2010 ADWOrganization of the PHP programs » History » Revision 3
Revision 2 (Neil Voss, 06/09/2010 08:39 AM) → Revision 3/4 (Neil Voss, 06/09/2010 08:48 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()
* Important base scripts:
** @checkAppionJob.php@ — follow the progress of the job (common to all scripts, except reconstructions, see @checkRefineJobs.php@)
** @index.php@ — provides the final report with methods section for any exemplar reconstructions
** @config.php@ — the customization file for the
** @@ —
** @@ —
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** @viewstack.php@ — the famous stack viewer
* 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