1. properties file can now be passed as a command-line argument

2. Updated license from 3.0 to 4.0

README.md

@@ -12,17 +12,17 @@ R2RML implementation written fully in Java 7, using Apache Jena 2.11, Spring 4.0
 
 ## Licence
 
-This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.
+This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 Unported License.
 
-http://creativecommons.org/licenses/by-nc/3.0/
+http://creativecommons.org/licenses/by-nc/4.0/
 
 You are free to use and distribute this work as long as you provide proper reference and respect the license terms.
 
 ## Publications
 
 1. N. Konstantinou, D. Kouis, N. Mitrou: ["Incremental Export of Relational Database Contents into RDF Graphs"](https://www.researchgate.net/publication/262098563_Incremental_Export_of_Relational_Database_Contents_into_RDF_Graphs). In 4th International Conference on Web Intelligence, Mining and Semantics (WIMS'14), Thessaloniki, Greece, June 2014 [(doi:10.1145/2611040.2611082)](http://dx.doi.org/10.1145/2611040.2611082) [(slides)](http://www.slideshare.net/nkons/wims14-v2)
 
-1. N. Konstantinou, D.E. Spanos, N. Houssos, N. Mitrou: ["Exposing Scholarly Information as Linked Open Data: RDFizing DSpace contents"](https://www.researchgate.net/publication/236881378_Exposing_Scholarly_Information_as_Linked_Open_Data_RDFizing_DSpace_contents). In The Electronic Library, Vol. 32, No. 6, 2014 (to appear)
+1. N. Konstantinou, D.E. Spanos, N. Houssos, N. Mitrou: ["Exposing Scholarly Information as Linked Open Data: RDFizing DSpace contents"](https://www.researchgate.net/publication/236881378_Exposing_Scholarly_Information_as_Linked_Open_Data_RDFizing_DSpace_contents). In The Electronic Library, Vol. 32, No. 6, 2014
 
 1. N. Konstantinou, D.E. Spanos, N. Mitrou: ["Transient and persistent RDF views over relational databases in the context of digital repositories"](https://www.researchgate.net/publication/258235039_Transient_and_persistent_RDF_views_over_relational_databases_in_the_context_of_digital_repositories). In 7th Metadata and Semantics Research Conference (MTSR'13), Thessaloniki, Greece, Springer, CCIS 390, pp. 342-354, November 2013 [(doi:10.1007/978-3-319-03437-9_33)](http://dx.doi.org/10.1007/978-3-319-03437-9_33) [(slides)](http://www.slideshare.net/nkons/transient-and-persistent-rdf-views-over-relational-databases-in-the-context-of-digital-repositories)
 

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>gr.seab</groupId>
 	<artifactId>r2rml-parser</artifactId>
-	<version>0.6</version>
+	<version>0.7</version>
 	<packaging>jar</packaging>
 	<name>R2RML Parser</name>
 	<properties>
@@ -114,11 +114,16 @@
 			<type>pom</type>
 			<version>2.11.2</version>
 		</dependency>
-                <dependency>
-                    <groupId>com.oracle</groupId>
-                    <artifactId>ojdbc6</artifactId>
-                    <version>11.2.0.3</version>
-                </dependency>
+			<dependency>
+			<groupId>com.oracle</groupId>
+			<artifactId>ojdbc6</artifactId>
+			<version>11.2.0.3</version>
+			</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+			<version>1.2</version>
+		</dependency>
 	</dependencies>
 
         <!-- Added for oracle JDBC driver -->
@@ -145,7 +150,7 @@
 		<developer>
 			<name>Nikolaos Konstantinou</name>
 			<email>nkons at cn.ntua.gr</email>
-			<url>https://www.researchgate.net/profile/Nikolaos_Konstantinou/</url>
+			<url>http://people.cn.ntua.gr/nkons/</url>
 			<organization>Hellenic Academic Libraries Link/National Technical University of Athens (HEAL-Link/NTUA)</organization>
 			<organizationUrl>http://www.seab.gr</organizationUrl>
 			<roles>

r2rml-parser.bat

@@ -1,4 +1,4 @@
 @echo off
-echo This is R2RML Parser 0.6-alpha
-java -Xms128m -Xmx1024m -cp "./*;./lib/*;" gr.seab.r2rml.beans.Main %1
-echo R2RML Parser 0.6-alpha. Done.
+echo This is R2RML Parser 0.7-alpha. Run with -h for help on options.
+java -Xms128m -Xmx1024m -cp "./*;./lib/*;" gr.seab.r2rml.beans.Main %1 %2
+echo R2RML Parser 0.7-alpha. Done.

r2rml-parser.sh

@@ -1,3 +1,3 @@
-echo "This is R2RML Parser 0.6-alpha"
-java -Xms128m -Xmx1024m -cp "./*;./lib/*;" -jar lib/r2rml-parser-0.6.jar -o true
-echo "R2RML Parser 0.6-alpha. Done."
+echo "This is R2RML Parser 0.7-alpha. Run with -h for help on options."
+java -Xms128m -Xmx1024m -cp "./*;./lib/*;" -jar lib/r2rml-parser-0.7.jar $1 $2
+echo "R2RML Parser 0.7-alpha. Done."

src/main/java/gr/seab/r2rml/beans/Database.java

@@ -1,9 +1,9 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
@@ -13,6 +13,7 @@
 
 import java.sql.Connection;
 import java.sql.ResultSet;
+import java.util.Properties;
 
 public interface Database {
 
@@ -22,4 +23,6 @@ public interface Database {
 
 	public void testQuery(String query);
 
+	public void setProperties(Properties properties);
+
 }

src/main/java/gr/seab/r2rml/beans/DatabaseImpl.java

@@ -1,17 +1,16 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
  * CONDITIONS OF ANY KIND, either express or implied.
  */
 package gr.seab.r2rml.beans;
 
-import java.io.FileInputStream;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.PreparedStatement;
@@ -35,28 +34,14 @@ public class DatabaseImpl implements Database {
 
 	private Connection connection;
 
-	private Properties properties = new Properties();
-
-	private String propertiesFilename;
+	private Properties properties;
 
 	private Util util;
 
 	public DatabaseImpl() {
 
 	}
 
-	/**
-	 * 
-	 */
-	public DatabaseImpl(String propertiesFilename) {
-		try {
-			properties.load(new FileInputStream(propertiesFilename));
-		} catch (Exception e) {
-			e.printStackTrace();
-			System.exit(1);
-		}
-	}
-
 	public Connection openConnection() {
 		log.info("Establishing source (relational) connection.");
 		if (connection == null) {
@@ -73,7 +58,7 @@ public Connection openConnection() {
 				log.info("Established source (relational) connection.");
 				return connection;
 			} catch (Exception e) {
-				e.printStackTrace();
+				log.error("Error establishing source (relational) connection! Please check your connection settings.");
 				System.exit(1);
 			}
 		} else {
@@ -92,7 +77,7 @@ public ResultSet query(String query) {
 			Statement statement = connection.createStatement(ResultSet.TYPE_SCROLL_SENSITIVE, ResultSet.CONCUR_UPDATABLE);
 			result = statement.executeQuery(query);
 		} catch (SQLException e) {
-			e.printStackTrace();
+			log.error("Error executing query! Query was: " + query);
 			System.exit(1);
 		}
 		return result;
@@ -114,19 +99,11 @@ public void testQuery(String query) {
 
 			preparedStatement.close();
 		} catch (SQLException e) {
-			e.printStackTrace();
+			log.error("Error testing query! Query was: " + query);
 			System.exit(1);
 		}
 	}
-
-	public String getPropertiesFilename() {
-		return propertiesFilename;
-	}
-
-	public void setPropertiesFilename(String propertiesFilename) {
-		this.propertiesFilename = propertiesFilename;
-	}
-
+
 	public Util getUtil() {
 		return util;
 	}

src/main/java/gr/seab/r2rml/beans/Generator.java

@@ -1,9 +1,9 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR

src/main/java/gr/seab/r2rml/beans/Main.java

@@ -1,9 +1,9 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
@@ -13,41 +13,91 @@
 
 import gr.seab.r2rml.entities.MappingDocument;
 
-import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.Calendar;
+import java.util.Properties;
 
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+import org.apache.commons.lang.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 
 public class Main {
 	private static final Logger log = LoggerFactory.getLogger(Main.class);
 
+	/**
+	 * The properties, as read from the properties file.
+	 */
+	private static Properties properties = new Properties();
+
 	public static void main(String[] args) {
 		Calendar c0 = Calendar.getInstance();
         long t0 = c0.getTimeInMillis();
-		String appContextFile = "app-context.xml";
-		if (args.length > 0) {
-			File f = new File(args[0]);
-			if (f.exists()) {
-				log.info("Spring context descriptor set to " + args[0]);
-				appContextFile = args[0];
-			} else {
-				log.info("File " + args[0] + " not in classpath, using app-context.xml instead");
+
+        CommandLineParser cmdParser = new PosixParser();
+
+        Options cmdOptions = new Options();
+        cmdOptions.addOption("p", "properties", true, "define the properties file. Example: r2rml-parser -p r2rml.properties");
+        cmdOptions.addOption("h", "print help", false, "help");
+
+		String propertiesFile = "r2rml.properties";
+
+		try {
+			CommandLine line = cmdParser.parse(cmdOptions, args);
+
+			if (line.hasOption("h")) {
+				HelpFormatter help = new HelpFormatter();
+				help.printHelp("r2rml-parser\n", cmdOptions);
+				System.exit(0);
 			}
-		} else {
-			log.info("Spring context file not provided, using app-context.xml");
+
+			if (line.hasOption("p")) {
+				propertiesFile = line.getOptionValue("p");
+			}
+		} catch (ParseException e1) {
+			//e1.printStackTrace();
+			log.error("Error parsing command line arguments.");
+			System.exit(1);
 		}
-		ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext(appContextFile);
+
+		try {
+			if (StringUtils.isNotEmpty(propertiesFile)) {
+				properties.load(new FileInputStream(propertiesFile));
+				log.info("Loaded properties from " + propertiesFile);
+			}
+		} catch (FileNotFoundException e) {
+			//e.printStackTrace();
+			log.error("Properties file not found (" + propertiesFile + ").");
+			System.exit(1);
+		} catch (IOException e) {
+			//e.printStackTrace();
+			log.error("Error reading properties file (" + propertiesFile + ").");
+			System.exit(1);
+		}
+
+		ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext("app-context.xml");
+
+		Database db = (Database) context.getBean("db");
+		db.setProperties(properties);
 
 		Parser parser = (Parser) context.getBean("parser");
+		parser.setProperties(properties);
+
 		MappingDocument mappingDocument = parser.parse();
 
 		mappingDocument.getTimestamps().add(t0); //0 Started
 		mappingDocument.getTimestamps().add(Calendar.getInstance().getTimeInMillis()); //1 Finished parsing. Starting generating result model.
 
 		Generator generator = (Generator) context.getBean("generator");
-		generator.setProperties(parser.getProperties());
+		generator.setProperties(properties);
 		generator.setResultModel(parser.getResultModel());
 
 		//Actually do the output

src/main/java/gr/seab/r2rml/beans/Parser.java

@@ -1,9 +1,9 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
@@ -24,9 +24,6 @@
 import gr.seab.r2rml.entities.sparql.LocalResultSet;
 import gr.seab.r2rml.entities.sql.SelectQuery;
 
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -96,7 +93,7 @@ public class Parser {
 	/**
 	 * The properties, as read from the properties file.
 	 */
-	private Properties properties = new Properties();
+	private Properties properties;
 
 	private boolean verbose;
 
@@ -105,21 +102,6 @@ public class Parser {
 	private Util util;
 
 	public Parser() {
-
-	}
-
-	public Parser(String propertiesFilename) {
-		this.propertiesFilename = propertiesFilename;
-		try {
-			if (StringUtils.isNotEmpty(propertiesFilename)) {
-				properties.load(new FileInputStream(propertiesFilename));
-				log.info("Loaded properties from " + propertiesFilename);
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
 	}
 
 	@SuppressWarnings("unchecked")

src/main/java/gr/seab/r2rml/beans/Util.java

@@ -1,9 +1,9 @@
 /**
- * Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported 
+ * Licensed under the Creative Commons Attribution-NonCommercial 4.0 Unported 
  * License (the "License"). You may not use this file except in compliance with
  * the License. You may obtain a copy of the License at:
  * 
- *  http://creativecommons.org/licenses/by-nc/3.0/
+ *  http://creativecommons.org/licenses/by-nc/4.0/
  *  
  * Unless required by applicable law or agreed to in writing, software distributed
  * under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR