Merge remote-tracking branch 'upstream/master'

IDE.md

@@ -1,48 +1,49 @@
 ## Working with IDEs
 
-The following instructions have been tested and confirmed working 
+The following instructions have been tested and confirmed working
 with Eclipse Kepler (4.3) and IntelliJ 12.1 on MacOSX.
 
 ### Eclipse
 1. Checkout the project from its repository, for example
-
-    ```git clone [email protected]:istlab/Alitheia-Core.git```
 
-2. Do the following 
-    ```
+    `git clone [email protected]:istlab/Alitheia-Core.git`
+
+2. Do the following
+  ```bash
     mvn clean install
     mvn -DdownloadJavadoc -Ddownloadsources eclipse:eclipse
-    ```
+  ```
 
-3. In Eclipse, choose Import->General->Existing Projects into Workspace.
+3. In Eclipse, choose `Import->General->Existing` Projects into Workspace.
 In the next dialogue,
 you enter the checkout directory and a list of project modules appears. Here
 you should select only the modules you will be working with.
 
-4. To debug, you run the debug.sh script from the top-level directory. This
+4. To debug, you run the `debug.sh` script from the top-level directory. This
 will start Alitheia Core in debug mode; initialisation will stop until an
 external debug is attached. To attach the eclipse debugger, click on the
-Run menu->Debug configurations, then select the Remote Java Application from
+`Run menu->Debug configurations`, then select the `Remote Java Application` from
 the list and click on the new launch configuration button. Add a name click
 debug. Eclipse will connect to the waiting virtual machine and will stop
 at any breakpoint you have set in the code.
 
 ### IntelliJ
 
 1. Checkout the project from its repository, for example
-    
-    ```git clone [email protected]:istlab/Alitheia-Core.git```
 
-2. Do the following 
-    ```
+    `git clone [email protected]:istlab/Alitheia-Core.git`
+
+2. Do the following
+
+  ```bash
     mvn clean install
     mvn -DdownloadJavadoc -Ddownloadsources intellij:intellij
-    ```
-    
-3. In IntelliJ, go to File->Open project and choose the Alitheia Core top-level 
+  ```
+
+3. In IntelliJ, go to `File->Open` project and choose the Alitheia Core top-level
 directory. Importing will start.
 
 4. To debug, create a debug configuration (Run->Debug->Edit Configurations) and
 then click on + and select Remote. Set port to 8000 and click Debug. Then run
-the debug.sh script on the top-level directory.
+the `debug.sh` script on the top-level directory.
 

README.md

@@ -1,7 +1,7 @@
 ## Introduction
 
 
-This is the source tree for Alitheia Core, a platform for 
+This is the source tree for Alitheia Core, a platform for
 software analytics and software engineering research.
 
 The README gives an overview of how the source tree is organised and sort
@@ -24,7 +24,7 @@ You can find the following files and directories here:
     version 2.
 
 `pom.xml`
-    As any other modern Java project, Alitheia Core uses maven for building. 
+    As any other modern Java project, Alitheia Core uses maven for building.
     We also use the Pax OSGi tools. You need to have those installed if
     you plan to add functionality or external libraries to Alitheia Core
 
@@ -54,33 +54,91 @@ Git must be installed. Git can be downloaded from: http://git-scm.com/download
 
 Without a Github account, the code can be checked out as follows:
 
-git clone git://github.com/istlab/Alitheia-Core.git
+`git clone git://github.com/istlab/Alitheia-Core.git`
 
 Courtesy of Github, a zip of the current latest version of the software
-can be downloaded.
-
-https://github.com/istlab/Alitheia-Core/zipball/master
+can be downloaded from https://github.com/istlab/Alitheia-Core/zipball/master.
 
 ### Compiling, running and developing
+Note: More instructions can be found at the online Quickstart guide at http://www.sqo-oss.org/quickstart.
 
 Alitheia Core is build using Maven (tested with version > 3). You can download
-Maven from the following link: http://maven.apache.org/
+Maven from the following link: http://maven.apache.org/.
+
+#### Choosing the Database Backend
+
+Alitheia Core supports two database backends: H2 and MySQL.
+
+ **Note: The configuration should always be enabled prior to compilation.**
+
+By default, Alitheia Core uses H2 (http://www.h2database.com/html/main.html) as
+its database backend. This should be ok for a local installation and experimentation, but in general it is recommended to use MySQL.
+
+##### Enabling Support for MySQL
+
+To enable support for MySQL the following steps must be followed:
+
+ 1. Edit the file `Alitheia­‐Core/pom.xml`:
+
+  a. Comment out the following lines:
+```xml
+<eu.sqooss.db>H2</eu.sqooss.db>
+<eu.sqooss.db.host>localhost</eu.sqooss.db.host>
+<eu.sqooss.db.schema>alitheia;LOCK_MODE=3;MULTI_THREADED=true</eu.sqooss.db.sche
+ma>
+<eu.sqooss.db.user>sa</eu.sqooss.db.user>
+<eu.sqooss.db.passwd></eu.sqooss.db.passwd>
+<eu.sqooss.db.conpool>c3p0</eu.sqooss.db.conpool>
+```
+  b. Uncomment the following lines:
+```xml
+<eu.sqooss.db>MySQL</eu.sqooss.db>
+<eu.sqooss.db.host>localhost</eu.sqooss.db.host>
+<eu.sqooss.db.schema>alitheia</eu.sqooss.db.schema>
+<eu.sqooss.db.user>alitheia</eu.sqooss.db.user>
+<eu.sqooss.db.passwd>alitheia</eu.sqooss.db.passwd>
+<eu.sqooss.db.conpool>c3p0</eu.sqooss.db.conpool>
+```
+ 2. Edit the MySQL main configuration file (usually named `/etc/my.cnf`) and add the
+  following lines:
+```
+default-­‐storage-­‐engine=innodb
+transaction_isolation=READ-­‐COMMITTED
+```
+The above lines enable innodb as default.
+
+ 3. Create an empty database named `alitheia`. Then create a database user named
+  `alitheia` with password `alitheia` and grant full control over the database
+(@localhost):
+```sql
+CREATE USER 'alitheia'@'localhost' IDENTIFIED BY 'alitheia';
+CREATE DATABASE alitheia;
+GRANT ALL PRIVILEGES ON alitheia.* TO alitheia@'localhost';
+```
+
+#### Building the project
 
 * To build the project, do:
 
   `mvn install`
 
-* To run Alitheia Core, you need to configure a database first. Consult the
-  online Quickstart guide at http://www.sqo-oss.org/quickstart
-  on how to do it. Then, run:
+#### Run the project
+
+* To run Alitheia Core, run:
 
   `mvn pax:provision`
 
   Then visit the web interface: [http://localhost:8080](http://localhost:8080)
 
+* To see the results of runned plugins of projects, run the following from the web folder:
+
+  ```mvn jetty:run```
+
+  Then visit the web interface: [http://localhost:8081](http://localhost:8081)
+
 * To debug Alitheia Core (on Unix-based systems):
 ```
-  mvn install pax:provision`
+  mvn install pax:provision
   [quit the OSGi prompt]
   ./debug.sh
 ```
@@ -94,3 +152,4 @@ Maven from the following link: http://maven.apache.org/
   Any tool can be used to write code for Alitheia Core, but using Eclipse will
   simplify things a lot. Instructions can be found in IDE.md
 
+

alitheia/core/src/test/java/eu/sqoooss/admin/test/AdminServiceImplTest.java → alitheia/core/src/test/java/eu/sqooss/admin/test/AdminServiceImplTest.java

@@ -1,4 +1,4 @@
-package eu.sqoooss.admin.test;
+package eu.sqooss.admin.test;
 
 import static org.junit.Assert.*;
 

alitheia/core/src/test/java/eu/sqoooss/admin/test/FailingAction.java → alitheia/core/src/test/java/eu/sqooss/admin/test/FailingAction.java

@@ -1,4 +1,4 @@
-package eu.sqoooss.admin.test;
+package eu.sqooss.admin.test;
 
 import eu.sqooss.service.admin.AdminActionBase;
 

alitheia/core/src/test/java/eu/sqoooss/admin/test/SucceedingAction.java → alitheia/core/src/test/java/eu/sqooss/admin/test/SucceedingAction.java

@@ -1,4 +1,4 @@
-package eu.sqoooss.admin.test;
+package eu.sqooss.admin.test;
 
 import eu.sqooss.service.admin.AdminActionBase;
 

pom.xml

@@ -169,8 +169,8 @@
         <configuration>
           <showWarnings>true</showWarnings>
           <showDeprecation>true</showDeprecation>
-          <source>1.6</source>
-          <target>1.6</target>
+          <source>1.7</source>
+          <target>1.7</target>
         </configuration>
       </plugin>
       <plugin>