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Developers guide » History » Version 50

Amber Herold, 08/10/2011 12:56 PM

1 1 Amber Herold 
h1. Developers guide
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This guide is primarily intended to help noobs to both Appion and Programming in general get up and running in the development environment that we have created at AMI.





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It is a good place to add notes, however basic, that may help someone else accomplish a task related to Appion software development.





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Parts of this guide are specific to machines and the environment that we have at AMI. Our apologies.





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# *System Overview*





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## Leginon





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### Scope





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### Windows Machine





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## Appion





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### Web Parts - web server





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### Python Parts - processing server





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### 3rd party apps





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## Clusters





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## "Myami code module diagram":http://emg.nysbc.org/projects/appion/wiki/Myami_code_diagram 





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# *Development Tools*





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## [[appion:AMI Redmine Quick Start Guide|Redmine quick start]] - issue reporting and adding documentation





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## [[AMI_Eclipse_Quick_Start_Guide|Eclipse quick start]] - setting up an integrated development environment





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## [[Subversion]] (SVN) - Tips for using our code repository





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# *Language and Technology Resources*





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## language specific tutorials, guides and tips





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### [[HTML notes]] 





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### [[CSS notes]] 





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### [[PHP notes]]





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### [[Python notes]] 





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### [[Javascript notes]]





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## [[General Best Practices]]





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## [[Coding standards|AMI's best practices]] 





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## [[Object Oriented Programming]]





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## [[Useful shell commands]]





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## [[MySQL_Notes|Getting started with MySQL]]





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# *Installing Appion for development*





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## Running the code from your sandbox





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# *Adding a new program to the pipeline*





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## General Instructions





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### Processing parts (Python)





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#### database access





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### Web Parts (PHP)





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#### launch page





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#### reporting page





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##### [[Using basicReport.inc]] for very simple PHP report pages





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#### database accesss





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## Adding a refinement method (single and multi model)





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### [[Adding refine python parts|Python wrapper for 3rd party programs]] (Anchi)





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### [[Adding refine runjob|Modifications to runJob.py]] (Christopher)





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### [[how to add a new refinement method|Uploading results to the databse]] (Dmitry)





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### [[Refine_Refactor_documentation|Adding the user interface]] (Amber)





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# *Testing*





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## [[Test datasets at AMI]]





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## [[Create Appion Session|Create Appion Session for testing purposes]]





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## [[Setup Local Databases | How to set up AMI databases on your local machine]]: Handy if you want to play with the databases without affecting anyone else.





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## [[Appion Testing|Automated testing]]





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## [[How to test upload images with your own sandbox]]





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## [[How to run manual picking and mask making]]





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# *Error Handling*





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## [[Error Handling|Error handling guide]]





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# *Adding pop-up Help*





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## [[adding popup help]]





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# *Making changes to database tables*





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## [[Database change procedure]] 





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# *Other stuff*





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## Where to find help





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## [[Common variables used]]





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## Appion Developer's Workshops





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### [[2010 Appion Developer Workshop]]





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### "2011 Appion Developer Workshop":http://emg.nysbc.org/projects/appion-workshop/wiki