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Deploying Domeo
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Step 1 - Libraries -
Step 2 - Environment -
Step 3 - Installing Git -
Step 4 - Clone the complete Domeo Repository -
Step 5 - Running the scripts -
Step 6 - Generating the war file -
Step 7 - Deploying the war file -
Step 8 - Database configuration -
Step 9 - Email configuration -
Step 10 - Proxy configuration -
Step 11 - General Info -
Step 12 - Start up!
After making sure Java 6 is installed, these are the libraries and tools needed:
Here is the archive of some of the latest Grails distributions: http://grails.org/download/archive/Grails
Here is the archive of the latest GWT distributions: http://code.google.com/p/google-web-toolkit/downloads/list
After all the necessary libraries have been downloaded, it is necessary to bind the environment variables.
In the file ./MacOSX/environment.plist bind
"GRAILS_HOME" = "/grails-2.0.3";
"GWT_HOME" = "/gwt-2.4.0";
Also in the file .bashrc file in the user’s home it is necessary to update the PATH by including the Grails /bin directory. Remember, it is necessary to logout and login again for all the variables changes to be loaded.
In order to build the project, it is necessary to download (clone) the code base through Git
[See how to clone the Domeo code here] (Cloning-the-codebase)
Some projects in the hierarchy contain a SETUP.TXT file. The scripts in those file has to be run in order to create the necessary directories and soft links. Particularly critical are the script in DomeoClientWrapper and Domeo projects.
Note: I know this is not very high tech, I will provide soon one single script for doing everything in one step.
In order to generate the war file properly you need to position in the root of the Domeo (domeo/Domeo) Grails project and to run the following grails instruction:
grails war
This will generate the war file in the directory Domeo/target
Deploy the war file in the webapp directory of Tomcat
Before starting the server, it is necessary to define the data source parameters. These have been externalized in the file Domeo-config.properties (case sensitive), which content will look similar to this:
# MySQL
dataSource.username = root
dataSource.password = ...
dataSource.url = jdbc:mysql://localhost/DomeoAlphaDev?useUnicode=true&characterEncoding=UTF-8
and this:
# Elastic Search
elastico.ip = xxx.xxx.xxx.xxx
elastico.port = 9200
elastico.database = domeo
elastico.collection = annotation
The Domeo-config.properties file has to be included in the Tomcat classpath.
Domeo uses the email system to send confirmations/requests/alerts to the users and administrators. Currently Domeo is setup to use a Gmail account. The credentials have to be set up in the previous configuration file and have to include the following properties:
grails.mail.host = smtp.gmail.com
grails.mail.port = 465
grails.mail.username = <email address of the Domeo system>
grails.mail.password = <password for the email address of the Domeo system>
grails.mail.default.from = <email address of the Domeo system>
If no email credential have been set up, Domeo is supposed to ignore the email instructions. However, it is strongly recommended to set the email up to assure a more efficient functioning of the system.
Domeo can be setup so that every call to external service happens through a proxy. In order to use a proxy add the following lines to the configuration file.
domeo.proxy.ip=<ip>
domeo.proxy.port=<port number>
In the configuration file it is important to add the general info of the instance:
domeo.subtitle=Annotation Toolkit
domeo.administrator=Dr. Paolo Ciccarese
domeo.admin.email.display=paolo dot ciccarese at gmail.com
domeo.admin.email.to=<email address>
domeo.organization=Massachusetts General Hospital
When Tomcat starts up you should be able to experience a logging similar to the following:
11 Mar 2013 15:38:56,567 conf.BootStrap ==========================================
11 Mar 2013 15:38:56,568 conf.BootStrap DOMEO ANNOTATION WEB TOOLKIT (v.2.0 Alpha, b.007)
11 Mar 2013 15:38:56,568 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,568 conf.BootStrap Designed and developed by Paolo Ciccarese
11 Mar 2013 15:38:56,568 conf.BootStrap for MIND Informatics Labs directed by Tim Clark
11 Mar 2013 15:38:56,568 conf.BootStrap A product of Massachusetts General Hospital, Boston, MA, USA (c) 2012
11 Mar 2013 15:38:56,568 conf.BootStrap ==========================================
11 Mar 2013 15:38:56,569 conf.BootStrap Bootstrapping....
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,569 conf.BootStrap ** Configuration externalization:
11 Mar 2013 15:38:56,569 conf.BootStrap [classpath:Domeo-config.properties, file:./Domeo-config.properties]
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,569 conf.BootStrap ** MongoDB Configuration
11 Mar 2013 15:38:56,570 conf.BootStrap url : [:]
11 Mar 2013 15:38:56,570 conf.BootStrap database : [:]
11 Mar 2013 15:38:56,570 conf.BootStrap collection : [:]
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,570 conf.BootStrap ** Elastic Search Configuration
11 Mar 2013 15:38:56,570 conf.BootStrap ip : 75.101.xxx.xxx
11 Mar 2013 15:38:56,570 conf.BootStrap port : 9200
11 Mar 2013 15:38:56,570 conf.BootStrap database : domeo
11 Mar 2013 15:38:56,571 conf.BootStrap collection : annotation
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,581 conf.BootStrap ** MySQL Configuration
11 Mar 2013 15:38:56,581 conf.BootStrap url : jdbc:mysql://localhost/DomeoAlphaDev?useUnicode=true&characterEncoding=UTF-8
11 Mar 2013 15:38:56,581 conf.BootStrap username : root
11 Mar 2013 15:38:56,581 conf.BootStrap password :
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
11 Mar 2013 15:38:56,582 conf.BootStrap ** Proxy Configuration
11 Mar 2013 15:38:56,582 conf.BootStrap proxy ip : [:]
11 Mar 2013 15:38:56,582 conf.BootStrap proxy port : [:]
11 Mar 2013 15:38:56,569 conf.BootStrap --------------------------------------------------------------------------------------
...
11 Mar 2013 15:38:56,885 conf.BootStrap Bootstrapping complete!
11 Mar 2013 15:38:56,885 conf.BootStrap ==========================================
| Server running. Browse to http://localhost:8080/Domeo