minor fixes

Author: ernesto

.classpath

@@ -13,6 +13,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" path="src/main/resources"/>
 	<classpathentry exported="true" kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

pom.xml

@@ -117,8 +117,16 @@
     <artifactId>log4j-core</artifactId>
     <version>2.13.3</version>
 </dependency>
-
-
+	<dependency>
+		<groupId>org.slf4j</groupId>
+        <artifactId>slf4j-log4j12</artifactId>
+        <version>1.7.31</version>
+	</dependency>
+    <dependency>
+		<groupId>org.slf4j</groupId>
+    	<artifactId>slf4j-api</artifactId>
+    	<version>1.7.31</version>
+    </dependency>
 <dependency>
 	<groupId>com.fasterxml.jackson.core</groupId>
 	<artifactId>jackson-annotations</artifactId>
@@ -207,6 +215,12 @@
           <include>**/*.txt</include>
           <include>**/*.gz</include>
         </includes>
+      </resource>
+      <resource>
+        <directory>src/main/resources</directory>
+        <includes>
+          <include>log4j.properties</include>          
+        </includes>
       </resource>      
     </resources>
 

src/main/java/uk/ac/ox/krr/logmap2/LogMap2_CommandLine.java

@@ -16,7 +16,7 @@ private static String getHelpMessage(){
 				"\t1. MATCHER. To use the matching functionality.\n" +
 				"\t2. IRI ontology 1. e.g.: http://myonto1.owl  or  file:/C://myonto1.owl  or  file:/usr/local/myonto1.owl\n" +
 				"\t3. IRI ontology 2. e.g.: http://myonto2.owl  or  file:/C://myonto2.owl  or  file:/usr/local/myonto2.owl\n" +
-				"\t4. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or C://output_path/\n or /C://output_path/\\n" +
+				"\t4. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or (windows) C://output_path/ or /C://output_path/\n" +
 				"\t5. Classify the input ontologies together with the mappings. e.g. true or false\n\n" +
 				"\tFor example: java -jar logmap2_standalone.jar MATCHER file:/home/ontos/cmt.owl file:/home/ontos/ekaw.owl /home/mappings/output/ true\n\n\n" +
 
@@ -25,7 +25,7 @@ private static String getHelpMessage(){
 				"\t2. IRI ontology 1. e.g.: http://myonto1.owl  or  file:/C://myonto1.owl  or  file:/usr/local/myonto1.owl\n" +
 				"\t3. IRI ontology 2. e.g.: http://myonto2.owl  or  file:/C://myonto2.owl  or  file:/usr/local/myonto2.owl\n" +
 				"\t4. Reference mappings (RDF alignment format). e.g.: /usr/local/reference_mappings.rdf\n" +
-				"\t5. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or C://output_path/\n or /C://output_path/\\n" +
+				"\t5. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or (windows) C://output_path/ or /C://output_path/\n" +
 				"\t6. Classify the input ontologies together with the mappings. e.g. true or false\n\n" +
 				"\tFor example: java -jar logmap2_standalone.jar EVALUATION file:/home/ontos/cmt.owl file:/home/ontos/ekaw.owl /home/refs/ref-cmt-ekaw.rdf /home/mappings/output/ true\n\n\n" +
 
@@ -36,8 +36,8 @@ private static String getHelpMessage(){
 				"\t4. Format mappings e.g.: OWL  or  RDF  or  TXT\n" +
 				"\t5. Full IRI or full Path:\n" +
 				"\t\ta. Full IRI of input mappings if OWL format. e.g.: file:/C://mymappings.owl  or  file:/usr/local/mymappings.owl  or http://mymappings.owl\n" +
-				"\t\tb. or Full path of input mappings if formats RDF or TXT. e.g.: C://mymappings.rdf  or  /usr/local/mymappings.txt\n" +
-				"\t6. Full output path for the repaired mappings: e.g. /usr/local/output_path or C://output_path\n or /C://output_path/\\n" +
+				"\t\tb. or Full path of input mappings if formats RDF or TXT. e.g.: C://mymappings.rdf  or /usr/local/mymappings.txt\n" +
+				"\t6. Full output path for the repaired mappings: e.g. /usr/local/output_path or (windows) C://output_path or /C://output_path/\n" +
 				"\t7. Extract modules for repair?: true or false\n" +
 				"\t8. Check satisfiability after repair using HermiT? true or false\n\n" +
 				"\tFor example: java -jar logmap2_standalone.jar DEBUGGER file:/home/ontos/cmt.owl file:/home/ontos/ekaw.owl " +
@@ -48,7 +48,7 @@ private static String getHelpMessage(){
 				"\t1. MATCHER. To use the matching functionality.\n" +
 				"\t2. IRI ontology 1. e.g.: http://myonto1.owl  or  file:/C://myonto1.owl  or  file:/usr/local/myonto1.owl\n" +
 				"\t3. IRI ontology 2. e.g.: http://myonto2.owl  or  file:/C://myonto2.owl  or  file:/usr/local/myonto2.owl\n" +
-				"\t4. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or C://output_path/\n or /C://output_path/\\n" +
+				"\t4. Full output path for mapping files and overlapping modules/fragments. e.g. /usr/local/output_path/ or (windows) C://output_path/ or /C://output_path/\n" +
 				"\tFor example: java -jar logmap2_standalone.jar LITE file:/home/ontos/cmt.owl file:/home/ontos/ekaw.owl /home/mappings/output/ \n\n\n" +
 
 

src/main/java/uk/ac/ox/krr/logmap2/LogMap2_Matcher.java

@@ -76,7 +76,7 @@ public LogMap2_Matcher(String iri_onto1, String iri_onto2, String reference, Str
 					);
 
 			System.out.println("Precision\tRecall\tF-score");
-			System.out.format("%.3f\t%.3f\t%.3f", StandardMeasures.getPrecision(), StandardMeasures.getRecall(), StandardMeasures.getFscore());
+			System.out.format("%.3f\t%.3f\t%.3f\n", StandardMeasures.getPrecision(), StandardMeasures.getRecall(), StandardMeasures.getFscore());
 
 
 

src/main/resources/log4j.properties

@@ -0,0 +1,16 @@
+#Root logger option
+log4j.rootLogger=ERROR, stdout
+log4j.rootLogger=INFO, file
+
+# Direct log messages to stdout
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Target=System.out
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p [%-30.30t] %-4L in %-20.20c{1} - %m%n
+
+
+# Define the file appender
+log4j.appender.file=org.apache.log4j.FileAppender
+log4j.appender.file.File=logmap-log.out
+log4j.appender.file.layout=org.apache.log4j.PatternLayout
+log4j.appender.file.layout.conversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p [%-30.30t] %-4L in %-20.20c{1} - %m%n