IGetDBWiki/GettingStarted: Difference between revisions

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This HowTo explains briefly how to get started with developing code for IGetDB project.
This HowTo explains briefly how to get started with developing code for IGetDB project.


== DB Access ==
== Code Example ==


All IGetDB projects are backed by the projectmanagement system [[GPMSWiki| GPMS]].
You can download some example source-code showing how to access an IGetDB mart and convert the results into a nice pie-chart: [[Media:IGetDBWiki$$GettingStarted$igetdb_1_0-tutorial.zip]]
To be able to work with IGetDB you need an account.


If you are a developer
== Setup of the IGetDB project class in GPMS 2 ==
send an email to:  [[MailTo(krunte DASH devel AT cebitec DOT uni DASH bielefeld DOT de)]] to get a
developer account.
== Version Control ==
IGetDB has dependencies on several CVS-controlled projects (IGetDB itself is in a Subversion repository, see below).


=== CVS ===
[http://www.cebitec.uni-bielefeld.de/groups/brf/internal/AdministrationOverview/SetupNewIGetDBProjectClass Setup of the IGetDB project class in GPMS 2 (internal wiki)]


* create a working direktory for CVS in your home named 'CVS'
== DB Access ==
* cd to that directory and get the projects needed to run emma:


<pre><nowiki>
All IGetDB projects are backed by the projectmanagement system [[GPMSWiki| GPMS]].
cvs checkout bioinfo/<name of project>
To be able to work with IGetDB you need an account.
</nowiki></pre>
 
You need to checkout the following projects:
* projectmanagement
* O2DBI
 
=== Subversion ===
* change into the directory <code><nowiki>CVS/bioinfo</nowiki></code> and execute
 
<pre><nowiki>
svn co http://svn.cebitec.uni-bielefeld.de/svn/igetdb/trunk igetdb
</nowiki></pre>


== Version Control ==
[[IGetDBWiki/GettingStarted/VersionControl| Version Control]]


== API Documentation ==
== API Documentation ==
Line 41: Line 25:
trouble then it's worth. To generate your own copy of the API
trouble then it's worth. To generate your own copy of the API
documentation, simply run <code><nowiki>ant doc</nowiki></code> in <code><nowiki>igetdb</nowiki></code> directory.
documentation, simply run <code><nowiki>ant doc</nowiki></code> in <code><nowiki>igetdb</nowiki></code> directory.
== Setting up the IGetDB-exporter for EMMA ==
[[IGetDBWiki/GettingStarted/EmmaPlugin| EMMA Plugin]]


== Web-Server ==
== Web-Server ==
 
[[IGetDBWiki/GettingStarted/WebServer| Web-Server]]
IGetDB should be able to run in any servlet-container, although it has been tested with Tomcat 5.5 only.


== Documentation ==
== Documentation ==
 
[[IGetDBWiki/GettingStarted/Documentation| Documentation]]
----
'''As developers we are also responsible for documentation. Please let's try the following conventions:'''
* document your code
* use the specific documentation tools of the domain
* use [[JavaDoc]] comments for documenting Java classes
* when using Eclipse use the Java formatter profile "Java Conventions"
* use POD for documenting Perl module
* use perlmodule Pod::Usage for documenting perl-scripts
* each script needs a usage message (see above)
* [[O2DBIWiki|O2DBI]]-documentation (will create POD-doku for server classes)
----
The other main source is the perldoc documentation. The generated [[O2DBIWiki|O2DBI]]-servermodules are pod documented. You can read them with:
<pre><nowiki>
perldoc module.pm
</nowiki></pre>
 
Other modules may also have pod-documetation but this is not guaranteed. The documentation found can also be incomplete or rather outdated. If you wish to generate the documentation for all perl modules you can do so be executing the shell script:
 
<pre><nowiki>
CVS/bioinfo/igetdb/share/exec/create_html_docs.pl
</nowiki></pre>
 
It generates an HTML version of the perldoc documentation in the directory 'CVS/bioinfo/igetdb/share/doc/html'.
 
Additional documentation can be found in CVS/bioinfo/igetdb/share/doc.


== Directory Structure ==
== Directory Structure ==
 
[[IGetDBWiki/GettingStarted/DirectoryStructure| Directory Structure]]
The directory `CVS/bioinfo/igetdb/` contains the specific components of the igetdb software:
 
* `/bin` start wrapper(s) for executable scripts in `/share/exec`.
To run a script in share exec type: `igetdb_start scriptname.pl -p project [options]`
* `/share` contains the main application code
** `/exec` executable scripts
** `/perl` contains perl code
*** `/IGetDB` contains perl code
**** `/WWW/` modules specific to the web front-end of IGetDB
**** `/DBmodules` modules accessing the backend, used by the www-modules
* `/www` contains web-server specific code and the document root
** `/cgi-bin' contains the cgi-scripts
*** `/templates' the HTML-templates for each page
* `/htdocs' contains the static HTML pages for the web front-end
** `/images' the images used for the web front-end
* `/log' contains logging files of the apache web server
* `/src` contains the database schema and code for generation of code and documentation

Latest revision as of 14:33, 28 October 2011

Getting Started

This HowTo explains briefly how to get started with developing code for IGetDB project.

Code Example

You can download some example source-code showing how to access an IGetDB mart and convert the results into a nice pie-chart: Media:IGetDBWiki$$GettingStarted$igetdb_1_0-tutorial.zip

Setup of the IGetDB project class in GPMS 2

Setup of the IGetDB project class in GPMS 2 (internal wiki)

DB Access

All IGetDB projects are backed by the projectmanagement system GPMS. To be able to work with IGetDB you need an account.

Version Control

Version Control

API Documentation

The API documentation of IGetDB is not checked in as this causes more trouble then it's worth. To generate your own copy of the API documentation, simply run ant doc in igetdb directory.

Setting up the IGetDB-exporter for EMMA

EMMA Plugin

Web-Server

Web-Server

Documentation

Documentation

Directory Structure

Directory Structure

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