merged with development + fixed bugs

.gitlab-ci.yml

@@ -14,3 +14,17 @@ cache:
 verify:
   script:
     - mvn test --batch-mode
+
+services:
+  - postgres:10.4
+  - name: microsoft/mssql-server-linux:latest
+    alias: sqlserver
+
+variables:
+    # Postgres
+  POSTGRES_DB: postgres
+  POSTGRES_USER: postgres
+  POSTGRES_PASSWORD: ""
+    # SQLServer
+  ACCEPT_EULA: Y
+  SA_PASSWORD: "YourSTRONG!Passw0rd"

README.md

@@ -123,3 +123,46 @@ try {
     logger.error(e.getMessage(), e);
 }
 ```
+
+### Testing
+#### RDBs
+Make sure you have [Docker](https://www.docker.com) running.
+
+Set the boolean constant ```LOCAL_TESTING``` in the file 'Mapper_RDBs_Test' to ```true``` for testing locally. 
+This causes the creation of the required Docker containers and adds the right connection string to the mapping files.
+
+Set the boolean constant ```LOCAL_TESTING``` in the file 'Mapper_RDBs_Test' to ```false``` for testing on / pushing to GitLab. 
+This makes sure that the containers running on GitLab are used and adds the right connection strings to the mapping files.
+
+##### Problems
+* A problem with Docker (can't start the container) causes the SQLServer tests to fail locally. These tests have been turned off.
+* A problem with Docker (can't start the container) causes the PostgreSQL tests to fail locally on windows 7 machines.
+
+# Dependencies
+
+|             Dependency             | License                                                            |
+|:----------------------------------:|--------------------------------------------------------------------|
+| com.spotify docker client          | Apache License 2.0                                                 |
+| com.h2database h2                  | Eclipse Public License 1.0 & Mozilla Public License 2.0            |
+| com.googlecode.zohhak              | GNU Lesser General Public License v3.0                             |
+| com.microsoft.sqlserver mssql-jdbc | MIT                                                                |
+| ch.vorbuger.mariaDB4j              | Apache License 2.0                                                 |
+| mysql-connector-java               | GNU General Public License v2.0                                    |
+| com.google.guava                   | Apache License 2.0                                                 |
+| javax.xml.parsers jaxp-api         | Apache License 2.0                                                 |
+| com.jayway.jsonpath                | Apache License 2.0                                                 |
+| junit                              | Eclipse Public License 1.0                                         |
+| org.eclipse.rdf4j rdf4j-runtime    | Eclipse Public License 1.0                                         |
+| commons-cli                        | Apache License 2.0                                                 |
+| com.opencsv opencsv                | Apache License 2.0                                                 |
+| commons-lang                       | Apache License 2.0                                                 |
+| ch.qos.logback                     | Eclipse Public License 1.0 & GNU Lesser General Public License 2.1 |
+
+# UML Diagrams
+## How to generate with IntelliJ IDEA
+(Requires Ultimate edition)
+
+* Right click on package: "be.ugent.rml"
+* Diagrams > Show Diagram > Java Class Diagrams
+* Choose what properties of the classes you want to show in the upper left corner
+* Export to file > .png  | Save diagram > .uml

buildNumber.properties

@@ -1,3 +1,3 @@
 #maven.buildNumber.plugin properties file
-#Tue Aug 07 15:31:45 CEST 2018
-buildNumber0=26
+#Thu Aug 09 14:05:44 CEST 2018
+buildNumber0=29

config_example.properties

@@ -1,4 +1,4 @@
 verbose = true
-mapping = path_to_mapping_file
-output = path_to_output_file
-help = true
+mappingfile = path_to_mapping_file
+outputfile = path_to_output_file
+help = false

pom.xml

@@ -60,6 +60,50 @@
             <artifactId>guava</artifactId>
             <version>23.0</version>
         </dependency>
+        <dependency>
+            <groupId>mysql</groupId>
+            <artifactId>mysql-connector-java</artifactId>
+            <version>8.0.11</version>
+        </dependency>
+        <dependency>
+            <groupId>ch.vorburger.mariaDB4j</groupId>
+            <artifactId>mariaDB4j</artifactId>
+            <version>2.2.3</version>
+        </dependency>
+        <dependency>
+            <groupId>postgresql</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>9.1-901-1.jdbc4</version>
+        </dependency>
+        <!-- jre version must be the same as the gitlab runner -->
+        <dependency>
+            <groupId>com.microsoft.sqlserver</groupId>
+            <artifactId>mssql-jdbc</artifactId>
+            <version>6.4.0.jre8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.googlecode.zohhak</groupId>
+            <artifactId>zohhak</artifactId>
+            <version>1.1.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.h2database</groupId>
+            <artifactId>h2</artifactId>
+            <version>1.4.197</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.spotify</groupId>
+            <artifactId>docker-client</artifactId>
+            <version>8.11.7</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.9.6</version>
+        </dependency>
     </dependencies>
 
     <build>
@@ -102,10 +146,10 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>2.17</version>
-                <configuration>
+<!--                <configuration>
                     <parallel>methods</parallel>
                     <threadCount>10</threadCount>
-                </configuration>
+                </configuration>-->
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>

src/main/java/be/ugent/rml/ApplyTemplateFunctionFactory.java

@@ -0,0 +1,37 @@
+package be.ugent.rml;
+
+import be.ugent.rml.functions.ApplyTemplateFunction;
+import be.ugent.rml.functions.Function;
+import be.ugent.rml.term.NamedNode;
+import be.ugent.rml.term.Term;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+public class ApplyTemplateFunctionFactory {
+
+    static Function generate(String genericTemplate, Term termType) {
+        return ApplyTemplateFunctionFactory.generate(genericTemplate, termType.equals(new NamedNode(NAMESPACES.RR + "IRI")));
+    }
+
+    static Function generate(String genericTemplate, boolean encodeURI) {
+        HashMap<String, List<Template>> parameters = new HashMap<>();
+        ArrayList<Template> temp = new ArrayList<>();
+        temp.add(Utils.parseTemplate(genericTemplate));
+        parameters.put("_TEMPLATE", temp);
+        return new ApplyTemplateFunction(parameters, encodeURI);
+    }
+
+    static Function generateWithConstantValue(String value) {
+        HashMap<String, List<Template>> parameters = new HashMap<>();
+        List<Template> temp = new ArrayList<>();
+        Template temp2 = new Template();
+        temp2.addElement(new TemplateElement(value, TEMPLATETYPE.CONSTANT));
+        temp.add(temp2);
+
+        parameters.put("_TEMPLATE", temp);
+
+        return new ApplyTemplateFunction(parameters);
+    }
+}

src/main/java/be/ugent/rml/DatabaseType.java

@@ -0,0 +1,85 @@
+package be.ugent.rml;
+
+/*
+    NOTE: Oracle is disabled because there are multiple drivers possible: http://www.orafaq.com/wiki/JDBC
+
+ */
+
+public class DatabaseType {
+
+    public static final String MYSQL = "com.mysql.cj.jdbc.Driver";
+    public static final String POSTGRES = "org.postgresql.Driver";
+    public static final String SQL_SERVER = "com.microsoft.sqlserver.jdbc.SQLServerDriver";
+    //public static final String ORACLE = "oracle.jdbc.driver.OracleDrive";
+    public static final String DB2 = "com.ibm.as400.access.AS400JDBCDriver";
+    /*
+    public static final String JAVA_DB = ;
+    public static final String SYBASE = ;
+    */
+
+    /*
+        Used to abstract as much as possible
+        Name fields are used to create JDBC connection strings in @RDBs
+     */
+    public enum Database {
+        MYSQL ("mysql"),
+        POSTGRES ("postgresql"),
+        SQL_SERVER ("sqlserver"),
+        //ORACLE (""),
+        DB2 ("as400");
+
+        private final String name;
+
+        private Database(String s) {
+            name = s;
+        }
+
+        public String toString() {
+            return this.name;
+        }
+    }
+
+    /*
+        Retrieves the Database enum type from a given (driver) string
+     */
+    public static Database getDBtype(String db) {
+        String db_lower = db.toLowerCase();
+        if (db_lower.contains("mysql")) {
+            return Database.MYSQL;
+        } else if (db_lower.contains("postgres")) {
+            return Database.POSTGRES;
+        } else if (db_lower.contains("sqlserver")) {
+            return Database.SQL_SERVER;
+        // } else if (db_lower.contains("oracle")) {
+        //    return Database.ORACLE;
+        } else if (db_lower.contains("ibm")) {
+            return Database.DB2;
+        } else {
+            throw new Error("Couldn't find a driver for the given DB: " + db);
+        }
+    }
+
+    /*
+        Retrieves the JDBC driver URL from a given Database enum type
+     */
+    public static String getDriver(Database db) {
+        switch(db) {
+            case MYSQL:
+                return MYSQL;
+
+            case POSTGRES:
+                return POSTGRES;
+
+            case SQL_SERVER:
+                return SQL_SERVER;
+
+         //   case ORACLE:
+         //       return ORACLE;
+
+            case DB2:
+                return DB2;
+            default:
+                throw new Error("Couldn't find a driver for the given DB: " + db);
+        }
+    }
+}