To the point: if the person you were five or ten years ago were to meet the person you are today, would you recognize yourself? What would you think? How about the reverse: if the person you are today were to meet the person you were five or ten years ago, what would you think?

I was the one being abused in an emotionally abusive relationship. I left.

If I attend , it might mean that I head down a basic science path. I’m not sure at what point I’d be able to mash tissue engineering into my career, if ever. Angiogenesis comes close, but isn’t really the same thing. Also, lots of friends here, but I’m worried that if I attend and become the ridiculous student I should have been as an undergrad, people will hold it against me. Social currency is money, of which I have and will have little.

If I attend , I can mash tissue engineering into my career immediately. There are at least three different laboratories I could rotate through that, at the very least, have collaborations which involve tissue engineering. I also have a few friends here, but they’re all in school and similarly busy. Social currency is intelligence, which is great.

If I attend , I’m not sure what I’d really be doing. Genetic Medicine research looks very interesting, but tissue engineering is not something that is done here. Few friends in the area. High cost of living without much justification. Social currency: connections.

Table below.

Goals

Create a Ruby on Rails development environment with Apache, MySQL, and PHP.

There are several possible ways of doing this, but since OS X is a Unix-based platform, I don’t see any reason to use pre-compiled packages like MacPorts and replacing the built-in software. Plus, this is supposed to be a learning experience.

Sources

http://maestric.com/doc/mac/apache_php_mysql_snow_leopard

http://michaelgracie.com/2009/09/23/plugging-mcrypt-into-php-on-mac-os-x-snow-leopard-10.6.1/

Basic Setup

OS X comes with Apache, Ruby, Rails, and PHP pre-loaded; the specific versions of each are dependent upon the installed version of OS X. In my case, I am starting with a fresh installation of Snow Leopard (10.6), and beginning by downloading all available System Updates, which brings my system to version 10.6.5, with Apache version 2.2.15, Ruby 1.8.7, Rails 2.3.5 , and PHP 5.3.3.

In order to use the pre-loaded Apache installation, go to “System Preferences” > “Sharing”  and check “Web Sharing”. This will enable the Apache web server. If you ever need to restart the server, either uncheck and re-check this box, or use the command <code>sudo apachectl restart</code> from the command line.

Next, we need a compiler, so we’ll install Apple’s Xcode Developer Tools, which can be found on the OS X installation CD/DVD and also online directly from Apple (http://developer.apple.com/technologies/tools/xcode.html). I have version 3.2.3 installed. I’m writing this up after having performed all of the updates, so the initial version may have been different.

MySQL

MySQL doesn’t come installed as part of the normal OS X distribution; just OS X Server. No problem; just download an OS X *.dmg package for MySQL Community Server: http://www.mysql.com/downloads/mysql/#downloads

Note: OS X Snow Leopard (10.6) and later compile in 64-bit C, so be sure to download the 64-bit version of MySQL (x86_64 suffix). This took me a while to figure out, as I had downloaded the 32-bit version for my 32-bit kernel. I thought it made sense. Version 5.1 should work just fine; I didn’t try 5.5.

Anyway, the MySQL *.dmg contains three files: the MySQL installer, the MySQL Startup Item installer, and the Preference Pane item. Install them in the order I have listed here. Once it’s installed, go ahead and try starting the server. The indicator in the Preference Pane item should turn green.

Edit /etc/profile and add “PATH=$PATH:/usr/local/mysql/bin”, otherwise you’ll have to type the full path to the mysql and mysqladmin executables in order to use them.

PHP

You’ll need to enable PHP by un-commenting a line beginning with “LoadModule php5_module…” in your Apache configuration file, typically found at /private/etc/apache2/apache2.conf.

Additionally, you’ll have to create a php.ini file in /etc/, which is most easily done by making a copy of “/etc/php.ini.default”. While you’re doing that, un-comment the line for your time zone, and enter a valid value. Additionally, change the three occurrences of “/var/mysql/mysql.sock” to “/tmp/mysql.sock” in order to point PHP at your MySQL installation.

I like using phpMyAdmin to manage my MySQL databases, so I’ll need to install this. The process is straightforward and well-documented. However, once you do this, you’ll notice that you’ll need PHP to have been compiled with the mcrypt extension, and the OS X distribution hasn’t been. Not to worry, Michael Gracie has a solution to that problem (http://michaelgracie.com/2009/09/23/plugging-mcrypt-into-php-on-mac-os-x-snow-leopard-10.6.1/).  Be sure to update the version numbers of the different software packages accordingly.

Restart the Apache server so these changes to php.ini take effect.

Ruby on Rails

I’m going to be using Rails 3.0, so I’ll need to update RubyGems with “sudo gem update –system” followed by “sudo gem update” to update all installed gems.

I’ll need to install a database adapter so that RoR can interface with MySQL. Rails 3 defaults to the mysql2 gem for MySQL databases, so we’ll install that with “sudo gem install mysql2 — –with-mysql-config=/usr/local/mysql/bin/mysql_config”.

I want to use the devise plugin for user authentication, so I’ll install that and its dependent gem, warden.

Finally, I want to use passenger to deploy my Rails application just to make my life easier: “sudo gem install passenger” followed by “sudo passenger-install-apache2-module” and follow the directions.

Done!

I was going to write more about configuring virtual hosts, but this post languished with “draft” status for over a week already.

The reason I used three models, rather than rolling the attributes of the third (ln2_locations) into the actual item was that in reality, we normally freeze down multiple vials with the same content at the same time.  I would like to implement this kind of mass assignment at a later time.

Anyway, it is often useful to be able to determine what we have stored, and how much of each different type of content is present. It’s one thing to know what the SQL code would be to retrieve these records; it’s another to convert that to an ActiveRecord query when you’re just learning.

What I would like to do is look at my items (cryovials), and pull out the unique content values (e.g. cell types), then go back and count how many vials I have with that content. It would be pretty easy to accomplish this as two separate statements, but that would involve iteration and two separate SQL queries. Best to leave it as one query where I count and select unique fields simultaneously:

Rails:

@summary = Ln2Location.select("count(*) count, contents").joins(:cryovial).where(:present => true).group(:contents)

SQL:

SELECT count(*) count, contents FROM `ln2_locations` INNER JOIN `cryovials` ON `cryovials`.`id` = `ln2_locations`.`cryovial_id` WHERE (`ln2_locations`.`present` = 1) GROUP BY contents

I’m selecting on Ln2Locations because there’s a property, “present,” which I’m using to select only the vials which haven’t been physically removed from the collection. Additionally, the relationship between the models is as follows:

class Cryovial < ActiveRecord::Base
# Relationships
belongs_to :user
has_many :dewars, :through => :ln2_location
has_many :ln2_locations
accepts_nested_attributes_for :ln2_locations

class Dewar < ActiveRecord::Base
# Relationships
belongs_to :laboratory
belongs_to :location
has_many :cryovials, :through < :ln2_locations

class Ln2Location < ActiveRecord::Base
# Relationships
belongs_to :dewar
belongs_to :cryovial

So only the child model, Ln2Locations, contains the foreign key that would be used to generate the join table.

- add desired attributes to migration file
- make added attributes accessible in model file
- either roll your own views or add fields to generated views

That’s it. It really isn’t difficult or different than making any other model.

I was worried that it would be complicated, and spent a lot of time reading about devise to be sure. It’s so easy, no one writes about it.

Optimizing your MySQL Application

Indexing for DB performance

details: http://www.railsbrain.com/api/rails-2.0.2/doc/index.html?a=M001468&name=add_index

I don’t plan to build a giant Rails application, but Rails is known to have scalability issues. Still good to be aware of these points.

I’ve bought the eBook version of the 4th edition of the Pragmatic Programmers’ Agile Web Development with Rails. It’s still in beta, but my main goal is to see how things have changed between Rails 2.x and Rails 3. The book also covers some basic user authentication, but it’s very simplistic. In the interest of getting my project up and going quickly, I looked into authlogic and devise/warden.

Both authlogic and devise/warden were highly recommended by mischa after building an application that did some direct comparisons of several different RoR user authentication solutions. Good enough for me. devise appears to be more lightweight, so I’ll try that one first.

A little bit about my server setup: I’m hosted with Lithium Hosting, which is a great deal and has fantastic customer service. They’re not paying me to pitch the service, though clicking the link above and then signing up for a plan gives me referral credits or something. It’s a shared hosting service, so I manage my site with cPanel if I need/want to, and I’ve added on SSH access to my account so I don’t really need to use cPanel.

Once the server upgraded to Rails 3.0/Ruby 1.8.7, a couple things happened: my rails apps stopped starting automatically (cPanel feature), cPanel could no longer start my rails apps, and I couldn’t create a new Rails app with a MySQL database.

Solutions:

1) install the mysql2 gem, which is the new mysql database adapter used by Rails 3. The compilers are disabled on my host, so this was done via support ticket.

2) add mongrel to my Gemfile,

#project/Gemfile
gem 'mongrel'

Mongrel isn’t automatically started in development mode. cPanel still won’t start my application, so starting the server is done via SSH with

rails server --port=[port]

So now I can create a new project

rails new project --database=mysql

and start the server. However, I don’t have a good way of authenticating users.

So, back to the support tickets to have both authlogic and devise installed. Once tech support has done that (seven minutes. really.), check if they’re installed for me:

gem server --port=[port]

and navigate to mysite.com:[port]. They’re not, run a couple commands from the command line:

gem install devise
gem install authlogic

Which should install the gems and make them available to me. Checking again as above, and both devise and authlogic are present. Add the appropriate lines to my Gemfile. Then, since I’m trying out devise first, install it:

rails generate devise:install

That’s all for now.

I’m writing this more to file this away somewhere I won’t accidentally delete it:


class CreateLn2Locations < ActiveRecord::Migration
def self.up
# create table
create_table :ln2_locations do |t|
t.integer :vial_id
t.integer :dewar_id
t.integer :canister
t.integer :cane
t.integer :position
t.boolean :present, :default => 1
t.date :date

t.timestamps
end

# remove table
drop_table :ln2_locations
end
end


Last night, I was almost doored by a guy getting out of his car. He opened his door, then kicked it out open even more without looking back. There were four other people on bicycles in front of me, and a patio full of restaurant patrons who would have seen if I had hit the door and gone through the window. Thank goodness I was already on the brake. Bike lanes are great, but I don’t really like being in the door zone. And so much for lights alerting drivers to my presence.