Appion

h1. AMI Eclipse Quick Start Guide

{{>toc}}

h2. 1 Get the Eclipse executable

First, you can try the executable that already has the plugins installed. Get *eclipse.tar.gz* from the Files tab here in Redmine. Just copy it to your machine, uncompress it and the executable is available within the eclipse directoy. No further installation steps are required.

If you want to install things yourself, this is what you need:

# Download eclipse from "here":http://www.eclipse.org/downloads/download.php?file=/technology/epp/downloads/release/galileo/SR1/eclipse-jee-galileo-SR1-linux-gtk-x86_64.tar.gz.

# Get the plugins:

## Subversion

## PHP

## Subversion connector

## pydev

# Copy it to somewhere on your local machine.

# Double click the eclipse executable to open. If using a machine that was setup with the AMI kickstart program, you will need to update java to use the 64 bit version. (Ask Christopher)

h2. 2 Create a Workspace and get the MyAMI code from Subversion

# Double click the eclipse executable found in the eclipse directory.

# When it opens, it will prompt you to choose a workspace. This workspace will hold a local copy of the myami code for you to work on. A good workspace location is a amiworkspace in your home directory. That is /home/username/amiworkspace.

# From the menu, select Window -> Open Perspective -> SVN Repository Exploring. This will open a view labeled SVN Repositories.

# Go to File -> New -> Repository Location.

# In the URL field type: http://emg.nysbc.org/svn/myami to get the Appion and Leginon code.

# Press the Finish button at the bottom of the dialog. A new repository will appear in the SVN Repositories view.

# Click on the arrow next to the repository icon to view the trunk, branches and tags associated with the repository.

# Click on the trunk to highlight it. Right click and select Checkout. This will get the code from the repo and put it in your workspace. When the operation completes, you will find a myami directory under amiworkspace in your home directory.

h2. 3 Configure your Development Environment

There are 2 types of development that you will most often do with the MyAMI code, Python for core processing and PHP for the web interface.

h3. 1 Setup the Python environment

Go to Window -> Preferences -> PyDev -> Editor -> Interpreter – python. Press the Auto Config button then press OK.

h3. 2 Setup the PHP environment

There are two ways to view the web applications that you are developing in your home directory. If you are developing on a machine that does not have a local Apache server, you can use the Cronus3 web server. The advantage of this is that all the image processing plugins are already installed on Cronus3 so you don't have to worry about them and you don't have to worry about making Apache work. If you do run Apache locally, you can take advantage of integrated debugging tools in Eclipse and learn more about how all the pieces of the project fit together since will will have to set more things up. 

Also note that the directions below will not get project_tools running. It is currently undergoing many changes and directions will be added when that process is complete.

h4. Use Cronus3 or Fly to view your web app

(Fly is a good choice since it is not a production server. You can create your own databases on Fly as well.)

# Open a terminal and go to your home directory: *$ cd ~*                                                 

# Create a directory called "ami_html" if it does not exist: *$ mkdir ami_html/*                                      

# Change directories to ami_html:  *$ cd ami_html*                                            

# Create a symbolic link to the web app directory in your workspace: *$ ln -s /home/[username]/amiworkspace/myami/myamiweb*   

# Try to browse to the project in a web browser ( http://cronus3/~username/myamiweb ). You should see an error because config.php failed to open. Keep reading "Create your config file" to fix this.

h4. Create your config file

*IMPORTANT:* Never check your local copy of the config files into Subversion. We don't want to share our database user information with the world.

# Change directories to the myamiweb project: *$ cd ~/amiworkspace/myami/myamiweb*

# Copy config.php.template to config.php: *$ cp config.php.template config.php*

# Open config.php for editting: *$ vi config.php*

# Make the following changes to config.php:

<pre>

// --- define dbem web tools base --- //

$BASE_PATH = "myamiweb";

define('BASE_URL', "/".$BASE_PATH."/");

// --- Set your leginon MySQL database server parameters

$DB_HOST        = "cronus4";

$DB_USER        = "usr_object";

$DB_PASS        = "";

$DB             = "dbemdata";

// --- XML test dataset

$XML_DATA = "test/viewerdata.xml";

// --- Project database URL

$PROJECT_URL = "http://cronus3.scripps.edu/~[username]/project_tools";

$PROJECT_DB_HOST = "cronus4";

$PROJECT_DB_USER = "usr_object";

$PROJECT_DB_PASS = "";

$PROJECT_DB = "project";

</pre>

Also modify config_processing.php:

<pre>

// --- Processing database --- //

$PROCESSING_DB_HOST = "cronus4";

$PROCESSING_DB_USER = "usr_object";

$PROCESSING_DB_PASS = "";

$PROCESSING_DB = ""; //--- leave empty,  set by projectdb

// --- Add as many processing hosts as you like --- //

$PROCESSING_HOSTS[]="guppy";

$PROCESSING_HOSTS[]="";

</pre>

h4. Use your local Apache server to view your web app (optional)

# Make sure you are logged in as root. ($ su)

# Make sure Apache is installed. There should be /etc/init.d/httpd on your machine. Start apache with $ /etc/init.d/httpd start. 

# Point a web browser to http://localhost/ and make sure you see the apache test page.

# Make sure Apache is configured for php

# the Apache config file is at /etc/httpd/conf

# web files should be at /var/www/html

## create  symbolic link to your workspace in /var/www/html

## Try to view at http://localhost/myamiweb 

## Not working because need the files on phpami

### go to phpami in your myamiweb workspace and create symbolic links to each file that remove the .php file extension

### put a symbolic link to this folder from user/share ( $ ln -s /home/amber/amiworkspace/myami/phpami php )

# To debug PHP issues check http://localhost/myamiweb/info.php

# For everything to work, you need to install plugins like the MRC module

h2. 4 Get a local copy of the databases (optional)

If you want to work on the databases and you would prefer to have a local copy to play with, read [[Setup Local Databases | How to set up a local copy of AMI databases]].

You also have an option of creating a copy of the database that you wish to work with on the fly server. You will name your DB with your name prepended to the name of the DB that is copied. You will need to update your Config file accordingly. You can work with your DB without affecting formal testing on fly or the production databases.

h2. 5 Run a Python Script

# Change perspective to PyDev. (Window->Open Perspective)

# Right click on the myami project and choose Properties

# Select PyDev - PYTHONPATH

# Under Source Folders select Add source folder

# Make sure myami is selected and press OK

# Build numextension

## Right click on numextension/setup.py and select Properties

## Select Run/Debug settings

## Select Edit

## Select the Arguments tab

## Under program arguments type _build_

## Select OK

## Right click on setup.py and select Run As->Python Run

# Run Leginon 

## Make sure the config files are set correctly (leginon.cfg, sinedon.cfg)

## Run leginon/syscheck.py by right clicking and selecting Run As->Python Run

## Right click on leginon/start.py and select Run As->Python Run

h2. 6 Merge a revision to another branch

# Commit your change and note the revision number.

# Go to the branch that you want to merge the code into and select Team->Merge.

# Under URL click Browse and select the trunk or branch that you already committed your changes to.

# In the revisions area, select the radio button next to Revisions: and click the Browse button.

# Select the revision that you wish to merge AND the revision immediately preceding yours.

# Select OK to close out the revision browser.

# Select the Preview Button to see what files will be merged.

# If it looks like the correct files, select the Ok button the close the preview and select OK again to execute the Merge.

# When it completes, Eclipse will open a synchronizing window where you can see the differences between your local, merged version of the files and the version held by SVN.

# If all the changes look correct, you may Commit the changes. Please include a comment in the commit message similar to the following:

bq. Merge from trunk r14376 and r14383 to 2.0 branch, Fix for Post-processing does not work with FREALIGN jobs , refs #657