ANDS SISS (DC4B) Project Files

Part-A: Extending the system features:
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0. Java doc is available in documentation/javadoc/index.html

1. To setup your Tomcat server v 7.0 instance in debugging mode:
    Eclipse -> Window -> Show View - > Project Explorer and select and expand 
    'Servers -> Apache Tomcat v7.0 at localhost-config' now double click the web.xml and make sure
    that debugging is defined within the <servlet> tags
    
    <servlet>
    ....
    ....
    <init-param>
      <param-name>debug</param-name>
      <param-value>1</param-value>
    </init-param>
    ....
    ....
    </servlet>
    
2. Extend with new R-scripts
Implement new R algorithms in scripts and then update the RscriptRead class and extend the ResultsLM 
class to use your newly updated R-script, such as:
    - Line fitting
    - Principal Component Analysis
    - Manova clustering

3. Extend new computeResults services class with addon computation algorithms such as:
    - BMCP (Bi-criterion Median Clustering)
    - MMCP (Multi-Median Clustering)
    - Jenks Natural Breaks

4. Implement automatic scripts to ingest of input data by scripting (bash scripts)

5. Export 'WAR' files instead so as to easily setup the java dependencies.

6. Setup the project as a Maven project to handle the building of the source with their 
dependencies automatically.

7. Extend web frontend interface descriptions to add more features. The frontend requires:
- jQuery 1.5.1
- jQuery-ui 1.8.11
- jQuery-form 2.84
- OpenLayers 2.11
- Extjs 3.4.0
- GeoExt 1.1
- Processingjs 1.2.3

Code Structure:

/canvas_pde
- Contain PDE files for visualising the statistical output.
- Requires Processingjs and HTML5 capable internet browsers such as Internet Explorer 9

/ext-3.4.0
- Contains Extjs 3.4.0

/geoext
- Contains GeoExt 1.1

/img
- Contains image files

/jquery-ui
- Contains jQuery 1.5.1 and jQuery-ui 1.8.11

/non-html5
- Contains support for internet browsers not supporting HTML5 (Internet Explorer 7 and 8)

/openlayers
- Contains OpenLayers 2.11

/processing
- Contains Processingjs 1.2.3

fieldset_style.css
- Styling for <fieldset>

ie_redirect.js
- Redirecting internet browsers which are not supporting HTML5

index.html
- Main html file

initial_loader.js
- Loading initial services such as Locations, Variables and Atom Feed

initial_loader.css
- Load initial styles

jquery.form.js
- Contains jQuery-form 2.84

map.js
- Contains source for the map object, data classification as well as user action and interface on the first tab (Map Interaction and Data classification)

map_style.css
- Styling for the map object

stat_forms.js
- Contains source for user action and interface on the second tab (Statistical Analysis)

stat_results.js
- Contains source to get the statistical output from user inputs on the statistical forms and visualise it.


Part-B: Debugging:
------------------------

1. If the R service backend is unable to be connected to:
    - The service runs on port 6311 by default, make sure the firewall opens localhost connections to this port
    - Do not enable 6311 to be accessed from an external location without going through a local process (servlet)
    - In the RserveCheck project:
        -  the ReadScript class has a JUnit test which describes how to load your Rscript
        - To start the local Rserve service on port 6311 access 
            http://localhost:8080/RserveCheck/Check?o=start
        - To stop the service go to: http://localhost:8080/RserveCheck/Check?o=stop
        - There should be debug logging to console and /tmp/server.log (default config in logback.xml) to help you
         debug the issue

2. Check the servlet errors/info/debug log, configured for each servlet in the logback.xml (by default /tmp/server.log)         

3. Check the system logs for apache web server
    This should be available in /var/log/apache2/
    
4. Check system logs for postgreSQL
    This should be available in /var/log/postgres/
        
5. Make sure you setup a logrotate on the default servlet logging (configured in logback.xml for each of the servlets) i.e., /tmp/server.log
otherwise the log file will continue to keep growing.

6. Also note, the servlet debugging (default /tmp/server.log) will be deleted on restart of the system.

7. If for some reason there are issues with the pre-compiled versions of the Database connectors, then you will need to manually compile them as shown below:
R project database connector installation:
a. Installing the required database connectors for R for PostgreSQL connector. To complete the steps below you need to make sure you have these utilities installed
    To install gcc (compiler and some default header files) 
        sudo apt-get install build-essential
b. To install the development headers for the libpq-dev (postgre sql devel library)
        sudo apt-get install libpq-dev
c. download RD-DBI for linux from: http://stat.bell-labs.com/RS-DBI/download/index.html
        wget  http://stat.bell-labs.com/RS-DBI/download/DBI/DBI_0.1-10.tar.gz
d. Install RD-DBI
        sudo R CMD INSTALL DBI-xxxxx.tar.gz
e. To install subversion - version control system
        sudo apt-get install subversion
f. To install the rpostgresql connector, download it from: http://code.google.com/p/rpostgresql/source/checkout documentation, i.e.,
        svn checkout http://rpostgresql.googlecode.com/svn/trunk/ rpostgresql-read-only
        cd rpostgresql-read-only
        tar zcvf rpostgresql.tar.gz RPostgreSQL
        sudo R CMD INSTALL rpostgresql.tar.gz
            
Rserve - a Binary R server installation:
1. Download a newer Rserve R package instead of the default provided by Ubuntu Linux OS 10.04 server:
        wget http://www.rforge.net/Rserve/snapshot/Rserve_1.7-0.tar.gz
        sudo R CMD INSTALL Rserve_xxxxxx.tar.gz
2. Download the Java application interfacing classes: These JARs are dependencies for the JAVA web services servlets
        wget http://www.rforge.net/Rserve/files/REngine.jar
        wget http://www.rforge.net/Rserve/files/RserveEngine.jar


Part-C: Miscellaneous:
------------------------------
Using the Default ubuntu Linux OS Tomcat Installation:
1. Install Tomcat packages in with apt-get or synaptic:
    sudo apt-get install tomcat6
2. Run the following command to edit tomcat-user.xml to enable Tomcat manager which will be used to deploy applications:
    sudo gedit /etc/tomcat6/tomcat-user.xml
3. Add these lines inside <tomcat-users></tomcat-users>:
    <role rolename="manager"/>
    <role rolename="admin"/>
    <user username="admin" password="password" roles="manager,admin"/>
4. Finally restart Tomcat:
    sudo /etc/init.d/tomcat6 restart

GeoServer Installation with the ubuntu OS system tomcat install:
GeoServer is packaged as a standalone servlet for use with existing servlet container applications such as Apache Tomcat and Jetty.
1. Download  GeoServer war file from the GeoServer Download page and pick the appropriate version to download.
2. Select Web archive on the download page.
3. Download and unpack the archive. Copy the file geoserver.war to the directory that contains Tomcat container application’s webapps.
4. Go to Tomcat manager (localhost:8080/manager/html) to deploy the war file.
For further GeoServer installation information go to: http://docs.geoserver.org/stable/en/user/installation/index.html