Rest server now also takes ch.psi.fda.home variable into account

FDA-106

ch.psi.fda/Readme.md

@@ -1,6 +1,9 @@
 # Overview
 This package holds the core functionality of FDA.
 
+# Usage
+use -Djava.util.logging.config.file=logging.properties` to configure logging
+
 # Development
 When checking out the project from the repository there is the `target/generated-sources/xjc` folder missing.
 After checking out the project execute `mvn compile` to create the folder and the required classes. 

ch.psi.fda/src/main/java/ch/psi/fda/rest/FdaServer.java

@@ -18,6 +18,7 @@ import org.glassfish.jersey.jackson.JacksonFeature;
 import org.glassfish.jersey.server.ResourceConfig;
 import org.glassfish.grizzly.http.server.HttpServer;
 
+import ch.psi.fda.install.ApplicationConfigurator;
 import sun.misc.Signal;
 import sun.misc.SignalHandler;
 
@@ -51,6 +52,10 @@ public class FdaServer {
 			return;
 		}
 
+		// set the correct environment variable based on ch.psi.fda.home variable
+		ApplicationConfigurator ac = new ApplicationConfigurator();
+		ac.initializeApplication();
+		
 		URI baseUri = UriBuilder.fromUri("http://" + hostname + "/").port(port).build();
 
 		ResourceBinder binder = new ResourceBinder();

ch.psi.fda/src/test/resources/home/config/logging.properties

@@ -11,4 +11,4 @@ java.util.logging.ConsoleHandler.level=ALL
 java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
 
 # Set the default logging level for the logger named com.mycompany
-ch.psi.level=ALL
+ch.psi.level=ALL