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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. |
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| == DB Access == | | == Code Example == |
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| 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.
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| 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
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| developer account.
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| == CVS ==
| | [http://www.cebitec.uni-bielefeld.de/groups/brf/internal/AdministrationOverview/SetupNewIGetDBProjectClass Setup of the IGetDB project class in GPMS 2 (internal wiki)] |
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| * 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:
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| <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>
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| You need to checkout the following projects:
| | == Version Control == |
| * igetdb
| | [[IGetDBWiki/GettingStarted/VersionControl| Version Control]] |
| * projectmanagement
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| * common
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| == API Documentation == | | == API Documentation == |
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| The API documentation of OntoDB is not checked in as this causes more | | 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 | | trouble then it's worth. To generate your own copy of the API |
| documentation, simply run the script | | documentation, simply run <code><nowiki>ant doc</nowiki></code> in <code><nowiki>igetdb</nowiki></code> directory. |
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| <pre><nowiki> | |
| CVS/bioinfo/ontodb/bin/create_html_doc.sh
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| </nowiki></pre> | |
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| | == Setting up the IGetDB-exporter for EMMA == |
| | [[IGetDBWiki/GettingStarted/EmmaPlugin| EMMA Plugin]] |
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| == Web-Server == | | == Web-Server == |
| | | [[IGetDBWiki/GettingStarted/WebServer| Web-Server]] |
| * goto CVS/bioinfo/igetdb/share/www
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| * edit apache2.sh: change `PORT=XXXX` to any free port on the webserver, and set CVS= to your CVS-directory
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| * login on a suitabel test-webserver using `qxterm` or `qrsh`
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| * in that shell execute:
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| <pre><nowiki>
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| CVS/bioinfo/igetdb/share/www/apache2.sh start
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| </nowiki></pre>
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| * try to open `http://SERVER:PORT` with your browser
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| * if nothing happens or you get an error message have a look at `CVS/bioinfo/igetdb/share/www/log/all.errors`
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| == Documentation == | | == Documentation == |
| | | [[IGetDBWiki/GettingStarted/Documentation| Documentation]] |
| ----
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| '''As developers we are also responsible for ducumentation. Please let's try the following conventions:
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| * document your code
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| * use the specific documentation tools of the domain
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| * use POD for documenting Perl module
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| * use perlmodule Pod::Usage for documenting perl-scripts
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| * each script needs a usage message (see above)
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| * [[O2DBIWiki|O2DBI]]-documentation (will create POD-doku for server classes)
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| '''
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| ----
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| The other main source is the perldoc documentation. The generated [[O2DBIWiki|O2DBI]]-servermodules are pod documented. You can read them with:
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| <pre><nowiki>
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| perldoc module.pm
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| </nowiki></pre>
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| 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:
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| <pre><nowiki>
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| CVS/bioinfo/igetdb/share/exec/create_html_docs.pl
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| </nowiki></pre>
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| It generates an HTML version of the perldoc documentation in the directory 'CVS/bioinfo/igetdb/share/doc/html'.
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| Additional documentation can be found in CVS/bioinfo/igetdb/share/doc.
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| == Directory Structure == | | == Directory Structure == |
| | | [[IGetDBWiki/GettingStarted/DirectoryStructure| Directory Structure]] |
| The directory `CVS/bioinfo/igetdb/` contains the specific components of the igetdb software:
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| * `/bin` start wrapper(s) for executable scripts in `/share/exec`.
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| To run a script in share exec type: `igetdb_start scriptname.pl -p project [options]`
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| * `/share` contains the main application code
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| ** `/exec` executable scripts
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| ** `/perl` contains perl code
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| *** `/IGetDB` contains perl code
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| **** `/WWW/` modules specific to the web front-end of IGetDB
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| **** `/DBmodules` modules accessing the backend, used by the www-modules
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| * `/www` contains web-server specific code and the document root
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| ** `/cgi-bin' contains the cgi-scripts
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| *** `/templates' the HTML-templates for each page
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| * `/htdocs' contains the static HTML pages for the web front-end
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| ** `/images' the images used for the web front-end
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| * `/log' contains logging files of the apache web server
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| * `/src` contains the database schema and code for generation of code and documentation
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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