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[DL-Learner SVN] SF.net SVN: dl-learner:[3495] trunk
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From: <jen...@us...> - 2011-12-09 13:52:52
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Revision: 3495
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3495&view=rev
Author: jenslehmann
Date: 2011-12-09 13:52:45 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
fixes for enrichment script
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java
trunk/components-core/src/main/java/org/dllearner/algorithms/refinement/ROLearner.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQuery.java
trunk/components-core/src/main/java/org/dllearner/reasoning/DIGHTTPConnector.java
trunk/components-core/src/main/java/org/dllearner/utilities/Files.java
trunk/components-core/src/main/java/org/dllearner/utilities/JamonMonitorLogger.java
trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/Start.java
trunk/scripts/src/main/java/org/dllearner/examples/Alzheimer.java
trunk/scripts/src/main/java/org/dllearner/examples/BreastTissue.java
trunk/scripts/src/main/java/org/dllearner/examples/Carcinogenesis.java
trunk/scripts/src/main/java/org/dllearner/examples/Cardiotocography.java
trunk/scripts/src/main/java/org/dllearner/examples/Heart.java
trunk/scripts/src/main/java/org/dllearner/examples/Mammographic.java
trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java
trunk/scripts/src/main/java/org/dllearner/examples/Mutagenesis.java
trunk/scripts/src/main/java/org/dllearner/examples/Parkinsons.java
trunk/scripts/src/main/java/org/dllearner/examples/Suramin.java
trunk/scripts/src/main/java/org/dllearner/scripts/CrossValidation.java
trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBible.java
trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -489,7 +489,7 @@
if (replaceSearchTree)
Files.createFile(new File(searchTreeFile), treeString);
else
- Files.appendFile(new File(searchTreeFile), treeString);
+ Files.appendToFile(new File(searchTreeFile), treeString);
}
// System.out.println(loop);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -507,7 +507,7 @@
if (replaceSearchTree)
Files.createFile(new File(searchTreeFile), treeString);
else
- Files.appendFile(new File(searchTreeFile), treeString);
+ Files.appendToFile(new File(searchTreeFile), treeString);
}
// System.out.println(loop);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -475,7 +475,7 @@
if (replaceSearchTree)
Files.createFile(searchTreeFile, treeString);
else
- Files.appendFile(searchTreeFile, treeString);
+ Files.appendToFile(searchTreeFile, treeString);
}
// Anzahl Schleifendurchläufe
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/refinement/ROLearner.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/refinement/ROLearner.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -521,7 +521,7 @@
if(replaceSearchTree)
Files.createFile(searchTreeFile, treeString);
else
- Files.appendFile(searchTreeFile, treeString);
+ Files.appendToFile(searchTreeFile, treeString);
}//write search tree
// Anzahl Schleifendurchläufe
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -357,7 +357,7 @@
File jamonlog = new File("log/jamon.html");
Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"
+ Files.appendToFile(jamonlog, "<xmp>\n"
+ JamonMonitorLogger.getStringForAllSortedByLabel());
System.exit(0);
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQuery.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQuery.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -245,7 +245,7 @@
Files.createFile(f, s + "\n");
logDeletedOnStart = true;
} else {
- Files.appendFile(f, s + "\n");
+ Files.appendToFile(f, s + "\n");
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/DIGHTTPConnector.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/DIGHTTPConnector.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/DIGHTTPConnector.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -176,7 +176,7 @@
osw.close();
if(protocolFile != null)
- Files.appendFile(protocolFile, "DIG code send to reasoner:\n\n"+send+"\n\n");
+ Files.appendToFile(protocolFile, "DIG code send to reasoner:\n\n"+send+"\n\n");
// receive answer
InputStream is = connection.getInputStream();
@@ -198,7 +198,7 @@
// }
if(protocolFile != null)
- Files.appendFile(protocolFile, "DIG code received from reasoner:\n\n"+answer+"\n\n");
+ Files.appendToFile(protocolFile, "DIG code received from reasoner:\n\n"+answer+"\n\n");
return answer.toString();
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/Files.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/Files.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/Files.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -186,7 +186,7 @@
* @param content
* Content of the file.
*/
- public static void appendFile(File file, String content) {
+ public static void appendToFile(File file, String content) {
try {
FileOutputStream fos = new FileOutputStream(file, true);
fos.write(content.getBytes());
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JamonMonitorLogger.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JamonMonitorLogger.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JamonMonitorLogger.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -168,7 +168,7 @@
public static void writeHTMLReport(String filename){
File jamonlog = new File(filename);
Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ Files.appendToFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
}
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -275,7 +275,7 @@
private void outputWriter(String output) {
if(writeToFile) {
- Files.appendFile(outputFile, output +"\n");
+ Files.appendToFile(outputFile, output +"\n");
System.out.println(output);
} else {
System.out.println(output);
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -199,7 +199,7 @@
// restrict tested number of entities per type (only for testing purposes);
// should be set to -1 in production mode
- private int maxEntitiesPerType = -1;
+ int maxEntitiesPerType = -1;
// number of axioms which will be learned/considered (only applies to
// some learners)
@@ -583,8 +583,11 @@
OWLNamedIndividual knowldegeBaseInd = f.getOWLNamedIndividual(IRI.create(ks.getEndpoint().getURL()));
ax = f.getOWLClassAssertionAxiom(EnrichmentVocabulary.SPARQLEndpoint, knowldegeBaseInd);
axioms.add(ax);
- ax = f.getOWLObjectPropertyAssertionAxiom(EnrichmentVocabulary.defaultGraph, knowldegeBaseInd, f.getOWLNamedIndividual(IRI.create(ks.getEndpoint().getDefaultGraphURIs().iterator().next())));
- axioms.add(ax);
+ if(!ks.getEndpoint().getDefaultGraphURIs().isEmpty()) {
+ // TODO: only writes one default graph
+ ax = f.getOWLObjectPropertyAssertionAxiom(EnrichmentVocabulary.defaultGraph, knowldegeBaseInd, f.getOWLNamedIndividual(IRI.create(ks.getEndpoint().getDefaultGraphURIs().iterator().next())));
+ axioms.add(ax);
+ }
ax = f.getOWLObjectPropertyAssertionAxiom(EnrichmentVocabulary.hasInput,
algorithmRunInd, knowldegeBaseInd);
axioms.add(ax);
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -22,6 +22,7 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.PrintStream;
import java.lang.reflect.InvocationTargetException;
import java.net.MalformedURLException;
import java.net.URL;
@@ -31,6 +32,8 @@
import java.util.Map;
import java.util.Map.Entry;
+import javax.xml.ws.http.HTTPException;
+
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
@@ -41,11 +44,14 @@
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.utilities.Files;
import org.semanticweb.owlapi.model.OWLAxiom;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
+import com.hp.hpl.jena.sparql.resultset.ResultSetException;
/**
* Enriches all of the LOD cloud.
@@ -124,19 +130,49 @@
// run enrichment
SparqlEndpoint se = endpoint.getValue();
String name = endpoint.getKey();
+
+ File f = new File(baseDir + name + ".ttl");
+ File log = new File(baseDir + name + ".log");
+
System.out.println("Enriching " + name + " using " + se);
Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference, false);
- e.start();
- // save results to a file
- SparqlEndpointKS ks = new SparqlEndpointKS(se);
- List<AlgorithmRun> runs = e.getAlgorithmRuns();
- List<OWLAxiom> axioms = new LinkedList<OWLAxiom>();
- for(AlgorithmRun run : runs) {
- axioms.addAll(e.toRDF(run.getAxioms(), run.getAlgorithm(), run.getParameters(), ks));
+
+ e.maxEntitiesPerType = 3; // hack for faster testing of endpoints
+
+ boolean success = false;
+ // run enrichment script - we make a case distinguish to see which kind of problems we get
+ // (could be interesting for statistics later on)
+ try {
+ e.start();
+ success = true;
+ } catch(StackOverflowError error) {
+ error.printStackTrace(new PrintStream(log));
+ Files.appendToFile(log, "stack overflows could be caused by cycles in class hierarchies");
+ error.printStackTrace();
+ } catch(ResultSetException ex) {
+ ex.printStackTrace(new PrintStream(log));
+ Files.appendToFile(log, ex.getMessage());
+ ex.printStackTrace();
+ } catch(QueryExceptionHTTP ex) {
+ ex.printStackTrace(new PrintStream(log));
+ Files.appendToFile(log, ex.getMessage());
+ ex.printStackTrace();
+ }
+// catch(Exception ex) {
+// System.out.println("class of exception: " + ex.getClass());
+// }
+
+ // save results to a file (TODO: check if enrichment format
+ if(success) {
+ SparqlEndpointKS ks = new SparqlEndpointKS(se);
+ List<AlgorithmRun> runs = e.getAlgorithmRuns();
+ List<OWLAxiom> axioms = new LinkedList<OWLAxiom>();
+ for(AlgorithmRun run : runs) {
+ axioms.addAll(e.toRDF(run.getAxioms(), run.getAlgorithm(), run.getParameters(), ks));
+ }
+ Model model = e.getModel(axioms);
+ model.write(new FileOutputStream(f), "TURTLE");
}
- Model model = e.getModel(axioms);
- File f = new File(baseDir + name + ".ttl");
- model.write(new FileOutputStream(f), "TURTLE");
}
}
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Start.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Start.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Start.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -216,7 +216,7 @@
// write JaMON report in HTML file
File jamonlog = new File("log/jamon.html");
Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ Files.appendToFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
}
/**
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Alzheimer.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Alzheimer.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Alzheimer.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -766,7 +766,7 @@
content.append("-\"" + getIndividual(key) + "\"\n");
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static void generateConfFile(File file) {
@@ -778,7 +778,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/alzheimer/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
// returns URI including quotationsmark (need for KBparser)
Modified: trunk/scripts/src/main/java/org/dllearner/examples/BreastTissue.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/BreastTissue.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/BreastTissue.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -296,7 +296,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/breasttissue/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generateExamples(File file, HashMap<String, Integer> patients, int i) {
@@ -311,7 +311,7 @@
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getURI(String name) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Carcinogenesis.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Carcinogenesis.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -268,7 +268,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/carcinogenesis/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(confTrainFile, confHeader);
+ Files.appendToFile(confTrainFile, confHeader);
// generating training examples
File trainingFilePositives = new File(prologDirectory + "train.f");
@@ -291,7 +291,7 @@
appendNegExamples(confTrainFile, negPTE1Examples);
if(createPTE1Conf) {
Files.clearFile(confPTE1File);
- Files.appendFile(confPTE1File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
+ Files.appendToFile(confPTE1File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
appendPosExamples(confPTE1File, posPTE1Examples);
appendNegExamples(confPTE1File, negPTE1Examples);
}
@@ -300,8 +300,8 @@
if(createPTE2Conf) {
File confPTE2File = new File("examples/carcinogenesis/testpte2.conf");
Files.clearFile(confPTE2File);
- Files.appendFile(confPTE2File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
- Files.appendFile(confPTE2File, getPTE2Examples());
+ Files.appendToFile(confPTE2File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
+ Files.appendToFile(confPTE2File, getPTE2Examples());
}
}
@@ -492,7 +492,7 @@
else
content.append("-\""+example.toString()+"\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
public static void appendNegExamples(File file, List<Individual> examples) {
@@ -503,7 +503,7 @@
else
content.append("+\""+example.toString()+"\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getAtomClass(String element, String atomType) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Cardiotocography.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Cardiotocography.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Cardiotocography.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -546,7 +546,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/cardiotocography/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generateExamples(File file, HashMap<String, Integer> patients, int i) {
@@ -561,7 +561,7 @@
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getURI(String name) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Heart.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Heart.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Heart.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -307,7 +307,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/heart/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generateExamples(File file) {
@@ -321,7 +321,7 @@
content.append("-\"" + getIndividual(key) + "\"\n");
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getURI(String name) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Mammographic.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Mammographic.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Mammographic.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -255,7 +255,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/mammographic/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generateExamples(File file) {
@@ -269,7 +269,7 @@
content.append("-\"" + getIndividual(key) + "\"\n");
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getURI(String name) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/MonogenicDiseases.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -361,61 +361,61 @@
String pt = rs.getString("phenotype");
if ((pt.toLowerCase().contains("polymorphism"))&&( neg_count<=negEx )) {
if (writeAlephFiles) {
- Files.appendFile(badFile, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(badFile, "deleterious(id"+mutationID+").\n");
}
if (writeYYFiles) {
- Files.appendFile(yybadFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
+ Files.appendToFile(yybadFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
}
if (cvAleph){
switch (kn) {
case 1:
aneg++;
- Files.appendFile(split1n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split1n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 2:
aneg++;
- Files.appendFile(split2n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split2n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 3:
aneg++;
- Files.appendFile(split3n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split3n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 4:
aneg++;
- Files.appendFile(split4n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split4n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 5:
aneg++;
- Files.appendFile(split5n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split5n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 6:
aneg++;
- Files.appendFile(split6n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split6n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 7:
aneg++;
- Files.appendFile(split7n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split7n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 8:
aneg++;
- Files.appendFile(split8n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split8n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 9:
aneg++;
- Files.appendFile(split9n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split9n, "deleterious(id"+mutationID+").\n");
if (aneg == neps) {aneg = 0; kn++;}
break;
case 10:
aneg++;
- Files.appendFile(split10n, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split10n, "deleterious(id"+mutationID+").\n");
// if (aneg == neps) {aneg = 0; kn++;}
break;
// case 11: // without comment its round negExamples / 10
@@ -427,61 +427,61 @@
}
if ((!pt.toLowerCase().contains("polymorphism"))&& ( pos_count<=posEx)) {
if (writeAlephFiles) {
- Files.appendFile(posFile, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(posFile, "deleterious(id"+mutationID+").\n");
}
if (writeYYFiles) {
- Files.appendFile(yyposFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
+ Files.appendToFile(yyposFile, "http://example.com/mutation/mutation#mutation"+mutationID+"\n");
}
if (cvAleph){
switch (kp) {
case 1:
apos++;
- Files.appendFile(split1f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split1f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 2:
apos++;
- Files.appendFile(split2f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split2f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 3:
apos++;
- Files.appendFile(split3f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split3f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 4:
apos++;
- Files.appendFile(split4f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split4f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 5:
apos++;
- Files.appendFile(split5f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split5f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 6:
apos++;
- Files.appendFile(split6f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split6f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 7:
apos++;
- Files.appendFile(split7f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split7f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 8:
apos++;
- Files.appendFile(split8f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split8f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 9:
apos++;
- Files.appendFile(split9f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split9f, "deleterious(id"+mutationID+").\n");
if (apos == peps) {apos = 0; kp++;}
break;
case 10:
apos++;
- Files.appendFile(split10f, "deleterious(id"+mutationID+").\n");
+ Files.appendToFile(split10f, "deleterious(id"+mutationID+").\n");
// if (apos == peps) {apos = 0; kp++;}
break;
// case 11: // without comments its round to posExamples / 10
@@ -712,7 +712,7 @@
confHeader += "\n";
}
- Files.appendFile(confFile, confHeader);
+ Files.appendToFile(confFile, confHeader);
if(!generatePosExampleClass) {
MonogenicDiseases.appendPosExamples(confFile, posExamples);
MonogenicDiseases.appendNegExamples(confFile, negExamples);
@@ -751,7 +751,7 @@
else
content.append("-\""+example.toString()+"\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
public static void appendNegExamples(File file, List<Individual> examples) {
@@ -762,6 +762,6 @@
else
content.append("+\""+example.toString()+"\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
}
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Mutagenesis.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Mutagenesis.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Mutagenesis.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -243,7 +243,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/mutagenesis/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generatePositiveExamples(String fileName)
@@ -439,7 +439,7 @@
else
content.append("-\"" + example.toString() + "\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
public static void appendNegExamples(File file, List<Individual> examples) {
@@ -450,7 +450,7 @@
else
content.append("+\"" + example.toString() + "\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getAtomClass(String element, String atomType) {
@@ -583,7 +583,7 @@
for (String negEx : negativeExamples) {
content.append("-\"" + getIndividual(negEx) + "\"\n");
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static BooleanDatatypePropertyAssertion getBooleanDatatypePropertyAssertion(
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Parkinsons.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Parkinsons.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Parkinsons.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -283,7 +283,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/parkinsons/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(file, confHeader);
+ Files.appendToFile(file, confHeader);
}
private static void generateExamples(File file) {
@@ -298,7 +298,7 @@
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
private static String getURI(String name) {
Modified: trunk/scripts/src/main/java/org/dllearner/examples/Suramin.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/Suramin.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/examples/Suramin.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -171,7 +171,7 @@
confHeader += "refexamples.writeSearchTree = false;\n";
confHeader += "refexamples.searchTreeFile = \"log/suramin/searchTree.log\";\n";
confHeader += "\n";
- Files.appendFile(confTrainFile, confHeader);
+ Files.appendToFile(confTrainFile, confHeader);
appendExamples(confTrainFile, posExamples);
}
@@ -382,7 +382,7 @@
content.append("-\""+getIndividual(compound.toString())+"\"\n");
}
}
- Files.appendFile(file, content.toString());
+ Files.appendToFile(file, content.toString());
}
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/CrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/CrossValidation.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/CrossValidation.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -374,7 +374,7 @@
private void outputWriter(String output) {
if(writeToFile) {
- Files.appendFile(outputFile, output +"\n");
+ Files.appendToFile(outputFile, output +"\n");
System.out.println(output);
} else {
System.out.println(output);
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBible.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBible.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBible.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -79,8 +79,8 @@
initLogger();
logger.info("Start");
Files.clearFile(file);
- Files.appendFile(file, "neg Ex random: "+RANDOMNEGATIVES+"\n");
- Files.appendFile(file, "negfactor : "+NEGFACTOR+"\n");
+ Files.appendToFile(file, "neg Ex random: "+RANDOMNEGATIVES+"\n");
+ Files.appendToFile(file, "negfactor : "+NEGFACTOR+"\n");
//String fileURL = new File(ontologyFile).toURI().toString();
@@ -113,7 +113,7 @@
for (NamedClass target : classesToRelearn) {
- Files.appendFile(file,"now learning: "+target+"\n");
+ Files.appendToFile(file,"now learning: "+target+"\n");
waitForInput();
positiveEx.clear();
@@ -138,7 +138,7 @@
if(negativeEx.size()<0) {
System.out.println(target);
waitForInput();
- Files.appendFile(file, "\tSKIPPED negEX "+negativeEx+"\n");
+ Files.appendToFile(file, "\tSKIPPED negEX "+negativeEx+"\n");
continue;
}
// reasoningService.prepareSubsumptionHierarchy();
@@ -151,7 +151,7 @@
e.printStackTrace();
}
waitForInput();
- Files.appendFile(file, "*************\n");
+ Files.appendToFile(file, "*************\n");
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBibleComparison.java 2011-12-09 12:54:27 UTC (rev 3494)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SemanticBibleComparison.java 2011-12-09 13:52:45 UTC (rev 3495)
@@ -237,7 +237,7 @@
public static void writeJamonLog(String filename){
File jamonlog = new File(filename);
Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ Files.appendToFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
}
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