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.
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Structure of root module |
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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.
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The src directory |
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