Project's Home Page
Table of Contents Document Overview The Project Repository Dependencies Building and Deploying OME
Project's Home Page II. The Project Repository

 
  SBDD>The Project Repository>Source code organization Previous   Next  
 
 
 
II-1. Source code organization
 

The OME source code and other related artifacts are all contained, under the CVS root, in a root module called OME.
The directories and files under the OME module are organized as follows. The top directories are:

  • doc: the SBDD and the Tags History are contained here, in the SBDD and TagsHistory subdirectories. The doc directory also contains a documentation page, docs.html, with links to the DB schema definition and documentation as well as links to the XML image and analysis module schema definitions and documentation.
  • images: contains images needed by the Joust JavaScript library that is used to build the HTML interface to OME.
  • src: contains the source code.
  • update: upgrade scripts for the DB schema, from one release to the next.
  • README: old trustworthy README file.
  Structure of root module
 
 

The src directory tree is organized as follows:

  • C: various analysis routines and image file conversion utilities.
  • crontab: a daily cron for PostgreSQL to run vacuum and analyze to optimize its look-ahead genetic query optimizer.
  • html: static pages that are used along with the Joust JavaScript library (whose code is contained in those pages) to define and manage the basic site structure.
  • JavaScript: contains JavaScript libraries and code to make up the SVG viewer. Here are also contained some HTML pages that implement a front-end to a directory tree browser, making use of the Joust JavaScript library.
  • java: contains UI widgets for the analysis engine.
  • perl2: the Web interface, the analysis engine, image import and export facility, the classes that wrap access to the OME DB. That is, the guts of the system. Also, some unit tests are included here as well as a handy Perl script, perlCheck.pl, that can be used to download and install the required Perl modules from our server.
  • SQL: the scripts that define the OME relational DB schema are in here. The Diagrams subdirectory contains a script, postgresql_autodoc.pl, that generates documentation from the DB schema.
  • xml: go there for the XML schema definitions related to the analysis engine and image.
  The src directory
 

 
 
 
  Top Project Repository Previous   Next