Project

General

Profile

Edit History

Appion Home ยป

Developers guide » History » Version 53

Anchi Cheng, 04/04/2012 09:27 PM

1 1 Amber Herold 
h1. Developers guide
2 





    3
    34
    Amber Herold
    
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.





    4
    
    
    
It is a good place to add notes, however basic, that may help someone else accomplish a task related to Appion software development.





    5
    
    
    
Parts of this guide are specific to machines and the environment that we have at AMI. Our apologies.





    6
    
    
    





    7
    24
    Amber Herold
    
# *System Overview*





    8
    7
    Amber Herold
    
## Leginon





    9
    
    
    
### Scope





    10
    
    
    
### Windows Machine





    11
    
    
    
## Appion





    12
    1
    Amber Herold
    
### Web Parts - web server





    13
    
    
    
### Python Parts - processing server





    14
    
    
    
### 3rd party apps





    15
    
    
    
## Clusters





    16
    29
    Amber Herold
    
## "Myami code module diagram":http://emg.nysbc.org/projects/appion/wiki/Myami_code_diagram 





    17
    20
    Amber Herold
    
 





    18
    24
    Amber Herold
    
# *Development Tools*





    19
    46
    Amber Herold
    
## [[appion:AMI Redmine Quick Start Guide|Redmine quick start]] - issue reporting and adding documentation





    20
    47
    Amber Herold
    
## [[AMI_Eclipse_Quick_Start_Guide|Eclipse quick start]] - setting up an integrated development environment





    21
    46
    Amber Herold
    
## [[Subversion]] (SVN) - Tips for using our code repository





    22
    22
    Amber Herold
    
 





    23
    46
    Amber Herold
    
# *Language and Technology Resources*





    24
    
    
    
## language specific tutorials, guides and tips





    25
    
    
    
### [[HTML notes]] 





    26
    
    
    
### [[CSS notes]] 





    27
    
    
    
### [[PHP notes]]





    28
    
    
    
### [[Python notes]] 





    29
    
    
    
### [[Javascript notes]]





    30
    50
    Amber Herold
    
## [[General Best Practices]]





    31
    46
    Amber Herold
    
## [[Coding standards|AMI's best practices]] 





    32
    1
    Amber Herold
    
## [[Object Oriented Programming]]





    33
    33
    Amber Herold
    
## [[Useful shell commands]]





    34
    
    
    
## [[MySQL_Notes|Getting started with MySQL]]





    35
    20
    Amber Herold
    
 





    36
    24
    Amber Herold
    
# *Installing Appion for development*





    37
    
    
    
## Running the code from your sandbox





    38
    1
    Amber Herold
    
 





    39
    24
    Amber Herold
    
# *Adding a new program to the pipeline*





    40
    30
    Amber Herold
    
## General Instructions





    41
    22
    Amber Herold
    
### Processing parts (Python)





    42
    
    
    
#### database access





    43
    
    
    
### Web Parts (PHP)





    44
    1
    Amber Herold
    
#### launch page





    45
    22
    Amber Herold
    
#### reporting page





    46
    23
    Amber Herold
    
##### [[Using basicReport.inc]] for very simple PHP report pages





    47
    22
    Amber Herold
    
#### database accesss





    48
    4
    Neil Voss
    
## Adding a refinement method (single and multi model)





    49
    26
    Amber Herold
    
### [[Adding refine python parts|Python wrapper for 3rd party programs]] (Anchi)





    50
    
    
    
### [[Adding refine runjob|Modifications to runJob.py]] (Christopher)





    51
    4
    Neil Voss
    
### [[how to add a new refinement method|Uploading results to the databse]] (Dmitry)





    52
    
    
    
### [[Refine_Refactor_documentation|Adding the user interface]] (Amber)





    53
    22
    Amber Herold
    
 





    54
    24
    Amber Herold
    
# *Testing*





    55
    38
    Amber Herold
    
## [[Test datasets at AMI]]





    56
    42
    Amber Herold
    
## [[Create Appion Session|Create Appion Session for testing purposes]]





    57
    41
    Amber Herold
    
## [[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.





    58
    23
    Amber Herold
    
## [[Appion Testing|Automated testing]]





    59
    36
    Amber Herold
    
## [[How to test upload images with your own sandbox]]





    60
    37
    Amber Herold
    
## [[How to run manual picking and mask making]]





    61
    22
    Amber Herold
    
 





    62
    39
    Amber Herold
    
# *Error Handling*





    63
    
    
    
## [[Error Handling|Error handling guide]]





    64
    22
    Amber Herold
    
 





    65
    1
    Amber Herold
    
# *Adding pop-up Help*





    66
    39
    Amber Herold
    
## [[adding popup help]]





    67
    6
    Amber Herold
    
 





    68
    49
    Amber Herold
    
# *Making changes to database tables*





    69
    
    
    
## [[Database change procedure]] 





    70
    
    
    
 





    71
    39
    Amber Herold
    
# *Other stuff*





    72
    
    
    
## Where to find help





    73
    51
    Amber Herold
    
## [[Appion tricks]]





    74
    39
    Amber Herold
    
## [[Common variables used]]





    75
    43
    Amber Herold
    
## Appion Developer's Workshops





    76
    44
    Amber Herold
    
### [[2010 Appion Developer Workshop]]





    77
    45
    Amber Herold
    
### "2011 Appion Developer Workshop":http://emg.nysbc.org/projects/appion-workshop/wiki





    78
    53
    Anchi Cheng
    
# [[Job submission vs direct Appion Script running from terminal]]  What are the differences in database logging and resource usage.