- // - runtime
-
- // learning examples:
- // - trains
- // - arches
- // - moral (simple)
- // - moral (complex)
- // - poker (pair)
- // - poker (straight)
- // - uncle (FORTE)
- // - more?
-
- String exampleBaseDir = "examples/";
- String gnuplotBaseDir = "log/gnuplot/";
- String statBaseDir = "log/stat/";
-
- File[] confFiles = new File[7];
- confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl.conf");
- confFiles[1] = new File(exampleBaseDir + "arch", "arch_owl.conf");
- confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl.conf");
- confFiles[3] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl.conf");
- confFiles[4] = new File(exampleBaseDir + "poker", "pair_owl.conf");
- confFiles[5] = new File(exampleBaseDir + "poker", "straight_owl.conf");
- confFiles[6] = new File(exampleBaseDir + "forte", "forte_uncle_owl.conf");
-
- String[] examples = new String[7];
- examples[0] = "trains";
- examples[1] = "arches";
- examples[2] = "moral reasoner (43 examples, simple)";
- examples[3] = "moral reasoner (43 examples, complex)";
- examples[4] = "poker (49 examples, pair)";
- examples[5] = "poker (55 examples, straight)";
- examples[6] = "uncle (FORTE data set)";
- int startExampleNr = 0;
-
- String[] algorithms = new String[3];
- algorithms[0] = "refinement";
- algorithms[1] = "gp";
- algorithms[2] = "hybrid";
-
- int[] algorithmRuns = {1,10,10};
- int startAlgorithmNr = 0;
-
- // Config.GP.maxConceptLength = 30;
- // Config.writeDIGProtocol = true;
- // Config.digProtocolFile = new File(statBaseDir, "dig.log");
-
- // do not plot anything
- // File[][][] gnuplotFiles = new File[examples.length][algorithms.length][3];
- // for(int i=0; i<examples.length; i++) {
- // for(int j=0; j<algorithms.length; j++) {
- // gnuplotFiles[i][j][0] = new File(gnuplotBaseDir, examples[i] + "_classification_" + algorithms[j] + ".data");
- // gnuplotFiles[i][j][1] = new File(gnuplotBaseDir, examples[i] + "_length_" + algorithms[j] + ".data");
- // gnuplotFiles[i][j][2] = new File(gnuplotBaseDir, examples[i] + "_runtime_" + algorithms[j] + ".data");
- // }
- //}
-
- File statFile = new File(statBaseDir, "statistics.txt");
- File statDetailsFile = new File(statBaseDir, "statistics_details.txt");
- String statString = "**automatically generated statistics**\n\n";
- String statDetailsString = statString;
-
- ComponentManager cm = ComponentManager.getInstance();
-
- // just set default options
-// ConfigurationManager confMgr = new ConfigurationManager();
-// confMgr.applyOptions();
-
- for(int exampleNr=startExampleNr; exampleNr < examples.length; exampleNr++) {
-
- // parse current conf file
- ConfParser learner = ConfParser.parseFile(confFiles[exampleNr]);
-
- String baseDir = confFiles[exampleNr].getParent();
-
- // read which files were imported (internal KB is ignored) and initialise reasoner
- Map<URL, OntologyFormat> imports = getImports(learner.getFunctionCalls(), confFiles[exampleNr]);
- //Map<URL, Class<? extends KnowledgeSource>> imports = Start.getImportedFiles(learner, baseDir);
-
- // detect specified positive and negative examples
- SortedSet<String> positiveExamples = learner.getPositiveExamples();
- SortedSet<String> negativeExamples = learner.getNegativeExamples();
- int nrOfExamples = positiveExamples.size() + negativeExamples.size();
-
- statString += "example: " + examples[exampleNr] + "\n\n";
-
- for(int algorithmNr=startAlgorithmNr; algorithmNr < algorithms.length; algorithmNr++) {
- // reset algorithm number (next example starts with first algorithm)
- startAlgorithmNr = 0;
-
- Stat classification = new Stat();
- Stat length = new Stat();
- Stat runtime = new Stat();
-
- for(int runNr=0; runNr < algorithmRuns[algorithmNr]; runNr++) {
-
- // create reasoner (this has to be done in this inner loop to
- // ensure that none of the algorithm benefits from e.g. caching
- // of previous reasoning requests
- // Reasoner reasoner = Main.createReasoner(new KB(), imports);
- // TODO: needs fixing
- KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
- ReasonerComponent reasoner = cm.reasoner(DIGReasoner.class, ks);
- ReasoningService rs = new ReasoningService(reasoner);
-
- // System.out.println(positiveExamples);
- // System.out.println(negativeExamples);
- // System.exit(0);
-
- // create learning problem
- // LearningProblem learningProblem = new LearningProblem(rs, positiveExamples, negativeExamples);
- LearningProblem learningProblem = cm.learningProblem(PosNegDefinitionLP.class, rs);
-
- // prepare reasoner for using subsumption and role hierarchy
- // TODO: currently, it is a small unfairness that each algorithm
- // uses the same reasoning object (e.g. the second algorithm may
- // have a small advantage if the reasoner cached reasoning requests
- // of the first algorithm)
-// Helper.autoDetectConceptsAndRoles(rs);
-// try {
-// reasoner.prepareSubsumptionHierarchy();
-// reasoner.prepareRoleHierarchy();
-// // improving the subsumption hierarchy makes only sense
-// // for the refinement based algorithm
-// if(algorithmNr==0)
-// reasoner.getSubsumptionHierarchy().improveSubsumptionHierarchy();
-// } catch (ReasoningMethodUnsupportedException e) {
-// e.printStackTrace();
-// }
-
- LearningAlgorithm learningAlgorithm = null;
- if(algorithmNr==0) {
- // Config.algorithm = Algorithm.REFINEMENT;
- // Config.Refinement.heuristic = Config.Refinement.Heuristic.FLEXIBLE;
-// Config.Refinement.horizontalExpansionFactor = 0.6;
-// Config.Refinement.quiet = true;
- // Config.percentPerLengthUnit = 0.05;
- // learningAlgorithm = new ROLearner(learningProblem);
- // learningAlgorithm = cm.learningAlgorithm(ROLearner.class, learningProblem);
- } else if(algorithmNr==1) {
- // Config.algorithm = Algorithm.GP;
-// Config.GP.algorithmType = GP.AlgorithmType.GENERATIONAL;
-//// Config.GP.selectionType = GP.SelectionType.RANK_SELECTION;
-// Config.GP.generations = 50;
-// Config.GP.useFixedNumberOfGenerations = true;
-// Config.GP.numberOfIndividuals = 201;
- // if(exampleNr == 3 || exampleNr == 4)
- // Config.GP.numberOfIndividuals = 51;
-// Config.GP.refinementProbability = 0;
-// Config.GP.mutationProbability = 0.02;
-// Config.GP.crossoverProbability = 0.8;
-// Config.GP.hillClimbingProbability = 0;
- // Config.percentPerLengthUnit = 0.005;
- // give GP a chance to find the long solution of the
- // uncle problem
- // if(exampleNr==3 || exampleNr==5 || exampleNr == 6)
- // Config.percentPerLengthUnit = 0.002;
- // learningAlgorithm = new GP(learningProblem);
- try {
- learningAlgorithm = cm.learningAlgorithm(GP.class, learningProblem, rs);
- } catch (LearningProblemUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- } else if(algorithmNr==2) {
- // Config.algorithm = Algorithm.HYBRID_GP;
-// Config.GP.algorithmType = GP.AlgorithmType.GENERATIONAL;
-// Config.GP.selectionType = GP.SelectionType.RANK_SELECTION;
-// Config.GP.generations = 50;
-// Config.GP.useFixedNumberOfGenerations = true;
-// Config.GP.numberOfIndividuals = 201;
- //if(exampleNr == 3 || exampleNr == 4)
- // Config.GP.numberOfIndividuals = 51;
-// Config.GP.refinementProbability = 0.65;
-// Config.GP.mutationProbability = 0.02;
-// Config.GP.crossoverProbability = 0.2;
-// Config.GP.hillClimbingProbability = 0;
- // Config.percentPerLengthUnit = 0.005;
- // if(exampleNr == 3 || exampleNr==5 || exampleNr==6)
-// Config.percentPerLengthUnit = 0.002;
- // learningAlgorithm = new GP(learningProblem);
- try {
- learningAlgorithm = cm.learningAlgorithm(GP.class, learningProblem, rs);
- } catch (LearningProblemUnsupportedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- // rs.resetStatistics();
-
- long algorithmStartTime = System.nanoTime();
- learningAlgorithm.start();
- long algorithmTime = System.nanoTime() - algorithmStartTime;
- // long algorithmTimeSeconds = algorithmTime / 1000000000;
-
- int conceptLength = learningAlgorithm.getBestSolution().getLength();
- Score bestScore = learningAlgorithm.getSolutionScore();
- int misClassifications = bestScore.getCoveredNegatives().size()
- + bestScore.getNotCoveredPositives().size();
- double classificationRatePercent = 100 * ((nrOfExamples - misClassifications) / (double) nrOfExamples);
-
- classification.addNumber(classificationRatePercent);
- length.addNumber(conceptLength);
- runtime.addNumber(algorithmTime);
-
- // free knowledge base to avoid memory leaks
- ((DIGReasoner) reasoner).releaseKB();
-
- statDetailsString += "example: " + examples[exampleNr] + "\n";
- statDetailsString += "algorithm: " + algorithms[algorithmNr] + "\n";
- statDetailsString += "learned concept: " + learningAlgorithm.getBestSolution() + "\n";
- statDetailsString += "classification: " + classificationRatePercent + "%\n";
- statDetailsString += "concept length: " + conceptLength + "\n";
- statDetailsString += "runtime: " + Helper.prettyPrintNanoSeconds(algorithmTime) + "\n\n";
-
- Files.createFile(statDetailsFile, statDetailsString);
-
- } // end run loop
-
- statString += "algorithm: " + algorithms[algorithmNr] + " (runs: " + algorithmRuns[algorithmNr] + ")\n";
- statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
- statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
- statString += "runtime: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getMean())) + " (standard deviation: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getStandardDeviation())) + ")\n\n";
-
- Files.createFile(statFile, statString);
-
- } // end algorithm loop
-
- } // end example loop
-
- }
-
- private static Map<URL, OntologyFormat> getImports(Map<String,List<List<String>>> functionCalls, File confFile) {
- Map<URL, OntologyFormat> importedFiles = new HashMap<URL, OntologyFormat>();
-
- OntologyFormat format = null;
- URL url = null;
-
- List<List<String>> imports = functionCalls.get("import");
-
- for (List<String> call : imports) {
-
- //if(call.get(0).equals("import")) {
-
- try {
- String fileString = call.get(1);
- if(fileString.startsWith("http:")) {
- url = new URL(fileString);
- } else {
- File f = new File(confFile.getParent(), 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, OntologyFormat.RDF_XML);
- else {
- String formatString = call.get(2);
- if (formatString.equals("RDF/XML"))
- format = OntologyFormat.RDF_XML;
- else
- format = OntologyFormat.N_TRIPLES;
- importedFiles.put(url, format);
- }
- // }
- }
-
- return importedFiles;
- }
-
- // erzeugt Statistiken für MLDM-Paper zur Verarbeitung mit GnuPlot
- // Vorsicht: Laufzeit von mehreren Stunden
-
- /**
- * Has been used to create the statistics for the MLDM 2007 paper.
- * Warning: this method runs for several hours
- *
- * @todo: This method has not been fully adapted to the base structure
- * changes. To reproduce the results, the method has to be implemented
- * properly.
- */
- @SuppressWarnings("unused")
- public static 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;
- long algorithmStartTime;
- 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);
- // TODO: set up knowledge source
- KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
- ReasonerComponent reasoner = cm.reasoner(DIGReasoner.class, ks);
- // reasoner.prepareSubsumptionHierarchy();
- // rs = new ReasoningService(reasoner);
- ReasoningService rs = cm.reasoningService(reasoner);
- // learningProblem = new LearningProblem(rs, posExamples, negExamples);
- learningProblem = cm.learningProblem(PosNegDefinitionLP.class, rs);
-
- // TODO: set up pos/neg examples
- cm.applyConfigEntry(learningProblem, "positiveExamples", null);
- cm.applyConfigEntry(learningProblem, "negativeExamples", null);
-
- 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));
- }
-
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-19 14:03:16
|
Revision: 902
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=902&view=rev
Author: kurzum
Date: 2008-05-19 07:03:09 -0700 (Mon, 19 May 2008)
Log Message:
-----------
started cleanup
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-05-19 13:11:24 UTC (rev 901)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-05-19 14:03:09 UTC (rev 902)
@@ -384,11 +384,12 @@
return algorithm.getBestSolutions(nrOfSolutions);
}
- //HACK
@Override
- public List<String> getBestSolutionsAsKBSyntax(int nrOfSolutions){
- return this.algorithm.getBestSolutionsAsKBSyntax(nrOfSolutions);
+ public synchronized List<Description> getGoodSolutions() {
+ return algorithm.getGoodSolutions();
}
+
+
@Override
public void stop() {
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-19 13:11:24 UTC (rev 901)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-19 14:03:09 UTC (rev 902)
@@ -472,6 +472,7 @@
logger.debug("size of candidate set: " + candidates.size());
boolean showOrderedSolutions = false;
printBestSolutions(20,showOrderedSolutions);
+
printStatistics(true);
if(stop)
@@ -1057,6 +1058,7 @@
return candidatesStable.last().getConcept();
}
+
public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
List<Description> best = new LinkedList<Description>();
int i=0;
@@ -1070,7 +1072,28 @@
return best;
}
- //HACK
+
+ /**
+ * returns the solutions, that have at least a certain quality
+ * either accuracy = 100% full solutions
+ * or accuracy > 100% - noise;
+ * @return
+ */
+ public synchronized List<Description> getGoodSolutions() {
+ List<Description> best = new LinkedList<Description>();
+
+ for(ExampleBasedNode n : candidatesStable.descendingSet()) {
+ if(n.getAccuracy(nrOfPositiveExamples, nrOfNegativeExamples)<(1-noise))
+ return best;
+ best.add(n.getConcept());
+
+ }
+ return best;
+ }
+
+
+
+ /*//HACK
public List<String> getBestSolutionsAsKBSyntax(int nrOfSolutions){
if(nrOfSolutions==0)nrOfSolutions=99999;
List<String> result = new LinkedList<String>();
@@ -1091,7 +1114,7 @@
}
}
return result;
- }
+ }*/
public void printBestSolutions(int nrOfSolutions, boolean showOrderedSolutions){
@@ -1109,8 +1132,19 @@
i++;
}
+ if(nrOfSolutions==0)
+ nrOfSolutions=solutions.size();
+ int a=0;
+ for(;a<nrOfSolutions && a < solutions.size();a++) {
+
+ logger.trace("nnn: "+solutions.get(a));
+ if(a==nrOfSolutions)
+ break ;
+
+ }
+
if(showOrderedSolutions) {
logger.trace("ordered by generality (most special solutions first):");
SubsumptionComparator sc = new SubsumptionComparator(rs);
Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-05-19 13:11:24 UTC (rev 901)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-05-19 14:03:09 UTC (rev 902)
@@ -57,17 +57,33 @@
*/
public abstract Description getBestSolution();
+
+
+ /**
+ * returns the best nrOfSolutions solutions
+ * regardless of quality, just depends on input int
+ * @param nrOfSolutions
+ * @return List<Description>
+ */
public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
List<Description> single = new LinkedList<Description>();
single.add(getBestSolution());
return single;
}
- //HACK
- public List<String> getBestSolutionsAsKBSyntax(int nrOfSolutions){
- return null;
+ /**
+ * returns the solutions, that have at least a certain quality
+ * either accuracy = 100%, i.e. full solutions
+ * or accuracy > 100% - noise;
+ * @return
+ */
+ public synchronized List<Description> getGoodSolutions() {
+ List<Description> single = new LinkedList<Description>();
+ single.add(getBestSolution());
+ return single;
}
+
/**
* Returns all learning problems supported by this component.
*/
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-19 13:11:24 UTC (rev 901)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-19 14:03:09 UTC (rev 902)
@@ -191,16 +191,16 @@
//igno.add(oneConcept.replaceAll("\"", ""));
- List<String> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
+ List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
System.out.println("concepts"+conceptresults);
//System.exit(0);
logger.debug("found nr of concepts:"+conceptresults.size());
SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
- for (String oneConcept : conceptresults) {
+ for (Description oneConcept : conceptresults) {
try{
System.out.println("oneconcept: "+oneConcept);
- SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(oneConcept), 200);
+ SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(oneConcept.toKBSyntaxString()), 200);
SortedSet<String> coveredInRest = new TreeSet<String>();
SortedSet<String> possibleNewCandidates = new TreeSet<String>();
SortedSet<String> notCoveredInTotal = new TreeSet<String>();
@@ -243,7 +243,7 @@
double accuracy= (double)i/rest.size();
double accuracy2= (double)a/totalSKOSset.size();
- logger.debug((new ResultCompare(oneConcept,instances,accuracy,accuracy2,instances.size(),
+ logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
//if(instances.size()>=0)System.out.println("size of instances "+instances.size());
Modified: trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java 2008-05-19 13:11:24 UTC (rev 901)
+++ trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java 2008-05-19 14:03:09 UTC (rev 902)
@@ -1,6 +1,7 @@
package org.dllearner.utilities.learn;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.SortedSet;
@@ -13,6 +14,7 @@
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.Description;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegLP;
@@ -114,7 +116,7 @@
//System.out.println( la.getBestSolution());;
}
- public List<String> learnDBpediaSKOS(SortedSet<String> posExamples,SortedSet<String> negExamples,
+ public List<Description> learnDBpediaSKOS(SortedSet<String> posExamples,SortedSet<String> negExamples,
String uri, SortedSet<String> ignoredConcepts, int recursiondepth,
boolean closeAfterRecursion, boolean randomizeCache, int resultsize, double noise){
@@ -193,7 +195,9 @@
sc.setTime();
la.start();
Statistics.addTimeLearning(sc.getTime());
- return la.getBestSolutionsAsKBSyntax(resultsize);
+ return la.getBestSolutions(resultsize);
+
+
//if(sc.getTime()/1000 >= 20)System.out.println("XXXMAX time reached");
//System.out.println("best"+la(20));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-20 14:00:26
|
Revision: 904
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=904&view=rev
Author: kurzum
Date: 2008-05-20 07:00:20 -0700 (Tue, 20 May 2008)
Log Message:
-----------
added RDFS reasoning to sparql
SparqlQueryDescriptionConvertRDFS
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java
Property Changed:
----------------
trunk/src/dl-learner/org/dllearner/kb/sparql/
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -1082,32 +1082,10 @@
- /*//HACK
- public List<String> getBestSolutionsAsKBSyntax(int nrOfSolutions){
- if(nrOfSolutions==0)nrOfSolutions=99999;
- List<String> result = new LinkedList<String>();
- for (Description d : solutions) {
-
- result.add(d.toKBSyntaxString());
- if(result.size()==nrOfSolutions)break;
- //if(result.size()==nrOfSolutions)break;
- }
- if(result.size()==0){
-
- for(ExampleBasedNode n : candidatesStable.descendingSet()) {
-
- result.add(n.getConcept().toKBSyntaxString());
- if(result.size()>=nrOfSolutions)
- return result;
-
- }
- }
- return result;
- }*/
public void printBestSolutions(int nrOfSolutions, boolean showOrderedSolutions){
- //QUALITY
+ //QUALITY: could be optimized
if(!logger.isTraceEnabled())
return;
//if(!logger.getLevel().toString().equalsIgnoreCase("TRACE"))return;
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -58,7 +58,7 @@
Iterator<StringTuple> it = s.iterator();
while (it.hasNext()) {
StringTuple t = (StringTuple) it.next();
- //RBC
+ //QUALITY: needs proper handling of ressource, could be done one step lower in the onion
if(!t.b.startsWith("http:"))continue;
// basically : if p is rdf:type then o is a class
Property changes on: trunk/src/dl-learner/org/dllearner/kb/sparql
___________________________________________________________________
Name: svn:ignore
+ SparqlQueryDescriptionConvertRDFS.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -410,8 +410,7 @@
}
public SparqlQueryThreaded sparqlQueryThreaded(String query){
- //RBC
- return new SparqlQueryThreaded(new Cache("cachet2"),this.sparqlQuery(query));
+ return new SparqlQueryThreaded(new Cache("cache"),this.sparqlQuery(query));
}
/* (non-Javadoc)
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -41,6 +41,7 @@
//private SparqlEndpoint se = null;
//private boolean RDFSReasoning = false;
+ private static int defaultLimit = 5;
private static Logger logger = Logger.getLogger(ComponentManager.class);
@@ -64,81 +65,94 @@
this.RDFSReasoning = RDFSReasoning;
}*/
- public String getSparqlQuery()
- {
- query="SELECT ?subject\nWHERE {"+query;
- query+="}\n";
- query+="LIMIT 5";
+ /*private String getSparqlQuery()
+ {
+ return getSparqlQuery(defaultLimit);
+ }*/
+
+ private String getSparqlQuery(int limit)
+ { // for old function see below
+ // it was using the object attribute in a strange way
+ // QUALITY: what if this function is called several times?? should be private maybe?
+ String tmpQuery=
+ "SELECT ?subject \nWHERE {"+query+
+ " }\n ";
+ if(limit>0) tmpQuery+="LIMIT "+limit;
+
+ query = tmpQuery;
return query;
}
- public String getSparqlQuery(int limit)
+ /* OLD FUNCTION keep for audit
+ * public String getSparqlQuery(int limit)
{ if(limit==0)limit=99999;
query="SELECT ?subject\nWHERE {"+query;
query+="}\n";
query+="LIMIT "+limit;
return query;
+ }*/
+
+
+
+
+
+ public static String getSparqlQuery(String descriptionKBSyntax) throws ParseException
+ {
+ return getSparqlQuery(descriptionKBSyntax, defaultLimit);
}
- public static String getSparqlSubclassQuery(String description)
- { String ret = "SELECT * \n";
- ret+= "WHERE {\n";
- ret+=" ?subject ?predicate <"+description+"> \n";
- ret+="}\n";
-
- return ret;
+ public static String getSparqlQuery(String descriptionKBSyntax, int limit) throws ParseException
+ {
+ Description d = KBParser.parseConcept(descriptionKBSyntax);
+ return getSparqlQuery(d, limit);
}
- public static String getSparqlQuery(String description) throws ParseException
+ public static String getSparqlQuery(Description description)
{
- Description d = KBParser.parseConcept(description);
- SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
- d.accept(visitor);
-
- //TODO ERROR see replace HACK
- String ret = visitor.getSparqlQuery();
- while (ret.contains("..")) {
- ret = ret.replace("..", ".");
- }
- return ret;
+ return getSparqlQuery(description, defaultLimit);
}
- public static String getSparqlQuery(String description, int limit) throws ParseException
- { if(limit==0)limit=99999;
- Description d = KBParser.parseConcept(description);
+ public static String getSparqlQuery(Description description, int limit)
+ {
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
- d.accept(visitor);
- //TODO ERROR see replace HACK
+ description.accept(visitor);
String ret = visitor.getSparqlQuery(limit);
+ //HACK see replace might be a good solution, needs testing
while (ret.contains("..")) {
ret = ret.replace("..", ".");
}
return ret;
}
+
+
+
+
+
/**
- * includes subclasses, costly function, because subclasses habe to be recieved first.
- * @param description
- * @param limit
+ * COMMENT: write some more
+ * includes subclasses, costly function, because subclasses have to be received first.
+ * @see conceptRewrite(String descriptionKBSyntax, SparqlEndpoint se, Cache c,
+ boolean simple)
+ * @param descriptionKBSyntax @see getSparqlQuery(Description description, int limit)
+ * @param limit @see getSparqlQuery(Description description, int limit)
* @param se
+ * @param c
+ * @param simple
* @return
* @throws ParseException
*/
- /*public static String getSparqlQueryIncludingSubclasses(String description, int limit, SparqlEndpoint se) throws ParseException
- { if(limit==0)limit=99999;
- Description d = KBParser.parseConcept(description);
- SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor(se, true);
- d.accept(visitor);
- return visitor.getSparqlQuery(limit);
- }*/
-
- public static String getSparqlQuery(Description description)
- {
- SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
- description.accept(visitor);
- return visitor.getSparqlQuery();
+ public static String getSparqlQueryIncludingSubclasses(String descriptionKBSyntax, int limit, SparqlEndpoint se,Cache c, boolean simple) throws ParseException
+ {
+ String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(descriptionKBSyntax, se, c, simple);
+
+ return getSparqlQuery(rewritten, limit);
+
}
+
+
+
/**
* Used for testing the Sparql Query converter.
*
@@ -225,8 +239,7 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Intersection)
*/
public void visit(Intersection description) {
- //TODO ERROR see replace HACK
-
+ // HACK see replace hacks in other functions
logger.trace("Intersection");
description.getChild(0).accept(this);
query+=".";
@@ -238,6 +251,7 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Union)
*/
public void visit(Union description) {
+ // HACK see replace hacks in other functions
logger.trace("Union");
query+="{";
description.getChild(0).accept(this);
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -17,6 +17,7 @@
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertRDFS;
import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.examples.AutomaticExampleFinderSKOSSPARQL;
@@ -200,7 +201,8 @@
for (Description oneConcept : conceptresults) {
try{
System.out.println("oneconcept: "+oneConcept);
- SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(oneConcept.toKBSyntaxString()), 200);
+ String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(oneConcept.toKBSyntaxString(), se, c, true);
+ SortedSet<String> instances = ae.queryConceptAsStringSet(rewritten, 200);
SortedSet<String> coveredInRest = new TreeSet<String>();
SortedSet<String> possibleNewCandidates = new TreeSet<String>();
SortedSet<String> notCoveredInTotal = new TreeSet<String>();
@@ -326,122 +328,5 @@
}
- /**
- *
- * @param description
- */
- public static SortedSet<String> getSubClasses(String description, int limit) {
- if(limit==0)limit=10;
- ResultSet rs = null;
- //System.out.println(description);
- SortedSet<String> alreadyQueried = new TreeSet<String>();
- try {
- String query = getSparqlSubclassQuery(description.replaceAll("\"", ""));
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- rs =SparqlQuery.JSONtoResultSet(JSON);
- LinkedList<String> remainingClasses = new LinkedList<String>();
-
- //make back
- //remainingClasses.addAll(getSubclassesFromResultSet(rs));
-
- alreadyQueried = new TreeSet<String>();
- alreadyQueried.add(description.replaceAll("\"", ""));
- alreadyQueried.addAll(getSubclassesFromResultSet(rs));
- //remainingClasses.addAll(alreadyQueried);
- return alreadyQueried;
-
- //SortedSet<String> remainingClasses = new JenaResultSetConvenience(rs).getStringListForVariable("subject");
-
-// while (remainingClasses.size()!=0){
-// SortedSet<String> tmpSet = new TreeSet<String>();
-// String tmp = remainingClasses.removeFirst();
-// //remainingClasses.remove(tmp);
-// query = SparqlQueryDescriptionConvertVisitor
-// .getSparqlSubclassQuery(tmp);
-// alreadyQueried.add(tmp);
-// if(alreadyQueried.size()==limit)break;
-// JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
-// rs =SparqlQuery.JSONtoResultSet(JSON);
-// tmpSet=getSubclassesFromResultSet(rs);
-// for (String string : tmpSet) {
-// if(!alreadyQueried.contains(string))
-// remainingClasses.add(string);
-// }
-// }
- //System.out.println(JSON);
-
-
- } catch (Exception e) {
-
- }
- System.out.println("subclasses "+alreadyQueried);
- System.out.println("nr of subclasses :"+alreadyQueried.size());
- return alreadyQueried;
- }
- public static SortedSet<String> getSubclassesFromResultSet(ResultSet rs)
- {
- SortedSet<String> result = new TreeSet<String>();
- List<ResultBinding> l = ResultSetFormatter.toList(rs);
- String p="",s="";
- for (ResultBinding resultBinding : l) {
-
- s=((resultBinding.get("subject").toString()));
- p=((resultBinding.get("predicate").toString()));
- if(p.equalsIgnoreCase("http://www.w3.org/2000/01/rdf-schema#subClassOf")){
- result.add(s);
- }
- }
- return result;
- }
-
- public static String getSparqlSubclassQuery(String description)
- { String ret = "SELECT * \n";
- ret+= "WHERE {\n";
- ret+=" ?subject ?predicate <"+description+"> \n";
- ret+="}\n";
-
- return ret;
- }
-
- public static String conceptRewrite(String description)
- { String quote = "\"";
- String ret="";
- String currentconcept="";
- int lastPos=0;
- SortedSet<String> subclasses=new TreeSet<String>();
-
- while ((lastPos=description.lastIndexOf(quote))!=-1){
- ret=description.substring(lastPos+1,description.length())+ret;
- description=description.substring(0,lastPos);
- //System.out.println(description);
- lastPos=description.lastIndexOf(quote);
- currentconcept=description.substring(lastPos+1,description.length());
- description=description.substring(0,lastPos);
- //replace
- //currentconcept="\"blabla\"";
- //System.out.println(currentconcept);
-
-
- subclasses = getSubClasses( currentconcept, 0);
-
- if (subclasses.size()==1)currentconcept="\""+currentconcept+"\"";
- else {
- LinkedList<Description> nc = new LinkedList<Description>();
- for (String one : subclasses) {
- nc.add(new NamedClass(one));
- }
- currentconcept=new Union(nc).toKBSyntaxString();
- }
-
- ret=currentconcept+ret;
- //ret+=description;
- }
- ret=description+ret;
- //System.out.println(ret);
- return ret;
- }
-
-
-
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -371,41 +371,9 @@
}
- /**
- * NOT WORKING
- * @param description
- */
- public void getSubClasses(String description) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlSubclassQuery(description.replace("\"", ""));
-
- rs = new SparqlQuery(query, se).send();
- System.out.println(query);
- //System.out.println(SparqlQuery.getAsXMLString(rs));
- System.out.println(rs.getResultVars());
- SortedSet<String> remainingClasses = new JenaResultSetConvenience(rs).getStringListForVariable("subject");
- SortedSet<String> alreadyQueried = new TreeSet<String>();
- alreadyQueried.add(description);
- while (remainingClasses.size()!=0){
- String tmp = remainingClasses.first();
- remainingClasses.remove(tmp);
- query = SparqlQueryDescriptionConvertVisitor
- .getSparqlSubclassQuery(tmp);
- alreadyQueried.add(tmp);
- rs = new SparqlQuery(query, se).send();
- remainingClasses.addAll(new JenaResultSetConvenience(rs).getStringListForVariable("subject"));
- }
- //System.out.println(JSON);
- System.out.println(alreadyQueried);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- }
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java 2008-05-19 14:12:01 UTC (rev 903)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java 2008-05-20 14:00:20 UTC (rev 904)
@@ -343,41 +343,8 @@
}
- /**
- * NOT WORKING
- * @param description
- */
- public void getSubClasses(String description) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlSubclassQuery(description.replace("\"", ""));
-
- rs = new SparqlQuery(query, se).send();
- System.out.println(query);
- //System.out.println(SparqlQuery.getAsXMLString(rs));
- System.out.println(rs.getResultVars());
- SortedSet<String> remainingClasses = new JenaResultSetConvenience(rs).getStringListForVariable("subject");
- SortedSet<String> alreadyQueried = new TreeSet<String>();
- alreadyQueried.add(description);
- while (remainingClasses.size()!=0){
- String tmp = remainingClasses.first();
- remainingClasses.remove(tmp);
- query = SparqlQueryDescriptionConvertVisitor
- .getSparqlSubclassQuery(tmp);
- alreadyQueried.add(tmp);
- rs = new SparqlQuery(query, se).send();
- remainingClasses.addAll(new JenaResultSetConvenience(rs).getStringListForVariable("subject"));
- }
- //System.out.println(JSON);
- System.out.println(alreadyQueried);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-20 16:41:52
|
Revision: 907
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=907&view=rev
Author: kurzum
Date: 2008-05-20 09:41:30 -0700 (Tue, 20 May 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLtest.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java 2008-05-20 14:25:48 UTC (rev 906)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -19,8 +19,6 @@
static Logger logger = Logger.getLogger(SparqlQueryDescriptionConvertRDFS.class);
-
-
/**
*
* replaces each String representing a concept in descriptionKBSyntax with a
@@ -83,7 +81,8 @@
}
/**
- * gets a SortedSet of all subclasses
+ * gets a SortedSet of all subclasses QUALITY: maybe it is better to have a
+ * parameter int depth, to choose a depth of subclass interference
*
* @see conceptRewrite(String descriptionKBSyntax, SparqlEndpoint se, Cache
* c, boolean simple )
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-20 14:25:48 UTC (rev 906)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -34,36 +34,9 @@
static SparqlEndpoint se;
private static Logger logger = Logger.getRootLogger();
- static String standardSettings="";
- static String algorithm="refexamples";
- static String standardSettingsRefexamples =
- "refexamples.minExecutionTimeInSeconds = 30;\n" +
- "refexamples.maxExecutionTimeInSeconds = 30;\n" +
- "//refexamples.guaranteeXgoodDescriptions = 10;\n" +
- "refexamples.logLevel=\"TRACE\";\n" +
- "refexamples.noisePercentage = 0.10;\n" +
- "refexamples.writeSearchTree = false;\n" +
- "refexamples.searchTreeFile = \"searchTree.txt\";\n" +
- "refexamples.replaceSearchTree = true;\n\n" ;
- static String standardSettingsRefinement =
- "refinement.minExecutionTimeInSeconds = 30;\n" +
- "refinement.maxExecutionTimeInSeconds = 30;\n" +
- "//refinement.guaranteeXgoodDescriptions = 10;\n" +
- "refinement.logLevel=\"TRACE\";\n" +
- "refinement.writeSearchTree = false;\n" +
- "refinement.searchTreeFile = \"searchTree.txt\";\n" +
- "refinement.replaceSearchTree = true;\n\n" ;
-
- static String standardDBpedia="" +
- "sparql.recursionDepth = 1;\n" +
- "sparql.predefinedFilter = \"YAGO\";\n" +
- "sparql.predefinedEndpoint = \"DBPEDIA\";\n";
- //"sparql.logLevel = \"INFO\";\n";
-
-
//vars
static boolean useRelated = false;
static boolean useSuperClasses = false;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-20 14:25:48 UTC (rev 906)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -16,7 +16,7 @@
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQL;
+import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.LearnSparql;
import org.dllearner.utilities.statistics.SimpleClock;
import org.dllearner.utilities.statistics.Statistics;
@@ -105,7 +105,7 @@
boolean closeAfterRecursion=true;
System.out.println(oneConcept);
- AutomaticExampleFinderSPARQL ae= new AutomaticExampleFinderSPARQL( se);
+ AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-20 14:25:48 UTC (rev 906)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -16,7 +16,7 @@
import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.examples.AutomaticExampleFinderRolesSPARQL;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQL;
+import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.learn.LearnSparql;
import org.dllearner.utilities.statistics.SimpleClock;
@@ -185,7 +185,7 @@
boolean closeAfterRecursion=false;
int numberOfTriples = 0;
for (String oneConcept : concepts) {
- AutomaticExampleFinderSPARQL ae= new AutomaticExampleFinderSPARQL( se);
+ AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
useRelated = true;
useSuperClasses = true;
useParallelClasses = false;
Deleted: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java 2008-05-20 14:25:48 UTC (rev 906)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -1,350 +0,0 @@
-package org.dllearner.utilities.examples;
-
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-
-import com.hp.hpl.jena.query.ResultSet;
-
-public class AutomaticExampleFinderSPARQL {
-
- private static Logger logger = Logger
- .getLogger(ComponentManager.class);
-
- private Cache c;
- private SparqlEndpoint se;
- private SortedSet<String> posExamples;
- private SortedSet<String> negExamples;
- public SortedSet<String> totalSKOSset;
- private int limit=1000;
-
-
- public AutomaticExampleFinderSPARQL(SparqlEndpoint se){
- this.c=new Cache("cachetemp");
- this.se=se;
- posExamples = new TreeSet<String>();
- negExamples = new TreeSet<String>();
- }
-
- public void initDBpedia(String concept, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
- dbpediaMakePositiveExamplesFromConcept( concept);
- SortedSet<String> keepForClean = new TreeSet<String>();
- keepForClean.addAll(this.posExamples);
-
- this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
-
-
- logger.trace("shrinking: pos Example size: "+posExamples.size());
-
- if(useRelated) {
- dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
- }
- if(useSuperclasses) {
- makeNegativeExamplesFromSuperClasses(concept);
- }
- if(useParallelClasses) {
- makeNegativeExamplesFromClassesOfInstances();
- }
- //clean
- negExamples.removeAll(keepForClean);
- logger.trace("neg Example size after cleaning: "+negExamples.size());
- this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
- logger.debug("pos Example size after shrinking: "+posExamples.size());
- logger.debug("neg Example size after shrinking: "+negExamples.size());
- logger.debug("Finished examples for concept: "+concept);
- }
-
- public void init(String concept, String namespace, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
- makePositiveExamplesFromConcept( concept);
- SortedSet<String> keepForClean = new TreeSet<String>();
- keepForClean.addAll(this.posExamples);
- this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
- logger.trace("shrinking: pos Example size: "+posExamples.size());
-
- if(useRelated) {
- makeNegativeExamplesFromRelatedInstances(this.posExamples,namespace);
- }
- if(useSuperclasses) {
- makeNegativeExamplesFromSuperClasses(concept);
- }
- if(useParallelClasses) {
- makeNegativeExamplesFromClassesOfInstances();
- }
- //clean
- negExamples.removeAll(keepForClean);
- logger.trace("neg Example size after cleaning: "+negExamples.size());
- this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
- logger.debug("pos Example size after shrinking: "+posExamples.size());
- logger.debug("neg Example size after shrinking: "+negExamples.size());
- logger.debug("Finished examples for concept: "+concept);
- }
-
-
-
- public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
- dbpediaMakePositiveExamplesFromConcept( concept);
- return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
-
- public SortedSet<String> getPosOnly(String concept, int limit){
- makePositiveExamplesFromConcept( concept);
- return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
-
- private void dbpediaMakePositiveExamplesFromConcept(String concept){
- logger.debug("making Positive Examples from Concept: "+concept);
- if(concept.contains("http://dbpedia.org/resource/Category:")) {
- this.posExamples = new JenaResultSetConvenience(dbpediaQuerySKOSConcept(concept,limit))
- .getStringListForVariable("subject");
- }else {
- this.posExamples = new JenaResultSetConvenience(queryConcept(concept,limit))
- .getStringListForVariable("subject");
- }
- logger.debug(" pos Example size: "+posExamples.size());
- }
-
- private void makePositiveExamplesFromConcept(String concept){
- logger.debug("making Positive Examples from Concept: "+concept);
- this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
- .getStringListForVariable("subject");
- logger.debug(" pos Example size: "+posExamples.size());
- }
-
-
-
- /*private void makePositiveExamplesFromConcept(String concept){
- logger.debug("making Positive Examples from Concept: "+concept);
- if(concept.contains("http://dbpedia.org/resource/Category:")) {
- this.posExamples = new JenaResultSetConvenience(querySKOSConcept(concept,0))
- .getStringListForVariable("subject");
- }else {
- this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
- .getStringListForVariable("subject");
- }
- logger.debug(" pos Example size: "+posExamples.size());
- }*/
-
-
-
-
-
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- dbpediaMakeNegativeExamplesFromRelatedInstances(string);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
-
- private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- makeNegativeExamplesFromRelatedInstances(string,namespace);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
-
-
- /**
- *
- * @param subject
- * @return
- */
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
- + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- this.negExamples.addAll(rsc.getStringListForVariable("o"));
-
-
- }
-
- private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), '"+namespace+"')).\n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- this.negExamples.addAll(rsc.getStringListForVariable("o"));
-
-
- }
-
-
- private void makeNegativeExamplesFromSuperClasses(String concept) {
-
- SortedSet<String> superClasses = new TreeSet<String>();
- superClasses.add(concept.replace("\"", ""));
- //logger.debug("before"+superClasses);
- superClasses = getSuperClasses( superClasses, 4);
- logger.debug("making neg Examples from "+superClasses.size()+" superclasses");
- JenaResultSetConvenience rsc;
- for (String oneSuperClass : superClasses) {
- logger.debug(oneSuperClass);
- rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", limit));
- this.negExamples.addAll(rsc.getStringListForVariable("subject"));
- }
- logger.debug(" neg Example size: "+negExamples.size());
- }
-
-
-
- private void makeNegativeExamplesFromClassesOfInstances() {
- logger.debug("making neg Examples from parallel classes");
- SortedSet<String> classes = new TreeSet<String>();
- //superClasses.add(concept.replace("\"", ""));
- //logger.debug("before"+superClasses);
- //superClasses = dbpediaGetSuperClasses( superClasses, 4);
- //logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
- JenaResultSetConvenience rsc;
- ResultSet rs=null;
- for (String instance : posExamples) {
- //System.out.println(instance);
- rs = getClassesForInstance(instance);
- //System.out.println(ResultSetFormatter.asXMLString(rs));
- rsc = new JenaResultSetConvenience(rs);
- classes.addAll(rsc.getStringListForVariable("subject"));
- //System.out.println(classes);
- }
- logger.debug("getting negExamples from "+classes.size()+" parallel classes");
- for (String oneClass : classes) {
- logger.debug(oneClass);
- rsc = new JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
- this.negExamples.addAll(rsc.getStringListForVariable("subject"));
- }
- logger.debug("neg Example size: "+negExamples.size());
-
- }
-
- private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
- SortedSet<String> ret = new TreeSet<String>();
- SortedSet<String> tmpset = new TreeSet<String>();
- ret.addAll(superClasses);
- //logger.debug(superClasses);
- JenaResultSetConvenience rsc;
-
- String query = "";
- for (; depth != 0 ; depth--) {
- for (String oneSuperClass : superClasses) {
-
- //tmp = oneSuperClass.replace("\"", "");
- query = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
- + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- rsc = new JenaResultSetConvenience(rs);
- tmpset.addAll(rsc.getStringListForVariable("superclass"));
-
- }
- ret.addAll(tmpset);
- //logger.debug(ret);
- superClasses.clear();
- superClasses.addAll(tmpset);
- tmpset.clear();
- }
- //logger.debug(concept);
- //logger.debug(query);
- return ret;
- }
-
-
-
- public ResultSet queryConcept(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println("JSON:\n"+JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
- if(limit==0)limit=99999;
- //
- ResultSet rs = null;
- try {
-
- String query = "SELECT * WHERE { \n " +
- "?subject " +
- "<http://www.w3.org/2004/02/skos/core#subject> " +
- "<" + SKOSconcept + "> \n" +
- "} LIMIT "+limit;
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public ResultSet getClassesForInstance(String instance) {
- ResultSet rs = null;
- try {
-
- String query = "SELECT ?subject WHERE { \n " +
- "<" + instance + ">"+
- " a " +
- "?subject " +
- "\n" +
- "} LIMIT "+limit;
- SparqlQuery sq = new SparqlQuery(query, se);
- //System.out.println(query);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public SortedSet<String> getPosExamples() {
- return posExamples;
- }
-
- public SortedSet<String> getNegExamples() {
- return negExamples;
- }
-
-
-
-
-
-
-}
Copied: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java (from rev 905, trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -0,0 +1,350 @@
+package org.dllearner.utilities.examples;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
+import org.dllearner.utilities.datastructures.SetManipulation;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+public class AutomaticExampleFinderSPARQLold {
+
+ private static Logger logger = Logger
+ .getLogger(ComponentManager.class);
+
+ private Cache c;
+ private SparqlEndpoint se;
+ private SortedSet<String> posExamples;
+ private SortedSet<String> negExamples;
+ public SortedSet<String> totalSKOSset;
+ private int limit=1000;
+
+
+ public AutomaticExampleFinderSPARQLold(SparqlEndpoint se){
+ this.c=new Cache("cachetemp");
+ this.se=se;
+ posExamples = new TreeSet<String>();
+ negExamples = new TreeSet<String>();
+ }
+
+ public void initDBpedia(String concept, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
+ dbpediaMakePositiveExamplesFromConcept( concept);
+ SortedSet<String> keepForClean = new TreeSet<String>();
+ keepForClean.addAll(this.posExamples);
+
+ this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
+
+
+ logger.trace("shrinking: pos Example size: "+posExamples.size());
+
+ if(useRelated) {
+ dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
+ }
+ if(useSuperclasses) {
+ makeNegativeExamplesFromSuperClasses(concept);
+ }
+ if(useParallelClasses) {
+ makeNegativeExamplesFromClassesOfInstances();
+ }
+ //clean
+ negExamples.removeAll(keepForClean);
+ logger.trace("neg Example size after cleaning: "+negExamples.size());
+ this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
+ logger.debug("pos Example size after shrinking: "+posExamples.size());
+ logger.debug("neg Example size after shrinking: "+negExamples.size());
+ logger.debug("Finished examples for concept: "+concept);
+ }
+
+ public void init(String concept, String namespace, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
+ makePositiveExamplesFromConcept( concept);
+ SortedSet<String> keepForClean = new TreeSet<String>();
+ keepForClean.addAll(this.posExamples);
+ this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
+ logger.trace("shrinking: pos Example size: "+posExamples.size());
+
+ if(useRelated) {
+ makeNegativeExamplesFromRelatedInstances(this.posExamples,namespace);
+ }
+ if(useSuperclasses) {
+ makeNegativeExamplesFromSuperClasses(concept);
+ }
+ if(useParallelClasses) {
+ makeNegativeExamplesFromClassesOfInstances();
+ }
+ //clean
+ negExamples.removeAll(keepForClean);
+ logger.trace("neg Example size after cleaning: "+negExamples.size());
+ this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
+ logger.debug("pos Example size after shrinking: "+posExamples.size());
+ logger.debug("neg Example size after shrinking: "+negExamples.size());
+ logger.debug("Finished examples for concept: "+concept);
+ }
+
+
+
+ public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
+ dbpediaMakePositiveExamplesFromConcept( concept);
+ return SetManipulation.fuzzyShrink(this.posExamples, limit);
+ }
+
+ public SortedSet<String> getPosOnly(String concept, int limit){
+ makePositiveExamplesFromConcept( concept);
+ return SetManipulation.fuzzyShrink(this.posExamples, limit);
+ }
+
+ private void dbpediaMakePositiveExamplesFromConcept(String concept){
+ logger.debug("making Positive Examples from Concept: "+concept);
+ if(concept.contains("http://dbpedia.org/resource/Category:")) {
+ this.posExamples = new JenaResultSetConvenience(dbpediaQuerySKOSConcept(concept,limit))
+ .getStringListForVariable("subject");
+ }else {
+ this.posExamples = new JenaResultSetConvenience(queryConcept(concept,limit))
+ .getStringListForVariable("subject");
+ }
+ logger.debug(" pos Example size: "+posExamples.size());
+ }
+
+ private void makePositiveExamplesFromConcept(String concept){
+ logger.debug("making Positive Examples from Concept: "+concept);
+ this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
+ .getStringListForVariable("subject");
+ logger.debug(" pos Example size: "+posExamples.size());
+ }
+
+
+
+ /*private void makePositiveExamplesFromConcept(String concept){
+ logger.debug("making Positive Examples from Concept: "+concept);
+ if(concept.contains("http://dbpedia.org/resource/Category:")) {
+ this.posExamples = new JenaResultSetConvenience(querySKOSConcept(concept,0))
+ .getStringListForVariable("subject");
+ }else {
+ this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
+ .getStringListForVariable("subject");
+ }
+ logger.debug(" pos Example size: "+posExamples.size());
+ }*/
+
+
+
+
+
+ private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
+ logger.debug("making examples from related instances");
+ for (String string : subject) {
+ dbpediaMakeNegativeExamplesFromRelatedInstances(string);
+ }
+ logger.debug(" negExample size: "+negExamples.size());
+ }
+
+ private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
+ logger.debug("making examples from related instances");
+ for (String string : subject) {
+ makeNegativeExamplesFromRelatedInstances(string,namespace);
+ }
+ logger.debug(" negExample size: "+negExamples.size());
+ }
+
+
+ /**
+ *
+ * @param subject
+ * @return
+ */
+ private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
+ + "}";
+
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ this.negExamples.addAll(rsc.getStringListForVariable("o"));
+
+
+ }
+
+ private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), '"+namespace+"')).\n"
+ + "}";
+
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ this.negExamples.addAll(rsc.getStringListForVariable("o"));
+
+
+ }
+
+
+ private void makeNegativeExamplesFromSuperClasses(String concept) {
+
+ SortedSet<String> superClasses = new TreeSet<String>();
+ superClasses.add(concept.replace("\"", ""));
+ //logger.debug("before"+superClasses);
+ superClasses = getSuperClasses( superClasses, 4);
+ logger.debug("making neg Examples from "+superClasses.size()+" superclasses");
+ JenaResultSetConvenience rsc;
+ for (String oneSuperClass : superClasses) {
+ logger.debug(oneSuperClass);
+ rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", limit));
+ this.negExamples.addAll(rsc.getStringListForVariable("subject"));
+ }
+ logger.debug(" neg Example size: "+negExamples.size());
+ }
+
+
+
+ private void makeNegativeExamplesFromClassesOfInstances() {
+ logger.debug("making neg Examples from parallel classes");
+ SortedSet<String> classes = new TreeSet<String>();
+ //superClasses.add(concept.replace("\"", ""));
+ //logger.debug("before"+superClasses);
+ //superClasses = dbpediaGetSuperClasses( superClasses, 4);
+ //logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
+ JenaResultSetConvenience rsc;
+ ResultSet rs=null;
+ for (String instance : posExamples) {
+ //System.out.println(instance);
+ rs = getClassesForInstance(instance);
+ //System.out.println(ResultSetFormatter.asXMLString(rs));
+ rsc = new JenaResultSetConvenience(rs);
+ classes.addAll(rsc.getStringListForVariable("subject"));
+ //System.out.println(classes);
+ }
+ logger.debug("getting negExamples from "+classes.size()+" parallel classes");
+ for (String oneClass : classes) {
+ logger.debug(oneClass);
+ rsc = new JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
+ this.negExamples.addAll(rsc.getStringListForVariable("subject"));
+ }
+ logger.debug("neg Example size: "+negExamples.size());
+
+ }
+
+ private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
+ SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<String> tmpset = new TreeSet<String>();
+ ret.addAll(superClasses);
+ //logger.debug(superClasses);
+ JenaResultSetConvenience rsc;
+
+ String query = "";
+ for (; depth != 0 ; depth--) {
+ for (String oneSuperClass : superClasses) {
+
+ //tmp = oneSuperClass.replace("\"", "");
+ query = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
+ + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
+ + "}";
+
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ rsc = new JenaResultSetConvenience(rs);
+ tmpset.addAll(rsc.getStringListForVariable("superclass"));
+
+ }
+ ret.addAll(tmpset);
+ //logger.debug(ret);
+ superClasses.clear();
+ superClasses.addAll(tmpset);
+ tmpset.clear();
+ }
+ //logger.debug(concept);
+ //logger.debug(query);
+ return ret;
+ }
+
+
+
+ public ResultSet queryConcept(String concept,int limit) {
+ ResultSet rs = null;
+ try {
+ String query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQuery(concept,limit);
+
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println("JSON:\n"+JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
+ public ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
+ if(limit==0)limit=99999;
+ //
+ ResultSet rs = null;
+ try {
+
+ String query = "SELECT * WHERE { \n " +
+ "?subject " +
+ "<http://www.w3.org/2004/02/skos/core#subject> " +
+ "<" + SKOSconcept + "> \n" +
+ "} LIMIT "+limit;
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
+ public ResultSet getClassesForInstance(String instance) {
+ ResultSet rs = null;
+ try {
+
+ String query = "SELECT ?subject WHERE { \n " +
+ "<" + instance + ">"+
+ " a " +
+ "?subject " +
+ "\n" +
+ "} LIMIT "+limit;
+ SparqlQuery sq = new SparqlQuery(query, se);
+ //System.out.println(query);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
+ public SortedSet<String> getPosExamples() {
+ return posExamples;
+ }
+
+ public SortedSet<String> getNegExamples() {
+ return negExamples;
+ }
+
+
+
+
+
+
+}
Copied: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLtest.java (from rev 905, trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQL.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLtest.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLtest.java 2008-05-20 16:41:30 UTC (rev 907)
@@ -0,0 +1,21 @@
+package org.dllearner.utilities.examples;
+
+import java.util.SortedSet;
+
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+
+public class AutomaticExampleFinderSPARQLtest {
+
+
+ private Cache c;
+ private SparqlEndpoint se;
+ private SortedSet<String> posExamples;
+ private SortedSet<String> negExamples;
+
+ static boolean useRelated = false;
+ static boolean useSuperClasses = false;
+ static boolean useParallelClasses = true;
+ static int poslimit = 10;
+ static int neglimit = 20;
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-21 15:07:08
|
Revision: 912
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=912&view=rev
Author: kurzum
Date: 2008-05-21 07:59:31 -0700 (Wed, 21 May 2008)
Log Message:
-----------
cleanup
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -82,6 +82,18 @@
this("cache");
} */
+ public static Cache getPersistentCache(){
+ Cache c = new Cache("cachePersistant");
+ c.setFreshnessInDays(365);
+ return c;
+ }
+
+ public static Cache getDefaultCache(){
+ Cache c = new Cache("cache");
+
+ return c;
+ }
+
/**
* Constructor for the cache itself.
*
@@ -242,5 +254,9 @@
return json;
}
}
+
+ public void setFreshnessInDays(int days){
+ freshnessSeconds = days * 24 * 60 * 60;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -112,6 +112,9 @@
return queryString;
}
+ /**
+ * @return String JSON
+ */
public String getResult() {
return json;
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -1,7 +1,8 @@
package org.dllearner.scripts;
-import java.util.LinkedList;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -10,222 +11,198 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
+import org.dllearner.core.ComponentManager;
import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.NamedClass;
-import org.dllearner.core.owl.Union;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertRDFS;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSKOSSPARQL;
-import org.dllearner.utilities.learn.LearnSparql;
-import org.dllearner.utilities.statistics.SimpleClock;
+import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL;
+import org.dllearner.utilities.examples.AutomaticPositiveExampleFinderSPARQL;
+import org.dllearner.utilities.examples.SPARQLTasks;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-
public class SKOS7030 {
- static Cache c;
- static SparqlEndpoint se;
+ private static SPARQLTasks sparqlTasks;
+
private static Logger logger = Logger.getRootLogger();
+ static boolean local = true;
+ static String url = "";
+ //LEARNING
+ static int recursiondepth=1;
+ static boolean closeAfterRecursion=true;
+ static boolean randomizeCache=false;
+ static double noise=15;
+ static int maxExecutionTimeInSeconds = 30;
+ static int guaranteeXgoodDescriptions = 40;
+ //static int limit=200;
- //vars
- static boolean useRelated = false;
- static boolean useSuperClasses = false;
- static boolean useParallelClasses = true;
- static int poslimit = 10;
- static int neglimit = 20;
- static int recursiondepth=1;
- static boolean closeAfterRecursion=true;
- static boolean randomizeCache=false;
- static int resultsize=20;
- static double noise=15;
- static int limit=200;
- static double percentage=0.3;
+ //examples
+ static int sparqlResultSize=2000;
+ static double percentOfSKOSSet=0.7;
+ static double negfactor=0.3;
+ SortedSet<String> posExamples = new TreeSet<String>();
+ SortedSet<String> fullPositiveSet = new TreeSet<String>();
+ SortedSet<String> fullminusposRest = new TreeSet<String>();
+ SortedSet<String> negExamples = new TreeSet<String>();
+
+
+
+
+
/**
* @param args
*/
public static void main(String[] args) {
- init();
- //logger.setLevel(Level.TRACE);
- Logger.getLogger(KnowledgeSource.class).setLevel(Level.WARN);
- //System.out.println(Logger.getLogger(SparqlQuery.class).getLevel());
- SimpleClock sc=new SimpleClock();
+ System.out.println("Start");
+ initLogger();
+ //parameters
- se = SparqlEndpoint.EndpointLOCALDBpedia();
-// String t="\"http://dbpedia.org/class/yago/Fiction106367107\"";
-// t="(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))";
-// //System.out.println(t);
-// //t="\"http://www.w3.org/2004/02/skos/core#subject\"";
-// //conceptRewrite(t);
-// //getSubClasses(t);
-//
-// AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);
-// try{
-// System.out.println("oneconcept: "+t);
-// SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(t), 200);
-// if(instances.size()>=0)System.out.println("size of instances "+instances.size());
-// if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
-// }catch (Exception e) {
-// e.printStackTrace();
-// }
- SortedSet<String> concepts = new TreeSet<String>();
+ if(local){
+ url = "http://139.18.2.37:8890/sparql";
+ sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointLOCALDBpedia());
+ }else{
+ url = "http://dbpedia.openlinksw.com:8890/sparql";
+ sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointDBpedia());
+ }
String prim="http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom";
String award=("http://dbpedia.org/resource/Category:Best_Actor_Academy_Award_winners");
- System.out.println(DBpediaSKOS(prim));
-// double acc1=0.0;
-// for (int i = 0; i < 5; i++) {
-// acc1+=DBpediaSKOS(prim);
-// }
-// System.out.println("accprim"+(acc1/5));
-//
-// double acc2=0.0;
-// for (int i = 0; i < 5; i++) {
-// acc2+=DBpediaSKOS(award);
-// }
-// System.out.println("accprim"+(acc2/5));
+ SKOS7030 s= new SKOS7030();
-// DBpediaSKOS(concepts.first());
-// DBpediaSKOS(concepts.first());
-// concepts.remove(concepts.first());
-// DBpediaSKOS(concepts.first());
-// DBpediaSKOS(concepts.first());
-// concepts.remove(concepts.first());
-// DBpediaSKOS(concepts.first());
-// DBpediaSKOS(concepts.first());
- //algorithm="refinement";
- //roles();
+ s.makeExamples(prim, percentOfSKOSSet, negfactor, sparqlResultSize);
+ //QUALITY s.posExamples
+ List<Description> conceptresults = s.learn(s.posExamples, s.negExamples);
+ logger.debug("found nr of concepts: "+conceptresults.size());
- /*System.out.println(Level.DEBUG.getClass());
- System.out.println(Level.toLevel("INFO"));
- System.out.println(Level.INFO);*/
- //System.exit(0);
+ for (Description oneConcept : conceptresults) {
+ s.evaluate(oneConcept, 1000);
+ }
+
+
+ System.out.println("Finished");
+
+ }
+ void evaluate(Description oneConcept, int sparqlResultLimit){
+ logger.debug("oneconcept: "+oneConcept);
+ SortedSet<String> instances = sparqlTasks.retrieveInstancesForConcept(oneConcept.toKBSyntaxString(), sparqlResultLimit);
- sc.printAndSet("Finished");
-
+ System.out.println(fullminusposRest.size());
+ System.out.println(instances.size());
+
+ SortedSet<String> coveredInRest = new TreeSet<String>(fullminusposRest);
+ coveredInRest.retainAll(instances);
+
+ System.out.println(fullminusposRest.size());
+ System.out.println(instances.size());
+ System.out.println(coveredInRest.size());
+
+
+
+ //SortedSet<String> possibleNewCandidates = new TreeSet<String>();
+ //SortedSet<String> notCoveredInTotal = new TreeSet<String>();
+
+
}
-
- static double DBpediaSKOS(String concept){
- se = SparqlEndpoint.EndpointLOCALDBpedia();
- //se = SparqlEndpoint.EndpointDBpedia();
- String url = "http://dbpedia.openlinksw.com:8890/sparql";
- url = "http://139.18.2.37:8890/sparql";
+ static void DBpediaSKOS(String SKOSConcept){
+
//concepts.add("http://dbpedia.org/resource/Category:Grammy_Award_winners");
//concepts.add("EXISTS \"http://dbpedia.org/property/grammyawards\".TOP");
- SortedSet<String> posExamples = new TreeSet<String>();
- SortedSet<String> negExamples = new TreeSet<String>();
+
//HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
//HashMap<String, String> result2 = new HashMap<String, String>();
//System.out.println(concepts.first());
//logger.setLevel(Level.TRACE);
- AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);
+
- ae.initDBpediaSKOS(concept,percentage , useRelated, useParallelClasses);
- posExamples = ae.getPosExamples();
- negExamples = ae.getNegExamples();
- for (String string2 : negExamples) {
- logger.debug("-"+string2);
- }
+// LearnSparql ls = new LearnSparql();
+//
+// //igno.add(oneConcept.replaceAll("\"", ""));
+//
+// List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
+//
+// System.out.println("concepts"+conceptresults);
+// //System.exit(0);
+//
+// SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
+// for (Description oneConcept : conceptresults) {
+// try{
+//
+//
+// int i=0;
+// int a=0;
+// for (String oneinst : instances) {
+// boolean inRest=false;
+// boolean inTotal=false;
+// for (String onerest : rest) {
+// if(onerest.equalsIgnoreCase(oneinst))
+// { i++; inRest=true; break;}
+//
+// }
+// if (inRest){coveredInRest.add(oneinst);};
+//
+// for (String onetotal : totalSKOSset) {
+// if(onetotal.equalsIgnoreCase(oneinst))
+// { a++; inTotal=true; break;}
+// }
+// if(!inRest && !inTotal){
+// possibleNewCandidates.add(oneinst);
+// }
+// }
+//
+// for (String onetotal : totalSKOSset) {
+// boolean mm=false;
+// for (String oneinst : instances) {
+// if(onetotal.equalsIgnoreCase(oneinst)){
+// mm=true;break;
+// }
+//
+// }
+// if(!mm)notCoveredInTotal.add(onetotal);
+//
+// }
+//
+//
+//
+// double accuracy= (double)i/rest.size();
+// double accuracy2= (double)a/totalSKOSset.size();
+//
+// logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
+// coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
+//
+// //if(instances.size()>=0)System.out.println("size of instances "+instances.size());
+// //if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
+// }catch (Exception e) {e.printStackTrace();}
+// }
- for (String string2 : posExamples) {
- logger.debug("+"+string2);
- }
- SortedSet<String> totalSKOSset= ae.totalSKOSset;
- SortedSet<String> rest= ae.rest;
- logger.debug(totalSKOSset);
- logger.debug(rest);
-
-
- LearnSparql ls = new LearnSparql();
-
- //igno.add(oneConcept.replaceAll("\"", ""));
-
- List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
-
- System.out.println("concepts"+conceptresults);
- //System.exit(0);
- logger.debug("found nr of concepts:"+conceptresults.size());
- SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
- for (Description oneConcept : conceptresults) {
- try{
- System.out.println("oneconcept: "+oneConcept);
- String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(oneConcept.toKBSyntaxString(), se, c, true);
- SortedSet<String> instances = ae.queryConceptAsStringSet(rewritten, 200);
- SortedSet<String> coveredInRest = new TreeSet<String>();
- SortedSet<String> possibleNewCandidates = new TreeSet<String>();
- SortedSet<String> notCoveredInTotal = new TreeSet<String>();
-
- int i=0;
- int a=0;
- for (String oneinst : instances) {
- boolean inRest=false;
- boolean inTotal=false;
- for (String onerest : rest) {
- if(onerest.equalsIgnoreCase(oneinst))
- { i++; inRest=true; break;}
-
- }
- if (inRest){coveredInRest.add(oneinst);};
-
- for (String onetotal : totalSKOSset) {
- if(onetotal.equalsIgnoreCase(oneinst))
- { a++; inTotal=true; break;}
- }
- if(!inRest && !inTotal){
- possibleNewCandidates.add(oneinst);
- }
- }
-
- for (String onetotal : totalSKOSset) {
- boolean mm=false;
- for (String oneinst : instances) {
- if(onetotal.equalsIgnoreCase(oneinst)){
- mm=true;break;
- }
-
- }
- if(!mm)notCoveredInTotal.add(onetotal);
-
- }
-
-
-
- double accuracy= (double)i/rest.size();
- double accuracy2= (double)a/totalSKOSset.size();
-
- logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
- coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
-
- //if(instances.size()>=0)System.out.println("size of instances "+instances.size());
- //if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
- }catch (Exception e) {e.printStackTrace();}
- }
-
// System.out.println(res.last());
// res.remove(res.last());
// System.out.println(res.last());
@@ -250,7 +227,7 @@
//
// }
//
- return 0.0;
+// return 0.0;
//System.out.println("AAAAAAAA");
@@ -268,7 +245,7 @@
- public static void init() {
+ public static void initLogger() {
SimpleLayout layout = new SimpleLayout();
// create logger (a simple logger which outputs
@@ -283,12 +260,11 @@
logger.addAppender(consoleAppender);
logger.addAppender(fileAppender);
logger.setLevel(Level.DEBUG);
- c = new Cache("cachetemp");
-
-
+ Logger.getLogger(KnowledgeSource.class).setLevel(Level.WARN);
+
}
- public static SortedSet<String> selectDBpediaConcepts(int number){
+ /*public static SortedSet<String> selectDBpediaConcepts(int number){
String query = "SELECT DISTINCT ?concept WHERE { \n" +
"[] a ?concept .FILTER (regex(str(?concept),'yago'))" +
" \n} \n"; //LIMIT "+number+"
@@ -298,8 +274,181 @@
ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+ }*/
+
+ public void makeExamples(String SKOSConcept, double percentOfSKOSSet , double negfactor, int sparqlResultSize){
+
+ //POSITIVES
+ AutomaticPositiveExampleFinderSPARQL apos = new AutomaticPositiveExampleFinderSPARQL(sparqlTasks);
+ apos.makePositiveExamplesFromSKOSConcept(SKOSConcept);
+ fullPositiveSet = apos.getPosExamples();
+
+ int poslimit=(int)Math.round(percentOfSKOSSet*fullPositiveSet.size());
+ int neglimit=(int)Math.round(poslimit*negfactor);
+
+ this.posExamples = SetManipulation.fuzzyShrink(fullPositiveSet,poslimit);
+
+
+
+ //NEGATIVES
+
+ AutomaticNegativeExampleFinderSPARQL aneg = new AutomaticNegativeExampleFinderSPARQL(fullPositiveSet,sparqlTasks);
+
+ aneg.makeNegativeExamplesFromParallelClasses(posExamples, sparqlResultSize);
+ SortedSet<String> negativeSet = aneg.getNegativeExamples(neglimit);
+
+ logger.debug("POSITIVE EXAMPLES");
+ for (String pos : posExamples) {
+ logger.debug("+"+pos);
+ }
+
+ logger.debug("NEGATIVE EXAMPLES");
+ for (String negs : negativeSet) {
+ logger.debug("-"+negs);
+ }
+
+
+
+ fullminusposRest = fullPositiveSet;
+ fullminusposRest.removeAll(posExamples);
+
+
+ logger.debug(fullPositiveSet);
+ logger.debug(fullminusposRest);
}
+ public List<Description> learn(SortedSet<String> posExamples, SortedSet<String> negExamples){
+
+ SortedSet<String> instances = new TreeSet<String>();
+ instances.addAll(posExamples);
+ instances.addAll(negExamples);
+
+
+ ComponentManager cm = ComponentManager.getInstance();
+ LearningAlgorithm la = null;
+ ReasoningService rs = null;
+ LearningProblem lp = null;
+ SparqlKnowledgeSource ks =null;
+ try {
+ Set<KnowledgeSource> sources = new HashSet<KnowledgeSource>();
+ ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
+ ReasonerComponent r = new FastInstanceChecker(sources);
+ rs = new ReasoningService(r);
+ //System.out.println("satisfy: "+rs.isSatisfiable());
+ lp = new PosNegDefinitionLP(rs);
+ ((PosNegLP) lp).setPositiveExamples(SetManipulation.stringToInd(posExamples));
+ ((PosNegLP) lp).setNegativeExamples(SetManipulation.stringToInd(negExamples));
+
+ la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
+
+ logger.debug("start learning");
+
+
+ //KNOWLEDGESOURCE
+ cm.applyConfigEntry(ks, "instances",instances);
+ cm.applyConfigEntry(ks, "url",url);
+ cm.applyConfigEntry(ks, "recursionDepth",recursiondepth);
+ cm.applyConfigEntry(ks, "closeAfterRecursion",closeAfterRecursion);
+ cm.applyConfigEntry(ks, "predefinedFilter","YAGO");
+ if(local)
+ cm.applyConfigEntry(ks, "predefinedEndpoint","LOCALDBPEDIA");
+ else {
+ cm.applyConfigEntry(ks, "predefinedEndpoint","DBPEDIA");
+ }
+ if(randomizeCache)
+ cm.applyConfigEntry(ks, "cacheDir","cache/"+System.currentTimeMillis()+"");
+ else {cm.applyConfigEntry(ks, "cacheDir",Cache.getDefaultCache());}
+
+ //LEARNINGALGORITHM
+ cm.applyConfigEntry(la,"useAllConstructor",false);
+ cm.applyConfigEntry(la,"useExistsConstructor",true);
+ cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
+ cm.applyConfigEntry(la,"useNegation",false);
+ cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
+ cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",maxExecutionTimeInSeconds);
+ cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",guaranteeXgoodDescriptions);
+ cm.applyConfigEntry(la,"writeSearchTree",false);
+ cm.applyConfigEntry(la,"searchTreeFile","log/SKOS.txt");
+ cm.applyConfigEntry(la,"replaceSearchTree",true);
+ cm.applyConfigEntry(la,"noisePercentage",noise);
+ //cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",999999);
+ cm.applyConfigEntry(la,"logLevel","TRACE");
+ /*if(ignoredConcepts.size()>0)
+ cm.applyConfigEntry(la,"ignoredConcepts",ignoredConcepts);
+ */
+
+ ks.init();
+ sources.add(ks);
+ r.init();
+ lp.init();
+ la.init();
+
+
+ la.start();
+ //Statistics.addTimeCollecting(sc.getTime());
+ //Statistics.addTimeLearning(sc.getTime());
+
+
+ return la.getGoodSolutions();
+
+ }catch (Exception e) {e.printStackTrace();}
+ return null;
+
+ }
+
+// String t="\"http://dbpedia.org/class/yago/Fiction106367107\"";
+// t="(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))";
+// //System.out.println(t);
+// //t="\"http://www.w3.org/2004/02/skos/core#subject\"";
+// //conceptRewrite(t);
+// //getSubClasses(t);
+//
+// AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);
+// try{
+// System.out.println("oneconcept: "+t);
+// SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(t), 200);
+// if(instances.size()>=0)System.out.println("size of instances "+instances.size());
+// if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
+// }catch (Exception e) {
+// e.printStackTrace();
+// }
+ //SortedSet<String> concepts = new TreeSet<String>();
+
+
+
+ //System.out.println(DBpediaSKOS(prim));
+// double acc1=0.0;
+// for (int i = 0; i < 5; i++) {
+// acc1+=DBpediaSKOS(prim);
+// }
+// System.out.println("accprim"+(acc1/5));
+//
+// double acc2=0.0;
+// for (int i = 0; i < 5; i++) {
+// acc2+=DBpediaSKOS(award);
+// }
+// System.out.println("accprim"+(acc2/5));
+
+// DBpediaSKOS(concepts.first());
+// DBpediaSKOS(concepts.first());
+// concepts.remove(concepts.first());
+// DBpediaSKOS(concepts.first());
+// DBpediaSKOS(concepts.first());
+// concepts.remove(concepts.first());
+// DBpediaSKOS(concepts.first());
+// DBpediaSKOS(concepts.first());
+ //algorithm="refinement";
+ //roles();
+
+ /*System.out.println(Level.DEBUG.getClass());
+ System.out.println(Level.toLevel("INFO"));
+ System.out.println(Level.INFO);*/
+ //System.exit(0);
+
+
+
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -14,8 +14,6 @@
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.LearnSparql;
import org.dllearner.utilities.statistics.SimpleClock;
@@ -107,7 +105,7 @@
System.out.println(oneConcept);
AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
- ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
+ //ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
posExamples = ae.getPosExamples();
negExamples = ae.getNegExamples();
@@ -183,6 +181,7 @@
}
+ //FIXME
public static SortedSet<String> selectDBpediaConcepts(int number){
String query = "SELECT DISTINCT ?concept WHERE { \n" +
"[] a ?concept .FILTER (regex(str(?concept),'yago'))" +
@@ -190,8 +189,9 @@
String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+ //JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ //return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+ return null;
}
public static SortedSet<String> initConcepts(){
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -13,9 +13,6 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticExampleFinderRolesSPARQL;
import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.learn.LearnSparql;
@@ -114,12 +111,12 @@
//HashMap<String, String> result2 = new HashMap<String, String>();
//System.out.println(concepts.first());
//logger.setLevel(Level.TRACE);
- AutomaticExampleFinderRolesSPARQL ae= new AutomaticExampleFinderRolesSPARQL( se);
+ //AutomaticExampleFinderRolesSPARQL ae= new AutomaticExampleFinderRolesSPARQL( se);
- ae.initDomainRange(roles.first(), poslimit, neglimit);
+ //ae.initDomainRange(roles.first(), poslimit, neglimit);
- posExamples = ae.getPosExamples();
- negExamples = ae.getNegExamples();
+ //posExamples = ae.getPosExamples();
+ //negExamples = ae.getNegExamples();
System.out.println(posExamples);
System.out.println(negExamples);
@@ -192,7 +189,7 @@
poslimit=10;
neglimit=10;
- ae.initDBpedia(concept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
+ //ae.initDBpedia(concept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
posExamples = ae.getPosExamples();
negExamples = ae.getNegExamples();
@@ -286,8 +283,9 @@
String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+ //JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ //return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+ return null;
}
Modified: trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -11,12 +11,9 @@
import org.apache.log4j.SimpleLayout;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
+import org.dllearner.utilities.examples.SPARQLTasks;
import org.dllearner.utilities.statistics.SimpleClock;
-import com.hp.hpl.jena.query.ResultSet;
-
public class SparqlEndpointTest {
private static Logger logger = Logger.getRootLogger();
static Set<String> working = new HashSet<String>();
@@ -65,22 +62,15 @@
SimpleClock sc = new SimpleClock();
try{
- String query ="" +
+ String SPARQLquery ="" +
"SELECT DISTINCT ?c " +
"WHERE {[] a ?c }" +
"LIMIT 100";
- query ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
-
- SparqlQuery s = new SparqlQuery(query,se);
+ SPARQLquery ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
+ int i = new SPARQLTasks(se).queryAsSet(SPARQLquery, "c").size();
- s.send();
- String result = s.getResult();
- ResultSet rs = SparqlQuery.JSONtoResultSet(result);
- JenaResultSetConvenience jsr = new JenaResultSetConvenience(rs);
- int i = jsr.getStringListForVariable("c").size();
-
working.add(sc.getAndSet("endpoint working: "+se.getURL()+" ("+((i==100)?"more than 100 concepts":"about "+i+" concepts")+" )"));
}catch (Exception e) {notworking.add(sc.getAndSet("endpoint NOT working: "+se.getURL()));}
}
Added: trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,9 @@
+package org.dllearner.utilities;
+
+/**
+ * provides convenience functions for timelogs
+ *
+ */
+public class JamonTimeLogger {
+
+}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -1,37 +0,0 @@
-package org.dllearner.utilities.datastructures;
-
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-
-public class JenaResultSetConvenience {
- ResultSet rs;
-
- public JenaResultSetConvenience(ResultSet rs) {
- super();
- this.rs = rs;
- }
-
- @SuppressWarnings("unchecked")
- public SortedSet<String> getStringListForVariable(String var){
- SortedSet<String> result = new TreeSet<String>();
-
- //String s=ResultSetFormatter.asXMLString(this.rs);
- List<ResultBinding> l = ResultSetFormatter.toList(this.rs);
-
- for (ResultBinding resultBinding : l) {
-
- result.add(resultBinding.get(var).toString());
-
- }
-
- return result;
-
- }
-
-
-}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -1,18 +1,12 @@
package org.dllearner.utilities.examples;
import java.util.SortedSet;
-import java.util.TreeSet;
import org.apache.log4j.Logger;
import org.dllearner.core.ComponentManager;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-
-import com.hp.hpl.jena.query.ResultSet;
-
+// keep this class it still needs to be worked in
public class AutomaticExampleFinderRolesSPARQL {
private static Logger logger = Logger
@@ -24,7 +18,7 @@
private SortedSet<String> negExamples;
private int roleLimit=1000;
-
+ /*
public AutomaticExampleFinderRolesSPARQL(SparqlEndpoint se){
this.c=new Cache("cachetemp");
this.se=se;
@@ -119,7 +113,7 @@
+ */
-
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -7,13 +7,8 @@
import org.dllearner.core.ComponentManager;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
import org.dllearner.utilities.datastructures.SetManipulation;
-import com.hp.hpl.jena.query.ResultSet;
-
public class AutomaticExampleFinderSKOSSPARQL {
private static Logger logger = Logger
@@ -35,8 +30,9 @@
negExamples = new TreeSet<String>();
}
+ @Deprecated
public void initDBpediaSKOS(String concept, double percent, boolean useRelated,boolean useParallelClasses) {
- dbpediaMakePositiveExamplesFromConcept( concept);
+ //dbpediaMakePositiveExamplesFromConcept( concept);
SortedSet<String> keepForClean = new TreeSet<String>();
keepForClean.addAll(this.posExamples);
totalSKOSset.addAll(this.posExamples);
@@ -55,12 +51,12 @@
logger.debug("rest: "+rest.size());
if(useRelated) {
- dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
+ //dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
}
if(useParallelClasses) {
int limit = this.posExamples.size();
- makeNegativeExamplesFromClassesOfInstances(limit);
+ //makeNegativeExamplesFromClassesOfInstances(limit);
}
//clean
negExamples.removeAll(keepForClean);
@@ -98,16 +94,8 @@
- public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
- dbpediaMakePositiveExamplesFromConcept( concept);
- return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
- public SortedSet<String> getPosOnly(String concept, int limit){
- makePositiveExamplesFromConcept( concept);
- return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
-
+ /*
private void dbpediaMakePositiveExamplesFromConcept(String concept){
logger.debug("making Positive Examples from Concept: "+concept);
if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -118,14 +106,15 @@
.getStringListForVariable("subject");
}
logger.debug("pos Example size: "+posExamples.size());
- }
+ }*/
+ /*
private void makePositiveExamplesFromConcept(String concept){
logger.debug("making Positive Examples from Concept: "+concept);
this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
.getStringListForVariable("subject");
logger.debug(" pos Example size: "+posExamples.size());
- }
+ }*/
@@ -145,60 +134,18 @@
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- dbpediaMakeNegativeExamplesFromRelatedInstances(string);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
- private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- makeNegativeExamplesFromRelatedInstances(string,namespace);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
-
/**
*
* @param subject
* @return
*/
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
- // SortedSet<String> result = new TreeSet<String>();
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
- + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- this.negExamples.addAll(rsc.getStringListForVariable("o"));
-
-
- }
- private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
- // SortedSet<String> result = new TreeSet<String>();
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), '"+namespace+"')).\n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- this.negExamples.addAll(rsc.getStringListForVariable("o"));
-
-
- }
-
+ /*
private void makeNegativeExamplesFromSuperClasses(String concept) {
SortedSet<String> superClasses = new TreeSet<String>();
@@ -213,109 +160,14 @@
this.negExamples.addAll(rsc.getStringListForVariable("subject"));
}
logger.debug(" neg Example size: "+negExamples.size());
- }
+ }*/
- private void makeNegativeExamplesFromClassesOfInstances(int limit) {
- logger.debug("making neg Examples from parallel classes");
- SortedSet<String> classes = new TreeSet<String>();
- //superClasses.add(concept.replace("\"", ""));
- //logger.debug("before"+superClasses);
- //superClasses = dbpediaGetSuperClasses( superClasses, 4);
- //logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
- JenaResultSetConvenience rsc;
- ResultSet rs=null;
- for (String instance : posExamples) {
- //System.out.println(instance);
- rs = getClassesForInstance(instance);
- //System.out.println(ResultSetFormatter.asXMLString(rs));
- rsc = new JenaResultSetConvenience(rs);
- classes.addAll(rsc.getStringListForVariable("subject"));
- //System.out.println(classes);
- }
- logger.debug("getting negExamples from "+classes.size()+" parallel classes");
- for (String oneClass : classes) {
- logger.debug(oneClass);
- rsc = new JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
- this.negExamples.addAll(rsc.getStringListForVariable("subject"));
- }
- logger.debug("neg Example size: "+negExamples.size());
-
- }
-
- private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
- SortedSet<String> ret = new TreeSet<String>();
- SortedSet<String> tmpset = new TreeSet<String>();
- ret.addAll(superClasses);
- //logger.debug(superClasses);
- JenaResultSetConvenience rsc;
-
- String query = "";
- for (; depth != 0 ; depth--) {
- for (String oneSuperClass : superClasses) {
-
- //tmp = oneSuperClass.replace("\"", "");
- query = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
- + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- rsc = new JenaResultSetConvenience(rs);
- tmpset.addAll(rsc.getStringListForVariable("superclass"));
-
- }
- ret.addAll(tmpset);
- //logger.debug(ret);
- superClasses.clear();
- superClasses.addAll(tmpset);
- tmpset.clear();
- }
- //logger.debug(concept);
- //logger.debug(query);
- return ret;
- }
-
-
- public ResultSet queryConcept(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println("JSON:\n"+JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
- public SortedSet<String> queryConceptAsStringSet(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- //System.out.println(query);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println("JSON:\n"+JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
- return new JenaResultSetConvenience(rs).getStringListForVariable("subject");
-
- }
-
+ /*
public ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
if(limit==0)limit=99999;
//
@@ -337,31 +189,10 @@
}
return rs;
- }
+ }*/
- public ResultSet getClassesForInstance(String instance) {
- ResultSet rs = null;
- try {
-
- String query = "SELECT ?subject WHERE { \n " +
- "<" + instance + ">"+
- " a " +
- "?subject " +
- "\n" +
- "} LIMIT 200";
- SparqlQuery sq = new SparqlQuery(query, se);
- //System.out.println(query);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
+
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
public SortedSet<String> getPosExamples() {
return posExamples;
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -7,13 +7,7 @@
import org.dllearner.core.ComponentManager;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-import com.hp.hpl.jena.query.ResultSet;
-
public class AutomaticExampleFinderSPARQLold {
private static Logger logger = Logger
@@ -33,7 +27,7 @@
posExamples = new TreeSet<String>();
negExamples = new TreeSet<String>();
}
-
+ /*
public void initDBpedia(String concept, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
dbpediaMakePositiveExamplesFromConcept( concept);
SortedSet<String> keepForClean = new TreeSet<String>();
@@ -62,43 +56,21 @@
logger.debug("Finished examples for concept: "+concept);
}
- public void init(String concept, String namespace, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
- makePositiveExamplesFromConcept( concept);
- SortedSet<String> keepForClean = new TreeSet<String>();
- keepForClean.addAll(this.posExamples);
- this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
- logger.trace("shrinking: pos Example size: "+posExamples.size());
-
- if(useRelated) {
- makeNegativeExamplesFromRelatedInstances(this.posExamples,namespace);
- }
- if(useSuperclasses) {
- makeNegativeExamplesFromSuperClasses(concept);
- }
- if(useParallelClasses) {
- makeNegativeExamplesFromClassesOfInstances();
- }
- //clean
- negExamples.removeAll(keepForClean);
- logger.trace("neg Example size after cleaning: "+negExamples.size());
- this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
- logger.debug("pos Example size after shrinking: "+posExamples.size());
- logger.debug("neg Example size after shrinking: "+negExamples.size());
- logger.debug("Finished examples for concept: "+concept);
- }
+ */
-
+ /*
public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
dbpediaMakePositiveExamplesFromConcept( concept);
return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
+ }*/
- public SortedSet<String> getPosOnly(String concept, int limit){
+ /*public SortedSet<String> getPosOnly(String concept, int limit){
makePositiveExamplesFromConcept( concept);
return SetManipulation.fuzzyShrink(this.posExamples, limit);
- }
+ }*/
+ /*
private void dbpediaMakePositiveExamplesFromConcept(String concept){
logger.debug("making Positive Examples from Concept: "+concept);
if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -110,16 +82,12 @@
}
logger.debug(" pos Example size: "+posExamples.size());
}
+ */
- private void makePositiveExamplesFromConcept(String concept){
- logger.debug("making Positive Examples from Concept: "+concept);
- this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
- .getStringListForVariable("subject");
- logger.debug(" pos Example size: "+posExamples.size());
- }
+
/*private void makePositiveExamplesFromConcept(String concept){
logger.debug("making Positive Examples from Concept: "+concept);
if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -136,29 +104,11 @@
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- dbpediaMakeNegativeExamplesFromRelatedInstances(string);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
- private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
- logger.debug("making examples from related instances");
- for (String string : subject) {
- makeNegativeExamplesFromRelatedInstances(string,namespace);
- }
- logger.debug(" negExample size: "+negExamples.size());
- }
- /**
- *
- * @param subject
- * @return
- */
- private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+
+ /*private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
// SortedSet<String> result = new TreeSet<String>();
String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
@@ -172,8 +122,8 @@
this.negExamples.addAll(rsc.getStringListForVariable("o"));
- }
-
+ }*/
+ /*
private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
// SortedSet<String> result = new TreeSet<String>();
@@ -187,27 +137,13 @@
this.negExamples.addAll(rsc.getStringListForVariable("o"));
- }
+ }*/
- private void makeNegativeExamplesFromSuperClasses(String concept) {
-
- SortedSet<String> superClasses = new TreeSet<String>();
- superClasses.add(concept.replace("\"", ""));
- //logger.debug("before"+superClasses);
- superClasses = getSuperClasses( superClasses, 4);
- logger.debug("making neg Examples from "+superClasses.size()+" superclasses");
- JenaResultSetConvenience rsc;
- for (String oneSuperClass : superClasses) {
- logger.debug(oneSuperClass);
- rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", limit));
- this.negExamples.addAll(rsc.getStringListForVariable("subject"));
- }
- logger.debug(" neg Example size: "+negExamples.size());
- }
+ /*
private void makeNegativeExamplesFromClassesOfInstances() {
logger.debug("making neg Examples from parallel classes");
SortedSet<String> classes = new TreeSet<String>();
@@ -233,107 +169,13 @@
}
logger.debug("neg Example size: "+negExamples.size());
- }
+ }*/
- private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
- SortedSet<String> ret = new TreeSet<String>();
- SortedSet<String> tmpset = new TreeSet<String>();
- ret.addAll(superClasses);
- //logger.debug(superClasses);
- JenaResultSetConvenience rsc;
-
- String query = "";
- for (; depth != 0 ; depth--) {
- for (String oneSuperClass : superClasses) {
-
- //tmp = oneSuperClass.replace("\"", "");
- query = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
- + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
- + "}";
-
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- rsc = new JenaResultSetConvenience(rs);
- tmpset.addAll(rsc.getStringListForVariable("superclass"));
-
- }
- ret.addAll(tmpset);
- //logger.debug(ret);
- superClasses.clear();
- superClasses.addAll(tmpset);
- tmpset.clear();
- }
- //logger.debug(concept);
- //logger.debug(query);
- return ret;
- }
- public ResultSet queryConcept(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println("JSON:\n"+JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
- public ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
- if(limit==0)limit=99999;
- //
- ResultSet rs = null;
- try {
-
- String query = "SELECT * WHERE { \n " +
- "?subject " +
- "<http://www.w3.org/2004/02/skos/core#subject> " +
- "<" + SKOSconcept + "> \n" +
- "} LIMIT "+limit;
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public ResultSet getClassesForInstance(String instance) {
- ResultSet rs = null;
- try {
-
- String query = "SELECT ?subject WHERE { \n " +
- "<" + instance + ">"+
- " a " +
- "?subject " +
- "\n" +
- "} LIMIT "+limit;
- SparqlQuery sq = new SparqlQuery(query, se);
- //System.out.println(query);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
public SortedSet<String> getPosExamples() {
return posExamples;
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -1,21 +1,145 @@
package org.dllearner.utilities.examples;
import java.util.SortedSet;
+import java.util.TreeSet;
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.utilities.datastructures.SetManipulation;
+import com.hp.hpl.jena.query.ResultSet;
+
public class AutomaticNegativeExampleFinderSPARQL {
+ // CHECK
+ private static Logger logger = Logger.getLogger(ComponentManager.class);
+
+ private SPARQLTasks sparqltasks;
+
+ private SortedSet<String> fullPositiveSet;
- private Cache c;
- private SparqlEndpoint se;
- private SortedSet<String> posExamples;
- private SortedSet<String> negExamples;
+ //static boolean useRelated = false;
+ private SortedSet<String> fromRelated;
+ //static boolean useSuperClasses = false;
+ private SortedSet<String> fromSuperclasses;
+ //static boolean useParallelClasses = true;
+ private SortedSet<String> fromParallelClasses;
- static boolean useRelated = false;
- static boolean useSuperClasses = false;
- static boolean useParallelClasses = true;
static int poslimit = 10;
static int neglimit = 20;
+
+ // CHECK all vars needed
+ public AutomaticNegativeExampleFinderSPARQL(
+ SortedSet<String> fullPositiveSet,
+ SPARQLTasks st) {
+ super();
+ this.fromParallelClasses = new TreeSet<String>();
+ this.fromRelated = new TreeSet<String>();
+ this.fromSuperclasses = new TreeSet<String>();
+
+ this.fullPositiveSet = fullPositiveSet;
+ this.sparqltasks = st;
+
+ }
+
+
+
+ public SortedSet<String> getNegativeExamples(int neglimit ) {
+
+ SortedSet<String> negatives = new TreeSet<String>();
+ negatives.addAll(fromParallelClasses);
+ negatives.addAll(fromRelated);
+ negatives.addAll(fromSuperclasses);
+ logger.debug("neg Example size before shrinking: " + negatives.size());
+ negatives = SetManipulation.fuzzyShrink(negatives,neglimit);
+ logger.debug("neg Example size after shrinking: " + negatives.size());
+ return negatives;
+ }
+
+ // CHECK namespace
+ public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances,
+ String namespace) {
+ logger.debug("making examples from related instances");
+ for (String oneInstance : instances) {
+ makeNegativeExamplesFromRelatedInstances(oneInstance, namespace);
+ }
+ logger.debug("|-negExample size from related: " + fromRelated.size());
+ }
+
+ private void makeNegativeExamplesFromRelatedInstances(String oneInstance, String objectnamespace) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String SPARQLquery = "SELECT * WHERE { \n" + "<" + oneInstance + "> " + "?p ?object. \n"
+ + "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}";
+
+ this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "object"));
+ this.fromRelated.removeAll(this.fullPositiveSet);
+
+ }
+
+ // QUALITY: weird function, best removed
+ public void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String SPARQLquery = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n" + "}";
+
+ this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "o"));
+
+ }
+
+ public void makeNegativeExamplesFromParallelClasses(SortedSet<String> positiveSet, int resultLimit){
+ makeNegativeExamplesFromClassesOfInstances(positiveSet, resultLimit);
+ }
+
+ public void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
+ int resultLimit) {
+ logger.debug("making neg Examples from parallel classes");
+ SortedSet<String> classes = new TreeSet<String>();
+ // superClasses.add(concept.replace("\"", ""));
+ // logger.debug("before"+superClasses);
+ // superClasses = dbpediaGetSuperClasses( superClasses, 4);
+ // logger.debug("getting negExamples from "+superClasses.size()+"
+ // superclasses");
+
+ for (String instance : positiveSet) {
+ classes.addAll(sparqltasks.getClassesForInstance(instance, resultLimit));
+ }
+ logger.debug("getting negExamples from " + classes.size() + " parallel classes");
+ for (String oneClass : classes) {
+ logger.debug(oneClass);
+ // rsc = new
+ // JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
+ this.fromParallelClasses.addAll(sparqltasks.retrieveInstancesForConcept("\"" + oneClass
+ + "\"", resultLimit));
+
+ }
+
+ this.fromParallelClasses.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example size from parallelclass: " + fromParallelClasses.size());
+
+ }
+
+ public void makeNegativeExamplesFromSuperClasses(String concept, int resultLimit) {
+
+ concept = concept.replaceAll("\"", "");
+ // superClasses.add(concept.replace("\"", ""));
+ // logger.debug("before"+superClasses);
+ SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, 4);
+ logger.debug("making neg Examples from " + superClasses.size() + " superclasses");
+
+ for (String oneSuperClass : superClasses) {
+ logger.debug(oneSuperClass);
+ this.fromSuperclasses.addAll(sparqltasks.retrieveInstancesForConcept("\""
+ + oneSuperClass + "\"", resultLimit));
+
+ }
+ this.fromSuperclasses.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example from superclass: " + fromSuperclasses.size());
+ }
+
}
Added: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,59 @@
+package org.dllearner.utilities.examples;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+
+public class AutomaticPositiveExampleFinderSPARQL {
+
+ //CHECK
+ private static Logger logger = Logger
+ .getLogger(ComponentManager.class);
+
+
+ private SPARQLTasks sparqltasks;
+
+ private SortedSet<String> posExamples;
+
+ public AutomaticPositiveExampleFinderSPARQL(SPARQLTasks st) {
+ super();
+
+ this.posExamples = new TreeSet<String>();
+ this.sparqltasks = st;
+ }
+
+ //QUALITY resultsize is not accounted for
+ public void makePositiveExamplesFromConcept(String conceptKBSyntax){
+ logger.debug("making Positive Examples from Concept: "+conceptKBSyntax);
+ this.posExamples = sparqltasks.retrieveInstancesForConcept(conceptKBSyntax, 0);
+ logger.debug(" pos Example size: "+posExamples.size());
+ }
+
+
+ //QUALITY resultsize is not accounted for
+ public void makePositiveExamplesFromRoleAndObject(String role, String object){
+ logger.debug("making Positive Examples from role: "+role+" and object: "+object);
+ this.posExamples = sparqltasks.retrieveDISTINCTSubjectsForRoleAndObject(role, object, 0);
+ logger.debug(" pos Example size: "+posExamples.size());
+ }
+
+ //QUALITY resultsize is not accounted for
+ public void makePositiveExamplesFromSKOSConcept(String SKOSConcept){
+ logger.debug("making Positive Examples from SKOSConcept: "+SKOSConcept);
+ this.posExamples = sparqltasks.retrieveInstancesForSKOSConcept(SKOSConcept, 0);
+ logger.debug(" pos Example size: "+posExamples.size());
+ }
+
+ public SortedSet<String> getPosExamples() {
+ return posExamples;
+ }
+
+
+
+
+
+}
Added: trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,216 @@
+package org.dllearner.utilities.examples;
+
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.sparql.core.ResultBinding;
+
+public class SPARQLTasks {
+
+ private Cache c;
+ private SparqlEndpoint se;
+
+ public SPARQLTasks(Cache c, SparqlEndpoint se) {
+ super();
+ this.c = c;
+ this.se = se;
+ }
+
+ public SPARQLTasks( SparqlEndpoint se) {
+ super();
+ this.c = null;
+ this.se = se;
+ }
+
+
+
+
+ /**
+ * QUALITY: doesn't seem optimal, check!
+ * get all superclasses up to a certain depth
+ * 1 means direct superclasses
+ * depth
+ * @param superClasses
+ * @param depth
+ * @return
+ */
+ public SortedSet<String> getSuperClasses(String oneClass, int depth) {
+ SortedSet<String> superClasses = new TreeSet<String>();
+ superClasses.add(oneClass);
+ SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<String> tmpset = new TreeSet<String>();
+ //ret.addAll(superClasses);
+ //logger.debug(superClasses);
+
+
+ String SPARQLquery = "";
+ for (; depth != 0 ; depth--) {
+ for (String oneSuperClass : superClasses) {
+ ...
[truncated message content] |
|
From: <ku...@us...> - 2008-05-22 14:10:35
|
Revision: 921
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=921&view=rev
Author: kurzum
Date: 2008-05-22 07:10:08 -0700 (Thu, 22 May 2008)
Log Message:
-----------
added jamon
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -46,6 +46,7 @@
import org.dllearner.refinementoperators.RhoDRDown;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.ConceptTransformation;
@@ -279,6 +280,7 @@
public void start() {
runtime=System.currentTimeMillis();
+ JamonMonitorLogger.getTimeMonitor(ExampleBasedROLComponent.class, "totalLearningTime").start();
// TODO: write a JUnit test for this problem (long-lasting or infinite loops because
// redundant children of a node are called recursively after when the node is extended
// twice)
@@ -432,9 +434,6 @@
// Anzahl Schleifendurchläufe
loop++;
-
-
-
}//end while
@@ -467,9 +466,13 @@
if(stop)
logger.info("Algorithm stopped.");
else
- logger.info("Algorithm terminated succesfully.");
+ logger.info("Algorithm terminated succesfully.");
+
+ JamonMonitorLogger.getTimeMonitor(ExampleBasedROLComponent.class, "totalLearningTime").stop();
}
+
+
// we apply the operator recursively until all proper refinements up
// to the maxmimum length are reached
private void extendNodeProper(ExampleBasedNode node, int maxLength) {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -32,7 +32,7 @@
import org.apache.log4j.Logger;
import org.dllearner.core.KnowledgeSource;
-import org.dllearner.utilities.statistics.Statistics;
+import org.dllearner.utilities.JamonMonitorLogger;
/**
* SPARQL query cache to avoid possibly expensive multiple queries. The queries
@@ -94,6 +94,10 @@
return c;
}
+ public static String getDefaultCacheDir(){
+ return "cache";
+ }
+
/**
* Constructor for the cache itself.
*
@@ -234,14 +238,21 @@
* @return Jena result set.
*/
public String executeSparqlQuery(SparqlQuery query) {
+ JamonMonitorLogger.getTimeMonitor(Cache.class, "TotalTimeExecuteSparqlQuery").start();
+ JamonMonitorLogger.increaseCount(Cache.class, "TotalQueries");
- Statistics.increaseQuery();
+
+ //Statistics.increaseQuery();
+
+ JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").start();
String result = getCacheEntry(query.getQueryString());
+ JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").stop();
+
if (result != null) {
logger.trace("got from cache");
-
- Statistics.increaseCachedQuery();
- return result;
+ JamonMonitorLogger.increaseCount(Cache.class, "SuccessfulHits");
+ //Statistics.increaseCachedQuery();
+ //return result;
} else {
//SimpleClock sc = new SimpleClock();
query.send();
@@ -251,8 +262,11 @@
addToCache(query.getQueryString(), json);
}
else json="";
- return json;
+ logger.warn("empty result: "+query.getQueryString());
+ //return json;
}
+ JamonMonitorLogger.getTimeMonitor(Cache.class, "TotalTimeExecuteSparqlQuery").stop();
+ return result;
}
public void setFreshnessInDays(int days){
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -25,6 +25,7 @@
import org.apache.log4j.Logger;
import org.dllearner.core.KnowledgeSource;
+import org.dllearner.utilities.JamonMonitorLogger;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
@@ -85,9 +86,11 @@
try{
//TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
- //SimpleClock sc=new SimpleClock();
+
+ JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").start();
rs = queryExecution.execSelect();
- //sc.printAndSet("rs to list");
+ JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
+
logger.debug("query SPARQL server ["+extraDebugInfo+"], retrieved: "+rs.getResultVars());
json=SparqlQuery.getAsJSON(rs);
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -25,6 +25,7 @@
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL;
import org.dllearner.utilities.examples.AutomaticPositiveExampleFinderSPARQL;
@@ -70,6 +71,7 @@
*/
public static void main(String[] args) {
System.out.println("Start");
+
initLogger();
//parameters
@@ -94,12 +96,13 @@
logger.debug("found nr of concepts: "+conceptresults.size());
for (Description oneConcept : conceptresults) {
- s.evaluate(oneConcept, 1000);
+ //s.evaluate(oneConcept, 1000);
}
System.out.println("Finished");
+ JamonMonitorLogger.printAll();
}
@@ -283,6 +286,8 @@
apos.makePositiveExamplesFromSKOSConcept(SKOSConcept);
fullPositiveSet = apos.getPosExamples();
+ //System.exit(0);
+
int poslimit=(int)Math.round(percentOfSKOSSet*fullPositiveSet.size());
int neglimit=(int)Math.round(poslimit*negfactor);
@@ -358,7 +363,7 @@
}
if(randomizeCache)
cm.applyConfigEntry(ks, "cacheDir","cache/"+System.currentTimeMillis()+"");
- else {cm.applyConfigEntry(ks, "cacheDir",Cache.getDefaultCache());}
+ else {cm.applyConfigEntry(ks, "cacheDir",Cache.getDefaultCacheDir());}
//LEARNINGALGORITHM
cm.applyConfigEntry(la,"useAllConstructor",false);
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -14,7 +14,6 @@
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.LearnSparql;
import org.dllearner.utilities.statistics.SimpleClock;
import org.dllearner.utilities.statistics.Statistics;
@@ -103,12 +102,12 @@
boolean closeAfterRecursion=true;
System.out.println(oneConcept);
- AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
+ //AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
//ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
- posExamples = ae.getPosExamples();
- negExamples = ae.getNegExamples();
+ //posExamples = ae.getPosExamples();
+ //negExamples = ae.getNegExamples();
for(recursiondepth=0;recursiondepth<4;recursiondepth++) {
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -13,7 +13,6 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.learn.LearnSparql;
import org.dllearner.utilities.statistics.SimpleClock;
@@ -23,6 +22,7 @@
public class SPARQLMassLearning {
+
static Cache c;
static SparqlEndpoint se;
private static Logger logger = Logger.getRootLogger();
@@ -182,7 +182,7 @@
boolean closeAfterRecursion=false;
int numberOfTriples = 0;
for (String oneConcept : concepts) {
- AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
+ //AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
useRelated = true;
useSuperClasses = true;
useParallelClasses = false;
@@ -190,8 +190,8 @@
poslimit=10;
neglimit=10;
//ae.initDBpedia(concept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
- posExamples = ae.getPosExamples();
- negExamples = ae.getNegExamples();
+ //posExamples = ae.getPosExamples();
+ //negExamples = ae.getNegExamples();
/*String tmp = concepts.first().replace("http://dbpedia.org/resource/Category:", "").replace("\"","");
@@ -223,33 +223,7 @@
}
- /***************************************************************************
- * *********************OLDCODE String
- * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
- * \"http://dbpedia.org/class/yago/Head110162991\")";
- *
- *
- * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
- * concepts.add("EXISTS
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
- * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
- * //concepts.add("ALL
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add(conj);
- * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
- * \"http://dbpedia.org/class/yago/Head110162991\")");
- *
- * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
- *
- * for (String kbsyntax : concepts) {
- * result.put(kbsyntax,queryConcept(kbsyntax)); }
- * System.out.println("************************"); for (String string :
- * result.keySet()) { System.out.println("KBSyntayString: "+string);
- * System.out.println("Query:\n"+result.get(string).hasNext());
- * System.out.println("************************"); }
- **************************************************************************/
+
Copied: trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java (from rev 920, trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -0,0 +1,101 @@
+package org.dllearner.utilities;
+
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlQuery;
+
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
+/**
+ * provides convenience functions for timelogs
+ *
+ */
+public class JamonMonitorLogger {
+
+
+ public static List<Monitor> getMonitorsSortedByLabel(){
+ MonitorFactory mf=(MonitorFactory)MonitorFactory.getFactory();
+ SortedSet<String> retMon = new TreeSet<String>();
+
+ @SuppressWarnings("unchecked")
+ Iterator<Monitor> it = mf.iterator();
+
+ while (it.hasNext()) {
+ Monitor monitor = (Monitor) it.next();
+ retMon.add(monitor.getLabel());
+ }
+
+ LinkedList<Monitor> l=new LinkedList<Monitor>();
+
+ for (String label : retMon) {
+ l.add(MonitorFactory.getTimeMonitor(label));
+ }
+
+ return l;
+ }
+
+
+
+ public static void printAll() {
+ List<Monitor> l= getMonitorsSortedByLabel();
+ for (int i = 0; i < l.size(); i++) {
+ Monitor monitor = l.get(i);
+ System.out.println(monitor);
+ }
+ }
+
+
+
+
+ public static String getMonitorPrefix(Class clazz){
+ String retval="";
+ if (clazz == SparqlQuery.class) {
+ retval= "Sparql:";
+ } else if (clazz == Cache.class) {
+ retval= "Sparql:";
+ } else if (clazz == Cache.class) {
+ retval= "Sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else if (clazz == ExampleBasedROLComponent.class) {
+ retval= "Learning:";
+ } else if (clazz == SparqlQuery.class) {
+ retval= "sparql:";
+ } else {
+ retval= "undefined:";
+ }
+ return retval+clazz.getSimpleName()+":";
+ }
+
+ public static Monitor getTimeMonitor(Class clazz, String label) {
+
+ String labeltmp = getMonitorPrefix(clazz)+label;
+ return MonitorFactory.getTimeMonitor(labeltmp);
+
+ }
+
+ public static void increaseCount (Class clazz, String label) {
+ MonitorFactory.getMonitor(getMonitorPrefix(clazz)+label, "#").add(1.0);
+ }
+
+
+
+
+}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -1,9 +0,0 @@
-package org.dllearner.utilities;
-
-/**
- * provides convenience functions for timelogs
- *
- */
-public class JamonTimeLogger {
-
-}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -45,7 +45,7 @@
public void makePositiveExamplesFromSKOSConcept(String SKOSConcept){
logger.debug("making Positive Examples from SKOSConcept: "+SKOSConcept);
this.posExamples = sparqltasks.retrieveInstancesForSKOSConcept(SKOSConcept, 0);
- logger.debug(" pos Example size: "+posExamples.size());
+ logger.debug("pos Example size: "+posExamples.size());
}
public SortedSet<String> getPosExamples() {
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-22 12:06:39 UTC (rev 920)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-22 14:10:08 UTC (rev 921)
@@ -90,7 +90,7 @@
"?subject " +
"<"+role+"> " +
"<" + object + "> \n" +
- "} LIMIT "+resultLimit;
+ "} "+limit(resultLimit);
return queryAsSet(SPARQLquery, "subject");
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-23 17:12:47
|
Revision: 924
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=924&view=rev
Author: kurzum
Date: 2008-05-23 10:12:31 -0700 (Fri, 23 May 2008)
Log Message:
-----------
fixed some bugs, sparqlqueries working again, added some time statistics
SKOS Script basically working
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlEndpoint.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/test/JenaHTTPTest.java
trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
Property Changed:
----------------
trunk/src/dl-learner/org/dllearner/test/
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -84,6 +84,7 @@
import org.dllearner.reasoning.FastRetrievalReasoner;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.datastructures.Datastructures;
import org.dllearner.utilities.datastructures.StringTuple;
import org.dllearner.utilities.owl.ConceptComparator;
@@ -134,6 +135,7 @@
Start start = null;
start = new Start(file);
start.start(inQueryMode);
+ JamonMonitorLogger.printAllSortedByLabel();
}
/**
Modified: trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -364,7 +364,7 @@
}
public static void initAllInstancesAndReasoners(){
- // Datei \xF6ffnen
+ // Datei oeffnen
BufferedReader in = null;
try {
in = new BufferedReader(new FileReader(allData));
@@ -423,7 +423,7 @@
}
public static void initAllInstancesWithoutReasoners(){
- // Datei \xF6ffnen
+ // Datei oeffnen
BufferedReader in = null;
try {
in = new BufferedReader(new FileReader(allData));
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -260,9 +260,13 @@
String json = query.getResult();
if (json!=null){
addToCache(query.getQueryString(), json);
+ result=json;
}
- else json="";
- logger.warn("empty result: "+query.getQueryString());
+ else {
+ json="";
+ logger.warn(Cache.class.getSimpleName()+"empty result: "+query.getQueryString());
+ }
+
//return json;
}
JamonMonitorLogger.getTimeMonitor(Cache.class, "TotalTimeExecuteSparqlQuery").stop();
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlEndpoint.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlEndpoint.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlEndpoint.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -132,6 +132,7 @@
ll.add(EndpointTalisBlogs());
ll.add(EndpointSWSchool());
ll.add(EndpointSparqlette());
+ ll.add(EndpointLOCALDBpedia());
return ll;
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -55,8 +55,8 @@
//examples
static int sparqlResultSize=2000;
- static double percentOfSKOSSet=0.7;
- static double negfactor=0.3;
+ static double percentOfSKOSSet=0.2;
+ static double negfactor=1.0;
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> fullPositiveSet = new TreeSet<String>();
SortedSet<String> fullminusposRest = new TreeSet<String>();
@@ -78,6 +78,7 @@
if(local){
url = "http://139.18.2.37:8890/sparql";
+ //RBC
sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointLOCALDBpedia());
}else{
url = "http://dbpedia.openlinksw.com:8890/sparql";
@@ -96,13 +97,14 @@
logger.debug("found nr of concepts: "+conceptresults.size());
for (Description oneConcept : conceptresults) {
+
//s.evaluate(oneConcept, 1000);
}
System.out.println("Finished");
- JamonMonitorLogger.printAll();
+ JamonMonitorLogger.printAllSortedByLabel();
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -188,6 +188,7 @@
String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ if(rs==null);
//JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
//return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
return null;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -175,12 +175,13 @@
//HashMap<String, String> result2 = new HashMap<String, String>();
//System.out.println(concepts.first());
//logger.setLevel(Level.TRACE);
- String concept=concepts.first();
- int i=0;
+
+ //String concept=concepts.first();
+ //int i=0;
Statistics.setCurrentLabel("0");
int recursiondepth=0;
boolean closeAfterRecursion=false;
- int numberOfTriples = 0;
+ //int numberOfTriples = 0;
for (String oneConcept : concepts) {
//AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);
useRelated = true;
@@ -257,6 +258,7 @@
String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ if(rs==null);
//JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
//return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
return null;
Property changes on: trunk/src/dl-learner/org/dllearner/test
___________________________________________________________________
Name: svn:ignore
+ JamonTest.java
Modified: trunk/src/dl-learner/org/dllearner/test/JenaHTTPTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/JenaHTTPTest.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/test/JenaHTTPTest.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -103,6 +103,8 @@
return ((end-start)/1000);
}
+ @Deprecated
+ @SuppressWarnings("all")
private static double httpQuery(String query) throws Exception
{
char value[]={13,10};
Modified: trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -3,6 +3,7 @@
import java.util.HashSet;
import java.util.LinkedList;
import java.util.Set;
+import java.util.SortedSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -11,6 +12,7 @@
import org.apache.log4j.SimpleLayout;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.examples.SPARQLTasks;
import org.dllearner.utilities.statistics.SimpleClock;
@@ -29,8 +31,8 @@
logger.removeAllAppenders();
logger.addAppender(fileAppender);
logger.addAppender(consoleAppender);
- logger.setLevel(Level.DEBUG);
- Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.INFO);
+ logger.setLevel(Level.TRACE);
+ Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.WARN);
//SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100
@@ -42,6 +44,7 @@
for (int j = 0; j < ll.size(); j++) {
testEndPoint(ll.get(j));
+ if(i==3)break;
logger.info("finished "+i+" of "+ll.size());
i++;
}
@@ -54,7 +57,7 @@
}
//set.add(SparqlEndpoint.);
-
+ JamonMonitorLogger.printAllSortedByLabel();
}
@@ -68,7 +71,8 @@
"LIMIT 100";
SPARQLquery ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
- int i = new SPARQLTasks(se).queryAsSet(SPARQLquery, "c").size();
+ SortedSet<String> tmp = new SPARQLTasks(se).queryAsSet(SPARQLquery, "c");
+ int i =tmp.size();
working.add(sc.getAndSet("endpoint working: "+se.getURL()+" ("+((i==100)?"more than 100 concepts":"about "+i+" concepts")+" )"));
Modified: trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/utilities/JamonMonitorLogger.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -19,41 +19,47 @@
*/
public class JamonMonitorLogger {
-
- public static List<Monitor> getMonitorsSortedByLabel(){
- MonitorFactory mf=(MonitorFactory)MonitorFactory.getFactory();
- SortedSet<String> retMon = new TreeSet<String>();
+ public static List<Monitor> getMonitors(){
+ //MonitorFactory mf=(MonitorFactory)MonitorFactory.getFactory();
+ LinkedList<Monitor> l=new LinkedList<Monitor>();
+
@SuppressWarnings("unchecked")
- Iterator<Monitor> it = mf.iterator();
-
+ Iterator<Monitor> it = MonitorFactory.getFactory().iterator();
+ //mf.iterator();
while (it.hasNext()) {
Monitor monitor = (Monitor) it.next();
- retMon.add(monitor.getLabel());
+
+ l.add(monitor);
}
- LinkedList<Monitor> l=new LinkedList<Monitor>();
+
- for (String label : retMon) {
+ /*for (String label : retMon) {
l.add(MonitorFactory.getTimeMonitor(label));
- }
+ }*/
return l;
}
- public static void printAll() {
- List<Monitor> l= getMonitorsSortedByLabel();
+ public static void printAllSortedByLabel() {
+ List<Monitor> l= getMonitors();
+ SortedSet<String> sset = new TreeSet<String>();
+
for (int i = 0; i < l.size(); i++) {
Monitor monitor = l.get(i);
- System.out.println(monitor);
+ sset.add(monitor.toString());
}
+ for (String onemon : sset) {
+ System.out.println(onemon);
+ }
}
-
+ @SuppressWarnings("all")
public static String getMonitorPrefix(Class clazz){
String retval="";
if (clazz == SparqlQuery.class) {
@@ -84,6 +90,9 @@
return retval+clazz.getSimpleName()+":";
}
+
+
+ @SuppressWarnings("all")
public static Monitor getTimeMonitor(Class clazz, String label) {
String labeltmp = getMonitorPrefix(clazz)+label;
@@ -91,8 +100,13 @@
}
+ @SuppressWarnings("all")
public static void increaseCount (Class clazz, String label) {
- MonitorFactory.getMonitor(getMonitorPrefix(clazz)+label, "#").add(1.0);
+ // MonitorFactory.getMonitor(getMonitorPrefix(clazz)+label, "#").add(1.0);
+ Monitor m = MonitorFactory.getMonitor(getMonitorPrefix(clazz)+label, "count");
+ // System.out.println(m);
+ m.setHits(m.getHits()+1);
+ //System.out.println(m);
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -1,23 +1,17 @@
package org.dllearner.utilities.examples;
-import java.util.SortedSet;
-
-import org.apache.log4j.Logger;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlEndpoint;
// keep this class it still needs to be worked in
public class AutomaticExampleFinderRolesSPARQL {
- private static Logger logger = Logger
- .getLogger(ComponentManager.class);
+// private static Logger logger = Logger
+// .getLogger(ComponentManager.class);
+//
+// private Cache c;
+// private SparqlEndpoint se;
+// private SortedSet<String> posExamples;
+// private SortedSet<String> negExamples;
+// private int roleLimit=1000;
- private Cache c;
- private SparqlEndpoint se;
- private SortedSet<String> posExamples;
- private SortedSet<String> negExamples;
- private int roleLimit=1000;
-
/*
public AutomaticExampleFinderRolesSPARQL(SparqlEndpoint se){
this.c=new Cache("cachetemp");
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -30,6 +30,7 @@
negExamples = new TreeSet<String>();
}
+
@Deprecated
public void initDBpediaSKOS(String concept, double percent, boolean useRelated,boolean useParallelClasses) {
//dbpediaMakePositiveExamplesFromConcept( concept);
@@ -55,7 +56,7 @@
}
if(useParallelClasses) {
- int limit = this.posExamples.size();
+ //int limit = this.posExamples.size();
//makeNegativeExamplesFromClassesOfInstances(limit);
}
//clean
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-23 10:03:01 UTC (rev 923)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-23 17:12:31 UTC (rev 924)
@@ -4,6 +4,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.apache.log4j.Logger;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
@@ -15,6 +16,9 @@
public class SPARQLTasks {
+ //CHECK
+ private static Logger logger = Logger
+ .getLogger(SPARQLTasks.class);
private Cache c;
private SparqlEndpoint se;
@@ -78,6 +82,7 @@
/**
+ * QUALITY: buggy because role doesn't work sometimes
* get subject with fixed role and object
* @param role
* @param object
@@ -95,7 +100,7 @@
return queryAsSet(SPARQLquery, "subject");
}
- public SortedSet<String> retrieveObjectsForSubjectAndRole(String subject, String role,int resultLimit) {
+ public SortedSet<String> retrieveObjectsForSubjectAndRole(String subject, String role, int resultLimit) {
String SPARQLquery =
"SELECT DISTINCT * WHERE { \n " +
"<" +subject+ "> "+
@@ -113,8 +118,8 @@
* @return
*/
public SortedSet<String> retrieveInstancesForSKOSConcept(String SKOSconcept,int resultLimit) {
- return retrieveDISTINCTSubjectsForRoleAndObject("http://www.w3.org/2004/02/skos/core#subject",
- SKOSconcept, resultLimit);
+ return queryPatternAsSet("?subject", "?predicate", "<"+SKOSconcept+">", "subject", resultLimit);
+ //return retrieveDISTINCTSubjectsForRoleAndObject("http://www.w3.org/2004/02/skos/core#subject",
}
@@ -157,6 +162,27 @@
}
+
+ /**
+ * query a pattern with a standard SPARQL query
+ * usage (?subject, ?predicate, <http:something> , subject )
+ * @param subject
+ * @param predicate
+ * @param object
+ * @param var
+ * @return
+ */
+ public SortedSet<String> queryPatternAsSet(String subject, String predicate, String object, String var, int resultLimit){
+ String SPARQLquery = "SELECT ?subject WHERE { \n " +
+ " " + subject +
+ " " + predicate +
+ " " + object +
+ " \n" +
+ "} "+limit(resultLimit);
+ return queryAsSet( SPARQLquery, var);
+ }
+
+
/**
* little higher level, executes query ,returns all resources for a variable
* @param SPARQLquery
@@ -166,12 +192,13 @@
public SortedSet<String> queryAsSet(String SPARQLquery, String var){
ResultSet rs = null;
try {
- rs = SparqlQuery.JSONtoResultSet(query(SPARQLquery));
+ String JSON = query(SPARQLquery);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
} catch (Exception e) {
e.printStackTrace();
}
- return getStringListForVariable(rs,"subject");
+ return getStringListForVariable(rs,var);
}
@@ -183,8 +210,10 @@
public String query(String SPARQLquery){
if(c==null){
SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
+ sq.extraDebugInfo+=se.getURL();
sq.send();
- return sq.getResult();
+ String JSON = sq.getResult();
+ return JSON;
}else{
return c.executeSparqlQuery(new SparqlQuery(SPARQLquery,se));
}
@@ -204,9 +233,7 @@
List<ResultBinding> l = ResultSetFormatter.toList(rs);
for (ResultBinding resultBinding : l) {
-
result.add(resultBinding.get(var).toString());
-
}
return result;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-26 12:02:42
|
Revision: 928
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=928&view=rev
Author: kurzum
Date: 2008-05-26 05:02:10 -0700 (Mon, 26 May 2008)
Log Message:
-----------
moved sparqltasks to sparql
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
Copied: trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java (from rev 927, trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -0,0 +1,273 @@
+package org.dllearner.kb.sparql;
+
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.sparql.core.ResultBinding;
+
+public class SPARQLTasks {
+
+ //CHECK
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger
+ .getLogger(SPARQLTasks.class);
+ private Cache c;
+ private SparqlEndpoint se;
+
+ public SPARQLTasks(Cache c, SparqlEndpoint se) {
+ super();
+ this.c = c;
+ this.se = se;
+ }
+
+ public SPARQLTasks( SparqlEndpoint se) {
+ super();
+ this.c = null;
+ this.se = se;
+ }
+
+
+
+
+ /**
+ * QUALITY: doesn't seem optimal, check!
+ * get all superclasses up to a certain depth
+ * 1 means direct superclasses
+ * depth
+ * @param superClasses
+ * @param depth
+ * @return
+ */
+ public SortedSet<String> getSuperClasses(String oneClass, int depth) {
+ SortedSet<String> superClasses = new TreeSet<String>();
+ superClasses.add(oneClass);
+ SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<String> tmpset = new TreeSet<String>();
+ //ret.addAll(superClasses);
+ //logger.debug(superClasses);
+
+
+ String SPARQLquery = "";
+ for (; depth != 0 ; depth--) {
+ for (String oneSuperClass : superClasses) {
+
+ //tmp = oneSuperClass.replace("\"", "");
+ SPARQLquery = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
+ + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
+ + "}";
+
+ tmpset.addAll(queryAsSet(SPARQLquery, "superclass"));
+
+ }
+ ret.addAll(tmpset);
+ //logger.debug(ret);
+ superClasses.clear();
+ superClasses.addAll(tmpset);
+ tmpset.clear();
+ }
+ //logger.debug(concept);
+ //logger.debug(query);
+ return ret;
+ }
+
+
+
+
+ /**
+ * QUALITY: buggy because role doesn't work sometimes
+ * get subject with fixed role and object
+ * @param role
+ * @param object
+ * @param resultLimit
+ * @return
+ */
+ public SortedSet<String> retrieveDISTINCTSubjectsForRoleAndObject(String role, String object,int resultLimit) {
+ String SPARQLquery =
+ "SELECT DISTINCT * WHERE { \n " +
+ "?subject " +
+ "<"+role+"> " +
+ "<" + object + "> \n" +
+ "} "+limit(resultLimit);
+
+ return queryAsSet(SPARQLquery, "subject");
+ }
+
+ public SortedSet<String> retrieveObjectsForSubjectAndRole(String subject, String role, int resultLimit) {
+ String SPARQLquery =
+ "SELECT DISTINCT * WHERE { \n " +
+ "<" +subject+ "> "+
+ "<"+role+"> " +
+ " ?object \n" +
+ "} LIMIT "+resultLimit;
+
+ return queryAsSet(SPARQLquery, "object");
+ }
+
+ /**
+ * all instances for a SKOS concept
+ * @param SKOSconcept
+ * @param resultLimit
+ * @return
+ */
+ public SortedSet<String> retrieveInstancesForSKOSConcept(String SKOSconcept,int resultLimit) {
+ return queryPatternAsSet("?subject", "?predicate", "<"+SKOSconcept+">", "subject", resultLimit);
+ //return retrieveDISTINCTSubjectsForRoleAndObject("http://www.w3.org/2004/02/skos/core#subject",
+ }
+
+
+
+ /**
+ * get all instances for a concept
+ * @param conceptKBSyntax
+ * @param sparqlResultLimit
+ * @return
+ */
+ public SortedSet<String> retrieveInstancesForConcept (String conceptKBSyntax,int sparqlResultLimit) {
+
+ String SPARQLquery = "";
+ try{
+ SPARQLquery = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQuery(conceptKBSyntax,sparqlResultLimit);
+ }catch (Exception e) {e.printStackTrace();}
+ return queryAsSet(SPARQLquery, "subject");
+ }
+
+
+
+
+ /**
+ * get all direct Classes of an instance
+ * @param instance
+ * @param resultLimit
+ * @return
+ */
+ public SortedSet<String> getClassesForInstance(String instance, int resultLimit) {
+
+ String SPARQLquery = "SELECT ?subject WHERE { \n " +
+ "<" + instance + ">"+
+ " a " +
+ "?subject " +
+ "\n" +
+ "} "+limit(resultLimit);
+
+ return queryAsSet(SPARQLquery, "subject");
+ }
+
+
+
+ public SortedSet<String> getDomain(String role,int resultLimit){
+
+ String SPARQLquery = "" +
+ "SELECT DISTINCT ?domain " +
+ "WHERE { \n" +
+ "?domain <" + role + "> " + " ?o. \n" +
+ "?domain a []\n." +
+ "FILTER (!isLiteral(?domain))." +
+ "}\n" + limit(resultLimit);
+
+ return queryAsSet(SPARQLquery, "domain");
+
+
+ }
+
+
+ public SortedSet<String> getRange(String role,int resultLimit){
+
+ String SPARQLquery = "" +
+ "SELECT DISTINCT ?range " +
+ "WHERE { \n" +
+ "?s <" + role + "> " + " ?range. \n" +
+ "?range a [].\n" +
+ "FILTER (!isLiteral(?range))." +
+ "}\n" + limit(resultLimit);
+
+ return queryAsSet(SPARQLquery, "range");
+
+ }
+
+
+
+ /**
+ * query a pattern with a standard SPARQL query
+ * usage (?subject, ?predicate, <http:something> , subject )
+ * @param subject
+ * @param predicate
+ * @param object
+ * @param var
+ * @return
+ */
+ public SortedSet<String> queryPatternAsSet(String subject, String predicate, String object, String var, int resultLimit){
+ String SPARQLquery = "SELECT ?subject WHERE { \n " +
+ " " + subject +
+ " " + predicate +
+ " " + object +
+ " \n" +
+ "} "+limit(resultLimit);
+ return queryAsSet( SPARQLquery, var);
+ }
+
+
+ /**
+ * little higher level, executes query ,returns all resources for a variable
+ * @param SPARQLquery
+ * @param var
+ * @return
+ */
+ public SortedSet<String> queryAsSet(String SPARQLquery, String var){
+ ResultSet rs = null;
+ try {
+ String JSON = query(SPARQLquery);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ return getStringListForVariable(rs,var);
+ }
+
+
+ /**
+ * lowlevel, executes query returns JSON
+ * @param SPARQLquery
+ * @return
+ */
+ public String query(String SPARQLquery){
+ if(c==null){
+ SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
+ sq.extraDebugInfo+=se.getURL();
+ sq.send();
+ String JSON = sq.getResult();
+ return JSON;
+ }else{
+ return c.executeSparqlQuery(new SparqlQuery(SPARQLquery,se));
+ }
+
+ }
+
+ private String limit(int resultLimit){
+ if(resultLimit>0)return " LIMIT "+resultLimit;
+ return "";
+ }
+
+
+ public static SortedSet<String> getStringListForVariable(ResultSet rs, String var){
+ SortedSet<String> result = new TreeSet<String>();
+
+ //String s=ResultSetFormatter.asXMLString(this.rs);
+ @SuppressWarnings("unchecked")
+ List<ResultBinding> l = ResultSetFormatter.toList(rs);
+
+ for (ResultBinding resultBinding : l) {
+ result.add(resultBinding.get(var).toString());
+ }
+
+ return result;
+
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-26 10:37:56 UTC (rev 927)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -20,6 +20,7 @@
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
@@ -29,7 +30,6 @@
import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL;
import org.dllearner.utilities.examples.AutomaticPositiveExampleFinderSPARQL;
-import org.dllearner.utilities.examples.SPARQLTasks;
public class SKOS7030 {
Modified: trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-26 10:37:56 UTC (rev 927)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -10,10 +10,10 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.utilities.JamonMonitorLogger;
-import org.dllearner.utilities.examples.SPARQLTasks;
import org.dllearner.utilities.statistics.SimpleClock;
public class SparqlEndpointTest {
Deleted: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-26 10:37:56 UTC (rev 927)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -1,152 +0,0 @@
-package org.dllearner.utilities.examples;
-
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.utilities.datastructures.SetManipulation;
-
-public class AutomaticNegativeExampleFinderSPARQL {
-
- // CHECK
- private static Logger logger = Logger.getLogger(ComponentManager.class);
-
- private SPARQLTasks sparqltasks;
-
- private SortedSet<String> fullPositiveSet;
-
- private SortedSet<String> fromRelated = new TreeSet<String>();
- private SortedSet<String> fromSuperclasses = new TreeSet<String>();;
- private SortedSet<String> fromParallelClasses = new TreeSet<String>();;
- private SortedSet<String> fromDomain = new TreeSet<String>();;
- private SortedSet<String> fromRange = new TreeSet<String>();;
-
- static int poslimit = 10;
- static int neglimit = 20;
-
- // CHECK separate posexamples and fullposset
- public AutomaticNegativeExampleFinderSPARQL(
- SortedSet<String> fullPositiveSet,
- SPARQLTasks st) {
- super();
- this.fullPositiveSet = fullPositiveSet;
- this.sparqltasks = st;
-
- }
-
-
-
- public SortedSet<String> getNegativeExamples(int neglimit ) {
-
- SortedSet<String> negatives = new TreeSet<String>();
- negatives.addAll(fromParallelClasses);
- negatives.addAll(fromRelated);
- negatives.addAll(fromSuperclasses);
- logger.debug("neg Example size before shrinking: " + negatives.size());
- negatives = SetManipulation.fuzzyShrink(negatives,neglimit);
- logger.debug("neg Example size after shrinking: " + negatives.size());
- return negatives;
- }
-
- // CHECK namespace
- public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances,
- String namespace) {
- logger.debug("making examples from related instances");
- for (String oneInstance : instances) {
- makeNegativeExamplesFromRelatedInstances(oneInstance, namespace);
- }
- logger.debug("|-negExample size from related: " + fromRelated.size());
- }
-
- private void makeNegativeExamplesFromRelatedInstances(String oneInstance, String objectnamespace) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String SPARQLquery = "SELECT * WHERE { \n" + "<" + oneInstance + "> " + "?p ?object. \n"
- + "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}";
-
- this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "object"));
- this.fromRelated.removeAll(this.fullPositiveSet);
-
- }
-
- // QUALITY: keep a while may still be needed
- /*public void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String SPARQLquery = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
- + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n" + "}";
-
- this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "o"));
-
- }*/
-
- public void makeNegativeExamplesFromParallelClasses(SortedSet<String> positiveSet, int resultLimit){
- makeNegativeExamplesFromClassesOfInstances(positiveSet, resultLimit);
- }
-
- public void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
- int resultLimit) {
- logger.debug("making neg Examples from parallel classes");
- SortedSet<String> classes = new TreeSet<String>();
- // superClasses.add(concept.replace("\"", ""));
- // logger.debug("before"+superClasses);
- // superClasses = dbpediaGetSuperClasses( superClasses, 4);
- // logger.debug("getting negExamples from "+superClasses.size()+"
- // superclasses");
-
- for (String instance : positiveSet) {
- classes.addAll(sparqltasks.getClassesForInstance(instance, resultLimit));
- }
- logger.debug("getting negExamples from " + classes.size() + " parallel classes");
- for (String oneClass : classes) {
- logger.debug(oneClass);
- // rsc = new
- // JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
- this.fromParallelClasses.addAll(sparqltasks.retrieveInstancesForConcept("\"" + oneClass
- + "\"", resultLimit));
-
- }
-
- this.fromParallelClasses.removeAll(this.fullPositiveSet);
- logger.debug("|-neg Example size from parallelclass: " + fromParallelClasses.size());
-
- }
-
- public void makeNegativeExamplesFromSuperClasses(String concept, int resultLimit) {
-
- concept = concept.replaceAll("\"", "");
- // superClasses.add(concept.replace("\"", ""));
- // logger.debug("before"+superClasses);
- SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, 4);
- logger.debug("making neg Examples from " + superClasses.size() + " superclasses");
-
- for (String oneSuperClass : superClasses) {
- logger.debug(oneSuperClass);
- this.fromSuperclasses.addAll(sparqltasks.retrieveInstancesForConcept("\""
- + oneSuperClass + "\"", resultLimit));
-
- }
- this.fromSuperclasses.removeAll(this.fullPositiveSet);
- logger.debug("|-neg Example from superclass: " + fromSuperclasses.size());
- }
-
- @SuppressWarnings("unused")
- private void makeNegativeExamplesFromDomain(String role, int resultLimit){
- logger.debug("making Negative Examples from Domain of : "+role);
- this.fromDomain.addAll(sparqltasks.getDomain(role, resultLimit));
- this.fromDomain.removeAll(this.fullPositiveSet);
- logger.debug("|-neg Example size from Domain: "+this.fromDomain.size());
- }
-
- @SuppressWarnings("unused")
- private void makeNegativeExamplesFromRange(String role, int resultLimit){
- logger.debug("making Negative Examples from Range of : "+role);
- this.fromRange.addAll(sparqltasks.getRange(role, resultLimit));
- this.fromRange.removeAll(this.fullPositiveSet);
- logger.debug("|-neg Example size from Range: "+this.fromRange.size());
- }
-
-
-}
Added: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -0,0 +1,153 @@
+package org.dllearner.utilities.examples;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.SPARQLTasks;
+import org.dllearner.utilities.datastructures.SetManipulation;
+
+public class AutomaticNegativeExampleFinderSPARQL {
+
+ // CHECK
+ private static Logger logger = Logger.getLogger(ComponentManager.class);
+
+ private SPARQLTasks sparqltasks;
+
+ private SortedSet<String> fullPositiveSet;
+
+ private SortedSet<String> fromRelated = new TreeSet<String>();
+ private SortedSet<String> fromSuperclasses = new TreeSet<String>();;
+ private SortedSet<String> fromParallelClasses = new TreeSet<String>();;
+ private SortedSet<String> fromDomain = new TreeSet<String>();;
+ private SortedSet<String> fromRange = new TreeSet<String>();;
+
+ static int poslimit = 10;
+ static int neglimit = 20;
+
+ // CHECK separate posexamples and fullposset
+ public AutomaticNegativeExampleFinderSPARQL(
+ SortedSet<String> fullPositiveSet,
+ SPARQLTasks st) {
+ super();
+ this.fullPositiveSet = fullPositiveSet;
+ this.sparqltasks = st;
+
+ }
+
+
+
+ public SortedSet<String> getNegativeExamples(int neglimit ) {
+
+ SortedSet<String> negatives = new TreeSet<String>();
+ negatives.addAll(fromParallelClasses);
+ negatives.addAll(fromRelated);
+ negatives.addAll(fromSuperclasses);
+ logger.debug("neg Example size before shrinking: " + negatives.size());
+ negatives = SetManipulation.fuzzyShrink(negatives,neglimit);
+ logger.debug("neg Example size after shrinking: " + negatives.size());
+ return negatives;
+ }
+
+ // CHECK namespace
+ public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances,
+ String namespace) {
+ logger.debug("making examples from related instances");
+ for (String oneInstance : instances) {
+ makeNegativeExamplesFromRelatedInstances(oneInstance, namespace);
+ }
+ logger.debug("|-negExample size from related: " + fromRelated.size());
+ }
+
+ private void makeNegativeExamplesFromRelatedInstances(String oneInstance, String objectnamespace) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String SPARQLquery = "SELECT * WHERE { \n" + "<" + oneInstance + "> " + "?p ?object. \n"
+ + "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}";
+
+ this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "object"));
+ this.fromRelated.removeAll(this.fullPositiveSet);
+
+ }
+
+ // QUALITY: keep a while may still be needed
+ /*public void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String SPARQLquery = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n" + "}";
+
+ this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "o"));
+
+ }*/
+
+ public void makeNegativeExamplesFromParallelClasses(SortedSet<String> positiveSet, int resultLimit){
+ makeNegativeExamplesFromClassesOfInstances(positiveSet, resultLimit);
+ }
+
+ public void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
+ int resultLimit) {
+ logger.debug("making neg Examples from parallel classes");
+ SortedSet<String> classes = new TreeSet<String>();
+ // superClasses.add(concept.replace("\"", ""));
+ // logger.debug("before"+superClasses);
+ // superClasses = dbpediaGetSuperClasses( superClasses, 4);
+ // logger.debug("getting negExamples from "+superClasses.size()+"
+ // superclasses");
+
+ for (String instance : positiveSet) {
+ classes.addAll(sparqltasks.getClassesForInstance(instance, resultLimit));
+ }
+ logger.debug("getting negExamples from " + classes.size() + " parallel classes");
+ for (String oneClass : classes) {
+ logger.debug(oneClass);
+ // rsc = new
+ // JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
+ this.fromParallelClasses.addAll(sparqltasks.retrieveInstancesForConcept("\"" + oneClass
+ + "\"", resultLimit));
+
+ }
+
+ this.fromParallelClasses.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example size from parallelclass: " + fromParallelClasses.size());
+
+ }
+
+ public void makeNegativeExamplesFromSuperClasses(String concept, int resultLimit) {
+
+ concept = concept.replaceAll("\"", "");
+ // superClasses.add(concept.replace("\"", ""));
+ // logger.debug("before"+superClasses);
+ SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, 4);
+ logger.debug("making neg Examples from " + superClasses.size() + " superclasses");
+
+ for (String oneSuperClass : superClasses) {
+ logger.debug(oneSuperClass);
+ this.fromSuperclasses.addAll(sparqltasks.retrieveInstancesForConcept("\""
+ + oneSuperClass + "\"", resultLimit));
+
+ }
+ this.fromSuperclasses.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example from superclass: " + fromSuperclasses.size());
+ }
+
+ @SuppressWarnings("unused")
+ private void makeNegativeExamplesFromDomain(String role, int resultLimit){
+ logger.debug("making Negative Examples from Domain of : "+role);
+ this.fromDomain.addAll(sparqltasks.getDomain(role, resultLimit));
+ this.fromDomain.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example size from Domain: "+this.fromDomain.size());
+ }
+
+ @SuppressWarnings("unused")
+ private void makeNegativeExamplesFromRange(String role, int resultLimit){
+ logger.debug("making Negative Examples from Range of : "+role);
+ this.fromRange.addAll(sparqltasks.getRange(role, resultLimit));
+ this.fromRange.removeAll(this.fullPositiveSet);
+ logger.debug("|-neg Example size from Range: "+this.fromRange.size());
+ }
+
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-26 10:37:56 UTC (rev 927)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -5,6 +5,7 @@
import org.apache.log4j.Logger;
import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.SPARQLTasks;
public class AutomaticPositiveExampleFinderSPARQL {
Deleted: trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-26 10:37:56 UTC (rev 927)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java 2008-05-26 12:02:10 UTC (rev 928)
@@ -1,277 +0,0 @@
-package org.dllearner.utilities.examples;
-
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-
-public class SPARQLTasks {
-
- //CHECK
- @SuppressWarnings("unused")
- private static Logger logger = Logger
- .getLogger(SPARQLTasks.class);
- private Cache c;
- private SparqlEndpoint se;
-
- public SPARQLTasks(Cache c, SparqlEndpoint se) {
- super();
- this.c = c;
- this.se = se;
- }
-
- public SPARQLTasks( SparqlEndpoint se) {
- super();
- this.c = null;
- this.se = se;
- }
-
-
-
-
- /**
- * QUALITY: doesn't seem optimal, check!
- * get all superclasses up to a certain depth
- * 1 means direct superclasses
- * depth
- * @param superClasses
- * @param depth
- * @return
- */
- public SortedSet<String> getSuperClasses(String oneClass, int depth) {
- SortedSet<String> superClasses = new TreeSet<String>();
- superClasses.add(oneClass);
- SortedSet<String> ret = new TreeSet<String>();
- SortedSet<String> tmpset = new TreeSet<String>();
- //ret.addAll(superClasses);
- //logger.debug(superClasses);
-
-
- String SPARQLquery = "";
- for (; depth != 0 ; depth--) {
- for (String oneSuperClass : superClasses) {
-
- //tmp = oneSuperClass.replace("\"", "");
- SPARQLquery = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
- + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
- + "}";
-
- tmpset.addAll(queryAsSet(SPARQLquery, "superclass"));
-
- }
- ret.addAll(tmpset);
- //logger.debug(ret);
- superClasses.clear();
- superClasses.addAll(tmpset);
- tmpset.clear();
- }
- //logger.debug(concept);
- //logger.debug(query);
- return ret;
- }
-
-
-
-
- /**
- * QUALITY: buggy because role doesn't work sometimes
- * get subject with fixed role and object
- * @param role
- * @param object
- * @param resultLimit
- * @return
- */
- public SortedSet<String> retrieveDISTINCTSubjectsForRoleAndObject(String role, String object,int resultLimit) {
- String SPARQLquery =
- "SELECT DISTINCT * WHERE { \n " +
- "?subject " +
- "<"+role+"> " +
- "<" + object + "> \n" +
- "} "+limit(resultLimit);
-
- return queryAsSet(SPARQLquery, "subject");
- }
-
- public SortedSet<String> retrieveObjectsForSubjectAndRole(String subject, String role, int resultLimit) {
- String SPARQLquery =
- "SELECT DISTINCT * WHERE { \n " +
- "<" +subject+ "> "+
- "<"+role+"> " +
- " ?object \n" +
- "} LIMIT "+resultLimit;
-
- return queryAsSet(SPARQLquery, "object");
- }
-
- /**
- * all instances for a SKOS concept
- * @param SKOSconcept
- * @param resultLimit
- * @return
- */
- public SortedSet<String> retrieveInstancesForSKOSConcept(String SKOSconcept,int resultLimit) {
- return queryPatternAsSet("?subject", "?predicate", "<"+SKOSconcept+">", "subject", resultLimit);
- //return retrieveDISTINCTSubjectsForRoleAndObject("http://www.w3.org/2004/02/skos/core#subject",
- }
-
-
-
- /**
- * get all instances for a concept
- * @param conceptKBSyntax
- * @param sparqlResultLimit
- * @return
- */
- public SortedSet<String> retrieveInstancesForConcept (String conceptKBSyntax,int sparqlResultLimit) {
-
- String SPARQLquery = "";
- try{
- SPARQLquery = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(conceptKBSyntax,sparqlResultLimit);
- }catch (Exception e) {e.printStackTrace();}
- return queryAsSet(SPARQLquery, "subject");
- }
-
-
-
-
- /**
- * get all direct Classes of an instance
- * @param instance
- * @param resultLimit
- * @return
- */
- public SortedSet<String> getClassesForInstance(String instance, int resultLimit) {
-
- String SPARQLquery = "SELECT ?subject WHERE { \n " +
- "<" + instance + ">"+
- " a " +
- "?subject " +
- "\n" +
- "} "+limit(resultLimit);
-
- return queryAsSet(SPARQLquery, "subject");
- }
-
-
-
- public SortedSet<String> getDomain(String role,int resultLimit){
-
- String SPARQLquery = "" +
- "SELECT DISTINCT ?domain " +
- "WHERE { \n" +
- "?domain <" + role + "> " + " ?o. \n" +
- "?domain a []\n." +
- "FILTER (!isLiteral(?domain))." +
- "}\n" + limit(resultLimit);
-
- return queryAsSet(SPARQLquery, "domain");
-
-
- }
-
-
- public SortedSet<String> getRange(String role,int resultLimit){
-
- String SPARQLquery = "" +
- "SELECT DISTINCT ?range " +
- "WHERE { \n" +
- "?s <" + role + "> " + " ?range. \n" +
- "?range a [].\n" +
- "FILTER (!isLiteral(?range))." +
- "}\n" + limit(resultLimit);
-
- return queryAsSet(SPARQLquery, "range");
-
- }
-
-
-
- /**
- * query a pattern with a standard SPARQL query
- * usage (?subject, ?predicate, <http:something> , subject )
- * @param subject
- * @param predicate
- * @param object
- * @param var
- * @return
- */
- public SortedSet<String> queryPatternAsSet(String subject, String predicate, String object, String var, int resultLimit){
- String SPARQLquery = "SELECT ?subject WHERE { \n " +
- " " + subject +
- " " + predicate +
- " " + object +
- " \n" +
- "} "+limit(resultLimit);
- return queryAsSet( SPARQLquery, var);
- }
-
-
- /**
- * little higher level, executes query ,returns all resources for a variable
- * @param SPARQLquery
- * @param var
- * @return
- */
- public SortedSet<String> queryAsSet(String SPARQLquery, String var){
- ResultSet rs = null;
- try {
- String JSON = query(SPARQLquery);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
- return getStringListForVariable(rs,var);
- }
-
-
- /**
- * lowlevel, executes query returns JSON
- * @param SPARQLquery
- * @return
- */
- public String query(String SPARQLquery){
- if(c==null){
- SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
- sq.extraDebugInfo+=se.getURL();
- sq.send();
- String JSON = sq.getResult();
- return JSON;
- }else{
- return c.executeSparqlQuery(new SparqlQuery(SPARQLquery,se));
- }
-
- }
-
- private String limit(int resultLimit){
- if(resultLimit>0)return " LIMIT "+resultLimit;
- return "";
- }
-
-
- public static SortedSet<String> getStringListForVariable(ResultSet rs, String var){
- SortedSet<String> result = new TreeSet<String>();
-
- //String s=ResultSetFormatter.asXMLString(this.rs);
- @SuppressWarnings("unchecked")
- List<ResultBinding> l = ResultSetFormatter.toList(rs);
-
- for (ResultBinding resultBinding : l) {
- result.add(resultBinding.get(var).toString());
- }
-
- return result;
-
- }
-
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-05-26 14:48:07
|
Revision: 929
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=929&view=rev
Author: kurzum
Date: 2008-05-26 07:48:00 -0700 (Mon, 26 May 2008)
Log Message:
-----------
intermediate
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/scripts/ResultCompare.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -1,5 +1,6 @@
package org.dllearner.kb.sparql;
+import java.util.LinkedList;
import java.util.List;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -12,10 +13,10 @@
public class SPARQLTasks {
- //CHECK
- @SuppressWarnings("unused")
+ //@SuppressWarnings("unused")
+ //LOGGER: SPARQLTasks
private static Logger logger = Logger
- .getLogger(SPARQLTasks.class);
+ .getLogger(SPARQLTasks.class);
private Cache c;
private SparqlEndpoint se;
@@ -76,9 +77,95 @@
}
-
+ /**
+ * gets a SortedSet of all subclasses QUALITY: maybe it is better to have a
+ * parameter int depth, to choose a depth of subclass interference
+ *
+ * @see conceptRewrite(String descriptionKBSyntax, SparqlEndpoint se, Cache
+ * c, boolean simple )
+ * @param description
+ * @param se
+ * @param c
+ * @param simple
+ * @return
+ */
+ public SortedSet<String> getSubClasses(String description, boolean simple) {
+ // ResultSet rs = null;
+ // System.out.println(description);
+ SortedSet<String> alreadyQueried = new TreeSet<String>();
+ try {
+
+ // initialisation get direct Subclasses
+ LinkedList<String> remainingClasses = new LinkedList<String>();
+
+ // collect remaining classes
+ remainingClasses.addAll(getDirectSubClasses(description.replaceAll("\"", "")));
+
+ // remainingClasses.addAll(alreadyQueried);
+
+ // alreadyQueried = new TreeSet<String>();
+ alreadyQueried.add(description.replaceAll("\"", ""));
+
+ if (simple) {
+ alreadyQueried.addAll(remainingClasses);
+ return alreadyQueried;
+ } else {
+
+ logger.warn("Retrieval auf all subclasses via SPARQL is cost intensive and might take a while");
+ while (remainingClasses.size() != 0) {
+ SortedSet<String> tmpSet = new TreeSet<String>();
+ String tmp = remainingClasses.removeFirst();
+ alreadyQueried.add(tmp);
+
+ tmpSet = getDirectSubClasses(tmp);
+ for (String string : tmpSet) {
+ if (!(alreadyQueried.contains(string))) {
+ remainingClasses.add(string);
+ }// if
+ }// for
+ }// while
+ }// else
+
+ } catch (Exception e) {
+
+ }
+
+ return alreadyQueried;
+ }
+
/**
+ * QUALITY: workaround for a sparql glitch {?a owl:subclassOf ?b} returns an
+ * empty set on some entpoints. returns all direct subclasses of String
+ * concept
+ *
+ * @param concept
+ * @return SortedSet of direct subclasses as String
+ */
+ private SortedSet<String> getDirectSubClasses(String concept) {
+ String SPARQLquery = "SELECT * \n";
+ SPARQLquery += "WHERE {\n";
+ SPARQLquery += " ?subject ?predicate <" + concept + "> \n";
+ SPARQLquery += "}\n";
+
+ ResultSet rs = queryAsResultSet(SPARQLquery);
+
+ SortedSet<String> subClasses = new TreeSet<String>();
+ @SuppressWarnings("unchecked")
+ List<ResultBinding> l = ResultSetFormatter.toList(rs);
+ String p = "", s = "";
+ for (ResultBinding resultBinding : l) {
+
+ s = ((resultBinding.get("subject").toString()));
+ p = ((resultBinding.get("predicate").toString()));
+ if (p.equalsIgnoreCase("http://www.w3.org/2000/01/rdf-schema#subClassOf")) {
+ subClasses.add(s);
+ }
+ }
+ return subClasses;
+ }
+
+ /**
* QUALITY: buggy because role doesn't work sometimes
* get subject with fixed role and object
* @param role
@@ -137,9 +224,26 @@
return queryAsSet(SPARQLquery, "subject");
}
+ /**
+ * get all instances for a concept including RDFS Reasoning
+ * @param conceptKBSyntax
+ * @param sparqlResultLimit
+ * @return
+ */
+ public SortedSet<String> retrieveInstancesForConceptIncludingSubclasses (String conceptKBSyntax,int sparqlResultLimit) {
+
+ String SPARQLquery = "";
+ try{
+ SPARQLquery = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQueryIncludingSubclasses(conceptKBSyntax,sparqlResultLimit,this,true);
+ }catch (Exception e) {e.printStackTrace();}
+ return queryAsSet(SPARQLquery, "subject");
+ }
+
+
/**
* get all direct Classes of an instance
* @param instance
@@ -232,8 +336,18 @@
/**
- * lowlevel, executes query returns JSON
+ * low level, executes query returns ResultSet
* @param SPARQLquery
+ * @return jena ResultSet
+ */
+ public ResultSet queryAsResultSet(String SPARQLquery){
+ return SparqlQuery.JSONtoResultSet(query(SPARQLquery));
+
+ }
+
+ /**
+ * low level, executes query returns JSON
+ * @param SPARQLquery
* @return
*/
public String query(String SPARQLquery){
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -1,7 +1,25 @@
+/**
+ * Copyright (C) 2007, Sebastian Hellmann
+ *
+ * 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.kb.sparql;
import java.util.LinkedList;
-import java.util.List;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -10,14 +28,17 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Union;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-//COMMENT: header
+/**
+ * @author Sebastian Hellmann
+ * Enables RDFS reasoning for the DL2SPARQL class
+ * by concept rewriting
+ * //QUALITY use SPARQLtasks
+ */
public class SparqlQueryDescriptionConvertRDFS {
- static Logger logger = Logger.getLogger(SparqlQueryDescriptionConvertRDFS.class);
+ //LOGGER: SparqlQueryDescriptionConvertVisitor
+ static Logger logger = Logger.getLogger(SparqlQueryDescriptionConvertVisitor.class);
/**
*
@@ -35,7 +56,7 @@
* RECOMMENDED for large hierarchies)
* @return the altered String
*/
- public static String conceptRewrite(String descriptionKBSyntax, SparqlEndpoint se, Cache c,
+ public static String conceptRewrite(String descriptionKBSyntax, SPARQLTasks st,
boolean simple) {
String quote = "\"";
String returnValue = "";
@@ -58,7 +79,7 @@
// System.out.println(currentconcept);
// subclasses are retrieved
- subclasses = getSubClasses(currentconcept, se, c, simple);
+ subclasses = st.getSubClasses(currentconcept, simple);
// if only one then keep
if (subclasses.size() == 1)
@@ -80,100 +101,6 @@
return returnValue;
}
- /**
- * gets a SortedSet of all subclasses QUALITY: maybe it is better to have a
- * parameter int depth, to choose a depth of subclass interference
- *
- * @see conceptRewrite(String descriptionKBSyntax, SparqlEndpoint se, Cache
- * c, boolean simple )
- * @param description
- * @param se
- * @param c
- * @param simple
- * @return
- */
- private static SortedSet<String> getSubClasses(String description, SparqlEndpoint se, Cache c,
- boolean simple) {
+
- // ResultSet rs = null;
- // System.out.println(description);
- SortedSet<String> alreadyQueried = new TreeSet<String>();
- try {
-
- // initialisation get direct Subclasses
- LinkedList<String> remainingClasses = new LinkedList<String>();
-
- // collect remaining classes
- remainingClasses.addAll(getDirectSubClasses(description.replaceAll("\"", ""), se, c));
-
- // remainingClasses.addAll(alreadyQueried);
-
- // alreadyQueried = new TreeSet<String>();
- alreadyQueried.add(description.replaceAll("\"", ""));
-
- if (simple) {
- alreadyQueried.addAll(remainingClasses);
- return alreadyQueried;
- } else {
-
- logger
- .warn("Retrieval auf all subclasses via SPARQL is cost intensive and might take a while");
- while (remainingClasses.size() != 0) {
- SortedSet<String> tmpSet = new TreeSet<String>();
- String tmp = remainingClasses.removeFirst();
- alreadyQueried.add(tmp);
-
- tmpSet = getDirectSubClasses(tmp, se, c);
- for (String string : tmpSet) {
- if (!(alreadyQueried.contains(string))) {
- remainingClasses.add(string);
- }// if
- }// for
- }// while
- }// else
-
- } catch (Exception e) {
-
- }
-
- return alreadyQueried;
- }
-
- /**
- * QUALITY: workaround for a sparql glitch {?a owl:subclassOf ?b} returns an
- * empty set on some entpoints. returns all direct subclasses of String
- * concept
- *
- * @param concept
- * @return SortedSet of direct subclasses as String
- */
- private static SortedSet<String> getDirectSubClasses(String concept, SparqlEndpoint se, Cache c) {
- String query = "SELECT * \n";
- query += "WHERE {\n";
- query += " ?subject ?predicate <" + concept + "> \n";
- query += "}\n";
-
- ResultSet rs = null;
- if (c == null) {
- rs = new SparqlQuery(query, se).send();
- } else {
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- rs = SparqlQuery.JSONtoResultSet(JSON);
- }
-
- SortedSet<String> subClasses = new TreeSet<String>();
- @SuppressWarnings("unchecked")
- List<ResultBinding> l = ResultSetFormatter.toList(rs);
- String p = "", s = "";
- for (ResultBinding resultBinding : l) {
-
- s = ((resultBinding.get("subject").toString()));
- p = ((resultBinding.get("predicate").toString()));
- if (p.equalsIgnoreCase("http://www.w3.org/2000/01/rdf-schema#subClassOf")) {
- subClasses.add(s);
- }
- }
- return subClasses;
- }
-
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -70,14 +70,13 @@
return getSparqlQuery(defaultLimit);
}*/
- private String getSparqlQuery(int limit)
+ private String getSparqlQuery(int resultLimit)
{ // for old function see below
// it was using the object attribute in a strange way
// QUALITY: what if this function is called several times?? should be private maybe?
String tmpQuery=
"SELECT ?subject \nWHERE {"+query+
- " }\n ";
- if(limit>0) tmpQuery+="LIMIT "+limit;
+ " }\n "+ limit(resultLimit);
query = tmpQuery;
return query;
@@ -112,11 +111,11 @@
return getSparqlQuery(description, defaultLimit);
}
- public static String getSparqlQuery(Description description, int limit)
+ public static String getSparqlQuery(Description description, int resultLimit)
{
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
description.accept(visitor);
- String ret = visitor.getSparqlQuery(limit);
+ String ret = visitor.getSparqlQuery(resultLimit);
//HACK see replace might be a good solution, needs testing
while (ret.contains("..")) {
ret = ret.replace("..", ".");
@@ -142,11 +141,11 @@
* @return
* @throws ParseException
*/
- public static String getSparqlQueryIncludingSubclasses(String descriptionKBSyntax, int limit, SparqlEndpoint se,Cache c, boolean simple) throws ParseException
+ public static String getSparqlQueryIncludingSubclasses(String descriptionKBSyntax, int resultLimit, SPARQLTasks st, boolean simple) throws ParseException
{
- String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(descriptionKBSyntax, se, c, simple);
+ String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(descriptionKBSyntax, st, simple);
- return getSparqlQuery(rewritten, limit);
+ return getSparqlQuery(rewritten, resultLimit);
}
@@ -341,6 +340,10 @@
logger.trace("DatatypeSomeRestriction");
}
+ private String limit(int resultLimit){
+ if(resultLimit>0)return " LIMIT "+resultLimit;
+ return "";
+ }
}
Deleted: trunk/src/dl-learner/org/dllearner/scripts/ResultCompare.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/ResultCompare.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/scripts/ResultCompare.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -1,83 +0,0 @@
-package org.dllearner.scripts;
-
-import java.util.SortedSet;
-
-public class ResultCompare implements Comparable<ResultCompare> {
- String concept;
- SortedSet<String> instances;
- double accuracy;
- double accuracy2;
- int nrOfInstances;
- SortedSet<String> coveredInRest;
- SortedSet<String> possibleNewCandidates;
- SortedSet<String> notCoveredInTotal;
-
-
- public ResultCompare(String concept, SortedSet<String> instances, double accuracy,
- double accuracy2, int nrOfInstances, SortedSet<String> coveredInRest,
- SortedSet<String> possibleNewCandidates, SortedSet<String> notCoveredInTotal) {
- super();
- this.concept = concept;
- this.instances = instances;
- this.accuracy = accuracy;
- this.accuracy2 = accuracy2;
- this.nrOfInstances = nrOfInstances;
- this.coveredInRest = coveredInRest;
- this.possibleNewCandidates = possibleNewCandidates;
- this.notCoveredInTotal = notCoveredInTotal;
- }
-
-
-
-
- public int compareTo(ResultCompare in) {
- ResultCompare obj = in;
- if(obj.accuracy > this.accuracy) return 1;
- else if(obj.accuracy == this.accuracy){
-
- if(obj.nrOfInstances<this.nrOfInstances)return 1;
- else if(obj.nrOfInstances>this.nrOfInstances)return -1;
- else return 1;
- //if(obj.nrOfInstances==this.nrOfInstances)return 0;
- }
- else {//if(obj.accuracy < this.accuracy){
- return -1;
- }
-
- }
-
-
-
-
- public String toStringFull(){
- String ret="";
- ret+="concept\t"+concept+"\n";
- ret+="instances\t"+instances+"\n";
- ret+="accuracy\t"+accuracy+"\n";
- ret+="nrOfInstances\t"+nrOfInstances+"\n";
- ret+="accuracy2\t"+accuracy2+"\n";
- ret+="coveredInRest("+coveredInRest.size()+")\t"+coveredInRest+"\n";
- ret+="possibleNewCandidates("+possibleNewCandidates.size()+")\t"+possibleNewCandidates+"\n";
- ret+="notCoveredInTotal("+notCoveredInTotal.size()+")\t"+notCoveredInTotal+"\n";
-
- return ret;
-
- }
-
- @Override
- public String toString(){
- String ret="";
- ret+="concept\t"+concept+"\n";
- //ret+="instances\t"+instances+"\n";
- ret+="accuracy\t"+accuracy+"\n";
- ret+="nrOfInstances\t"+nrOfInstances+"\n";
- ret+="accuracy2\t"+accuracy2+"\n";
- //ret+="coveredInRest("+coveredInRest.size()+")\t"+coveredInRest+"\n";
- //ret+="possibleNewCandidates("+possibleNewCandidates.size()+")\t"+possibleNewCandidates+"\n";
- //ret+="notCoveredInTotal("+notCoveredInTotal.size()+")\t"+notCoveredInTotal+"\n";
-
- return ret;
-
- }
-
-}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -47,19 +47,14 @@
static int maxExecutionTimeInSeconds = 30;
static int guaranteeXgoodDescriptions = 40;
- //static int limit=200;
-
-
-
-
//examples
static int sparqlResultSize=2000;
static double percentOfSKOSSet=0.2;
static double negfactor=1.0;
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> fullPositiveSet = new TreeSet<String>();
- SortedSet<String> fullminusposRest = new TreeSet<String>();
+ SortedSet<String> fullPosSetWithoutPosExamples = new TreeSet<String>();
SortedSet<String> negExamples = new TreeSet<String>();
@@ -78,13 +73,14 @@
if(local){
url = "http://139.18.2.37:8890/sparql";
- //RBC
sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointLOCALDBpedia());
}else{
url = "http://dbpedia.openlinksw.com:8890/sparql";
sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointDBpedia());
}
+ System.out.println(sparqlTasks.getDomain("http://dbpedia.org/property/predecessor", 1000));
+
String prim="http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom";
String award=("http://dbpedia.org/resource/Category:Best_Actor_Academy_Award_winners");
@@ -92,164 +88,93 @@
SKOS7030 s= new SKOS7030();
s.makeExamples(prim, percentOfSKOSSet, negfactor, sparqlResultSize);
- //QUALITY s.posExamples
- List<Description> conceptresults = s.learn(s.posExamples, s.negExamples);
+
+ List<Description> conceptresults = s.learn();
logger.debug("found nr of concepts: "+conceptresults.size());
+ System.out.println(conceptresults);
- for (Description oneConcept : conceptresults) {
+ int x=0;
+
+ SortedSet<ResultMostCoveredInRest> res = new TreeSet<ResultMostCoveredInRest>();
+ for (Description concept : conceptresults) {
+ if(x++==100)break;
+ res.add(s.evaluate(concept, 1000));
- //s.evaluate(oneConcept, 1000);
+ }
+
+ x=0;
+ for (ResultMostCoveredInRest resultMostCoveredInRest : res) {
+ if(x++==10)break;
+ System.out.println(resultMostCoveredInRest.concept);
+ System.out.println(resultMostCoveredInRest.accuracy);
+ System.out.println(resultMostCoveredInRest.retrievedInstancesSize);
+
}
+ s.print(res.first().concept, 1000);
System.out.println("Finished");
JamonMonitorLogger.printAllSortedByLabel();
}
- void evaluate(Description oneConcept, int sparqlResultLimit){
- logger.debug("oneconcept: "+oneConcept);
- SortedSet<String> instances = sparqlTasks.retrieveInstancesForConcept(oneConcept.toKBSyntaxString(), sparqlResultLimit);
+ void print(Description concept, int sparqlResultLimit){
+ logger.debug("evaluating concept: "+concept);
+// SortedSet<String> instances = sparqlTasks.retrieveInstancesForConcept(oneConcept.toKBSyntaxString(), sparqlResultLimit);
+ SortedSet<String> instances =
+ sparqlTasks.retrieveInstancesForConceptIncludingSubclasses(
+ concept.toKBSyntaxString(),sparqlResultLimit);
- System.out.println(fullminusposRest.size());
- System.out.println(instances.size());
-
- SortedSet<String> coveredInRest = new TreeSet<String>(fullminusposRest);
+ SortedSet<String> coveredInRest = new TreeSet<String>(fullPosSetWithoutPosExamples);
coveredInRest.retainAll(instances);
+
- System.out.println(fullminusposRest.size());
- System.out.println(instances.size());
- System.out.println(coveredInRest.size());
+ SortedSet<String> coveredTotal = new TreeSet<String>(fullPositiveSet);
+ coveredTotal.retainAll(instances);
+ SortedSet<String> notCoveredInRest = new TreeSet<String>(fullPosSetWithoutPosExamples);
+ notCoveredInRest.retainAll(coveredInRest);
+ System.out.println(notCoveredInRest);
- //SortedSet<String> possibleNewCandidates = new TreeSet<String>();
- //SortedSet<String> notCoveredInTotal = new TreeSet<String>();
+ SortedSet<String> notCoveredTotal = new TreeSet<String>(fullPositiveSet);
+ notCoveredTotal.retainAll(coveredTotal);
+ System.out.println(notCoveredTotal);
-
}
-
- static void DBpediaSKOS(String SKOSConcept){
+ ResultMostCoveredInRest evaluate(Description concept, int sparqlResultLimit){
+ logger.debug("evaluating concept: "+concept);
+// SortedSet<String> instances = sparqlTasks.retrieveInstancesForConcept(oneConcept.toKBSyntaxString(), sparqlResultLimit);
+ SortedSet<String> instances =
+ sparqlTasks.retrieveInstancesForConceptIncludingSubclasses(
+ concept.toKBSyntaxString(),sparqlResultLimit);
+ SortedSet<String> coveredInRest = new TreeSet<String>(fullPosSetWithoutPosExamples);
+ coveredInRest.retainAll(instances);
- //concepts.add("http://dbpedia.org/resource/Category:Grammy_Award_winners");
- //concepts.add("EXISTS \"http://dbpedia.org/property/grammyawards\".TOP");
+ SortedSet<String> coveredTotal = new TreeSet<String>(fullPositiveSet);
+ coveredTotal.retainAll(instances);
+ SortedSet<String> notCoveredInRest = new TreeSet<String>(fullPosSetWithoutPosExamples);
+ notCoveredInRest.retainAll(coveredInRest);
- //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
- //HashMap<String, String> result2 = new HashMap<String, String>();
- //System.out.println(concepts.first());
- //logger.setLevel(Level.TRACE);
+ SortedSet<String> notCoveredTotal = new TreeSet<String>(fullPositiveSet);
+ notCoveredTotal.retainAll(coveredTotal);
+ double acc = (double) (coveredInRest.size() / fullPosSetWithoutPosExamples.size());
+ System.out.println("Accuracy: "+acc);
+ return new ResultMostCoveredInRest(concept,acc,instances.size());
-
-
-// LearnSparql ls = new LearnSparql();
-//
-// //igno.add(oneConcept.replaceAll("\"", ""));
-//
-// List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
-//
-// System.out.println("concepts"+conceptresults);
-// //System.exit(0);
-//
-// SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
-// for (Description oneConcept : conceptresults) {
-// try{
-//
-//
-// int i=0;
-// int a=0;
-// for (String oneinst : instances) {
-// boolean inRest=false;
-// boolean inTotal=false;
-// for (String onerest : rest) {
-// if(onerest.equalsIgnoreCase(oneinst))
-// { i++; inRest=true; break;}
-//
-// }
-// if (inRest){coveredInRest.add(oneinst);};
-//
-// for (String onetotal : totalSKOSset) {
-// if(onetotal.equalsIgnoreCase(oneinst))
-// { a++; inTotal=true; break;}
-// }
-// if(!inRest && !inTotal){
-// possibleNewCandidates.add(oneinst);
-// }
-// }
-//
-// for (String onetotal : totalSKOSset) {
-// boolean mm=false;
-// for (String oneinst : instances) {
-// if(onetotal.equalsIgnoreCase(oneinst)){
-// mm=true;break;
-// }
-//
-// }
-// if(!mm)notCoveredInTotal.add(onetotal);
-//
-// }
-//
-//
-//
-// double accuracy= (double)i/rest.size();
-// double accuracy2= (double)a/totalSKOSset.size();
-//
-// logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
-// coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
-//
-// //if(instances.size()>=0)System.out.println("size of instances "+instances.size());
-// //if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
-// }catch (Exception e) {e.printStackTrace();}
-// }
-
-// System.out.println(res.last());
-// res.remove(res.last());
-// System.out.println(res.last());
-// res.remove(res.last());
-// System.out.println(res.last());
-// res.remove(res.last());
-//
-
- //double percent=0.80*(double)res.size();;
-// double acc=res.first().accuracy;
-// logger.debug(res.first().toStringFull());
-// res.remove(res.first());
-// logger.debug(res.first().toStringFull());
-// res.remove(res.first());
-// int i=0;
-// while (res.size()>0){
-// logger.debug(res.first());
-// res.remove(res.first());
-// //if(res.size()<=percent)break;
-// if(i>50)break;
-// i++;
-//
-// }
-//
-// return 0.0;
-
-
- //System.out.println("AAAAAAAA");
- //System.exit(0);
- //"relearned concept: ";
- //cf.writeSPARQL(confname, posExamples, negExamples, url, new TreeSet<String>(),standardSettings,algorithm);
- //
-
- //Statistics.print();
+
}
-
-
-
public static void initLogger() {
SimpleLayout layout = new SimpleLayout();
@@ -302,7 +227,7 @@
AutomaticNegativeExampleFinderSPARQL aneg = new AutomaticNegativeExampleFinderSPARQL(fullPositiveSet,sparqlTasks);
aneg.makeNegativeExamplesFromParallelClasses(posExamples, sparqlResultSize);
- SortedSet<String> negativeSet = aneg.getNegativeExamples(neglimit);
+ this.negExamples = aneg.getNegativeExamples(neglimit);
logger.debug("POSITIVE EXAMPLES");
for (String pos : posExamples) {
@@ -310,27 +235,35 @@
}
logger.debug("NEGATIVE EXAMPLES");
- for (String negs : negativeSet) {
+ for (String negs : this.negExamples) {
logger.debug("-"+negs);
}
- fullminusposRest = fullPositiveSet;
- fullminusposRest.removeAll(posExamples);
+ fullPosSetWithoutPosExamples = fullPositiveSet;
+ fullPosSetWithoutPosExamples.removeAll(posExamples);
logger.debug(fullPositiveSet);
- logger.debug(fullminusposRest);
+ logger.debug(fullPosSetWithoutPosExamples);
}
- public List<Description> learn(SortedSet<String> posExamples, SortedSet<String> negExamples){
+ public List<Description> learn(){
SortedSet<String> instances = new TreeSet<String>();
- instances.addAll(posExamples);
- instances.addAll(negExamples);
+ instances.addAll(this.posExamples);
+ instances.addAll(this.negExamples);
+ logger.info("Start Learning with");
+ logger.info("positive examples: \t"+posExamples.size());
+ logger.info("negative examples: \t"+negExamples.size());
+ logger.info("instances \t"+instances.size());
+
+
+
+
ComponentManager cm = ComponentManager.getInstance();
LearningAlgorithm la = null;
@@ -344,8 +277,8 @@
rs = new ReasoningService(r);
//System.out.println("satisfy: "+rs.isSatisfiable());
lp = new PosNegDefinitionLP(rs);
- ((PosNegLP) lp).setPositiveExamples(SetManipulation.stringToInd(posExamples));
- ((PosNegLP) lp).setNegativeExamples(SetManipulation.stringToInd(negExamples));
+ ((PosNegLP) lp).setPositiveExamples(SetManipulation.stringToInd(this.posExamples));
+ ((PosNegLP) lp).setNegativeExamples(SetManipulation.stringToInd(this.negExamples));
la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
@@ -454,8 +387,57 @@
System.out.println(Level.INFO);*/
//System.exit(0);
+ private class ResultCompare implements Comparable<ResultCompare>{
+ Description concept ;
+ double accuracy = 0.0;
+ int retrievedInstancesSize=0;
+
+ public int compareTo(ResultCompare o2) {
+ return 0;
+ }
+ public boolean equals(ResultCompare o2){
+ return this.concept.equals(o2.concept);
+ }
+
+
+ public ResultCompare(Description conceptKBSyntax, double accuracy, int retrievedInstancesSize) {
+ super();
+ this.concept = conceptKBSyntax;
+ this.accuracy = accuracy;
+ this.retrievedInstancesSize = retrievedInstancesSize;
+ }
+
+
+ }
+
+ private class ResultMostCoveredInRest extends ResultCompare{
+
+ public ResultMostCoveredInRest(Description concept, double accuracy,
+ int retrievedInstancesSize) {
+ super(concept, accuracy, retrievedInstancesSize);
+
+ }
+ public int compareTo(ResultMostCoveredInRest o2) {
+ if(this.equals(o2))return 0;
+
+ if(this.accuracy > o2.accuracy){
+ return 1;
+ }
+ else if(this.accuracy == o2.accuracy) {
+ if(this.retrievedInstancesSize < o2.retrievedInstancesSize )
+ return 1;
+ else if(this.retrievedInstancesSize > o2.retrievedInstancesSize){
+ return -1;
+ }
+ else return this.concept.toKBSyntaxString().compareTo(o2.concept.toKBSyntaxString());
+ }else {
+ return -1;
+ }
+
+ }
+
+ }
-
}
Added: trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -0,0 +1,89 @@
+package org.dllearner.utilities.datastructures;
+
+import java.util.SortedSet;
+
+import org.dllearner.core.owl.Description;
+
+public class ResultConceptSorter implements Comparable<ResultConceptSorter> {
+ String concept;
+ SortedSet<String> instances;
+ double accuracy;
+ double accuracy2;
+ int nrOfInstances;
+ SortedSet<String> coveredInRest;
+ SortedSet<String> possibleNewCandidates;
+ SortedSet<String> notCoveredInTotal;
+
+
+ public ResultConceptSorter(String concept, SortedSet<String> instances, double accuracy,
+ double accuracy2, int nrOfInstances, SortedSet<String> coveredInRest,
+ SortedSet<String> possibleNewCandidates, SortedSet<String> notCoveredInTotal) {
+ super();
+ this.concept = concept;
+ this.instances = instances;
+ this.accuracy = accuracy;
+ this.accuracy2 = accuracy2;
+ this.nrOfInstances = nrOfInstances;
+ this.coveredInRest = coveredInRest;
+ this.possibleNewCandidates = possibleNewCandidates;
+ this.notCoveredInTotal = notCoveredInTotal;
+ }
+
+
+
+
+ public int compareTo(ResultConceptSorter in) {
+ ResultConceptSorter obj = in;
+ if(obj.accuracy > this.accuracy) return 1;
+ else if(obj.accuracy == this.accuracy){
+
+ if(obj.nrOfInstances<this.nrOfInstances)return 1;
+ else if(obj.nrOfInstances>this.nrOfInstances)return -1;
+ else return 1;
+ //if(obj.nrOfInstances==this.nrOfInstances)return 0;
+ }
+ else {//if(obj.accuracy < this.accuracy){
+ return -1;
+ }
+
+ }
+
+
+
+
+ public String toStringFull(){
+ String ret="";
+ ret+="concept\t"+concept+"\n";
+ ret+="instances\t"+instances+"\n";
+ ret+="accuracy\t"+accuracy+"\n";
+ ret+="nrOfInstances\t"+nrOfInstances+"\n";
+ ret+="accuracy2\t"+accuracy2+"\n";
+ ret+="coveredInRest("+coveredInRest.size()+")\t"+coveredInRest+"\n";
+ ret+="possibleNewCandidates("+possibleNewCandidates.size()+")\t"+possibleNewCandidates+"\n";
+ ret+="notCoveredInTotal("+notCoveredInTotal.size()+")\t"+notCoveredInTotal+"\n";
+
+ return ret;
+
+ }
+
+ @Override
+ public String toString(){
+ String ret="";
+ ret+="concept\t"+concept+"\n";
+ //ret+="instances\t"+instances+"\n";
+ ret+="accuracy\t"+accuracy+"\n";
+ ret+="nrOfInstances\t"+nrOfInstances+"\n";
+ ret+="accuracy2\t"+accuracy2+"\n";
+ //ret+="coveredInRest("+coveredInRest.size()+")\t"+coveredInRest+"\n";
+ //ret+="possibleNewCandidates("+possibleNewCandidates.size()+")\t"+possibleNewCandidates+"\n";
+ //ret+="notCoveredInTotal("+notCoveredInTotal.size()+")\t"+notCoveredInTotal+"\n";
+
+ return ret;
+
+ }
+
+
+
+
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -10,7 +10,7 @@
public class AutomaticNegativeExampleFinderSPARQL {
- // CHECK
+ // LOGGER: ComponentManager
private static Logger logger = Logger.getLogger(ComponentManager.class);
private SPARQLTasks sparqltasks;
@@ -26,7 +26,13 @@
static int poslimit = 10;
static int neglimit = 20;
- // CHECK separate posexamples and fullposset
+
+ /**
+ * takes as input a full positive set to make sure no negatives are added as positives
+ *
+ * @param fullPositiveSet
+ * @param SPARQLTasks st
+ */
public AutomaticNegativeExampleFinderSPARQL(
SortedSet<String> fullPositiveSet,
SPARQLTasks st) {
@@ -38,6 +44,11 @@
+ /**
+ * aggregates all collected neg examples
+ * @param neglimit
+ * @return
+ */
public SortedSet<String> getNegativeExamples(int neglimit ) {
SortedSet<String> negatives = new TreeSet<String>();
@@ -50,12 +61,18 @@
return negatives;
}
- // CHECK namespace
+
+ /**
+ * makes neg ex from related instances, that take part in a role R(pos,neg)
+ * filters all objects, that don't use the given namespace
+ * @param instances
+ * @param objectNamespace
+ */
public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances,
- String namespace) {
+ String objectNamespace) {
logger.debug("making examples from related instances");
for (String oneInstance : instances) {
- makeNegativeExamplesFromRelatedInstances(oneInstance, namespace);
+ makeNegativeExamplesFromRelatedInstances(oneInstance, objectNamespace);
}
logger.debug("|-negExample size from related: " + fromRelated.size());
}
@@ -83,11 +100,16 @@
}*/
+ /**
+ * makes neg ex from classes, the pos ex belong to
+ * @param positiveSet
+ * @param resultLimit
+ */
public void makeNegativeExamplesFromParallelClasses(SortedSet<String> positiveSet, int resultLimit){
makeNegativeExamplesFromClassesOfInstances(positiveSet, resultLimit);
}
- public void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
+ private void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
int resultLimit) {
logger.debug("making neg Examples from parallel classes");
SortedSet<String> classes = new TreeSet<String>();
@@ -115,6 +137,11 @@
}
+ /**
+ * if pos ex derive from one class, then neg ex are taken from a superclass
+ * @param concept
+ * @param resultLimit
+ */
public void makeNegativeExamplesFromSuperClasses(String concept, int resultLimit) {
concept = concept.replaceAll("\"", "");
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-26 12:02:10 UTC (rev 928)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java 2008-05-26 14:48:00 UTC (rev 929)
@@ -9,7 +9,7 @@
public class AutomaticPositiveExampleFinderSPARQL {
- //CHECK
+ // LOGGER: ComponentManager
private static Logger logger = Logger
.getLogger(ComponentManager.class);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-06-04 12:07:51
|
Revision: 938
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=938&view=rev
Author: jenslehmann
Date: 2008-06-04 05:07:48 -0700 (Wed, 04 Jun 2008)
Log Message:
-----------
removed black hole for exceptions in SparqlQuery
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQuery.java
trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQueryClasses.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -30,7 +30,6 @@
import org.apache.log4j.Logger;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
-import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.Score;
import org.dllearner.core.config.BooleanConfigOption;
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -70,7 +70,6 @@
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.KBFile;
import org.dllearner.kb.OWLFile;
-import org.dllearner.kb.extraction.TypedSparqlQuery;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegInclusionLP;
@@ -85,7 +84,6 @@
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
-import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.datastructures.Datastructures;
import org.dllearner.utilities.datastructures.StringTuple;
import org.dllearner.utilities.owl.ConceptComparator;
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQuery.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQuery.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -96,7 +96,7 @@
// .getSparqlEndpoint(), cache, uri.toString(), sparqlQueryString);
SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
- query.extraDebugInfo=uri.toString();
+// query.extraDebugInfo=uri.toString();
String JSON = cache.executeSparqlQuery(query);
ResultSet rs = SparqlQuery.JSONtoResultSet(JSON);
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQueryClasses.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQueryClasses.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/TypedSparqlQueryClasses.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -64,7 +64,7 @@
+ "}";
SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
- query.extraDebugInfo=uri.toString();
+// query.extraDebugInfo=uri.toString();
ResultSet rs = SparqlQuery.JSONtoResultSet(cache.executeSparqlQuery(query));
List<ResultBinding> l = ResultSetFormatter.toList(rs);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -353,7 +353,7 @@
public String query(String SPARQLquery){
if(c==null){
SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
- sq.extraDebugInfo+=se.getURL();
+// sq.extraDebugInfo+=se.getURL();
sq.send();
String JSON = sq.getResult();
return JSON;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -21,6 +21,7 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
import org.apache.log4j.Logger;
@@ -44,13 +45,12 @@
private static Logger logger = Logger.getLogger(KnowledgeSource.class);
- public String extraDebugInfo = "";
private boolean isRunning = false;
private String queryString;
private QueryEngineHTTP queryExecution;
private SparqlEndpoint endpoint;
private String json = null;
- private SparqlQueryException sendException=null;
+// private SparqlQueryException sendException=null;
/**
* Standard constructor.
@@ -83,25 +83,24 @@
queryExecution.addNamedGraph(ngu);
}
- try{
- //TODO remove after overnext Jena release
- HttpQuery.urlLimit = 3*1024 ;
+ //TODO remove after overnext Jena release
+ HttpQuery.urlLimit = 3*1024 ;
- JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").start();
- rs = queryExecution.execSelect();
- JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
+ JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").start();
+ rs = queryExecution.execSelect();
+ JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
- logger.debug("query SPARQL server ["+extraDebugInfo+"], retrieved: "+rs.getResultVars());
- json=SparqlQuery.getAsJSON(rs);
+ logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
+ json=SparqlQuery.getAsJSON(rs);
- logger.trace(rs.getResultVars().toString());
- } catch (Exception e){
- sendException=new SparqlQueryException(e.getMessage());
- logger.debug(e.getMessage());
- //e.printStackTrace();
- logger.debug("Exception when querying Sparql Endpoint in " + this.getClass());
- logger.debug(queryString);
- }
+ logger.trace(rs.getResultVars().toString());
+// } catch (Exception e){
+// sendException=new SparqlQueryException(e.getMessage());
+// logger.debug(e.getMessage());
+// //e.printStackTrace();
+// logger.debug("Exception when querying Sparql Endpoint in " + this.getClass());
+// logger.debug(queryString);
+// }
isRunning = false;
return rs;
}
@@ -130,9 +129,9 @@
return queryExecution;
}
- public SparqlQueryException getException(){
- return sendException;
- }
+// public SparqlQueryException getException(){
+// return sendException;
+// }
public boolean hasCompleted() {
return (json != null);
@@ -163,10 +162,11 @@
// possible Jena bug: Jena modifies the result set during
// JSON transformation, so we need to get it back
resultSet = JSONtoResultSet(baos.toString());
- try{
+ try {
return baos.toString("UTF-8");
- }catch (Exception e){
- return baos.toString();
+ } catch (UnsupportedEncodingException e) {
+ // should never happen as UTF-8 is supported
+ throw new Error(e);
}
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -29,7 +29,6 @@
import org.dllearner.algorithms.gp.GP;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.KnowledgeSource;
-import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.OntologyFormat;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningService;
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-04 11:50:54 UTC (rev 937)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-04 12:07:48 UTC (rev 938)
@@ -302,25 +302,17 @@
* method will block until learning is completed.
*
* @param id Session ID.
+ * @param format The format of the result string: "manchester", "kb", "dl".
* @return The best solution found.
* @throws ClientNotKnownException
- */
+ */
@WebMethod
- public String learn(int id) throws ClientNotKnownException {
- ClientState state = getState(id);
- state.getLearningAlgorithm().start();
- return state.getLearningAlgorithm().getBestSolution().toString();
- }
-
- @WebMethod
public String learn(int id, String format) throws ClientNotKnownException {
ClientState state = getState(id);
state.getLearningAlgorithm().start();
- // ResultSet resultSet=SparqlQuery.JSONtoResultSet(state.getQuery(id).getResult());
Description solution = state.getLearningAlgorithm().getBestSolution();
if(format == "manchester")
- return solution.toManchesterSyntaxString(state.getReasoningService().getBaseURI(), new HashMap<String,String>()).
- replace("\"", "");
+ return solution.toManchesterSyntaxString(state.getReasoningService().getBaseURI(), new HashMap<String,String>());
else if(format == "kb")
return solution.toKBSyntaxString();
else
@@ -528,8 +520,6 @@
public String getAsJSON(int sessionID, int queryID) throws ClientNotKnownException, SparqlQueryException
{
ClientState state = getState(sessionID);
- SparqlQueryException exception=null;
- if ((exception=state.getQuery(queryID).getSparqlQuery().getException())!=null) throw exception;
return state.getQuery(queryID).getResult();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <Jen...@us...> - 2008-06-05 10:43:29
|
Revision: 942
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=942&view=rev
Author: JensLehmann
Date: 2008-06-05 03:43:24 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
updated statistics and cross validation script
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -163,19 +163,20 @@
options.add(new BooleanConfigOption("elitism", "specifies whether to use elitism in selection", true));
StringConfigOption algorithmType = new StringConfigOption("algorithmType", "algorithm type", "steadyState");
algorithmType.setAllowedValues(new String[] {"generational", "steadyState"});
- DoubleConfigOption mutationProb = new DoubleConfigOption("mutationProbablitiy", "mutation probability", 0.03);
+ options.add(algorithmType);
+ DoubleConfigOption mutationProb = new DoubleConfigOption("mutationProbability", "mutation probability", 0.03);
mutationProb.setLowerLimit(0.0);
mutationProb.setUpperLimit(1.0);
options.add(mutationProb);
- DoubleConfigOption crossoverProb = new DoubleConfigOption("crossoverProbablitiy", "crossover probability", 0.95);
+ DoubleConfigOption crossoverProb = new DoubleConfigOption("crossoverProbability", "crossover probability", 0.95);
crossoverProb.setLowerLimit(0.0);
crossoverProb.setUpperLimit(1.0);
options.add(crossoverProb);
- DoubleConfigOption hillClimbingProb = new DoubleConfigOption("hillClimbingProbablitiy", "hill climbing probability", 0.0);
+ DoubleConfigOption hillClimbingProb = new DoubleConfigOption("hillClimbingProbability", "hill climbing probability", 0.0);
hillClimbingProb.setLowerLimit(0.0);
hillClimbingProb.setUpperLimit(1.0);
options.add(hillClimbingProb);
- DoubleConfigOption refinementProb = new DoubleConfigOption("refinementProbablitiy", "refinement operator probability (values higher than 0 turn this into a hybrid GP algorithm - see publication)", 0.00);
+ DoubleConfigOption refinementProb = new DoubleConfigOption("refinementProbability", "refinement operator probability (values higher than 0 turn this into a hybrid GP algorithm - see publication)", 0.00);
refinementProb.setLowerLimit(0.0);
refinementProb.setUpperLimit(1.0);
options.add(refinementProb);
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -104,6 +104,7 @@
private LearningAlgorithm la;
private LearningProblem lp;
private ReasoningService rs;
+ private ReasonerComponent rc;
/**
* Entry point for CLI interface.
@@ -183,10 +184,10 @@
// step 2: detect used reasoner
ConfFileOption reasonerOption = parser.getConfOptionsByName("reasoner");
- ReasonerComponent reasoner = cm.reasoner(getReasonerClass(reasonerOption), sources);
- configureComponent(cm, reasoner, componentPrefixMapping, parser);
- initComponent(cm, reasoner);
- rs = cm.reasoningService(reasoner);
+ rc = cm.reasoner(getReasonerClass(reasonerOption), sources);
+ configureComponent(cm, rc, componentPrefixMapping, parser);
+ initComponent(cm, rc);
+ rs = cm.reasoningService(rc);
// step 3: detect learning problem
ConfFileOption problemOption = parser.getConfOptionsByName("problem");
@@ -754,6 +755,10 @@
return lp;
}
+ public ReasonerComponent getReasonerComponent() {
+ return rc;
+ }
+
public ReasoningService getReasoningService() {
return rs;
}
@@ -829,4 +834,6 @@
return laClass;
}
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -35,7 +35,6 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningMethodUnsupportedException;
-import org.dllearner.core.ReasoningService;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
@@ -100,7 +99,7 @@
private SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
private SortedSet<Individual> individuals;
- private ReasoningService rs;
+// private ReasoningService rs;
private OWLAPIReasoner rc;
private Set<KnowledgeSource> sources;
@@ -177,7 +176,7 @@
atomicRoles = rc.getAtomicRoles();
individuals = rc.getIndividuals();
- rs = new ReasoningService(rc);
+// rs = new ReasoningService(rc);
// TODO: some code taken from Helper.createFlatABox, but pasted here
// because additional things need to
@@ -187,9 +186,9 @@
logger.debug("dematerialising concepts");
- for (NamedClass atomicConcept : rs.getAtomicConcepts()) {
+ for (NamedClass atomicConcept : rc.getAtomicConcepts()) {
- SortedSet<Individual> pos = rs.retrieval(atomicConcept);
+ SortedSet<Individual> pos = rc.retrieval(atomicConcept);
classInstancesPos.put(atomicConcept, pos);
if(defaultNegation) {
@@ -199,7 +198,7 @@
// on the carcinogenesis data set (and probably others), so we have to
// be careful here
Negation negatedAtomicConcept = new Negation(atomicConcept);
- classInstancesNeg.put(atomicConcept, rs.retrieval(negatedAtomicConcept));
+ classInstancesNeg.put(atomicConcept, rc.retrieval(negatedAtomicConcept));
}
@@ -521,32 +520,32 @@
* @see org.dllearner.core.Reasoner#prepareSubsumptionHierarchy(java.util.Set)
*/
public void prepareSubsumptionHierarchy(Set<NamedClass> allowedConcepts) {
- rs.prepareSubsumptionHierarchy();
+ rc.prepareSubsumptionHierarchy(allowedConcepts);
}
@Override
public SubsumptionHierarchy getSubsumptionHierarchy() {
- return rs.getSubsumptionHierarchy();
+ return rc.getSubsumptionHierarchy();
}
@Override
public void prepareRoleHierarchy(Set<ObjectProperty> allowedRoles) {
- rs.prepareRoleHierarchy(allowedRoles);
+ rc.prepareRoleHierarchy(allowedRoles);
}
@Override
public ObjectPropertyHierarchy getRoleHierarchy() {
- return rs.getRoleHierarchy();
+ return rc.getRoleHierarchy();
}
@Override
public void prepareDatatypePropertyHierarchy(Set<DatatypeProperty> allowedRoles) {
- rs.prepareDatatypePropertyHierarchy(allowedRoles);
+ rc.prepareDatatypePropertyHierarchy(allowedRoles);
}
@Override
public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
- return rs.getDatatypePropertyHierarchy();
+ return rc.getDatatypePropertyHierarchy();
}
@Override
@@ -554,7 +553,7 @@
// Negation neg = new Negation(subConcept);
// Intersection c = new Intersection(neg,superConcept);
// return fastRetrieval.calculateSets(c).getPosSet().isEmpty();
- return rs.subsumes(superConcept, subConcept);
+ return rc.subsumes(superConcept, subConcept);
}
/**
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -474,6 +474,9 @@
private TreeSet<Description> getMoreSpecialConcepts(Description concept) {
Set<Set<OWLClass>> classes = null;
try {
+// System.out.println(OWLAPIDescriptionConvertVisitor.getOWLDescription(concept));
+// System.out.println(getSubsumptionHierarchy());
+// System.out.println(reasoner);
classes = reasoner.getSubClasses(OWLAPIDescriptionConvertVisitor.getOWLDescription(concept));
} catch (OWLReasonerException e) {
e.printStackTrace();
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -34,6 +34,7 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
+import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.BooleanValueRestriction;
import org.dllearner.core.owl.DataRange;
Modified: trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -115,7 +115,8 @@
}
LearningProblem lp = start.getLearningProblem();
- ReasoningService rs = start.getReasoningService();
+// ReasoningService rs = start.getReasoningService();
+// start.getReasoningService().releaseKB();
// the training and test sets used later on
List<Set<Individual>> trainingSetsPos = new LinkedList<Set<Individual>>();
@@ -194,7 +195,6 @@
try {
start = new Start(file);
} catch (ComponentInitException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
}
lp = start.getLearningProblem();
@@ -206,17 +206,17 @@
// System.out.println("neg: " + neg.size());
// System.exit(0);
- // es fehlt init zwischendurch
-
- if(la == null)
- la = start.getLearningAlgorithm();
+ la = start.getLearningAlgorithm();
// init again, because examples have changed
try {
+// start.getReasonerComponent().init();
+ lp.init();
la.init();
} catch (ComponentInitException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
+
long algorithmStartTime = System.nanoTime();
la.start();
long algorithmDuration = System.nanoTime() - algorithmStartTime;
@@ -224,6 +224,7 @@
Description concept = la.getBestSolution();
+ ReasoningService rs = start.getReasoningService();
Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
Set<Individual> tmp3 = rs.instanceCheck(concept, testSetsNeg.get(currFold));
@@ -258,7 +259,7 @@
System.out.println(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
// free all resources
- start.getReasoningService().releaseKB();
+ rs.releaseKB();
cm.freeAllComponents();
}
@@ -312,7 +313,7 @@
return splits;
}
- private String statOutput(DecimalFormat df, Stat stat, String unit) {
+ public static String statOutput(DecimalFormat df, Stat stat, String unit) {
String str = "av. " + df.format(stat.getMean()) + unit;
str += " (deviation " + df.format(stat.getStandardDeviation()) + unit + "; ";
str += "min " + df.format(stat.getMin()) + unit + "; ";
Modified: trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -22,6 +22,7 @@
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
+import java.text.DecimalFormat;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -49,6 +50,8 @@
*/
public class PaperStatistics {
+ private static DecimalFormat df = new DecimalFormat();
+
/**
* Points to the current statistic generation function.
*
@@ -82,7 +85,7 @@
// learning examples:
// - trains
- // - arches
+ // - arches => left out, insufficiently many examples
// - moral (simple)
// - moral (complex)
// - poker (pair)
@@ -95,22 +98,22 @@
String statBaseDir = "log/stat/";
File[] confFiles = new File[1];
-// confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl");
- confFiles[0] = new File(exampleBaseDir + "arch", "arch");
-// confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl");
-// confFiles[3] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl");
-// confFiles[4] = new File(exampleBaseDir + "poker", "pair_owl");
-// confFiles[5] = new File(exampleBaseDir + "poker", "straight_owl");
-// confFiles[6] = new File(exampleBaseDir + "forte", "forte_uncle_owl");
+ confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl");
+// confFiles[0] = new File(exampleBaseDir + "arch", "arch");
+ confFiles[1] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl");
+ confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl");
+ confFiles[3] = new File(exampleBaseDir + "poker", "pair_owl");
+ confFiles[4] = new File(exampleBaseDir + "poker", "straight_owl");
+ confFiles[5] = new File(exampleBaseDir + "forte", "forte_uncle_owl");
String[] examples = new String[7];
examples[0] = "trains";
- examples[1] = "arches";
- examples[2] = "moral reasoner (43 examples, simple)";
- examples[3] = "moral reasoner (43 examples, complex)";
- examples[4] = "poker (49 examples, pair)";
- examples[5] = "poker (55 examples, straight)";
- examples[6] = "uncle (FORTE data set)";
+// examples[0] = "arches";
+ examples[1] = "moral reasoner (43 examples, simple)";
+ examples[2] = "moral reasoner (43 examples, complex)";
+ examples[3] = "poker (49 examples, pair)";
+ examples[4] = "poker (55 examples, straight)";
+ examples[5] = "uncle (FORTE data set)";
int startExampleNr = 0;
// for any example, we create conf files for each configuration to be tested
@@ -121,6 +124,8 @@
algorithmPostfix[3] = "_hybrid";
int startAlgorithmNr = 0;
+ int[] folds = new int[] {5,5,5,5,5,5};
+
File statFile = new File(statBaseDir, "statistics.txt");
String statString = "**automatically generated statistics**\n\n";
@@ -132,16 +137,22 @@
File confFile = new File(confFiles[exampleNr] + algorithmPostfix[algorithmNr] + ".conf");
- CrossValidation cv = new CrossValidation(confFile, 5, false);
- Stat classification = new Stat();
- Stat length = new Stat();
- Stat runtime = new Stat();
+ System.out.println("running " + folds[exampleNr] + " fold cross validation on " + confFile);
+ CrossValidation cv = new CrossValidation(confFile, folds[exampleNr], false);
+ Stat accuracy = cv.getAccuracy();
+ Stat length = cv.getLength();
+ Stat runtime = cv.getRuntime();
+
statString += "conf file: " + confFile + "\n";
- statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
- statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
- statString += "runtime: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getMean())) + " (standard deviation: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getStandardDeviation())) + ")\n\n";
+// statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
+// statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
+// statString += "runtime: " + runtime.getMean() + " (standard deviation: " + runtime.getStandardDeviation() + ")\n\n";
+ statString += "accuracy: " + CrossValidation.statOutput(df, accuracy, "%") + "\n";
+ statString += "length: " + CrossValidation.statOutput(df, length, "") + "\n";
+ statString += "runtime: " + CrossValidation.statOutput(df, runtime, "s") + "\n\n";
+
Files.createFile(statFile, statString);
} // end algorithm loop
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sk...@us...> - 2008-06-10 15:52:33
|
Revision: 954
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=954&view=rev
Author: sknappe
Date: 2008-06-10 08:51:54 -0700 (Tue, 10 Jun 2008)
Log Message:
-----------
Added Manipulator Interface and changed classes accordingly
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Configuration.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java
trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulator.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java
trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/kb/extraction/DBpediaNavigatorManipulator.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ManipulatorType.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulators.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -152,6 +152,5 @@
@Override
public Score getSolutionScore() {
return learner.getSolutionScore();
- }
-
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -41,7 +41,7 @@
// expands all directly connected nodes
@Override
- public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulators m) {
Set<StringTuple> s = tsq.getTupelForResource(this.uri);
// see manipulator
@@ -85,7 +85,7 @@
// gets the types for properties recursively
@Override
- public void expandProperties(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public void expandProperties(TypedSparqlQueryInterface tsq, Manipulators m) {
}
/*
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Configuration.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Configuration.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Configuration.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -32,7 +32,7 @@
private SparqlEndpoint endpoint;
private SparqlQueryType sparqlQueryType;
- private Manipulator manipulator;
+ private Manipulators manipulator;
// the following needs to be moved to
// class extraction algorithm or manipulator
private int recursiondepth;
@@ -43,7 +43,7 @@
public String cacheDir="cache";
public Configuration(SparqlEndpoint specificSparqlEndpoint,
- SparqlQueryType sparqlQueryType, Manipulator manipulator,
+ SparqlQueryType sparqlQueryType, Manipulators manipulator,
int recursiondepth, boolean getAllSuperClasses,
boolean closeAfterRecursion, String cacheDir) {
this.endpoint = specificSparqlEndpoint;
@@ -64,7 +64,7 @@
}
- public Manipulator getManipulator() {
+ public Manipulators getManipulator() {
return this.manipulator;
}
Added: trunk/src/dl-learner/org/dllearner/kb/extraction/DBpediaNavigatorManipulator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/DBpediaNavigatorManipulator.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/DBpediaNavigatorManipulator.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -0,0 +1,120 @@
+/**
+ * Copyright (C) 2007, Sebastian Hellmann
+ *
+ * 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.kb.extraction;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Set;
+
+import org.dllearner.utilities.datastructures.StringTuple;
+
+/**
+ * Used to manipulate retrieved tupels, identify blanknodes, etc.
+ *
+ * @author Sebastian Hellmann
+ *
+ */
+public class DBpediaNavigatorManipulator implements Manipulators{
+ public final String subclass = "http://www.w3.org/2000/01/rdf-schema#subClassOf";
+ public final String type = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type";
+ final String objectProperty = "http://www.w3.org/2002/07/owl#ObjectProperty";
+ final String classns = "http://www.w3.org/2002/07/owl#Class";
+ final String thing = "http://www.w3.org/2002/07/owl#Thing";
+
+ public String blankNodeIdentifier = "bnode";
+ public int breakSuperClassRetrievalAfter = 200;
+ public LinkedList<StringTuple> replacePredicate;
+ public LinkedList<StringTuple> replaceObject;
+
+ // Set<String> classproperties;
+
+ public DBpediaNavigatorManipulator(String blankNodeIdentifier,
+ int breakSuperClassRetrievalAfter,
+ LinkedList<StringTuple> replacePredicate,
+ LinkedList<StringTuple> replaceObject) {
+ this.blankNodeIdentifier = blankNodeIdentifier;
+ this.replaceObject = replaceObject;
+ this.replacePredicate = replacePredicate;
+ this.breakSuperClassRetrievalAfter = breakSuperClassRetrievalAfter;
+ // Set<String> classproperties = new HashSet<String>();
+ // classproperties.add(subclass);
+
+ }
+
+ /**
+ * this checks for consistency and manipulates the tuples, before they get
+ * triple
+ *
+ * @param tuples
+ * tuples for the node
+ * @param node
+ * @return
+ */
+ public Set<StringTuple> check(Set<StringTuple> tuples, Node node) {
+ Set<StringTuple> toRemove = new HashSet<StringTuple>();
+ Iterator<StringTuple> it = tuples.iterator();
+ while (it.hasNext()) {
+ StringTuple t = (StringTuple) it.next();
+
+ replacePredicate(t);
+ replaceObject(t);
+
+
+ // remove <rdf:type, owl:class>
+ // this is done to avoid transformation to owl:subclassof
+ if (t.a.equals(type) && t.b.equals(classns)
+ && node instanceof ClassNode) {
+ toRemove.add(t);
+ }
+
+ // all with type class
+ if (t.b.equals(classns) && node instanceof ClassNode) {
+ toRemove.add(t);
+ }
+
+ // remove all instances with owl:type thing
+ if (t.a.equals(type) && t.b.equals(thing)
+ && node instanceof InstanceNode) {
+ toRemove.add(t);
+ }
+
+ }
+ tuples.removeAll(toRemove);
+
+ return tuples;
+ }
+
+ private void replacePredicate(StringTuple t) {
+ for (StringTuple rep : replacePredicate) {
+ if (rep.a.equals(t.a)) {
+ t.a = rep.b;
+ }
+ }
+ }
+
+ private void replaceObject(StringTuple t) {
+ for (StringTuple rep : replaceObject) {
+ if (rep.a.equals(t.a)) {
+ t.a = rep.b;
+ }
+ }
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -34,7 +34,7 @@
public class ExtractionAlgorithm {
private Configuration configuration;
- private Manipulator manipulator;
+ private Manipulators manipulator;
private int recursionDepth = 1;
// private boolean getAllSuperClasses = true;
// private boolean closeAfterRecursion = true;
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -47,7 +47,7 @@
// expands all directly connected nodes
@Override
- public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulators m) {
Set<StringTuple> s = tsq.getTupelForResource(uri);
// see Manipulator
@@ -86,7 +86,7 @@
// gets the types for properties recursively
@Override
- public void expandProperties(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public void expandProperties(TypedSparqlQueryInterface tsq, Manipulators m) {
for (PropertyNode one : properties) {
one.expandProperties(tsq, m);
}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -47,7 +47,7 @@
public void useConfiguration(SparqlQueryType SparqlQueryType,
- SparqlEndpoint SparqlEndpoint, Manipulator manipulator,
+ SparqlEndpoint SparqlEndpoint, Manipulators manipulator,
int recursiondepth, boolean getAllSuperClasses,
boolean closeAfterRecursion, String cacheDir) {
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulator.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulator.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -32,7 +32,7 @@
* @author Sebastian Hellmann
*
*/
-public class Manipulator {
+public class Manipulator implements Manipulators{
public final String subclass = "http://www.w3.org/2000/01/rdf-schema#subClassOf";
public final String type = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type";
final String objectProperty = "http://www.w3.org/2002/07/owl#ObjectProperty";
Added: trunk/src/dl-learner/org/dllearner/kb/extraction/ManipulatorType.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ManipulatorType.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ManipulatorType.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -0,0 +1,23 @@
+package org.dllearner.kb.extraction;
+
+import java.util.LinkedList;
+
+import org.dllearner.utilities.datastructures.StringTuple;
+
+
+/**
+ * Used to get the right manipulator
+ *
+ * @author Sebastian Knappe
+ *
+ */
+public class ManipulatorType {
+
+ public static Manipulators getManipulatorByName(String predefinedManipulator,String blankNodeIdentifier, int breakSuperClassRetrievalAfter, LinkedList<StringTuple> replacePredicate,LinkedList<StringTuple> replaceObject)
+ {
+ if (predefinedManipulator.equals("DBPEDIA-NAVIGATOR")) return new DBpediaNavigatorManipulator(blankNodeIdentifier,
+ breakSuperClassRetrievalAfter, replacePredicate, replaceObject);
+ else return new Manipulator(blankNodeIdentifier,
+ breakSuperClassRetrievalAfter, replacePredicate, replaceObject);
+ }
+}
Added: trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulators.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulators.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Manipulators.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -0,0 +1,15 @@
+package org.dllearner.kb.extraction;
+
+import java.util.Set;
+
+import org.dllearner.utilities.datastructures.StringTuple;
+
+public interface Manipulators {
+
+ public int breakSuperClassRetrievalAfter = 200;
+ public final String subclass = "http://www.w3.org/2000/01/rdf-schema#subClassOf";
+ public final String type = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type";
+ public String blankNodeIdentifier = "bnode";
+
+ public Set<StringTuple> check(Set<StringTuple> tuples, Node node);
+}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -55,7 +55,7 @@
* @return Vector<Node> all Nodes that are new because of expansion
*/
public abstract Vector<Node> expand(
- TypedSparqlQueryInterface typedSparqlQuery, Manipulator manipulator);
+ TypedSparqlQueryInterface typedSparqlQuery, Manipulators manipulator);
/**
* gets type defs for properties like rdf:type SymmetricProperties
@@ -65,7 +65,7 @@
* @return Vector<Node>
*/
public abstract void expandProperties(
- TypedSparqlQueryInterface typedSparqlQuery, Manipulator manipulator);
+ TypedSparqlQueryInterface typedSparqlQuery, Manipulators manipulator);
/**
* output
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -53,13 +53,13 @@
// Property Nodes are normally not expanded,
// this function is never called
@Override
- public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public Vector<Node> expand(TypedSparqlQueryInterface tsq, Manipulators m) {
return null;
}
// gets the types for properties recursively
@Override
- public void expandProperties(TypedSparqlQueryInterface tsq, Manipulator m) {
+ public void expandProperties(TypedSparqlQueryInterface tsq, Manipulators m) {
b.expandProperties(tsq, m);
Set<StringTuple> s = tsq.getTupelForResource(uri);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -46,6 +46,8 @@
import org.dllearner.core.owl.KB;
import org.dllearner.kb.extraction.Manager;
import org.dllearner.kb.extraction.Manipulator;
+import org.dllearner.kb.extraction.ManipulatorType;
+import org.dllearner.kb.extraction.Manipulators;
import org.dllearner.parser.KBParser;
import org.dllearner.reasoning.DIGConverter;
import org.dllearner.reasoning.JenaOWLDIGConverter;
@@ -73,6 +75,7 @@
private int recursionDepth = recursionDepthDefault;
private String predefinedFilter = null;
private String predefinedEndpoint = null;
+ private String predefinedManipulator = "STANDARD";
private Set<String> predList = new HashSet<String>();
private Set<String> objList = new HashSet<String>();
// private Set<String> classList;
@@ -136,7 +139,8 @@
"the mode of the SPARQL Filter, use one of YAGO,SKOS,YAGOSKOS , YAGOSPECIALHIERARCHY, TEST"));
options.add(new StringConfigOption("predefinedEndpoint",
"the mode of the SPARQL Filter, use one of DBPEDIA, LOCAL, GOVTRACK, REVYU, MYOPENLINK, FACTBOOK"));
-
+ options.add(new StringConfigOption("predefinedManipulator",
+ "the mode of the Manipulator, use one of STANDARD, DBPEDIA-NAVIGATOR"));
options.add(new StringSetConfigOption("predList",
"list of all ignored roles"));
options.add(new StringSetConfigOption("objList",
@@ -220,6 +224,8 @@
predefinedEndpoint = ((String) entry.getValue()).toUpperCase();
} else if (option.equals("predefinedFilter")) {
predefinedFilter = ((String) entry.getValue()).toUpperCase();
+ } else if (option.equals("predefinedManipulator")) {
+ predefinedManipulator = ((String) entry.getValue()).toUpperCase();
} else if (option.equals("format")) {
format = (String) entry.getValue();
} else if (option.equals("dumpToFile")) {
@@ -292,7 +298,7 @@
Manager m = new Manager();
SparqlQueryType sparqlQueryType = null;
// get Options for Manipulator
- Manipulator manipulator = new Manipulator(blankNodeIdentifier,
+ Manipulators manipulator = ManipulatorType.getManipulatorByName(predefinedManipulator, blankNodeIdentifier,
breakSuperClassRetrievalAfter, replacePredicate, replaceObject);
// get Options for endpoints
Modified: trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-10 15:48:27 UTC (rev 953)
+++ trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-10 15:51:54 UTC (rev 954)
@@ -23,6 +23,7 @@
import java.util.Set;
import java.util.TreeSet;
+import org.dllearner.algorithms.DBpediaNavigationSuggestor;
import org.dllearner.algorithms.RandomGuesser;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ComponentManager;
@@ -35,6 +36,7 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.reasoning.DIGReasoner;
+import org.dllearner.reasoning.OWLAPIReasoner;
/**
* Test for component based design.
@@ -55,12 +57,12 @@
// create knowledge source
KnowledgeSource source = cm.knowledgeSource(OWLFile.class);
- String example = "examples/family/father.owl";
+ String example = "examples/family/uncle.owl";
cm.applyConfigEntry(source, "url", new File(example).toURI().toString());
source.init();
// create DIG reasoning service with standard settings
- ReasonerComponent reasoner = cm.reasoner(DIGReasoner.class, source);
+ ReasonerComponent reasoner = cm.reasoner(OWLAPIReasoner.class, source);
// ReasoningService rs = cm.reasoningService(DIGReasonerNew.class, source);
reasoner.init();
ReasoningService rs = cm.reasoningService(reasoner);
@@ -68,29 +70,31 @@
// create a learning problem and set positive and negative examples
LearningProblem lp = cm.learningProblem(PosNegDefinitionLP.class, rs);
Set<String> positiveExamples = new TreeSet<String>();
- positiveExamples.add("http://example.com/father#stefan");
- positiveExamples.add("http://example.com/father#markus");
- positiveExamples.add("http://example.com/father#martin");
+ positiveExamples.add("http://localhost/foo#heinz");
+ positiveExamples.add("http://localhost/foo#alex");
Set<String> negativeExamples = new TreeSet<String>();
- negativeExamples.add("http://example.com/father#heinz");
- negativeExamples.add("http://example.com/father#anna");
- negativeExamples.add("http://example.com/father#michelle");
+ negativeExamples.add("http://localhost/foo#jan");
+ negativeExamples.add("http://localhost/foo#anna");
+ negativeExamples.add("http://localhost/foo#hanna");
cm.applyConfigEntry(lp, "positiveExamples", positiveExamples);
cm.applyConfigEntry(lp, "negativeExamples", negativeExamples);
+
lp.init();
+
// create the learning algorithm
LearningAlgorithm la = null;
try {
- la = cm.learningAlgorithm(RandomGuesser.class, lp, rs);
+ la = cm.learningAlgorithm(DBpediaNavigationSuggestor.class, lp, rs);
} catch (LearningProblemUnsupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- cm.applyConfigEntry(la, "numberOfTrees", 100);
- cm.applyConfigEntry(la, "maxDepth", 5);
- la.init();
-
+ try{
+ la.init();
+ }catch (Exception e){
+ }
+
// start the algorithm and print the best concept found
la.start();
System.out.println(la.getBestSolution());
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|
|
From: <sk...@us...> - 2008-06-10 16:51:13
|
Revision: 955
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=955&view=rev
Author: sknappe
Date: 2008-06-10 09:51:06 -0700 (Tue, 10 Jun 2008)
Log Message:
-----------
I don't use SparqlQueryThreaded anymore
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/server/ClientState.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-10 15:51:54 UTC (rev 954)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-10 16:51:06 UTC (rev 955)
@@ -66,7 +66,7 @@
//DEFAULTS
static int recursionDepthDefault = 1;
-
+ private boolean useCache=true;
// ConfigOptions
public URL url;
// String host;
@@ -164,6 +164,8 @@
options.add(new BooleanConfigOption("learnDomain",
"learns the Domain for a Role"));
+ options.add(new BooleanConfigOption("useCache",
+ "If true a Cache is used"));
options.add(new BooleanConfigOption("learnRange",
"learns the Range for a Role"));
options.add(new StringConfigOption("role",
@@ -232,7 +234,9 @@
dumpToFile = (Boolean) entry.getValue();
} else if (option.equals("useLits")) {
useLits = (Boolean) entry.getValue();
- } else if (option.equals("getAllSuperClasses")) {
+ } else if (option.equals("useCache")) {
+ useCache = (Boolean) entry.getValue();
+ }else if (option.equals("getAllSuperClasses")) {
getAllSuperClasses = (Boolean) entry.getValue();
/*
* TODO remaove } else if (option.equals("learnDomain")) {
@@ -415,9 +419,6 @@
return new SparqlQuery(query, endpoint);
}
- public SparqlQueryThreaded sparqlQueryThreaded(String query){
- return new SparqlQueryThreaded(new Cache("cache"),this.sparqlQuery(query));
- }
/* (non-Javadoc)
* @see org.dllearner.core.KnowledgeSource#toKB()
@@ -431,6 +432,14 @@
public URL getNTripleURL(){
return dumpFile;
}
+
+ public boolean getUseCache(){
+ return useCache;
+ }
+
+ public String getCacheDir(){
+ return cacheDir;
+ }
/*public static void main(String[] args) throws MalformedURLException {
String query = "SELECT ?pred ?obj\n"
Modified: trunk/src/dl-learner/org/dllearner/server/ClientState.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-06-10 15:51:54 UTC (rev 954)
+++ trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-06-10 16:51:06 UTC (rev 955)
@@ -34,6 +34,7 @@
import org.dllearner.core.ReasoningService;
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryThreaded;
/**
@@ -51,7 +52,7 @@
private Set<KnowledgeSource> knowledgeSources = new HashSet<KnowledgeSource>();
- private Map<Integer, SparqlQueryThreaded> queryIDs = new HashMap<Integer, SparqlQueryThreaded>();
+ private Map<Integer, SparqlQuery> queryIDs = new HashMap<Integer, SparqlQuery>();
private LearningProblem learningProblem;
@@ -73,7 +74,7 @@
return id;
}
- private int generateQueryID(SparqlQueryThreaded query) {
+ private int generateQueryID(SparqlQuery query) {
int id;
Random rand = new Random();
do {
@@ -83,11 +84,11 @@
return id;
}
- public int addQuery(SparqlQueryThreaded query){
+ public int addQuery(SparqlQuery query){
return this.generateQueryID(query);
}
- public SparqlQueryThreaded getQuery(int id){
+ public SparqlQuery getQuery(int id){
return queryIDs.get(id);
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-10 15:51:54 UTC (rev 954)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-10 16:51:06 UTC (rev 955)
@@ -61,6 +61,7 @@
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.SparqlQueryException;
import org.dllearner.kb.sparql.SparqlQueryThreaded;
+import org.dllearner.kb.sparql.Cache;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegInclusionLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
@@ -536,11 +537,16 @@
{
final ClientState state = getState(sessionID);
Component component = state.getComponent(componentID);
- final int id=state.addQuery(((SparqlKnowledgeSource)component).sparqlQueryThreaded(query));
+ final SparqlKnowledgeSource ks=(SparqlKnowledgeSource)component;
+ final int id=state.addQuery(ks.sparqlQuery(query));
Thread sparqlThread = new Thread() {
@Override
public void run() {
- state.getQuery(id).send();
+ if (ks.getUseCache()){
+ Cache cache=new Cache(ks.getCacheDir());
+ cache.executeSparqlQuery(state.getQuery(id));
+ }
+ else state.getQuery(id).send();
}
};
sparqlThread.start();
@@ -552,8 +558,13 @@
{
ClientState state = getState(sessionID);
Component component = state.getComponent(componentID);
- SparqlQueryThreaded sparql=((SparqlKnowledgeSource)component).sparqlQueryThreaded(query);
- sparql.send();
+ SparqlKnowledgeSource ks=(SparqlKnowledgeSource)component;
+ SparqlQuery sparql=ks.sparqlQuery(query);
+ if (ks.getUseCache()){
+ Cache cache=new Cache(ks.getCacheDir());
+ cache.executeSparqlQuery(sparql);
+ }
+ else sparql.send();
return sparql.getResult();
}
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|
|
From: <lor...@us...> - 2008-06-17 10:53:46
|
Revision: 963
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=963&view=rev
Author: lorenz_b
Date: 2008-06-17 03:53:42 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
added method getInconsistentClasses() to class OWLAPIReasoner and interface ReasonerComponent
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-15 13:46:32 UTC (rev 962)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-17 10:53:42 UTC (rev 963)
@@ -38,6 +38,7 @@
import org.dllearner.core.owl.ObjectPropertyHierarchy;
import org.dllearner.core.owl.SubsumptionHierarchy;
import org.dllearner.utilities.datastructures.SortedSetTuple;
+import org.semanticweb.owl.model.OWLClass;
/**
* @author Jens Lehmann
@@ -255,4 +256,7 @@
public abstract void releaseKB();
+ public Set<OWLClass> getInconsistentClasses() throws ReasoningMethodUnsupportedException{
+ throw new ReasoningMethodUnsupportedException();
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-15 13:46:32 UTC (rev 962)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-17 10:53:42 UTC (rev 963)
@@ -938,5 +938,17 @@
public boolean hasDatatypeSupport() {
return true;
}
+
+ @Override
+ public Set<OWLClass> getInconsistentClasses(){
+
+ try {
+ return reasoner.getInconsistentClasses();
+ } catch (OWLReasonerException e) {
+ e.printStackTrace();
+ throw new Error("Inconsistens classes check error in OWL API.");
+ }
+
+ }
}
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|
|
From: <sk...@us...> - 2008-06-17 17:04:01
|
Revision: 966
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=966&view=rev
Author: sknappe
Date: 2008-06-17 10:03:58 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
Changed the classes to work without SparqlQueryThreaded
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-17 16:33:03 UTC (rev 965)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-17 17:03:58 UTC (rev 966)
@@ -34,6 +34,8 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.utilities.JamonMonitorLogger;
+import com.hp.hpl.jena.query.ResultSet;
+
/**
* SPARQL query cache to avoid possibly expensive multiple queries. The queries
* and their results are written to files. A cache has an associated cache
@@ -249,15 +251,17 @@
JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").stop();
if (result != null) {
+ query.setJson(result);
+ query.setRunning(false);
logger.trace("got from cache");
JamonMonitorLogger.increaseCount(Cache.class, "SuccessfulHits");
//Statistics.increaseCachedQuery();
//return result;
} else {
//SimpleClock sc = new SimpleClock();
- query.send();
//sc.printAndSet("query");
- String json = query.getResult();
+ ResultSet rs= query.send();
+ String json = SparqlQuery.getAsJSON(rs);
if (json!=null){
addToCache(query.getQueryString(), json);
result=json;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-17 16:33:03 UTC (rev 965)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-17 17:03:58 UTC (rev 966)
@@ -354,8 +354,8 @@
if(c==null){
SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
// sq.extraDebugInfo+=se.getURL();
- sq.send();
- String JSON = sq.getResult();
+ ResultSet rs=sq.send();
+ String JSON = SparqlQuery.getAsJSON(rs);
return JSON;
}else{
return c.executeSparqlQuery(new SparqlQuery(SPARQLquery,se));
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-17 16:33:03 UTC (rev 965)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-17 17:03:58 UTC (rev 966)
@@ -49,7 +49,8 @@
private String queryString;
private QueryEngineHTTP queryExecution;
private SparqlEndpoint endpoint;
- private String json = null;
+ private ResultSet rs;
+ private String json;
// private SparqlQueryException sendException=null;
/**
@@ -69,9 +70,8 @@
public ResultSet send() {
isRunning = true;
- ResultSet rs=null;
logger.trace(queryString);
-
+
String service = endpoint.getURL().toString();
logger.trace(endpoint.getURL().toString());
// Jena access to SPARQL endpoint
@@ -91,8 +91,7 @@
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
- json=SparqlQuery.getAsJSON(rs);
-
+
logger.trace(rs.getResultVars().toString());
// } catch (Exception e){
// sendException=new SparqlQueryException(e.getMessage());
@@ -114,13 +113,6 @@
return queryString;
}
- /**
- * @return String JSON
- */
- public String getResult() {
- return json;
- }
-
public boolean isRunning() {
return isRunning;
}
@@ -133,10 +125,6 @@
// return sendException;
// }
- public boolean hasCompleted() {
- return (json != null);
- }
-
/**
* sends a query and returns XML
*
@@ -184,4 +172,19 @@
return ResultSetFactory.fromJSON(bais);
}
+ public String getJson() {
+ return json;
+ }
+
+ public void setJson(String json) {
+ this.json = json;
+ }
+
+ public void setRunning(boolean running){
+ this.isRunning=running;
+ }
+
+ public ResultSet getResultSet(){
+ return rs;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-17 16:33:03 UTC (rev 965)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-17 17:03:58 UTC (rev 966)
@@ -521,15 +521,22 @@
public String getAsJSON(int sessionID, int queryID) throws ClientNotKnownException, SparqlQueryException
{
ClientState state = getState(sessionID);
- return state.getQuery(queryID).getResult();
+ ResultSet resultSet=null;
+ String json=null;
+ if ((json=state.getQuery(queryID).getJson())!=null) return json;
+ else if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsJSON(resultSet);
+ else return SparqlQuery.getAsJSON(state.getQuery(queryID).send());
}
@WebMethod
public String getAsXMLString(int sessionID, int queryID) throws ClientNotKnownException
{
ClientState state = getState(sessionID);
- ResultSet resultSet=SparqlQuery.JSONtoResultSet(state.getQuery(queryID).getResult());
- return SparqlQuery.getAsXMLString(resultSet);
+ ResultSet resultSet=null;
+ String json=null;
+ if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsXMLString(resultSet);
+ else if ((json=state.getQuery(queryID).getJson())!=null) return SparqlQuery.getAsXMLString(SparqlQuery.JSONtoResultSet(json));
+ else return SparqlQuery.getAsXMLString(state.getQuery(queryID).send());
}
@WebMethod
@@ -543,6 +550,7 @@
@Override
public void run() {
if (ks.getUseCache()){
+ state.getQuery(id).setRunning(true);
Cache cache=new Cache(ks.getCacheDir());
cache.executeSparqlQuery(state.getQuery(id));
}
@@ -562,10 +570,9 @@
SparqlQuery sparql=ks.sparqlQuery(query);
if (ks.getUseCache()){
Cache cache=new Cache(ks.getCacheDir());
- cache.executeSparqlQuery(sparql);
+ return cache.executeSparqlQuery(sparql);
}
- else sparql.send();
- return sparql.getResult();
+ else return SparqlQuery.getAsJSON(sparql.send());
}
@WebMethod
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From: <sk...@us...> - 2008-06-17 17:05:11
|
Revision: 967
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=967&view=rev
Author: sknappe
Date: 2008-06-17 10:05:00 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
Changed the classes to work without SparqlQueryThreaded
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/server/ClientState.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryThreaded.java
Deleted: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryThreaded.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryThreaded.java 2008-06-17 17:03:58 UTC (rev 966)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryThreaded.java 2008-06-17 17:05:00 UTC (rev 967)
@@ -1,41 +0,0 @@
-package org.dllearner.kb.sparql;
-
-/**
- * The class is used for threaded querying of a Sparql Endpoint.
- * @author Sebastian Knappe
- *
- */
-public class SparqlQueryThreaded {
- private Cache cache;
- private SparqlQuery query;
- private String result;
-
- public SparqlQueryThreaded(Cache cache, SparqlQuery query)
- {
- this.cache=cache;
- this.query=query;
- this.result=null;
- }
-
- public void stop() {
- query.getExecution().abort();
- result=null;
- }
-
- public boolean isRunning() {
- return result==null;
- }
-
- public void send()
- {
- result=cache.executeSparqlQuery(query);
- }
-
- public SparqlQuery getSparqlQuery(){
- return query;
- }
-
- public String getResult(){
- return result;
- }
-}
Modified: trunk/src/dl-learner/org/dllearner/server/ClientState.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-06-17 17:03:58 UTC (rev 966)
+++ trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-06-17 17:05:00 UTC (rev 967)
@@ -35,7 +35,6 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryThreaded;
/**
* Stores the state of a DL-Learner client session.
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-17 17:03:58 UTC (rev 966)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-17 17:05:00 UTC (rev 967)
@@ -60,7 +60,6 @@
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.SparqlQueryException;
-import org.dllearner.kb.sparql.SparqlQueryThreaded;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegInclusionLP;
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|
|
From: <sk...@us...> - 2008-06-18 18:26:52
|
Revision: 972
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=972&view=rev
Author: sknappe
Date: 2008-06-18 11:26:41 -0700 (Wed, 18 Jun 2008)
Log Message:
-----------
changed to work without SparqlQueryThreaded
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-18 18:25:58 UTC (rev 971)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-18 18:26:41 UTC (rev 972)
@@ -265,6 +265,7 @@
if (json!=null){
addToCache(query.getQueryString(), json);
result=json;
+ query.setJson(result);
}
else {
json="";
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-18 18:25:58 UTC (rev 971)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-18 18:26:41 UTC (rev 972)
@@ -23,11 +23,13 @@
import java.io.ByteArrayOutputStream;
import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
+import java.util.Iterator;
import org.apache.log4j.Logger;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.utilities.JamonMonitorLogger;
+import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetFormatter;
@@ -69,7 +71,7 @@
*/
public ResultSet send() {
- isRunning = true;
+ //isRunning = true;
logger.trace(queryString);
String service = endpoint.getURL().toString();
@@ -85,11 +87,10 @@
//TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
-
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").start();
rs = queryExecution.execSelect();
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
-
+
logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
logger.trace(rs.getResultVars().toString());
@@ -100,7 +101,7 @@
// logger.debug("Exception when querying Sparql Endpoint in " + this.getClass());
// logger.debug(queryString);
// }
- isRunning = false;
+ //isRunning = false;
return rs;
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-18 18:25:58 UTC (rev 971)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-18 18:26:41 UTC (rev 972)
@@ -552,8 +552,13 @@
state.getQuery(id).setRunning(true);
Cache cache=new Cache(ks.getCacheDir());
cache.executeSparqlQuery(state.getQuery(id));
+ state.getQuery(id).setRunning(false);
}
- else state.getQuery(id).send();
+ else{
+ state.getQuery(id).setRunning(true);
+ state.getQuery(id).send();
+ state.getQuery(id).setRunning(false);
+ }
}
};
sparqlThread.start();
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|
|
From: <hee...@us...> - 2008-06-23 11:12:45
|
Revision: 976
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=976&view=rev
Author: heeroyuy
Date: 2008-06-23 04:11:48 -0700 (Mon, 23 Jun 2008)
Log Message:
-----------
-bug fixes
-removed unnecessary outputs
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-22 11:09:36 UTC (rev 975)
+++ trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-23 11:11:48 UTC (rev 976)
@@ -72,7 +72,6 @@
test.iterator().next();
Description d1 = new ObjectSomeRestriction(test.iterator().next(), new Thing());
test.remove(rs.getAtomicRolesList().iterator().next());
- System.out.println("TADA: "+d1);
simpleSuggestions.add(d1);
}
return simpleSuggestions;
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-22 11:09:36 UTC (rev 975)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-23 11:11:48 UTC (rev 976)
@@ -195,8 +195,6 @@
try {
if(source instanceof OWLAPIOntology)
{
- System.out.println(source instanceof OWLAPIOntology);
- System.out.println("JUHU es geht");
OWLOntology ontology = ((OWLAPIOntology)source).getOWLOntolgy();
owlAPIOntologies.add(ontology);
allImports.addAll(manager.getImportsClosure(ontology));
@@ -216,7 +214,6 @@
}
else
{
- System.out.println(":'S");
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(url.toURI());
owlAPIOntologies.add(ontology);
allImports.addAll(manager.getImportsClosure(ontology));
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-06-22 11:09:36 UTC (rev 975)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-06-23 11:11:48 UTC (rev 976)
@@ -438,20 +438,28 @@
public void setPositiveConcept()
{
SortedSet<Individual> individuals = null;
- for(Iterator<NamedClass> i = rs.getAtomicConcepts().iterator(); i.hasNext();)
+ if(!aktuell.getRootObject().toString().equals("Thing"))
{
- if(individuals==null)
+ for(Iterator<NamedClass> i = rs.getAtomicConcepts().iterator(); i.hasNext();)
{
- NamedClass concept = i.next();
- if(concept.toString().endsWith("#"+aktuell.getRootObject().toString()))
+ if(individuals==null)
{
- if(rs.retrieval(concept)!=null){
- individual = rs.retrieval(concept);
- break;
+ NamedClass concept = i.next();
+ if(concept.toString().endsWith("#"+aktuell.getRootObject().toString()))
+ {
+ if(rs.retrieval(concept)!=null)
+ {
+ individual = rs.retrieval(concept);
+ break;
+ }
}
}
}
}
+ else
+ {
+ individual = rs.getIndividuals();
+ }
}
/**
@@ -463,9 +471,12 @@
public boolean setPositivExamplesChecked(String indi)
{
boolean isChecked = false;
- if(individual.toString().contains(indi))
+ if(individual != null)
{
- isChecked = true;
+ if(individual.toString().contains(indi))
+ {
+ isChecked = true;
+ }
}
return isChecked;
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java 2008-06-22 11:09:36 UTC (rev 975)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java 2008-06-23 11:11:48 UTC (rev 976)
@@ -177,7 +177,6 @@
public void clear() {
- System.out.println("Und jetzt bin ich hier :-)");
dllearner.unsetEverything();
dllearner.makeView();
handleVerifyEditorContents();
@@ -194,8 +193,6 @@
return restrictionCreatorPanel.createRestrictions();
}
else if(tabbedPane.getSelectedComponent() == dllearner){
- System.out.println("die loesungen:"+dllearner.getSollutions());
-
return dllearner.getSollutions();
}
return super.getEditedObjects();
@@ -478,7 +475,6 @@
*/
public OWLDescription getSollution()
{
- System.out.println(model.getSolution());
return model.getSolution();
}
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|
|
From: <ku...@us...> - 2008-06-24 17:05:38
|
Revision: 979
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=979&view=rev
Author: kurzum
Date: 2008-06-24 10:04:10 -0700 (Tue, 24 Jun 2008)
Log Message:
-----------
made an extra log file just fo sparql in folder log/sparql.txt
SparqlQuery method send should not return resultSet.
Therefore I marked it deprecated.
It is a possible source of errors, because it can only be used/traversed once.
e.g.
SparqlQuery.getAsXML(ResulSet);
SparqlQuery.getAsXML(ResulSet);
will produce an error on second call.
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-24 12:08:34 UTC (rev 978)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-24 17:04:10 UTC (rev 979)
@@ -64,9 +64,9 @@
import org.dllearner.core.config.StringConfigOption;
import org.dllearner.core.config.StringSetConfigOption;
import org.dllearner.core.config.StringTupleListConfigOption;
-import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.KBFile;
import org.dllearner.kb.OWLFile;
@@ -120,18 +120,24 @@
// create logger (a simple logger which outputs
// its messages to the console and a log file)
+
SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- FileAppender fileAppender = null;
+ FileAppender fileAppenderNormal = null;
+ File f = new File("log/sparql.txt");
try {
- fileAppender = new FileAppender(layout, "log/log.txt", false);
+ fileAppenderNormal = new FileAppender(layout, "log/log.txt", false);
+ f.delete();
+ f.createNewFile();
} catch (IOException e) {
e.printStackTrace();
}
+
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.addAppender(fileAppender);
+ logger.addAppender(fileAppenderNormal);
logger.setLevel(Level.DEBUG);
+
// Logger.getLogger(KnowledgeSource.class).setLevel(Level.WARN);
// Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.WARN);
// Logger.getLogger(TypedSparqlQuery.class).setLevel(Level.WARN);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-24 12:08:34 UTC (rev 978)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-24 17:04:10 UTC (rev 979)
@@ -31,11 +31,8 @@
import java.util.LinkedList;
import org.apache.log4j.Logger;
-import org.dllearner.core.KnowledgeSource;
import org.dllearner.utilities.JamonMonitorLogger;
-import com.hp.hpl.jena.query.ResultSet;
-
/**
* SPARQL query cache to avoid possibly expensive multiple queries. The queries
* and their results are written to files. A cache has an associated cache
@@ -61,7 +58,8 @@
*/
public class Cache implements Serializable {
- private static Logger logger = Logger.getLogger(KnowledgeSource.class);
+ private static Logger logger = Logger.getLogger(Cache.class);
+
private static final long serialVersionUID = 843308736471742205L;
@@ -237,39 +235,41 @@
*
* @param query
* The SPARQL query.
- * @return Jena result set.
+ * @return Jena result set in JSON format
*/
public String executeSparqlQuery(SparqlQuery query) {
JamonMonitorLogger.getTimeMonitor(Cache.class, "TotalTimeExecuteSparqlQuery").start();
JamonMonitorLogger.increaseCount(Cache.class, "TotalQueries");
-
-
- //Statistics.increaseQuery();
-
+
JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").start();
String result = getCacheEntry(query.getQueryString());
JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").stop();
if (result != null) {
- query.setJson(result);
- query.setRunning(false);
- logger.trace("got from cache");
+ //query.setJson(result);
+
+ query.setRunning(false);
+ SparqlQuery.writeToSpecialLog("***********\nJSON retrieved from cache");
+ SparqlQuery.writeToSpecialLog(query.getQueryString());
+ SparqlQuery.writeToSpecialLog(query.getEndpoint().getURL().toString());
JamonMonitorLogger.increaseCount(Cache.class, "SuccessfulHits");
- //Statistics.increaseCachedQuery();
- //return result;
+
} else {
- //SimpleClock sc = new SimpleClock();
- //sc.printAndSet("query");
- ResultSet rs= query.send();
- String json = SparqlQuery.getAsJSON(rs);
+
+ //ResultSet rs= query.send();
+ query.send();
+ String json = query.getJson();
if (json!=null){
addToCache(query.getQueryString(), json);
+ SparqlQuery.writeToSpecialLog("result added to cache: "+json);
result=json;
query.setJson(result);
}
else {
json="";
+ result="";
logger.warn(Cache.class.getSimpleName()+"empty result: "+query.getQueryString());
+ SparqlQuery.writeToSpecialLog("empty result for : "+query.getQueryString());
}
//return json;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-24 12:08:34 UTC (rev 978)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-24 17:04:10 UTC (rev 979)
@@ -21,15 +21,13 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.FileWriter;
import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
-import java.util.Iterator;
import org.apache.log4j.Logger;
-import org.dllearner.core.KnowledgeSource;
import org.dllearner.utilities.JamonMonitorLogger;
-import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetFormatter;
@@ -45,13 +43,14 @@
*/
public class SparqlQuery {
- private static Logger logger = Logger.getLogger(KnowledgeSource.class);
+ private static Logger logger = Logger.getLogger(SparqlQuery.class);
+
private boolean isRunning = false;
private String queryString;
private QueryEngineHTTP queryExecution;
private SparqlEndpoint endpoint;
- private ResultSet rs;
+ //private ResultSet rs;
private String json;
// private SparqlQueryException sendException=null;
@@ -66,16 +65,26 @@
this.endpoint = endpoint;
}
+
+
+
+
/**
* Sends a SPARQL query using the Jena library.
+ * should return JSON String
+ * needs refactoring
+ * @return ResultSet
*/
+ @Deprecated
public ResultSet send() {
-
+ ResultSet rs;
//isRunning = true;
- logger.trace(queryString);
+ writeToSpecialLog("***********\nNew Query:");
+ writeToSpecialLog(queryString);
+ writeToSpecialLog(endpoint.getURL().toString());
String service = endpoint.getURL().toString();
- logger.trace(endpoint.getURL().toString());
+
// Jena access to SPARQL endpoint
queryExecution = new QueryEngineHTTP(service, queryString);
for (String dgu : endpoint.getDefaultGraphURIs()) {
@@ -91,17 +100,20 @@
rs = queryExecution.execSelect();
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
+
logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
-
- logger.trace(rs.getResultVars().toString());
-// } catch (Exception e){
-// sendException=new SparqlQueryException(e.getMessage());
-// logger.debug(e.getMessage());
-// //e.printStackTrace();
-// logger.debug("Exception when querying Sparql Endpoint in " + this.getClass());
-// logger.debug(queryString);
-// }
- //isRunning = false;
+ writeToSpecialLog("query SPARQL server, retrieved: "+rs.getResultVars());
+ writeToSpecialLog("Results from ResultSet");
+
+ json = SparqlQuery.getAsJSON(rs);
+ writeToSpecialLog(json);
+ rs = SparqlQuery.JSONtoResultSet(json);
+ while (rs.hasNext()){
+ writeToSpecialLog("Result: "+rs.nextBinding());
+ }
+
+ isRunning = false;
+ rs = SparqlQuery.JSONtoResultSet(json);
return rs;
}
@@ -114,6 +126,10 @@
return queryString;
}
+ public SparqlEndpoint getEndpoint() {
+ return endpoint;
+ }
+
public boolean isRunning() {
return isRunning;
}
@@ -185,7 +201,18 @@
this.isRunning=running;
}
- public ResultSet getResultSet(){
+ public static void writeToSpecialLog(String s){
+ try{
+ FileWriter fw = new FileWriter("log/sparql.txt",true);
+ fw.write(s+"\n");
+ fw.flush();
+ fw.close();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ /*public ResultSet getResultSet(){
return rs;
- }
+ }*/
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-24 12:08:34 UTC (rev 978)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-24 17:04:10 UTC (rev 979)
@@ -51,16 +51,16 @@
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.config.ConfigOption;
-import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.OWLFile;
+import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.SparqlQueryException;
-import org.dllearner.kb.sparql.Cache;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegInclusionLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
@@ -72,8 +72,6 @@
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.datastructures.Datastructures;
-import com.hp.hpl.jena.query.ResultSet;
-
/**
* DL-Learner web service interface.
*
@@ -520,10 +518,10 @@
public String getAsJSON(int sessionID, int queryID) throws ClientNotKnownException, SparqlQueryException
{
ClientState state = getState(sessionID);
- ResultSet resultSet=null;
+ //ResultSet resultSet=null;
String json=null;
if ((json=state.getQuery(queryID).getJson())!=null) return json;
- else if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsJSON(resultSet);
+ //else if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsJSON(resultSet);
else return SparqlQuery.getAsJSON(state.getQuery(queryID).send());
}
@@ -531,10 +529,10 @@
public String getAsXMLString(int sessionID, int queryID) throws ClientNotKnownException
{
ClientState state = getState(sessionID);
- ResultSet resultSet=null;
+ //ResultSet resultSet=null;
String json=null;
- if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsXMLString(resultSet);
- else if ((json=state.getQuery(queryID).getJson())!=null) return SparqlQuery.getAsXMLString(SparqlQuery.JSONtoResultSet(json));
+ //if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsXMLString(resultSet);
+ if ((json=state.getQuery(queryID).getJson())!=null) return SparqlQuery.getAsXMLString(SparqlQuery.JSONtoResultSet(json));
else return SparqlQuery.getAsXMLString(state.getQuery(queryID).send());
}
@@ -590,7 +588,6 @@
public void stopSparqlThread(int sessionID, int queryID) throws ClientNotKnownException
{
ClientState state = getState(sessionID);
-
state.getQuery(queryID).stop();
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java 2008-06-24 12:08:34 UTC (rev 978)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java 2008-06-24 17:04:10 UTC (rev 979)
@@ -20,6 +20,7 @@
package org.dllearner.server;
import java.io.BufferedReader;
+import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.InetSocketAddress;
@@ -29,6 +30,7 @@
import javax.xml.ws.Endpoint;
import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
@@ -46,14 +48,28 @@
public class DLLearnerWSStart {
public static void main(String[] args) {
-
- // create web service logger
- SimpleLayout layout = new SimpleLayout();
+
+ //create web service logger
+ SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
Logger logger = Logger.getRootLogger();
+
+ FileAppender fileAppenderNormal = null;
+ File f = new File("log/sparql.txt");
+ try {
+ fileAppenderNormal = new FileAppender(layout, "log/log.txt", false);
+ f.delete();
+ f.createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
+ logger.addAppender(fileAppenderNormal);
logger.setLevel(Level.INFO);
+
InetSocketAddress isa = new InetSocketAddress("localhost", 8181);
HttpServer server = null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2008-06-25 20:33:28
|
Revision: 980
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=980&view=rev
Author: lorenz_b
Date: 2008-06-25 13:33:25 -0700 (Wed, 25 Jun 2008)
Log Message:
-----------
changed return type of method getInconsistentClasses() to NamedClass
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-24 17:04:10 UTC (rev 979)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-25 20:33:25 UTC (rev 980)
@@ -256,7 +256,7 @@
public abstract void releaseKB();
- public Set<OWLClass> getInconsistentClasses() throws ReasoningMethodUnsupportedException{
+ public Set<NamedClass> getInconsistentClasses() throws ReasoningMethodUnsupportedException{
throw new ReasoningMethodUnsupportedException();
}
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-24 17:04:10 UTC (rev 979)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-25 20:33:25 UTC (rev 980)
@@ -937,15 +937,18 @@
}
@Override
- public Set<OWLClass> getInconsistentClasses(){
+ public Set<NamedClass> getInconsistentClasses(){
+ Set<NamedClass> concepts = new HashSet<NamedClass>();
try {
- return reasoner.getInconsistentClasses();
+ for(OWLClass concept : reasoner.getInconsistentClasses())
+ concepts.add(new NamedClass(concept.getURI().toString()));
+
} catch (OWLReasonerException e) {
e.printStackTrace();
- throw new Error("Inconsistens classes check error in OWL API.");
+ throw new Error("Inconsistent classes check error in OWL API.");
}
-
+ return concepts;
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-06-26 15:22:06
|
Revision: 984
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=984&view=rev
Author: kurzum
Date: 2008-06-26 08:21:53 -0700 (Thu, 26 Jun 2008)
Log Message:
-----------
main format for sparqlquery is json now
hope it doesn't produce so much errors now anymore
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
trunk/src/dl-learner/org/dllearner/test/JenaQueryToResultSpeedTest.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -246,12 +246,13 @@
JamonMonitorLogger.getTimeMonitor(Cache.class, "ReadTime").stop();
if (result != null) {
- //query.setJson(result);
+ query.setJson(result);
query.setRunning(false);
- SparqlQuery.writeToSpecialLog("***********\nJSON retrieved from cache");
- SparqlQuery.writeToSpecialLog(query.getQueryString());
- SparqlQuery.writeToSpecialLog(query.getEndpoint().getURL().toString());
+ SparqlQuery.writeToSparqlLog("***********\nJSON retrieved from cache");
+ SparqlQuery.writeToSparqlLog(query.getQueryString());
+ SparqlQuery.writeToSparqlLog(query.getEndpoint().getURL().toString());
+ SparqlQuery.writeToSparqlLog("JSON: "+result);
JamonMonitorLogger.increaseCount(Cache.class, "SuccessfulHits");
} else {
@@ -261,7 +262,7 @@
String json = query.getJson();
if (json!=null){
addToCache(query.getQueryString(), json);
- SparqlQuery.writeToSpecialLog("result added to cache: "+json);
+ SparqlQuery.writeToSparqlLog("result added to cache: "+json);
result=json;
query.setJson(result);
}
@@ -269,7 +270,7 @@
json="";
result="";
logger.warn(Cache.class.getSimpleName()+"empty result: "+query.getQueryString());
- SparqlQuery.writeToSpecialLog("empty result for : "+query.getQueryString());
+ SparqlQuery.writeToSparqlLog("empty result for : "+query.getQueryString());
}
//return json;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SPARQLTasks.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -354,8 +354,8 @@
if(c==null){
SparqlQuery sq = new SparqlQuery(SPARQLquery,se);
// sq.extraDebugInfo+=se.getURL();
- ResultSet rs=sq.send();
- String JSON = SparqlQuery.getAsJSON(rs);
+ sq.send();
+ String JSON = sq.getJson();
return JSON;
}else{
return c.executeSparqlQuery(new SparqlQuery(SPARQLquery,se));
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -45,7 +45,6 @@
import org.dllearner.core.config.StringTupleListConfigOption;
import org.dllearner.core.owl.KB;
import org.dllearner.kb.extraction.Manager;
-import org.dllearner.kb.extraction.Manipulator;
import org.dllearner.kb.extraction.ManipulatorType;
import org.dllearner.kb.extraction.Manipulators;
import org.dllearner.parser.KBParser;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -47,11 +47,12 @@
private boolean isRunning = false;
+ private boolean wasExecuted = false;
private String queryString;
private QueryEngineHTTP queryExecution;
private SparqlEndpoint endpoint;
//private ResultSet rs;
- private String json;
+ private String json = null;
// private SparqlQueryException sendException=null;
/**
@@ -61,7 +62,8 @@
* @param endpoint
*/
public SparqlQuery(String queryString, SparqlEndpoint endpoint) {
- this.queryString = queryString;
+ // QUALITY there seems to be a bug in ontowiki
+ this.queryString = queryString.replaceAll("\n", " ");
this.endpoint = endpoint;
}
@@ -71,17 +73,18 @@
/**
* Sends a SPARQL query using the Jena library.
- * should return JSON String
- * needs refactoring
- * @return ResultSet
+ * main format is JSON use method getasjson
+ *
+ * @return nothing
*/
- @Deprecated
- public ResultSet send() {
+
+ public void send() {
+ wasExecuted = true;
ResultSet rs;
//isRunning = true;
- writeToSpecialLog("***********\nNew Query:");
- writeToSpecialLog(queryString);
- writeToSpecialLog(endpoint.getURL().toString());
+ writeToSparqlLog("***********\nNew Query:");
+ writeToSparqlLog(queryString);
+ writeToSparqlLog(endpoint.getURL().toString());
String service = endpoint.getURL().toString();
@@ -94,6 +97,7 @@
queryExecution.addNamedGraph(ngu);
}
+
//TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").start();
@@ -101,20 +105,17 @@
JamonMonitorLogger.getTimeMonitor(SparqlQuery.class, "httpTime").stop();
- logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
- writeToSpecialLog("query SPARQL server, retrieved: "+rs.getResultVars());
- writeToSpecialLog("Results from ResultSet");
+ logger.debug("query length: "+queryString.length()+" | ENDPOINT: "+endpoint.getURL().toString());
+ //writeToSparqlLog("query: "+queryString+ " | ENDPOINT: "+endpoint.getURL().toString());
+
+
json = SparqlQuery.getAsJSON(rs);
- writeToSpecialLog(json);
- rs = SparqlQuery.JSONtoResultSet(json);
- while (rs.hasNext()){
- writeToSpecialLog("Result: "+rs.nextBinding());
- }
+ writeToSparqlLog("JSON: "+json);
+
isRunning = false;
- rs = SparqlQuery.JSONtoResultSet(json);
- return rs;
+
}
public void stop() {
@@ -143,7 +144,7 @@
// }
/**
- * sends a query and returns XML
+ * Converts Jena result set to XML.
*
* @return String xml
*/
@@ -188,12 +189,25 @@
//System.out.println("JSON " + json);
return ResultSetFactory.fromJSON(bais);
}
+
+ /**
+ * Converts from JSON to xml format.
+ *
+ * @param json
+ * A JSON representation if a SPARQL query result.
+ * @return A Jena ResultSet.
+ */
+ public static String JSONtoXML(String json) {
+ return getAsXMLString(JSONtoResultSet(json));
+ }
public String getJson() {
+ if(wasExecuted == false){this.send();}
return json;
}
public void setJson(String json) {
+ this.wasExecuted=true;
this.json = json;
}
@@ -201,7 +215,7 @@
this.isRunning=running;
}
- public static void writeToSpecialLog(String s){
+ public static void writeToSparqlLog(String s){
try{
FileWriter fw = new FileWriter("log/sparql.txt",true);
fw.write(s+"\n");
@@ -212,7 +226,13 @@
}
}
- /*public ResultSet getResultSet(){
- return rs;
- }*/
+ public ResultSet getResultSet(){
+ if(getJson() == null) {return null;}
+ else return JSONtoResultSet(json) ;
+ }
+
+ public String getXMLString(){
+ if(getJson() == null) {return null;}
+ else return JSONtoXML(json) ;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -519,21 +519,39 @@
{
ClientState state = getState(sessionID);
//ResultSet resultSet=null;
- String json=null;
- if ((json=state.getQuery(queryID).getJson())!=null) return json;
+ String json = null;
+ try {
+ json = state.getQuery(queryID).getJson();
+ }catch (Exception e) {
+ e.printStackTrace();
+ throw new SparqlQueryException("SparqlQuery failed"+e.toString());
+ }
+
+ if(json == null) { throw new SparqlQueryException("SparqlQuery failed JSON was null");}
+ return json;
+ //if ((json=state.getQuery(queryID).getJson())!=null) return json;
//else if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsJSON(resultSet);
- else return SparqlQuery.getAsJSON(state.getQuery(queryID).send());
+ //else return SparqlQuery.getAsJSON(state.getQuery(queryID).send());
}
@WebMethod
- public String getAsXMLString(int sessionID, int queryID) throws ClientNotKnownException
+ public String getAsXMLString(int sessionID, int queryID) throws ClientNotKnownException, SparqlQueryException
{
ClientState state = getState(sessionID);
- //ResultSet resultSet=null;
- String json=null;
+
+ String xml = null;
+ try{
+ xml = state.getQuery(queryID).getXMLString();
+ }catch (Exception e) {
+ e.printStackTrace();
+ throw new SparqlQueryException("SparqlQuery failed"+e.toString());
+ }
+
+ if(xml == null) throw new SparqlQueryException("SparqlQuery failed xml was null");
+ return xml;
//if ((resultSet=state.getQuery(queryID).getResultSet())!=null) return SparqlQuery.getAsXMLString(resultSet);
- if ((json=state.getQuery(queryID).getJson())!=null) return SparqlQuery.getAsXMLString(SparqlQuery.JSONtoResultSet(json));
- else return SparqlQuery.getAsXMLString(state.getQuery(queryID).send());
+ //if ((json=state.getQuery(queryID).getJson())!=null) return SparqlQuery.getAsXMLString(SparqlQuery.JSONtoResultSet(json));
+ //else return SparqlQuery.getAsXMLString(state.getQuery(queryID).send());
}
@WebMethod
@@ -574,7 +592,7 @@
Cache cache=new Cache(ks.getCacheDir());
return cache.executeSparqlQuery(sparql);
}
- else return SparqlQuery.getAsJSON(sparql.send());
+ else return sparql.getJson();
}
@WebMethod
Modified: trunk/src/dl-learner/org/dllearner/test/JenaQueryToResultSpeedTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/JenaQueryToResultSpeedTest.java 2008-06-26 10:44:36 UTC (rev 983)
+++ trunk/src/dl-learner/org/dllearner/test/JenaQueryToResultSpeedTest.java 2008-06-26 15:21:53 UTC (rev 984)
@@ -22,7 +22,6 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
-import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFormatter;
@@ -54,14 +53,14 @@
SparqlEndpoint sse = SparqlEndpoint.EndpointDBpedia();
SparqlQuery sqJena = new SparqlQuery(queryString, sse);
// first query is not counted
- ResultSet rs = sqJena.send();
- SparqlQuery.getAsXMLString(rs);
+ sqJena.send();
+ sqJena.getXMLString();
long now = System.currentTimeMillis();
long tmp = now;
for (int i = 0; i < howOften; i++) {
- rs = sqJena.send();
- SparqlQuery.getAsXMLString(rs);
+ sqJena.send();
+ sqJena.getXMLString();
p("Jena as XML needed: "
+ (System.currentTimeMillis() - tmp));
tmp = System.currentTimeMillis();
@@ -83,8 +82,8 @@
for (int i = 0; i < howOften; i++) {
// sqJena.getAsList();
- ResultSet rs = sqJena.send();
- ResultSetFormatter.toList(rs);
+ sqJena.send();
+ ResultSetFormatter.toList(sqJena.getResultSet());
p("Jena as List needed: "
+ (System.currentTimeMillis() - tmp));
tmp = System.currentTimeMillis();
@@ -100,14 +99,14 @@
SparqlEndpoint sse = SparqlEndpoint.EndpointDBpedia();
SparqlQuery sqJena = new SparqlQuery(queryString, sse);
// first query is not counted
- ResultSet rs = sqJena.send();
- SparqlQuery.getAsJSON(rs);
+ sqJena.send();
+ sqJena.getJson();
long now = System.currentTimeMillis();
long tmp = now;
for (int i = 0; i < howOften; i++) {
- rs = sqJena.send();
- SparqlQuery.getAsJSON(rs);
+ sqJena.send();
+ sqJena.getJson();
p("Jena as JSON needed: "
+ (System.currentTimeMillis() - tmp));
tmp = System.currentTimeMillis();
@@ -123,15 +122,15 @@
SparqlEndpoint sse = SparqlEndpoint.EndpointDBpedia();
SparqlQuery sqJena = new SparqlQuery(queryString, sse);
// first query is not counted
- ResultSet rs = sqJena.send();
- SparqlQuery.getAsJSON(rs);
+ sqJena.send();
+ sqJena.getJson();
long now = System.currentTimeMillis();
long tmp = now;
for (int i = 0; i < howOften; i++) {
// System.out.println(sqJena.getAsJSON());
- rs = sqJena.send();
- String json = SparqlQuery.getAsJSON(rs);
+ sqJena.send();
+ String json = sqJena.getJson();
SparqlQuery.JSONtoResultSet(json);
p("Jena as JSON and back needed: "
+ (System.currentTimeMillis() - tmp));
@@ -150,8 +149,8 @@
SparqlQuery sqJena = new SparqlQuery(queryString, sse);
// SparqlQueryConventional sqConv=new SparqlQueryConventional(sse);
- ResultSet rs = sqJena.send();
- System.out.println(SparqlQuery.getAsXMLString(rs));
+ sqJena.send();
+ System.out.println(sqJena.getJson());
// System.out.println(sqConv.getAsXMLString(""));
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-06-27 14:28:52
|
Revision: 986
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=986&view=rev
Author: jenslehmann
Date: 2008-06-27 07:28:48 -0700 (Fri, 27 Jun 2008)
Log Message:
-----------
extension of abstract LearningAlgorithm class and many subsequent (possibly code-breaking) changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/core/Score.java
trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
trunk/src/dl-learner/org/dllearner/gui/MiniGUI.java
trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
trunk/src/dl-learner/org/dllearner/learningproblems/ScoreThreeValued.java
trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java
trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/scripts/TestValidation.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/LearningPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptTransformation.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -26,6 +26,7 @@
import java.util.List;
import java.util.Map;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -277,8 +278,13 @@
}
@Override
- public Description getBestSolution() {
+ public Description getCurrentlyBestDescription() {
return bestDefinition;
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+ return new EvaluatedDescription(bestDefinition,bestScore);
}
@Override
@@ -286,4 +292,22 @@
stop = true;
}
+ /* (non-Javadoc)
+ * @see org.dllearner.core.LearningAlgorithm#pause()
+ */
+ @Override
+ public void pause() {
+ // TODO Auto-generated method stub
+
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.LearningAlgorithm#resume()
+ */
+ @Override
+ public void resume() {
+ // TODO Auto-generated method stub
+
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -24,6 +24,7 @@
import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -145,12 +146,35 @@
}
@Override
- public Description getBestSolution() {
- return learner.getBestSolution();
+ public Description getCurrentlyBestDescription() {
+ return learner.getCurrentlyBestDescription();
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+ return learner.getCurrentlyBestEvaluatedDescription();
}
@Override
public Score getSolutionScore() {
return learner.getSolutionScore();
}
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.LearningAlgorithm#pause()
+ */
+ @Override
+ public void pause() {
+ // TODO Auto-generated method stub
+
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.LearningAlgorithm#resume()
+ */
+ @Override
+ public void resume() {
+ // TODO Auto-generated method stub
+
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -25,6 +25,7 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.gp.Program;
import org.dllearner.algorithms.gp.GPUtilities;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -117,8 +118,13 @@
}
@Override
- public Description getBestSolution() {
+ public Description getCurrentlyBestDescription() {
return bestDefinition;
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+ return new EvaluatedDescription(bestDefinition,bestScore);
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -1,9 +1,8 @@
package org.dllearner.algorithms;
-import java.util.Set;
-import java.util.List;
import java.util.*;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -25,9 +24,14 @@
//this.learningProblem = learningProblem;
}
- public Description getBestSolution()
+ public Description getCurrentlyBestDescription()
{
return bestSollution;
+ }
+
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription()
+ {
+ return new EvaluatedDescription(bestSollution, solutionScore);
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -30,6 +30,7 @@
import java.util.Map.Entry;
import org.dllearner.algorithms.hybridgp.Psi;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -948,9 +949,14 @@
}
@Override
- public Description getBestSolution() {
+ public Description getCurrentlyBestDescription() {
+ return bestConcept;
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
// return fittestIndividual.getTree();
- return bestConcept;
+ return new EvaluatedDescription(bestConcept,bestScore);
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -25,9 +25,11 @@
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
+import java.util.SortedSet;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -391,21 +393,24 @@
}
@Override
- public Description getBestSolution() {
+ public Description getCurrentlyBestDescription() {
return algorithm.getBestSolution();
}
@Override
- public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
- return algorithm.getBestSolutions(nrOfSolutions);
+ public synchronized SortedSet<Description> getCurrentlyBestDescriptions() {
+ return algorithm.getCurrentlyBestDescriptions();
}
@Override
- public synchronized List<Description> getGoodSolutions() {
- return algorithm.getGoodSolutions();
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+ return new EvaluatedDescription(algorithm.getBestSolution(),algorithm.getSolutionScore());
}
-
+ @Override
+ public synchronized SortedSet<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions() {
+ return algorithm.getCurrentlyBestEvaluatedDescriptions();
+ }
@Override
public void stop() {
@@ -415,14 +420,15 @@
public ExampleBasedNode getStartNode() {
return algorithm.getStartNode();
}
+
+ @Override
+ public void pause() {
+ // TODO: not implemented
+ }
+
+ @Override
+ public void resume() {
+ // TODO: not implemented
+ }
-
- /*public void printBestSolutions(int nrOfSolutions){
-
- algorithm.printBestSolutions(nrOfSolutions);
- }*/
-
-
-
-
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -33,6 +33,7 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.Score;
@@ -455,8 +456,7 @@
String KBSyntax="KBSyntax:\n";
for(Description c : solutions) {
logger.info(show+": " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
- // watch for String.replace Quick hack
- manchester+=show+": "+c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).replace("\"", "")+"\n";
+ manchester+=show+": "+c.toManchesterSyntaxString(baseURI, new HashMap<String,String>())+"\n";
KBSyntax+=show+": " + c.toKBSyntaxString()+"\n";
if(show>=5){break;} show++;
}
@@ -1059,43 +1059,34 @@
return candidatesStable.last().getConcept();
}
-
- public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
- List<Description> best = new LinkedList<Description>();
+ public SortedSet<Description> getCurrentlyBestDescriptions() {
+ SortedSet<Description> best = new TreeSet<Description>();
int i=0;
+ int nrOfSolutions = 200;
for(ExampleBasedNode n : candidatesStable.descendingSet()) {
-
- best.add(n.getConcept());
- if(i==nrOfSolutions)
- return best;
+ best.add(n.getConcept());
+ if(i==nrOfSolutions)
+ return best;
i++;
}
return best;
}
-
- /**
- * returns the solutions, that have at least a certain quality
- * either accuracy = 100% full solutions
- * or accuracy > 100% - noise;
- * @return
- */
- public synchronized List<Description> getGoodSolutions() {
- List<Description> best = new LinkedList<Description>();
-
- for(ExampleBasedNode n : candidatesStable.descendingSet()) {
- if(n.getAccuracy(nrOfPositiveExamples, nrOfNegativeExamples)<(1-noise))
- return best;
- best.add(n.getConcept());
-
+ public SortedSet<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions() {
+ int count = 0;
+ SortedSet<ExampleBasedNode> rev = candidatesStable.descendingSet();
+ SortedSet<EvaluatedDescription> cbd = new TreeSet<EvaluatedDescription>();
+ for(ExampleBasedNode eb : rev) {
+ cbd.add(new EvaluatedDescription(eb.getConcept(), getScore(eb.getConcept())));
+ // return a maximum of 200 elements (we need a maximum, because the
+ // candidate set can be very large)
+ if(count > 200)
+ return cbd;
+ count++;
}
- return best;
+ return cbd;
}
-
-
-
-
public void printBestSolutions(int nrOfSolutions, boolean showOrderedSolutions){
//QUALITY: could be optimized
if(!logger.isTraceEnabled())
@@ -1136,6 +1127,13 @@
return learningProblem.computeScore(getBestSolution());
}
+ private Score getScore(Description d) {
+ if(posOnly)
+ return posOnlyLearningProblem.computeScore(d);
+ else
+ return learningProblem.computeScore(d);
+ }
+
public ExampleBasedNode getStartNode() {
return startNode;
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -14,6 +14,7 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
+import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -1033,8 +1034,13 @@
}
@Override
- public Description getBestSolution() {
+ public Description getCurrentlyBestDescription() {
return candidatesStable.last().getConcept();
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+ return new EvaluatedDescription(candidatesStable.last().getConcept(), getSolutionScore());
}
public void printBestSolutions(int nrOfSolutions){
@@ -1050,7 +1056,7 @@
}
@Override
- public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
+ public synchronized List<Description> getCurrentlyBestDescriptions(int nrOfSolutions) {
List<Description> best = new LinkedList<Description>();
int i=0;
for(Node n : candidatesStable.descendingSet()) {
@@ -1065,9 +1071,9 @@
@Override
public Score getSolutionScore() {
if(posOnly)
- return posOnlyLearningProblem.computeScore(getBestSolution());
+ return posOnlyLearningProblem.computeScore(getCurrentlyBestEvaluatedDescription().getDescription());
else
- return learningProblem.computeScore(getBestSolution());
+ return learningProblem.computeScore(getCurrentlyBestEvaluatedDescription().getDescription());
}
Added: trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -0,0 +1,108 @@
+/**
+ * Copyright (C) 2007-2008, 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.core;
+
+import java.util.Set;
+
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.learningproblems.ScoreTwoValued;
+
+/**
+ * This represents a class description, which has been
+ * evaluated by the learning algorithm, i.e. it has been checked
+ * which examples it covers. It can be used as return value for
+ * learning algorithms to make it easier for applications to
+ * assess how good an offered class description is and how it
+ * classifies particular examples.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class EvaluatedDescription {
+
+ private Description description;
+ private Score score;
+
+ public EvaluatedDescription(Description description, Score score) {
+ this.description = description;
+ this.score = score;
+ }
+
+ public EvaluatedDescription(Description description, Set<Individual> posAsPos, Set<Individual> posAsNeg, Set<Individual> negAsPos, Set<Individual> negAsNeg) {
+ this.description = description;
+ // usually core methods should not depend on methods outside of the core package (except utilities)
+ // in this case, this is just a convenience constructor
+ score = new ScoreTwoValued(posAsPos, posAsNeg, negAsPos, negAsNeg);
+ }
+
+ public Description getDescription() {
+ return description;
+ }
+
+ public int getDescriptionLength() {
+ return description.getLength();
+ }
+
+ public int getDescriptionDepth() {
+ return description.getDepth();
+ }
+
+ /**
+ * @return
+ * @see org.dllearner.core.Score#getAccuracy()
+ */
+ public double getAccuracy() {
+ return score.getAccuracy();
+ }
+
+ /**
+ * @return
+ * @see org.dllearner.core.Score#getCoveredNegatives()
+ */
+ public Set<Individual> getCoveredNegatives() {
+ return score.getCoveredNegatives();
+ }
+
+ /**
+ * @return
+ * @see org.dllearner.core.Score#getCoveredPositives()
+ */
+ public Set<Individual> getCoveredPositives() {
+ return score.getCoveredPositives();
+ }
+
+ /**
+ * @return
+ * @see org.dllearner.core.Score#getNotCoveredNegatives()
+ */
+ public Set<Individual> getNotCoveredNegatives() {
+ return score.getNotCoveredNegatives();
+ }
+
+ /**
+ * @return
+ * @see org.dllearner.core.Score#getNotCoveredPositives()
+ */
+ public Set<Individual> getNotCoveredPositives() {
+ return score.getNotCoveredPositives();
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -1,5 +1,5 @@
/**
- * Copyright (C) 2007, Jens Lehmann
+ * Copyright (C) 2007-2008, Jens Lehmann
*
* This file is part of DL-Learner.
*
@@ -22,73 +22,188 @@
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.core.owl.Description;
+import org.dllearner.utilities.owl.ConceptTransformation;
/**
+ * Abstract superclass of all learning algorithm implementations.
+ * Includes support for anytime learning algorithms and resumable
+ * learning algorithms. Provides methods for filtering the best
+ * descriptions found by the algorithm. As results of the algorithm,
+ * you can either get only descriptions or evaluated descriptions.
+ * Evaluated descriptions have information about accuracy and
+ * example coverage associated with them. However, retrieving those
+ * may require addition reasoner queries, because the learning
+ * algorithms usually use but do not necessarily store this information.
+ *
* @author Jens Lehmann
*
*/
public abstract class LearningAlgorithm extends Component {
/**
- * Starts the algorithm.
- *
+ * Starts the algorithm. It runs until paused, stopped, or
+ * a termination criterion has been reached.
*/
public abstract void start();
-
/**
- * Stops the algorithm gracefully.
- *
+ * Pauses the algorithm (not all algorithms need to implement
+ * this operation).
*/
+ public void pause() { };
+
+ /**
+ * Resumes the algorithm (not all algorithms need to implement
+ * this operation). You can use this method to continue
+ * an algorithm run even after a termination criterion has been
+ * reached. It will run until paused, stopped, or terminated
+ * again.
+ */
+ public void resume() { };
+
+ /**
+ * Stops the algorithm gracefully. A stopped algorithm cannot be resumed anymore.
+ * Use this method for cleanup and freeing memory.
+ */
public abstract void stop();
-
+
/**
* Every algorithm must be able to return the score of the
* best solution found.
+ *
* @return Best score.
*/
+ @Deprecated
public abstract Score getSolutionScore();
/**
- * Returns the best solutions obtained so far.
- * @return Best solution.
+ * @see #getCurrentlyBestEvaluatedDescription()
*/
- public abstract Description getBestSolution();
+ public abstract Description getCurrentlyBestDescription();
+ /**
+ * @see #getCurrentlyBestEvaluatedDescriptions()
+ */
+ public SortedSet<Description> getCurrentlyBestDescriptions() {
+ TreeSet<Description> ds = new TreeSet<Description>();
+ ds.add(getCurrentlyBestDescription());
+ return ds;
+ }
+ /**
+ * @see #getCurrentlyBestEvaluatedDescriptions(int)
+ */
+ public synchronized List<Description> getCurrentlyBestDescriptions(int nrOfDescriptions) {
+ return getCurrentlyBestDescriptions(nrOfDescriptions, false);
+ }
/**
- * returns the best nrOfSolutions solutions
- * regardless of quality, just depends on input int
- * @param nrOfSolutions
- * @return List<Description>
+ * @see #getCurrentlyBestEvaluatedDescriptions(int,double,boolean)
*/
- public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
- List<Description> single = new LinkedList<Description>();
- single.add(getBestSolution());
- return single;
+ public synchronized List<Description> getCurrentlyBestDescriptions(int nrOfDescriptions, boolean filterNonMinimalDescriptions) {
+ SortedSet<Description> currentlyBest = getCurrentlyBestDescriptions();
+ List<Description> returnList = new LinkedList<Description>();
+ int count = 0;
+ for(Description ed : currentlyBest) {
+ // return if we have sufficiently many descriptions
+ if(count >= nrOfDescriptions)
+ return returnList;
+
+ if(!filterNonMinimalDescriptions || ConceptTransformation.isDescriptionMinimal(ed))
+ returnList.add(ed);
+
+ count++;
+ }
+ return returnList;
+ }
+
+ /**
+ * Returns the best descriptions obtained so far.
+ * @return Best class description found so far.
+ */
+ public abstract EvaluatedDescription getCurrentlyBestEvaluatedDescription();
+
+ /**
+ * Returns a sorted set of the best descriptions found so far. We
+ * assume that they are ordered such that the best ones come in
+ * first.
+ * @return Best class descriptions found so far.
+ */
+ public SortedSet<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions() {
+ TreeSet<EvaluatedDescription> ds = new TreeSet<EvaluatedDescription>();
+ ds.add(getCurrentlyBestEvaluatedDescription());
+ return ds;
}
/**
- * returns the solutions, that have at least a certain quality
- * either accuracy = 100%, i.e. full solutions
- * or accuracy > 100% - noise;
- * @return
+ * Returns a filtered list of currently best class descriptions.
+ *
+ * @param nrOfDescriptions Maximum number of restrictions. Use Integer.MAX_VALUE
+ * if you do not want this filter to be active.
+ *
+ * @param accuracyThreshold Minimum accuracy. All class descriptions with lower
+ * accuracy are disregarded. Specify a value between 0.0 and 1.0. Use 0.0 if
+ * you do not want this filter to be active.
+ *
+ * @param filterNonMinimalDescriptions If true, non-minimal descriptions are
+ * filtered, e.g. ALL r.TOP (being equivalent to TOP), male AND male (can be
+ * shortened to male). Currently, non-minimal descriptions are just skipped,
+ * i.e. they are completely omitted from the return list. Later, implementation
+ * might be changed to return shortened versions of those descriptions.
+ *
+ * @return A list of currently best class descriptions.
*/
- public synchronized List<Description> getGoodSolutions() {
- List<Description> single = new LinkedList<Description>();
- single.add(getBestSolution());
- return single;
+ public synchronized List<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions(int nrOfDescriptions, double accuracyThreshold, boolean filterNonMinimalDescriptions) {
+ SortedSet<EvaluatedDescription> currentlyBest = getCurrentlyBestEvaluatedDescriptions();
+ List<EvaluatedDescription> returnList = new LinkedList<EvaluatedDescription>();
+ int count = 0;
+ for(EvaluatedDescription ed : currentlyBest) {
+ // once we hit a description with a below threshold accuracy, we simply return
+ // because learning algorithms are advised to order descriptions by accuracy,
+ // so we won't find any concept with higher accuracy in the remaining list
+ if(ed.getAccuracy() < accuracyThreshold)
+ return returnList;
+
+ // return if we have sufficiently many descriptions
+ if(count >= nrOfDescriptions)
+ return returnList;
+
+ if(!filterNonMinimalDescriptions || ConceptTransformation.isDescriptionMinimal(ed.getDescription()))
+ returnList.add(ed);
+
+ count++;
+ }
+ return returnList;
}
+ /**
+ * Return the best currently found concepts up to some maximum
+ * count (no minimality filter used).
+ * @param nrOfDescriptions Maximum number of descriptions returned.
+ * @return Return value is getCurrentlyBestDescriptions(nrOfDescriptions, 0.0, false).
+ */
+ public synchronized List<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions(int nrOfDescriptions) {
+ return getCurrentlyBestEvaluatedDescriptions(nrOfDescriptions, 0.0, false);
+ }
/**
+ * Returns a fraction of class descriptions with sufficiently high accuracy.
+ * @param accuracyThreshold Only return solutions with this accuracy or higher.
+ * @return Return value is getCurrentlyBestDescriptions(Integer.MAX_VALUE, accuracyThreshold, false).
+ */
+ public synchronized List<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions(double accuracyThreshold) {
+ return getCurrentlyBestEvaluatedDescriptions(Integer.MAX_VALUE, accuracyThreshold, false);
+ }
+
+ /**
* Returns all learning problems supported by this component.
*/
public static Collection<Class<? extends LearningProblem>> supportedLearningProblems() {
return new LinkedList<Class<? extends LearningProblem>>();
}
-
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/Score.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/Score.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/core/Score.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -1,3 +1,23 @@
+/**
+ * Copyright (C) 2007-2008, 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.core;
import java.util.Set;
@@ -4,9 +24,26 @@
import org.dllearner.core.owl.Individual;
+/**
+ * The score class is used to store how well a class description did
+ * on a learning problem.
+ *
+ * @author Jens Lehmann
+ *
+ */
public abstract class Score {
+
+ // accuracy
+ public abstract double getAccuracy();
+
+ // example coverage
+ public abstract Set<Individual> getCoveredPositives();
+ public abstract Set<Individual> getCoveredNegatives();
+ public abstract Set<Individual> getNotCoveredPositives();
+ public abstract Set<Individual> getNotCoveredNegatives();
+
+ // older methods (not frequently used anymore)
public abstract double getScore();
-
/**
* The score of a concept depends on how good it classifies the
* examples of a learning problem and the length of the concept
@@ -20,9 +57,4 @@
*/
public abstract Score getModifiedLengthScore(int newLength);
- public abstract Set<Individual> getCoveredPositives();
- public abstract Set<Individual> getCoveredNegatives();
- public abstract Set<Individual> getNotCoveredPositives();
-
- // public abstract int getNrOfMiss
}
Modified: trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -284,7 +284,7 @@
//System.out.println("best"+la.getBestSolution());
}catch (Exception e) {e.printStackTrace();}
- return la.getBestSolution();
+ return la.getCurrentlyBestDescription();
}
static KB getKB(SortedSet<Integer> lines){
Modified: trunk/src/dl-learner/org/dllearner/gui/MiniGUI.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/MiniGUI.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/gui/MiniGUI.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -198,7 +198,7 @@
// wait for a solution (note that not all learning problems have a
// solution (100% accuracy), so one usually has to run the algorithm in its own
// thread, such that it can be aborted after some time
- Description solution = la.getBestSolution();
+ Description solution = la.getCurrentlyBestDescription();
solutionDisplay.setText(solution.toString());
}
}
Modified: trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -172,9 +172,9 @@
infoArea.setText("");
// best solutions
- if (config.getLearningAlgorithm().getBestSolutions(5) != null) {
+ if (config.getLearningAlgorithm().getCurrentlyBestEvaluatedDescriptions(5) != null) {
infoArea.append("Best solutions: \n\n"
- + listToString(config.getLearningAlgorithm().getBestSolutions(10)) + "\n");
+ + listToString(config.getLearningAlgorithm().getCurrentlyBestEvaluatedDescriptions(10)) + "\n");
}
// solution score
// if (config.getLearningAlgorithm().getSolutionScore() != null)
@@ -257,7 +257,7 @@
if (millis > 0)
time += millis + "ms ";
if (false)
- time += mikros + "\xB5s ";
+ time += mikros + "�s ";
if (false)
time += nanos + "ns ";
return time;
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/ScoreThreeValued.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/ScoreThreeValued.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/ScoreThreeValued.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -233,6 +233,22 @@
@Override
public Score getModifiedLengthScore(int newLength) {
return new ScoreThreeValued(newLength, accuracyPenalty, errorPenalty, penaliseNeutralExamples, percentPerLengthUnit, posClassified, neutClassified, negClassified, posExamples, neutExamples, negExamples);
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Score#getAccuracy()
+ */
+ @Override
+ public double getAccuracy() {
+ return accuracy;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Score#getNotCoveredNegatives()
+ */
+ @Override
+ public Set<Individual> getNotCoveredNegatives() {
+ return negAsNeg;
}
}
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -1,3 +1,23 @@
+/**
+ * Copyright (C) 2007-2008, 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.learningproblems;
import java.util.Set;
@@ -6,10 +26,15 @@
import org.dllearner.core.owl.Individual;
/**
+ * Calculates accuracy and score (with respect to some length penalty) of
+ * a class description.
*
- * TODO: accuracy-Berechnung (positive+negative Beispiele muessen dafuer bekannt sein)
+ * TODO: In fact, a score value influencing a learning algorithm
+ * should not be calculated here, but rather in a separate heuristic
+ * as there are many methods to calculate such a value. This class
+ * should only be used for computing example coverage, accuracy etc.
*
- * @author jl
+ * @author Jens Lehmann
*
*/
public class ScoreTwoValued extends Score {
@@ -19,11 +44,15 @@
private Set<Individual> negAsPos;
private Set<Individual> negAsNeg;
private double score;
- private double classificationScore;
+ private double accuracy;
private int nrOfExamples;
private int conceptLength;
private double percentPerLengthUnit;
+ public ScoreTwoValued(Set<Individual> posAsPos, Set<Individual> posAsNeg, Set<Individual> negAsPos, Set<Individual> negAsNeg) {
+ this(0,0,posAsPos,posAsNeg,negAsPos,posAsPos);
+ }
+
public ScoreTwoValued(int conceptLength, double percentPerLengthUnit, Set<Individual> posAsPos, Set<Individual> posAsNeg, Set<Individual> negAsPos, Set<Individual> negAsNeg) {
this.conceptLength = conceptLength;
this.percentPerLengthUnit = percentPerLengthUnit;
@@ -36,15 +65,22 @@
}
private void computeScore() {
- // - Anzahl falscher Klassifikationen
- classificationScore = - posAsNeg.size() - negAsPos.size();
- // Anteil falscher Klassifikationen (Zahl zwischen -1 und 0)
- classificationScore = classificationScore / (double) nrOfExamples;
- // Berücksichtigung des Längenfaktors
- score = classificationScore - percentPerLengthUnit * conceptLength;
+ // compute accuracy
+ accuracy = posAsPos.size() + negAsNeg.size();
+ accuracy = accuracy / (double) nrOfExamples;
+ // compute score
+ score = accuracy - 1 - percentPerLengthUnit * conceptLength;
}
@Override
+ public double getAccuracy() {
+ return accuracy;
+ }
+
+ /**
+ * score = accuracy - 1 - length * length penalty
+ */
+ @Override
public double getScore() {
return score;
}
@@ -53,7 +89,7 @@
public String toString() {
String str = "";
str += "score: " + score + "\n";
- str += "accuracy: " + (1 + classificationScore) + "\n";
+ str += "accuracy: " + accuracy + "\n";
str += "posAsPos (" + posAsPos.size() + "): " + posAsPos + "\n";
str += "positive examples classified as negative (" + posAsNeg.size() + "): " + posAsNeg + "\n";
str += "negative examples classified as positive (" + negAsPos.size() + "): " + negAsPos + "\n";
@@ -74,16 +110,15 @@
public Set<Individual> getNotCoveredPositives() {
return posAsNeg;
}
-
- /*
+
@Override
- public double getModifiedLengthScore(int newLength) {
- return classificationScore - Config.percentPerLengthUnit * newLength;
- }
- */
+ public Set<Individual> getNotCoveredNegatives() {
+ return negAsNeg;
+ }
@Override
public Score getModifiedLengthScore(int newLength) {
return new ScoreTwoValued(newLength, percentPerLengthUnit, posAsPos, posAsNeg, negAsPos, negAsNeg);
- }
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -222,7 +222,7 @@
long algorithmDuration = System.nanoTime() - algorithmStartTime;
runtime.addNumber(algorithmDuration/(double)1000000000);
- Description concept = la.getBestSolution();
+ Description concept = la.getCurrentlyBestDescription();
ReasoningService rs = start.getReasoningService();
Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -89,7 +89,7 @@
s.makeExamples(prim, percentOfSKOSSet, negfactor, sparqlResultSize);
- List<Description> conceptresults = s.learn();
+ SortedSet<Description> conceptresults = s.learn();
logger.debug("found nr of concepts: "+conceptresults.size());
System.out.println(conceptresults);
@@ -249,7 +249,7 @@
logger.debug(fullPosSetWithoutPosExamples);
}
- public List<Description> learn(){
+ public SortedSet<Description> learn(){
SortedSet<String> instances = new TreeSet<String>();
instances.addAll(this.posExamples);
@@ -330,7 +330,7 @@
//Statistics.addTimeLearning(sc.getTime());
- return la.getGoodSolutions();
+ return la.getCurrentlyBestDescriptions();
}catch (Exception e) {e.printStackTrace();}
return null;
Modified: trunk/src/dl-learner/org/dllearner/scripts/TestValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/TestValidation.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/scripts/TestValidation.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -57,7 +57,7 @@
Start start = new Start(new File(filenameTrain));
start.start(false);
- Description solution = start.getLearningAlgorithm().getBestSolution();
+ Description solution = start.getLearningAlgorithm().getCurrentlyBestDescription();
logger.setLevel(Level.WARN);
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -308,7 +308,7 @@
public String learn(int id, String format) throws ClientNotKnownException {
ClientState state = getState(id);
state.getLearningAlgorithm().start();
- Description solution = state.getLearningAlgorithm().getBestSolution();
+ Description solution = state.getLearningAlgorithm().getCurrentlyBestDescription();
if(format.equals("manchester"))
return solution.toManchesterSyntaxString(state.getReasoningService().getBaseURI(), new HashMap<String,String>());
else if(format.equals("kb"))
@@ -342,13 +342,13 @@
@WebMethod
public String getCurrentlyBestConcept(int id) throws ClientNotKnownException {
ClientState state = getState(id);
- return state.getLearningAlgorithm().getBestSolution().toString();
+ return state.getLearningAlgorithm().getCurrentlyBestEvaluatedDescription().toString();
}
@WebMethod
public String[] getCurrentlyBestConcepts(int id, int nrOfConcepts) throws ClientNotKnownException {
ClientState state = getState(id);
- List<Description> bestConcepts = state.getLearningAlgorithm().getBestSolutions(nrOfConcepts);
+ List<Description> bestConcepts = state.getLearningAlgorithm().getCurrentlyBestDescriptions(nrOfConcepts);
List<String> conc=new LinkedList<String>();
Iterator<Description> iter=bestConcepts.iterator();
while (iter.hasNext())
@@ -612,7 +612,7 @@
@WebMethod
public int[] getConceptDepth(int id, int nrOfConcepts) throws ClientNotKnownException {
ClientState state = getState(id);
- List<Description> bestConcepts = state.getLearningAlgorithm().getBestSolutions(nrOfConcepts);
+ List<Description> bestConcepts = state.getLearningAlgorithm().getCurrentlyBestDescriptions(nrOfConcepts);
Iterator<Description> iter=bestConcepts.iterator();
int[] length=new int[bestConcepts.size()];
int i=0;
@@ -626,7 +626,7 @@
@WebMethod
public int[] getConceptArity(int id, int nrOfConcepts) throws ClientNotKnownException {
ClientState state = getState(id);
- List<Description> bestConcepts = state.getLearningAlgorithm().getBestSolutions(nrOfConcepts);
+ List<Description> bestConcepts = state.getLearningAlgorithm().getCurrentlyBestDescriptions(nrOfConcepts);
Iterator<Description> iter=bestConcepts.iterator();
int[] arity=new int[bestConcepts.size()];
int i=0;
Modified: trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -97,7 +97,7 @@
// start the algorithm and print the best concept found
la.start();
- System.out.println(la.getBestSolution());
+ System.out.println(la.getCurrentlyBestEvaluatedDescription());
}
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/LearningPanelDescriptor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/LearningPanelDescriptor.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/LearningPanelDescriptor.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -69,7 +69,7 @@
la = getWizardModel().getOre().start();//started endlosen Algorithmus
- publish(la.getBestSolutions(10));
+ publish(la.getCurrentlyBestDescriptions(10));
List<Description> result = getWizardModel().getOre().getLearningResults(100);
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -177,15 +177,15 @@
}
public Description getLearningResult(){
- return la.getBestSolution();
+ return la.getCurrentlyBestDescription();
}
- public List<Description> getSolutions(){
- return la.getGoodSolutions();
- }
+// public List<Description> getSolutions(){
+// return la.getCurrentlyBestDescriptions();
+// }
public List<Description> getLearningResults(int anzahl){
- return la.getBestSolutions(anzahl);
+ return la.getCurrentlyBestDescriptions(anzahl);
}
/**
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -224,9 +224,9 @@
*/
private void addToListModel()
{
- for(int j = 0;j<la.getBestSolutions(anzahl).size();j++)
+ for(int j = 0;j<la.getCurrentlyBestEvaluatedDescriptions(anzahl).size();j++)
{
- suggestModel.add(j,la.getBestSolutions(anzahl).get(j));
+ suggestModel.add(j,la.getCurrentlyBestEvaluatedDescriptions(anzahl).get(j));
}
}
@@ -352,7 +352,7 @@
error = "Learning succesful";
// start the algorithm and print the best concept found
la.start();
- description = new Description[la.getBestSolutions(anzahl).size()];
+ description = new Description[la.getCurrentlyBestEvaluatedDescriptions(anzahl).size()];
addToListModel();
view.renderErrorMessage(error);
view.getRunButton().setEnabled(true);
Modified: trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptTransformation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptTransformation.java 2008-06-27 13:44:33 UTC (rev 985)
+++ trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptTransformation.java 2008-06-27 14:28:48 UTC (rev 986)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, 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.utilities.owl;
import java.util.Collections;
@@ -21,8 +40,11 @@
import org.dllearner.core.owl.ObjectQuantorRestriction;
import org.dllearner.core.owl.Thing;
-// ev. kann man diese Klasse später in ein anderes Paket ziehen, da sie nicht direkt mit
-// refinement zu tun hat
+/**
+ * Concept transformation and concept checking methods.
+ *
+ * @author Jens Lehmann
+ */
public class ConceptTransformation {
public static long cleaningTimeNs = 0;
@@ -386,4 +408,39 @@
return concept;
}
+ /**
+ * Method to determine, whether a class description is minimal,
+ * e.g. \forall r.\top (\equiv \top) or male \sqcup male are not
+ * minimal. This method performs heuristic sanity checks (it will
+ * not try to find semantically equivalent shorter descriptions).
+ * @param description Input description.
+ * @return True if a superfluous construct has been found.
+ */
+ public static boolean isDescriptionMinimal(Description description) {
+ ConceptComparator cc = new ConceptComparator();
+ int length = description.getLength();
+ int length2 = ConceptTransformation.getShortConcept(description, cc).getLength();
+ if(length2 < length)
+ return false;
+ if(ConceptTransformation.findEquivalences(description))
+ return false;
+ return true;
+ }
+
+ private static boolean findEquivalences(Description description) {
+ // \exists r.\bot \equiv \bot
+ if(description instanceof ObjectSomeRestriction && description.getChild(0) instanceof Nothing)
+ return true;
+ // \forall r.\top \equiv \top
+ if(description instanceof ObjectAllRestriction && description.getChild(0) instanceof Thing)
+ return true;
+ // check children
+ for(Description child : description.getChildren()) {
+ if(findEquivalences(child))
+ return true;
+ }
+ // false if none of the checks was successful
+ return false;
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-06-28 07:28:20
|
Revision: 991
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=991&view=rev
Author: jenslehmann
Date: 2008-06-28 00:28:11 -0700 (Sat, 28 Jun 2008)
Log Message:
-----------
- comparator for evaluated descriptions
- fixed some warnings
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, 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.algorithms;
import java.util.*;
@@ -4,79 +23,80 @@
import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.LearningAlgorithm;
-import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.Score;
import org.dllearner.core.owl.*;
-public class SimpleSuggestionLearningAlgorithm extends LearningAlgorithm implements Runnable{
+/**
+ * TODO: Javadoc
+ * TODO: Extend such that it can really be used as learning algorithm.
+ *
+ * @author Christian Kötteritzsch
+ *
+ */
+public class SimpleSuggestionLearningAlgorithm extends LearningAlgorithm implements Runnable {
-private Score solutionScore;
-private boolean stop = false;
-private Description bestSollution;
-private Set<Description> simpleSuggestions;
-private LearningProblem learningProblem;
+ private boolean stop = false;
+ private Score solutionScore;
+ private Description bestSollution;
+ private Set<Description> simpleSuggestions;
- public SimpleSuggestionLearningAlgorithm()
- {
- //this.learningProblem = learningProblem;
+ public SimpleSuggestionLearningAlgorithm() {
+ // this.learningProblem = learningProblem;
}
-
- public Description getCurrentlyBestDescription()
- {
+
+ @Override
+ public Description getCurrentlyBestDescription() {
return bestSollution;
- }
-
- public EvaluatedDescription getCurrentlyBestEvaluatedDescription()
- {
+ }
+
+ @Override
+ public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
return new EvaluatedDescription(bestSollution, solutionScore);
}
-
-
- public void stop()
- {
+
+ @Override
+ public void stop() {
stop = true;
}
-
- public void start()
- {
-
+
+ @Override
+ public void start() {
+
}
-
- public <T> void applyConfigEntry(ConfigEntry<T> entry)
- {
-
+
+ @Override
+ public <T> void applyConfigEntry(ConfigEntry<T> entry) {
+
}
-
- public void init()
- {
-
+
+ @Override
+ public void init() {
+
}
-
- public Score getSolutionScore()
- {
+
+ @Override
+ public Score getSolutionScore() {
return solutionScore;
}
-
- public void run()
- {
-
+
+ public void run() {
+
}
-
- public Set<Description> getSimpleSuggestions(ReasoningService rs,Set<Individual> indi) {
+
+ public Set<Description> getSimpleSuggestions(ReasoningService rs, Set<Individual> indi) {
// EXISTS property.TOP
// ESISTS hasChild
// EXISTS hasChild.male
- simpleSuggestions= new HashSet<Description>();
- List<ObjectProperty> test=rs.getAtomicRolesList();
- while(test.iterator().hasNext())
- {
- test.iterator().next();
- Description d1 = new ObjectSomeRestriction(test.iterator().next(), new Thing());
- test.remove(rs.getAtomicRolesList().iterator().next());
- simpleSuggestions.add(d1);
+ simpleSuggestions = new HashSet<Description>();
+ List<ObjectProperty> test = rs.getAtomicRolesList();
+ while (test.iterator().hasNext()) {
+ test.iterator().next();
+ Description d1 = new ObjectSomeRestriction(test.iterator().next(), new Thing());
+ test.remove(rs.getAtomicRolesList().iterator().next());
+ simpleSuggestions.add(d1);
}
return simpleSuggestions;
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -398,7 +398,7 @@
}
@Override
- public synchronized SortedSet<Description> getCurrentlyBestDescriptions() {
+ public synchronized List<Description> getCurrentlyBestDescriptions() {
return algorithm.getCurrentlyBestDescriptions();
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -50,6 +50,7 @@
import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.ConceptTransformation;
+import org.dllearner.utilities.owl.EvaluatedDescriptionComparator;
/**
* Implements the example based refinement operator learning
@@ -167,6 +168,8 @@
// comparator used to create ordered sets of concepts
private ConceptComparator conceptComparator = new ConceptComparator();
+ // comparator for evaluated descriptions
+ private EvaluatedDescriptionComparator edComparator = new EvaluatedDescriptionComparator();
// utility variables
private DecimalFormat df = new DecimalFormat();
@@ -1059,8 +1062,8 @@
return candidatesStable.last().getConcept();
}
- public SortedSet<Description> getCurrentlyBestDescriptions() {
- SortedSet<Description> best = new TreeSet<Description>();
+ public List<Description> getCurrentlyBestDescriptions() {
+ List<Description> best = new LinkedList<Description>();
int i=0;
int nrOfSolutions = 200;
for(ExampleBasedNode n : candidatesStable.descendingSet()) {
@@ -1075,7 +1078,7 @@
public SortedSet<EvaluatedDescription> getCurrentlyBestEvaluatedDescriptions() {
int count = 0;
SortedSet<ExampleBasedNode> rev = candidatesStable.descendingSet();
- SortedSet<EvaluatedDescription> cbd = new TreeSet<EvaluatedDescription>();
+ SortedSet<EvaluatedDescription> cbd = new TreeSet<EvaluatedDescription>(edComparator);
for(ExampleBasedNode eb : rev) {
cbd.add(new EvaluatedDescription(eb.getConcept(), getScore(eb.getConcept())));
// return a maximum of 200 elements (we need a maximum, because the
Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -88,8 +88,8 @@
/**
* @see #getCurrentlyBestEvaluatedDescriptions()
*/
- public SortedSet<Description> getCurrentlyBestDescriptions() {
- TreeSet<Description> ds = new TreeSet<Description>();
+ public List<Description> getCurrentlyBestDescriptions() {
+ List<Description> ds = new LinkedList<Description>();
ds.add(getCurrentlyBestDescription());
return ds;
}
@@ -105,7 +105,7 @@
* @see #getCurrentlyBestEvaluatedDescriptions(int,double,boolean)
*/
public synchronized List<Description> getCurrentlyBestDescriptions(int nrOfDescriptions, boolean filterNonMinimalDescriptions) {
- SortedSet<Description> currentlyBest = getCurrentlyBestDescriptions();
+ List<Description> currentlyBest = getCurrentlyBestDescriptions();
List<Description> returnList = new LinkedList<Description>();
int count = 0;
for(Description ed : currentlyBest) {
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -34,7 +34,6 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
-import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.BooleanValueRestriction;
import org.dllearner.core.owl.DataRange;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -89,7 +89,7 @@
s.makeExamples(prim, percentOfSKOSSet, negfactor, sparqlResultSize);
- SortedSet<Description> conceptresults = s.learn();
+ List<Description> conceptresults = s.learn();
logger.debug("found nr of concepts: "+conceptresults.size());
System.out.println(conceptresults);
@@ -249,7 +249,7 @@
logger.debug(fullPosSetWithoutPosExamples);
}
- public SortedSet<Description> learn(){
+ public List<Description> learn(){
SortedSet<String> instances = new TreeSet<String>();
instances.addAll(this.posExamples);
Modified: trunk/src/dl-learner/org/dllearner/test/ComponentTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/test/ComponentTest.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -24,7 +24,6 @@
import java.util.TreeSet;
import org.dllearner.algorithms.DBpediaNavigationSuggestor;
-import org.dllearner.algorithms.RandomGuesser;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.KnowledgeSource;
@@ -35,7 +34,6 @@
import org.dllearner.core.ReasoningService;
import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.PosNegDefinitionLP;
-import org.dllearner.reasoning.DIGReasoner;
import org.dllearner.reasoning.OWLAPIReasoner;
/**
Modified: trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java 2008-06-27 16:49:46 UTC (rev 990)
+++ trunk/src/dl-learner/org/dllearner/utilities/datastructures/ResultConceptSorter.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -2,8 +2,7 @@
import java.util.SortedSet;
-import org.dllearner.core.owl.Description;
-
+// class is not used anywhere and is not documented - delete?
public class ResultConceptSorter implements Comparable<ResultConceptSorter> {
String concept;
SortedSet<String> instances;
Added: trunk/src/dl-learner/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java 2008-06-28 07:28:11 UTC (rev 991)
@@ -0,0 +1,61 @@
+/**
+ * Copyright (C) 2007-2008, 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.utilities.owl;
+
+import java.util.Comparator;
+
+import org.dllearner.core.EvaluatedDescription;
+
+/**
+ * Comparator for evaluated descriptions, which orders them by
+ * accuracy as first criterion, length as second criterion, and
+ * syntactic structure as third criterion.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class EvaluatedDescriptionComparator implements Comparator<EvaluatedDescription> {
+
+ ConceptComparator cc = new ConceptComparator();
+
+ /* (non-Javadoc)
+ * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+ */
+ @Override
+ public int compare(EvaluatedDescription ed1, EvaluatedDescription ed2) {
+ double acc1 = ed1.getAccuracy();
+ double acc2 = ed2.getAccuracy();
+ if(acc1 > acc2)
+ return 1;
+ else if(acc1 < acc2)
+ return -1;
+ else {
+ int length1 = ed1.getDescriptionLength();
+ int length2 = ed2.getDescriptionLength();
+ if(length1 < length2)
+ return 1;
+ else if(length1 > length2)
+ return -1;
+ else
+ return cc.compare(ed1.getDescription(), ed2.getDescription());
+ }
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-06-30 08:56:15
|
Revision: 992
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=992&view=rev
Author: jenslehmann
Date: 2008-06-30 01:56:11 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
- added convenience method to get SPARQL query for evaluated description
- fixed all warnings (you should now have zero errors, zero warnings, zero notices)
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java
trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
trunk/src/dl-learner/org/dllearner/tools/ore/NegExampleRepairDialog.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -53,12 +53,12 @@
*/
public class DBpediaNavigationSuggestor extends LearningAlgorithm {
- private ReasoningService rs;
+// private ReasoningService rs;
private ExampleBasedROLComponent learner;
private static String defaultSearchTreeFile = "log/searchTree.txt";
public DBpediaNavigationSuggestor(LearningProblem learningProblem, ReasoningService rs) {
- this.rs=rs;
+// this.rs=rs;
if(learningProblem instanceof PosNegLP) {
PosNegLP lp = (PosNegLP) learningProblem;
this.learner=new ExampleBasedROLComponent(lp, rs);
Modified: trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/algorithms/SimpleSuggestionLearningAlgorithm.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -38,7 +38,7 @@
*/
public class SimpleSuggestionLearningAlgorithm extends LearningAlgorithm implements Runnable {
- private boolean stop = false;
+// private boolean stop = false;
private Score solutionScore;
private Description bestSollution;
private Set<Description> simpleSuggestions;
@@ -59,7 +59,7 @@
@Override
public void stop() {
- stop = true;
+// stop = true;
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -23,6 +23,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.learningproblems.ScoreTwoValued;
/**
@@ -41,11 +42,24 @@
private Description description;
private Score score;
+ /**
+ * Constructs an evaluated description using its score.
+ * @param description The description, which was evaluated.
+ * @param score The score of the description.
+ */
public EvaluatedDescription(Description description, Score score) {
this.description = description;
this.score = score;
}
+ /**
+ * Constructs an evaluated description using example coverage.
+ * @param description The description, which was evaluated.
+ * @param posAsPos Positive examples classified as positive by (i.e. instance of) the description.
+ * @param posAsNeg Positive examples classified as negative by (i.e. not instance of) the description.
+ * @param negAsPos Negative examples classified as positive by (i.e. instance of) the description.
+ * @param negAsNeg Negative examples classified as negative by (i.e. not instance of) the description.
+ */
public EvaluatedDescription(Description description, Set<Individual> posAsPos, Set<Individual> posAsNeg, Set<Individual> negAsPos, Set<Individual> negAsNeg) {
this.description = description;
// usually core methods should not depend on methods outside of the core package (except utilities)
@@ -53,20 +67,29 @@
score = new ScoreTwoValued(posAsPos, posAsNeg, negAsPos, negAsNeg);
}
+ /**
+ * Gets the description, which was evaluated.
+ * @return The underlying description.
+ */
public Description getDescription() {
return description;
}
+ /**
+ * @see org.dllearner.core.owl.Description#getLength()
+ */
public int getDescriptionLength() {
return description.getLength();
}
+ /**
+ * @see org.dllearner.core.owl.Description#getDepth()
+ */
public int getDescriptionDepth() {
return description.getDepth();
}
/**
- * @return
* @see org.dllearner.core.Score#getAccuracy()
*/
public double getAccuracy() {
@@ -74,7 +97,6 @@
}
/**
- * @return
* @see org.dllearner.core.Score#getCoveredNegatives()
*/
public Set<Individual> getCoveredNegatives() {
@@ -82,7 +104,6 @@
}
/**
- * @return
* @see org.dllearner.core.Score#getCoveredPositives()
*/
public Set<Individual> getCoveredPositives() {
@@ -90,7 +111,6 @@
}
/**
- * @return
* @see org.dllearner.core.Score#getNotCoveredNegatives()
*/
public Set<Individual> getNotCoveredNegatives() {
@@ -98,11 +118,24 @@
}
/**
- * @return
* @see org.dllearner.core.Score#getNotCoveredPositives()
*/
public Set<Individual> getNotCoveredPositives() {
return score.getNotCoveredPositives();
}
+ /**
+ * Returns a SPARQL query to get instances of this description
+ * from a SPARQL endpoint. Of course, results may be incomplete,
+ * because no inference is done. The SPARQL query is a straightforward
+ * translation without any attempts to perform e.g. subclass
+ * inferencing.
+ *
+ * @param limit The maximum number of results. Corresponds to LIMIT
+ * in SPARQL.
+ * @return A SPARQL query of the underlying description.
+ */
+ public String getSparqlQuery(int limit) {
+ return SparqlQueryDescriptionConvertVisitor.getSparqlQuery(description, limit);
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -38,7 +38,6 @@
import org.dllearner.core.owl.ObjectPropertyHierarchy;
import org.dllearner.core.owl.SubsumptionHierarchy;
import org.dllearner.utilities.datastructures.SortedSetTuple;
-import org.semanticweb.owl.model.OWLClass;
/**
* @author Jens Lehmann
Modified: trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -20,6 +20,7 @@
this.ontology = onto;
}
+ @Override
public <T> void applyConfigEntry(ConfigEntry<T> entry) throws InvalidConfigOptionValueException
{
@@ -30,21 +31,25 @@
return ontology;
}
+ @Override
public KB toKB()
{
throw new Error("OWL -> KB conversion not implemented yet.");
}
+ @Override
public void init()
{
}
+ @Override
public void export(File file, OntologyFormat format)
{
}
+ @Override
public String toDIG(URI kbURI)
{
return null;
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -52,9 +52,9 @@
StringTuple t = (StringTuple) it.next();
try {
// substitute rdf:type with owl:subclassof
- if (t.a.equals(m.type) || t.a.equals(m.subclass)) {
+ if (t.a.equals(Manipulators.type) || t.a.equals(Manipulators.subclass)) {
ClassNode tmp = new ClassNode(new URI(t.b));
- properties.add(new PropertyNode(new URI(m.subclass), this,
+ properties.add(new PropertyNode(new URI(Manipulators.subclass), this,
tmp));
Nodes.add(tmp);
} else {
@@ -67,9 +67,9 @@
// if o is a blank node expand further
// TODO this needs a lot more work
- if (t.b.startsWith(m.blankNodeIdentifier)) {
+ if (t.b.startsWith(Manipulators.blankNodeIdentifier)) {
tmp.expand(tsq, m);
- System.out.println(m.blankNodeIdentifier);
+ System.out.println(Manipulators.blankNodeIdentifier);
System.out.println("XXXXX" + t.b);
}
// Nodes.add(tmp);
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ExtractionAlgorithm.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -131,7 +131,7 @@
Node next = instances.remove(0);
logger.trace("Getting classes for: " + next);
classes.addAll(next.expand(tsqc, manipulator));
- if (classes.size() >= manipulator.breakSuperClassRetrievalAfter) {
+ if (classes.size() >= Manipulators.breakSuperClassRetrievalAfter) {
break;
}
}
@@ -155,7 +155,7 @@
// if(i % 50==0)System.out.println("got "+i+" extra classes,
// max: "+manipulator.breakSuperClassRetrievalAfter);
i++;
- if (i >= manipulator.breakSuperClassRetrievalAfter) {
+ if (i >= Manipulators.breakSuperClassRetrievalAfter) {
break;
}
}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -64,7 +64,7 @@
// basically : if p is rdf:type then o is a class
// else it is an instance
try {
- if (t.a.equals(m.type)) {
+ if (t.a.equals(Manipulators.type)) {
ClassNode tmp = new ClassNode(new URI(t.b));
classes.add(tmp);
Nodes.add(tmp);
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/PropertyNode.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -67,7 +67,7 @@
while (it.hasNext()) {
StringTuple t = (StringTuple) it.next();
try {
- if (t.a.equals(m.type)) {
+ if (t.a.equals(Manipulators.type)) {
specialTypes.add(t.b);
}
} catch (Exception e) {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -1,6 +1,24 @@
+/**
+ * Copyright (C) 2007-2008, 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.kb.sparql;
-
import java.util.HashMap;
import java.util.SortedSet;
import java.util.Stack;
@@ -34,7 +52,9 @@
/**
* Converter from DL-Learner descriptions to a corresponding SPARQL query
* to get all instances that are described by this description.
+ *
* @author Sebastian Knappe
+ * @author Sebastian Hellmann
*
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -83,7 +83,7 @@
String prim="http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom";
- String award=("http://dbpedia.org/resource/Category:Best_Actor_Academy_Award_winners");
+// String award=("http://dbpedia.org/resource/Category:Best_Actor_Academy_Award_winners");
SKOS7030 s= new SKOS7030();
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/NegExampleRepairDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/NegExampleRepairDialog.java 2008-06-28 07:28:11 UTC (rev 991)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/NegExampleRepairDialog.java 2008-06-30 08:56:11 UTC (rev 992)
@@ -22,7 +22,6 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
-import org.dllearner.reasoning.OWLAPIReasoner;
import org.semanticweb.owl.model.OWLOntologyChange;
import org.semanticweb.owl.model.RemoveAxiom;
@@ -49,17 +48,17 @@
private ORE ore;
private Individual ind;
- private OWLAPIReasoner reasoner;
+// private OWLAPIReasoner reasoner;
private Description actualDesc;
private Description newDesc;
- private Individual object;
+// private Individual object;
public NegExampleRepairDialog(Individual ind, JDialog dialog, ORE ore){
super(dialog, "Repair negative example", true);
this.ind = ind;
this.ore = ore;
- this.reasoner = ore.reasoner2;
+// this.reasoner = ore.reasoner2;
init();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-06-30 14:38:12
|
Revision: 995
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=995&view=rev
Author: jenslehmann
Date: 2008-06-30 07:37:58 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
descriptions can now be converted to OWL/XML making it easier for clients to use their structure
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIRenderers.java
Modified: trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-06-30 14:12:50 UTC (rev 994)
+++ trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-06-30 14:37:58 UTC (rev 995)
@@ -25,9 +25,12 @@
import org.dllearner.core.owl.Individual;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.learningproblems.ScoreTwoValued;
+import org.dllearner.reasoning.OWLAPIDescriptionConvertVisitor;
+import org.dllearner.utilities.owl.OWLAPIRenderers;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
+import org.semanticweb.owl.model.OWLDescription;
/**
* This represents a class description, which has been
@@ -151,6 +154,8 @@
JSONObject object = new JSONObject();
try {
object.put("descriptionManchesterSyntax", description.toManchesterSyntaxString(null, null));
+ OWLDescription d = OWLAPIDescriptionConvertVisitor.getOWLDescription(description);
+ object.put("descriptionOWLXML", OWLAPIRenderers.toOWLXMLSyntax(d));
object.put("accuracy", score.getAccuracy());
object.put("coveredPositives", getJSONArray(score.getCoveredPositives()));
object.put("coveredNegatives", getJSONArray(score.getCoveredNegatives()));
Modified: trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIRenderers.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIRenderers.java 2008-06-30 14:12:50 UTC (rev 994)
+++ trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIRenderers.java 2008-06-30 14:37:58 UTC (rev 995)
@@ -22,9 +22,13 @@
import java.io.StringWriter;
import java.net.URI;
+import org.coode.owlapi.owlxml.renderer.OWLXMLObjectRenderer;
+import org.coode.owlapi.owlxml.renderer.OWLXMLWriter;
+import org.coode.xml.XMLWriterNamespaceManager;
import org.semanticweb.owl.apibinding.OWLManager;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLOntologyManager;
import uk.ac.manchester.cs.owl.mansyntaxrenderer.ManchesterOWLSyntaxObjectRenderer;
@@ -51,11 +55,32 @@
return sw.toString();
}
+ /**
+ * Converts an OWL API description to an OWL/XML syntax string.
+ *
+ * @param description Input OWLDescription.
+ * @return OWL/XML syntax string.
+ */
+ public static String toOWLXMLSyntax(OWLDescription description) {
+ StringWriter sw = new StringWriter();
+ // set up default namespace and prefixes
+ XMLWriterNamespaceManager ns = new XMLWriterNamespaceManager("http://example.com");
+ ns.setPrefix("owl2", "http://www.w3.org/2006/12/owl2-xml#");
+ OWLXMLWriter oxw = new OWLXMLWriter(sw, ns);
+ OWLXMLObjectRenderer renderer = new OWLXMLObjectRenderer(oxw);
+ description.accept(renderer);
+ return sw.toString();
+ }
+
public static void main(String args[]) {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLDataFactory factory = manager.getOWLDataFactory();
- OWLDescription d = factory.getOWLClass(URI.create("http://example.com/test"));
- String s = toManchesterOWLSyntax(d);
+ OWLDescription a1 = factory.getOWLClass(URI.create("http://example.com/test#a1"));
+ OWLDescription a2 = factory.getOWLClass(URI.create("http://example.com/test#a2"));
+ OWLObjectProperty r = factory.getOWLObjectProperty(URI.create("http://example.com/test#r"));
+ OWLDescription d3 = factory.getOWLObjectSomeRestriction(r, a2);
+ OWLDescription d = factory.getOWLObjectIntersectionOf(a1,d3);
+ String s = toOWLXMLSyntax(d);
System.out.println(s);
}
}
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