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2010 ADWOrganization of the PHP programs » History » Revision 2

Revision 1 (Neil Voss, 06/09/2010 08:19 AM) → Revision 2/4 (Neil Voss, 06/09/2010 08:39 AM)

h1. Organization of the PHP programs 

 * Location: 
 ** /myami/myamiweb/processing 

 * Sub Folders: 
 ** @inc@ — include directory, common libraries like @appionlib@ 
 ** @js@ — javascript directory, contains @help.js@ the help pop-up window text 
 ** @img@ — image director, contains images like program logos (e.g., EMAN, Appion, Spider) and check, cross, and ext icons for image assessor 
 ** @css@ — style sheets, custom look and feel of website, usually not modified 

 * The include (@inc@) folder 
 ** @appionloop.inc@ — contains the common interface for all appionLoop programs (CTF estimators, Particle pickers, and Make Stack) 
 ** -@euler.inc@- — depricated on the fly Euler plot generation script, was way too slow moved to python 
 ** @menuprocessing.php@ — a single, giant function that generates the menu on the left side of all appion pages 
 ** @particledata.inc@ — collection of all database queries, e.g., getStackIds(), getParticlesFromImageId(), getPixelSizeFromImgId(), or getStackIdFromReconId() 
 ** @processing.inc@ — functions that are common to all Appion pages, e.g., processing_header(), referenceBox(), submitAppionJob(), getProjectId() 
 ** @summarytables.inc@ — provides summary tables that are common on many pages, e.g., stacksummarytable(), alignstacksummarytable(), and modelsummarytable() 

 * Ideal flow for a job process: 
 ** _select program_ (e.g., @selectParticleAlignment.php@) — a selection page for each program that provides a detailed description to help user decide which on to use 
 ** _run Appion script_ (e.g., @runDogPicker.php@) — setup parameters and run the program 
 ** @checkAppionJob.php@ — follow the progress of the job (common to all scripts, except reconstructions, see @checkRefineJobs.php@) 
 ** _process summary_ (e.g., @stackhierarchy.php@) — show all runs of that process type, e.g., stacks 
 ** _process report_ (e.g., @stackreport.php@ — report on a particular run of that process type, e.g. stack id 12