CoGe - Greentea

CoGe Greentea is a metrics and analytics engine for the CoGe platform written on Clojure's web framework Noir.

How To: Deploy on a Server via Apache Webserver

Prerequisites:

(You can install these CLI tools using your linux distributions preferred package manager)

Apache2 - with plugins
libapache2-mod-proxy-html - For proxying the running port to the correct endpoints.
libxml2-dev
Maven - For Clojure Dependencies
Git - For cloning repos in from github
[Leiningen] - Automate Clojure projects without setting your hair on fire. [Leiningen]: https://github.com/technomancy/leiningen

Configuring Greentea to the Database

Once you have all the prerequisites installed, you need to get the Greentea (Analytics) repo from Github. Run:

$ git clone https://github.com/LyonsLab/Greentea.git

TODO: Create a method of loading settings into Analytics from a configuration file so there's no need to unsafely fudge with the code.

Open "Greentea/src/greentea/db.clj" in your favorite text editor.

Modify from line 9:

  defdb cogedb                                                                   
      (mysql {:db "<DB>;"                                                            
      :user "<DB USER>;"                                                          
      :host "<DB HOST (probably localhost)>"
      :port "<DB&nbsp;PORT (remove this line if default)>"
      :password "<DB PASSWORD>"})

Write to the file. Make sure not to push any sensitive information back to Github!

Get Greentea Running:

Inside the cloned directory run:

$ lein run &

This should pull in all the required dependencies'''*''' and start a Jetty servlet running on port 3456.
Check localhost:3456 to verify that the analytics platform is running.

Configure Apache to Proxy the Servlet Port to the /greentea Endpoint:

Now to setup apache to point localhost/greentea/ to port 3456.

Open '/etc/apache2/apache.conf' (or another conf location) in your favorite editor and add these lines:

  RewriteEngine On 
  NameVirtualHost *:90 
  Listen 90
  
  <VirtualHost *:90> 
    ServerAdmin coge.genome@gmail.com ServerName localhost 
    #ServerAlias geco.com.analytics
    ErrorLog /home/rchasman/logs/error.log 
    CustomLog <PATH>/logs/access.log combined 
    LogLevel warn
      
   <Directory <PATH>/Greentea/resources/public/>     
        AllowOverride All                                                        
        Order Allow,Deny                                                         
        Allow from all                                                           
   </Directory>
   
    DocumentRoot <PATH>/Greentea/resources/public                    
      
    ProxyPass /analytics/ http://localhost:3456/analytics/                       
    ProxyPassReverse /analytics/ http://localhost:3456/analytics/                
      
    ProxyPass /analytics http://localhost:3456/analytics/                        
    ProxyPassReverse /analytics http://localhost:3456/analytics/                 
      
    ProxyPass /greentea/ http://localhost:3456/greentea/                         
    ProxyPassReverse /greentea/ http://localhost:3456/greentea/                  
      
    ProxyPass /greentea http://localhost:3456/greentea/                          
    ProxyPassReverse /greentea http://localhost:3456/greentea/                   
  </VirtualHost>

These lines proxy calls to /greentea and /greentea/ to port 3456 so that we don't have to type any ugly numbers to reach our site.

Finally, run:

sudo services apache2 restart

If it says OK, it means the server should be started and you should be able to point a browser at it.

If everything was configured properly point your browser to /Greentea and Greentea should be up and running!

*In the case of a common dependency issue with iplant-clojure-commons:

We need to point to the missing dependency manually:

Run:

$ git clone https://github.com/iPlantCollaborativeOpenSource/iplant-clojure-commons.git

In the iplant-clojure-commons directory, run:

$ lein uberjar

In lein 2.0 this will create a file at "/iplant-clojure-commons/clojure-commons-1.3.3-SNAPSHOT-standalone.jar"

Replacing with appropriate , run:

$ mvn install:install-file -DgroupId=org.iplantc -DartifactId=clojure-commons -Dversion=1.3.3-SNAPSHOT -Dpackaging=jar -Dfile=<PATH>/iplant-clojure-commons/clojure-commons-1.3.3-SNAPSHOT-standalone.jar

Now try :

$ lein clean

and then

$ lein run

The dependency issue should be resolved.

rchasman / Greentea