##General Information This repository includes the servlet based middleware part of the Alazen project.

##Setup

1. Pack the content of the build/classes folder, the lib/ folder, the dl_genomic_files.bas script in src/ and the web.xml file into a .war file (see here [1] as a reference). ALternatively you can use the createWAR.bash script lying in the repository. As of right now, using the script will not include the web pages. If you want to include the web pages you can get these from the frontend team [2]
2. Set up a servlet container, following, the process will be described with an Apache Tomcat 8.0 (i.e. here [3])
3. Move into the root directory of the Tomcat server. Navigate into the webapps/ directory and copy the .war-archive into it. Start the Server via the startup.sh script in bin/, the Tomcat should now deploy the application. If you have not included the web pages you should now put them into webapps/Alazen/ directory.
4. If you want to use name search and prefix search navigate into webapps/Alazen/WEB-INF/classes and execute dl_genomic_files.bash. The execution of the file will take several minutes.
5. Restart the server. The server will now initiate the servlet. This will take several minutes. Even if the script says that Tomcat started, the web application will not be available until the initialization process has finished.

##Usage

1. Make sure you are in the wifi network of the instute for computer science Humboldt University Berlin and that the initialization process has finished.
2. In your browser, open 141.20.37.114:10000/MiddlewareServlet/
3. You should now see the web page you deployed into webapps/Alazen and use the system

Information: By accessing http://141.20.37.114:10000/MiddlewareServlet/QueryReceiver you should be able to send requests to the middleware system without using the frontend. Make sure to use the query exchange format specified in the specification [4] in section 3 when using the application this way

[1] https://docs.oracle.com/javaee/7/tutorial/packaging003.htm

[2] https://github.com/hu-semesterprojekt-genombrowser/Alazen-GUI

[3] http://tomcat.apache.org/

[4] https://github.com/hu-semesterprojekt-genombrowser/Alazen/blob/master/finaleDokumente/projektSpezifikation/Projektspezifikation_final.pdf