Difference between revisions of "Installation"

Revision as of 16:30, 20 January 2007

Installing mx

These are somewhat brief and should evolve as more people attempt to install. Feel free to add questions right here.

Required Software

MySQL (http://www.mysql.com/)

• You need at least MySQL 4.1.14 to install the tables. 4.1.10 and previous will load, but several queries (mostly Matrix related) will not work. We have not investigated whether they can be modified to work with 4.1.10 or earlier. MySQL 5.n is in use on development and production servers. Its easiest to install the community addition with the startup item too, then reboot. You'll want to secure your mysql installation.

• There are many examples of how to install and secure MySQL on your machine available on whe world-wide web. If you are using OS X chances are you have a copy installed already (it will need configuration if you haven't already done so).

Ruby

• If you don't already have ruby you can find more about it here. We run mx under 1.82 or 1.84. We recommend building it from source. Get it the source here.

RubyGems

Its easiest to install several Ruby packages (including Rails) through the Ruby package manager RubyGems.

Rails (http://www.rubyonrails.org/)

Install Rails with

       gem install rails --include dependencies
     

More information on installing Rails may be found at the URL above. We have developed primarily on Rails version 1.1.12, and production is now using 1.1.16. For security reasons you should be using 1.1.16 or higher.

You'll also need RedCloth, a simple markup language that is used in various places.

       gem install redcloth    

ImageMagik (optional) (http://www.imagemagick.org/script/index.php)

• NOTE: This is optional, and not required for MorphBank images.

• mx uses ImageMagik to handle images. At present it is set to do this through a PHP call (due to the drastic speed increase this provides).
• See the image.rb model to eliminate the need for PHP.
• The tool 'convert' must be in your PATH, and in the default setting so must PHP, i.e. when you type 'convert' or 'php' at the command prompt you should get a short status line indicating they executed.

Files and images uploaded to mx are stored in /public/files

If you are on a PC create the following folders in /public

       files
       files/big
       files/medium
       files/original
       files/thumb

On a *nix system you'll need the same structure, but note that you can also use a symbolic link to keep your images elsewhere.

Platform Specific Notes

OS X

• You should have [Apple's develop tools installed before installing mx. Later versions of OS X come with it installed, if you can do

 gcc -v 

and see 3.n you're probably ok.

• You may have to use 'sudo' in front of your commands when installing, like

sudo gem install rails --include dependencies

• You need to be running Ruby version 1.8.2 or higher (tested on 1.8.2)
• OS X updates **WILL** break your installation by (re)installing Ruby to /usr/bin. Their version (at least in 10.3.9) is incompatible with mx. The easiest way to get around this is to simply rename the OS X version ruby in /usr/local/bin to something like ruby_old like this:

cd /usr/local/bin
mv ruby ruby_old

• Test your version of ruby at the path by entering

  ruby -v

x86 (Windows 2000/XP)

• The db/rake tasks for rebuilding are apparently borked at present matt 19:40, 16 January 2007 (CST)

*nix Specific Notes

Installation

Basic steps

1. Install the required software (see above).
2. Download the mx source.
3. Build the database(s).
4. Configure the database for startup.

Detailed installation steps

Download mx source

1. Get it from [Sourceforge] *OR*
2. Checking out a copy via SVN (only available to developers at present)

Build the database

The easiest way to install the database is to open a terminal or command prompt and navigate to the /db folder at the root of the mx code (you should see the tables.sql file there). Once there logon to mysql as an administrator. The process to install from scratch will look like something like this (don't forget the ';' for mysql commands):

       cd <path_to_rails>/db
       mysql -u root -p
       <enter password>
       create database mx_development;
       use mx_development;
       source tables.sql;
       

Build the production databases the same way:

       create database mx_production;
       use mx_production;
       source tables.sql;

If you have access to a master copy of the data from production (talk to your administrator to see if this is possible) you'll not need to follow the instructions below, but do:

cd <mx root>/db
rake restore_last file=<dumped production data>

4) Add an administrator to the mx tables

These steps all require that you are using the MySQL client

       mysql -u root -p 
       <enter password>

You'll need to add a MySQL account so that the app can access the database:

       GRANT ALL PRIVILEGES ON mx_development.* TO 'mx'@'localhost' IDENTIFIED BY 'MmmXxx';

A single user with administrator privileges will have to be manually added to the 'people' tables prior to using mx. Once this user is added additional users can be added from the mx interface.

       use database mx_development;
       insert into people (first_name, last_name, login, password, is_admin,
         creates_projects) values ('joe', 'smith', 'jsmith', sha1('foosomepwdbar'), 1,1);
       

• IMPORTANT - you must wrap 'foo' and 'bar' around your password in the above line. In the example above the password for 'jsmith' is 'somepwd' #

While in the MySQL client you'll also want to add a root node to your taxonomic names hierarchy (assumes the admin you created has id 1).

       insert into taxon_names (name, l, r, creator_id, updator_id) values ('root', 1, 2, 1, 1);

Usage (development mode)

Using the server/application

To test/develop in development mode navigate to the root of your installation and type

       ruby script/server

Open a web browser and browse to

       127.0.0.1:3000

You should see a login page. If you see the mx page but no login fields then you have not correctly added your administrator user.

Once logged in navigate to

       127.0.0.1:3000/admin

to create new projects.

You can also navigate to

       127.0.0.1:3000/account/signup

to add regular users.

Rebuilding the tables

If you've downloaded a new version of mx, or have a new copy of the tables you can rebuild the tables several ways.

Using rake

Navigate to /db and do

rake --tasks

You'll see a list of options that you can run in that directory. The dumped data goes into /dumps.

To rebuild the tables with the *current* data do this

rake reload

So if you have acquired a copy of data from someone else you can do something like this:

 rake restore file=<your file like 2007_01_10_173343.sql>

Note that its assumed that the data is in /dumps.

Using SQL statements

If you just want to rebuild the tables (*prior* to their being any data, all data will be LOST via this method) you can repeat the building commands:

cd <trunk>/db
mysql -u <username, e.g. root> -p
drop database mx_development;
create database mx_development;
use mx_development;
source tables.sql;

If you have data that you want to maintain then do a

rake dump_data 

prior to the sequence above. Then repeat the rake restore.

Usage (production mode)

<under construction>

Production installation follows, for the most part, the same installation process as above. See the Rails homepage for setting up the server. Note that only users with accounts can see data in a clean installation of mx, i.e. you must manually configure the installation to make data available to the public.