Difference between revisions of "Installation"

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* '''IMPORTANT:''' Don't even bother trying to get Leopard's preinstalled MySQL to work with Rails '''if''' it's the 64 bit version.  It's basically impossible at this point.  Save yourself the headache, install the 32 bit version then add the mysql gem.
 
* '''IMPORTANT:''' Don't even bother trying to get Leopard's preinstalled MySQL to work with Rails '''if''' it's the 64 bit version.  It's basically impossible at this point.  Save yourself the headache, install the 32 bit version then add the mysql gem.
  
=== [http://www2.ruby-lang.org/en/20020102.html Ruby] ===  
+
=== [http://www.ruby-lang.org/en/ Ruby] ===  
  
* If you don't already have Ruby (most *nix systems come with it installed) you can find more about it [http://www.ruby-lang.org here]. We run mx under 1.8.7 and in some cases 1.8.6.  We recommend building from source.  Get it the source [http://www2.ruby-lang.org/en/20020102.html here]. Test your version of ruby at the path by entering:   
+
* If you don't already have Ruby (most *nix systems come with it installed) you can find more about it [http://www.ruby-lang.org here]. Ruby v. 1.8.7 or higher is now required.  We recommend building from source.  Get the source [http://www.ruby-lang.org/en/ here]. Test your version of ruby at the path by entering:   
  
 
  ruby -v
 
  ruby -v

Revision as of 10:54, 9 February 2011

Overview

mx can be installed locally for development or testing purposes or on a server. If you're seriously considering supporting a mx installation in your lab or workplace you should have an intermediate to advanced programmer or server admin on your team. Because of the relatively rapid updates to mx we recommend that you consider using the edge branch. Alternatively you could contact an admin of an existing installation and collaborate with them.

Required Software

MySQL

  • MySQL 5.n is in use on development and production servers. Its easiest to install the community addition with the startup item, then reboot.
  • 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).
  • IMPORTANT: Don't even bother trying to get Leopard's preinstalled MySQL to work with Rails if it's the 64 bit version. It's basically impossible at this point. Save yourself the headache, install the 32 bit version then add the mysql gem.

Ruby

  • If you don't already have Ruby (most *nix systems come with it installed) you can find more about it here. Ruby v. 1.8.7 or higher is now required. We recommend building from source. Get the source here. Test your version of ruby at the path by entering:
ruby -v

Under Debian 5 (installing 1.8.7 as of 2010-09-28) use

sudo apt-get install ruby

RubyGems

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

Rails

Production is now using Rails 2.3.10. Install the required version with the -v flag.

  • Do (appending --no-rdoc will speed things up, but not install local documentation):
 gem install rails --include-dependencies --no-rdoc

Optional Software

ImageMagik

  • NOTE: This is optional, and not required for MorphBank images.
  • The tools 'convert' and 'identify' must be in your systems PATH, copying them to /usr/bin generally works. You do not need a rubygem hook.
  • Ensure that you have created the necessary paths for storing the images.
  • If possible install the additional jpg, tiff, png, and gs libraries before installing ImageMagick, this will let you handle additional image formats.

Passenger

  • Used only on a production server.
  • If you are running passenger, on CentOS/RHEL 5 servers there is a default daily chron that deletes some necessary passenger files in /tmp/passenger.PID. The easiest way to deal with this is to set the PassengerTempDir in the apache conf to something else, like so:
 PassengerTempDir /some_other_tmp_dir

Legacy notes on installation

Installation

Basic steps

  1. Install the required software (see above).
  2. Download the mx source and required gems.
  3. Build the database(s).
  4. Configure the database for startup.
  5. Configure your folders
  6. Start the server

Detailed installation steps

Download mx source

The preferred method is now to checkout the source from Sourceforge using [SVN]].

The (most) stable branch is the trunk, though it presently lags significantly behind edge (see comments in intro):

svn co https://mx-database.svn.sourceforge.net/svnroot/mx-database/trunk your_local_folder_name_here

For developers or those wanting to see the latest changes an edge branch that should be relatively stable but may contain production restricting commits is here:

svn co https://mx-database.svn.sourceforge.net/svnroot/mx-database/branches/edge your_local_folder_name_here

Several site-specific branches are being added, these are not recommended as a base for new installs but do provide a lot of example code. To grab everything you can just do:

 svn co https://mx-database.svn.sourceforge.net/svnroot/mx-database your_local_folder_name_here

We will also continue occasionally to filter and provide non-svn [packages of the source], though expect these to lag significantly behind the svn versions.

Get the required gems

Depending on the checkout you downloaded you might need to install the ruby-debug gem first.

sudo gem install ruby-debug

You need various Ruby gems listed in the environment.rb. The easiest way to install them all is to enter your mx folder (you should see the folders 'app', 'config' etc. if you are in the right place) and type:

sudo rake gems:install

To install the bioruby gem you can do:

sudo gem install bio

Note that the native mysql gem is nearly always problematic, and you might have to work at getting it installed. You can try:

  sudo env ARCHFLAGS="-arch i386" gem install mysql -- --with-mysql-config=/usr/local/mysql/bin/mysql_config

On RHEL (after yum install mysql-devel) this worked:

gem install mysql -- --with-mysql-config=/usr/lib64/mysql/mysql_config 

On Ubuntu 9.10 (see also here) this worked:

sudo apt-get install libmysqlclient-dev
sudo gem install mysql

See here, or here, and more recently here for other possible solutions if you have no luck with the above.

Build the database

As of 0.2.1590 mx is setup to use the Rails migrations.

If you haven't yet create the databases (don't forget the ';' for mysql commands):

       mysql -u root -p
       <enter password>
       create database mx_test;
       create database mx_development;
       create database mx_production;
       

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';

Repeat the above but swap out the word development for 'test' and 'production'.

Then exit mysql and create the development database with the rake task (you may need to prefix with 'sudo'):

       rake db:migrate RAILS_ENV=development

You can create the production database like so if necessary:

       rake db:migrate RAILS_ENV=production

To create the test database do

       rake db:test:clone_structure

Anytime the source is updated just repeat the rake db:migrate and your database will be updated if there are changes. There are several rake tasks available for dumping and restoring data, make sure to check them out.

Adding an administrator and root to the taxon tree

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.

       mysql -u root -p
       <enter password>
       use 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 (this assumes the admin you created has id 1).

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

To start adding real taxa after you create a project make this root taxon visible via the visibility view in the "Taxon names" tab. Then the root will available as the parent of the highest taxonomic level included in your taxa list. Use the visibility list in the Taxon names tab to make root visible

Configure the environment.rb file

Open the

  /config/environment.rb 

file in a text editor. At the bottom you'll some variables under the header Local Configuration. Provide values for:

HOME_SERVER = 'your-server.com'
HELP_WIKI = 'hymenoptera.tamu.edu/wiki'  

To use/link to the existing help in this wiki (a good idea!) use 'hymenoptera.tamu.edu/wiki' for HELP_WIKI.

You may also change the various FOO_PATHs if your local configuration is setup differently.

You'll need to grab GoogleMaps API keys and add them for BOTH of:

 GMAPS_KEY_PRODUCTION
 GMAPS_KEY_DEVELOPMENT

Finally, replace the emails in

   ExceptionNotifier.exception_recipients = %w(joe@schmoe.com bob@gmail.com)

with those you want e-mails to be sent to when errors are thrown.

Specific to *nix systems: check the path of your MySQL socket

By default, the path of mysql.sock is set to

  /tmp/mysql.sock

However, several distributions do not use this path. To change it edit the file

  config/database.yml

and replace the 3 occurrences of

  socket: /tmp/mysql.sock

by your actual path. For instance in Ubuntu

 socket: /var/run/mysqld/mysqld.sock

Configuring file and image storage

Edit the /config/initializers/local_config.rb file and configure the various FILE_PATH variables, they can be left is if needed. If left is they correspond to the folders that you'll need to create below in the /public folder.

       files
       files/images
       files/images/big
       files/images/medium
       files/images/original
       files/images/thumb
       files/pdfs
       files/datasets
       files/chromatograms

On a *nix syste you can also use a symbolic link to keep your images, pdfs, and datasets elsewhere.

Start the server (development)

ruby script/server

Navigate to [127.0.0.1:3000 127.0.0.1:3000]

Troubleshooting

Configuring my.cnf

If you get a 'Mysql::Error: Got a packet bigger than 'max_allowed_packet' bytes:' you can add the following line to your my.cnf under [mysqld]: 'max_allowed_packet = 32M;'.

Usage (development)

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.

Upgrading

Once you have mx installed upgrading should be relatively straightforward. First, make a backup of both the database and the application, we assume you know where your data reside by this point, and we assume that you know that things can go horribly wrong. After backing up replace the old source with the new (see below for comments). Then, make sure you have the required Rails/Gems (plugins are included in the source already). Finally, run the rake task to update the database like so:

rake db:migrate RAILS_ENV=<development|production>

Its always a good idea to run the test suite as well, this will give you a good idea of what possible problems you might still have.

rake test

Production with no customizations

We don't have Capistrano working, so essentially you'll have to devise your own method of rolling to production, we use an SVN checkout for now.

Production with customizations

in progress

If you have begun to build public front ends you know where your custom code resides (/public, /app/models/public, /app/controllers/public, /app/views/public), manage these as you like.

Usage (production)

<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.

If you plan to set up a production installation of mx, it would be a good idea to read chapter 27 of Agile Web Development with Rails, second edition.

Misc. (Server config. etc.)

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