Appion

h1. Developers guide

Proposed content:

 

# System Overview

## Leginon

### Scope

### Windows Machine

## Appion

### Web Parts - web server

### Python Parts - processing server

### 3rd party apps

## Clusters

 

# Development Tools

## [[appion:AMI Redmine Quick Start Guide|Redmine]]

## Eclipse

## SVN

 

# Languages and Technology

## html, css, PHP, Python, Javascript, mySQL

## [[Coding standards|best practices for these]] 

 

# Installing Appion for development

# Myami Code Tree

# Running the code from your sandbox

 

# Adding a new program to the pipeline

## General Insructions

### python parts

#### [[how to add a new refinement method]] (single and multi-model)

### Web Parts

#### launch page

#### [[Refine_Refactor_documentation|How to add a launch form for a new refine type]]

##### parameter checking

#### reporting pages

### Database Parts

#### python side

#### PHP side

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

### Python wrapper for 3rd party programs (Anchi)

### Modifications to runJob.py (Christopher)

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

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

# Testing

# [[Error Handling]]

# Issue reporting and life-cycle

## [[appion:Issue Workflow Tutorial]]: A guide to setting the Issue status.

# Checking your code into the main trunk

# Appion/Leginon Release Versioning

# Adding Documentation

# Adding pop-up Help

# Where to find help

h2. Common variables used

* $outdir is the directory that contains the disk, session, jobtype, but not the runname: For example: /data/appion/10dec16a/extract

* $rundir = $outdir + runname, For example: /data/appion/10dec16a/extract/dogrun1

note: appion python code only accepts $rundir

* $description 

* $commit

* $command

* $sessiondata'

* $sessionid vs. $sessionId vs. $expid vs. $expId

* $apix vs. $pixelsize

* $box vs. $boxsize

h2. variable dump

<pre>

cd ~/myami/myamiweb/processing

cat *.php | grep '\$[A-Za-z]' | sed 's/\$_[A-Za-z]*//' | sed 's/[^$]*\(\$[A-Za-z0-9]*\)[^$]*/\1 \

/g' | sort | uniq -c | sort -rn | head -50

</pre>

<# of occurrences> <variable name>

<pre>

1066 $command 

1001 $particle 

 943 $ 

 854 $expId 

 630 $i 

 387 $formAction 

 385 $html 

 366 $javascript 

 349 $outdir 

 337 $projectId 

 327 $runname 

 326 $sessionId 

 299 $extra 

 213 $description 

 200 $graph 

 198 $stackid 

 198 $sessioninfo 

 186 $apix 

 180 $sessiondata 

 162 $display 

 160 $title 

 158 $templatetable 

 157 $user 

 136 $line 

 131 $javafunctions 

 127 $heading 

 126 $numpart 

 125 $jobinfo 

 117 $errors 

 114 $stackinfo 

 110 $t 

 110 $key 

 109 $s 

 108 $templateinfo 

 101 $sessionpath 

  98 $bin 

  96 $tomogram 

  96 $sub 

  96 $nproc 

  96 $filename 

  94 $stackId 

  91 $headinfo 

  90 $sessionname 

  90 $data 

  89 $j 

  89 $cmd 

  89 $box 

  89 $alignId 

  86 $r 

</pre>

h3. [[Appion Testing|Automated testing]]

h3. [[Using basicReport.inc]] for PHP report pages