GENOMEPRO 2.0
Code Directory Structure:
-------------------------
website: -- source code of all the web site components
database: -- backups of database structure and schema
installationGuide: -- how to install GenomePro on a fresh server
userManual: -- simple guide on how to use GenomePro 2.0
Web Site Directory Structure:
-----------------------------
> var
> www
> html
> avatars -- user avatars
> *.jpg
> *.png
> ...
> config
> config.php -- contains PHP definitions (global variables)
> core
> core.php -- in every PHP page. autoloads all libraries
> delivery -- FTP section. password protected user files
> user1
> index.php -- copied from helpers/ftp. makes viewing nicer
> uploads -- files uploaded by user. some form of DNA
> u1_file1.*
> u1_file2.*
> ...
> results -- result of tools arranged by folders
> u1_out1 -- the actual name of these folders contain job id
> *.*
> ...
> u1_out2
> *.*
> ...
> ...
> ...
> helpers
> cron
> cron.helper.php -- locks crons from running over each other.
> db_cleaner.php -- runs once a day. cleans uncomfirmed users for now.
> file_validator.php -- validates uploaded files for validity.
> job_processor.php -- processes jobs from the database and stores results.
> ftp
> index.php -- this gets copied when user created or password changed.
> mailer -- PHPMailer stuff. only kept the bare minimum.
> *.* -- we're using a GenomePro gmail to send emails.
> ...
> db_helper.php -- currently empty. Poor guy never got love.
> format_helper.php -- functions stored here that format dates, etc.
> system_helper.php -- super versatile guy. Moves files, creates FTP for users, and more.
> libraries -- the models of the site
> Database.php -- the only model that runs queries and returns results of queries.
> File.php -- contains functions to grab and set files from and to the database.
> Job.php -- same as files, but with jobs instead.
> Template.php -- the pseudo-mvc guy. this is the controllers means to communicate with view.
> Tool.php -- same as files, but with tools instead.
> User.php -- same as files, but with users instead.
> Validator.php -- just checks up on formatting, like when registering, passwords match, etc.
> programs -- run of the mill location where C programs are stored.
> source -- any source files, sample input, trashy stuff stored here.
> *.*
> ...
> extract -- one of the programs GenomePro uses.
> extract.exe -- the actual executable. most programs follow this format.
> probes
> probes.exe
> ...
> templates -- HTML code for the site. Controllers pull from here onto TEMPLATE.
> css
> *.*
> ...
> data
> *.*
> ...
> fonts
> *.*
> ...
> ...
> about.php -- the views of the site.
> charts.php
> contact.php
> ...
> about.php -- although similar name, don't be confused! These are the controllers.
> charts.php
> contact.php
> ...
GenomePro Site:
----------------
http://genomepro.cis.fiu.edu/