IGetDBWiki/GettingStarted: Difference between revisions

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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$$GettingStarted$igetdb_1_0-tutorial.zip]]
You can download some example source-code showing how to access an IGetDB mart and convert the results into a nice pie-chart: [[Media:IGetDBWiki$$GettingStarted$igetdb_1_0-tutorial.zip]]
== Setup of the IGetDB project class in GPMS 2 ==
[http://www.cebitec.uni-bielefeld.de/groups/brf/internal/AdministrationOverview/SetupNewIGetDBProjectClass Setup of the IGetDB project class in GPMS 2 (internal wiki)]


== DB Access ==
== DB Access ==


All IGetDB projects are backed by the projectmanagement system [[GPMSWiki| GPMS]].
All IGetDB projects are backed by the projectmanagement system [[GPMSWiki| GPMS]].
To be able to work with IGetDB you need an account.
To be able to work with IGetDB you need an account.
 
If you are a developer
send an email to:  [[MailTo(krunte AT cebitec DOT uni DASH bielefeld DOT de)]] to get a
developer account.


== Version Control ==
== Version Control ==
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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 ==
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== 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-documentation 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: `gendb_start scriptname.pl -p project [options]`
* `/share` contains all shared files
** `/exec` executable scripts, such as the importer scripts GenDB->IGetDB and SAMS->IGetDB
** `/doc` contains written and generated (e.g. `ant doc`) documentation
* `/WebContent` contains web-server specific code and the document root
** `/META-INF` contains a default version of the MANIFEST.MF file required for the `.war` file
** `/WEB-INF` contains the servlet configuration file `web.xml`
*** `/lib` contains all the `.jar` files the application is depending on
* `/src` contains the database schema and source code
** `/conf` contains all the configuration and resource files that are to be included into the `.war` file
** `/java` contains the Java source code

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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