A “spike” application for Prescription Drug Monitoring Program (PDMP) research and experimentation, implements the protocol described in doc/srpp.txt. A client-side implementation is also available; it’s a plugin module for the OpenMRS electronic health record system. See github.com/project-pdmp/openmrs-module-pdmp for that code.
Copyright 2012, 2013 The MITRE Corporation
Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Spike installation and configuration is typical for a Rails application:
-
Clone the repository.
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Run “bundle install” to install the components that Spike depends on.
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Run “rake db:create” then run “rake db:migrate” to create the database and schema.
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Run “rake db:seed” to add reference data to the database. This command will create an administrative user ID and password and print them on the console.
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Run “rails server” to start the application.
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Go to localhost:3000/ and use the user ID and password from step 4 to sign in.
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Add your value-added features. You might find the following resources handy:
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The Getting Started Guide: guides.rubyonrails.org/getting_started.html
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Ruby on Rails Tutorial Book: www.railstutorial.org/
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If you’d like, please contribute bug fixes and enhancements back to
this project so others can benefit from them (and you can benefit from having a smaller patch kit).
Sometimes your application goes wrong. Fortunately there are a lot of tools that will help you debug it and get it back on the rails.
First area to check is the application log files. Have “tail -f” commands running on the server.log and development.log. Rails will automatically display debugging and runtime information to these files. Debugging info will also be shown in the browser on requests from 127.0.0.1.
You can also log your own messages directly into the log file from your code using the Ruby logger class from inside your controllers. Example:
class WeblogController < ActionController::Base def destroy @weblog = Weblog.find(params[:id]) @weblog.destroy logger.info("#{Time.now} Destroyed Weblog ID ##{@weblog.id}!") end end
The result will be a message in your log file along the lines of:
Mon Oct 08 14:22:29 +1000 2007 Destroyed Weblog ID #1!
More information on how to use the logger is at www.ruby-doc.org/core/
Also, Ruby documentation can be found at www.ruby-lang.org/. There are several books available online as well:
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Programming Ruby: www.ruby-doc.org/docs/ProgrammingRuby/ (Pickaxe)
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Learn to Program: pine.fm/LearnToProgram/ (a beginners guide)
These two books will bring you up to speed on the Ruby language and also on programming in general.
Debugger support is available through the debugger command when you start your Mongrel or WEBrick server with –debugger. This means that you can break out of execution at any point in the code, investigate and change the model, and then, resume execution! You need to install ruby-debug to run the server in debugging mode. With gems, use sudo gem install ruby-debug. Example:
class WeblogController < ActionController::Base def index @posts = Post.all debugger end end
So the controller will accept the action, run the first line, then present you with a IRB prompt in the server window. Here you can do things like:
>> @posts.inspect
=> "[#<Post:0x14a6be8
@attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>,
#<Post:0x14a6620
@attributes={"title"=>"Rails", "body"=>"Only ten..", "id"=>"2"}>]"
>> @posts.first.title = "hello from a debugger"
=> "hello from a debugger"
…and even better, you can examine how your runtime objects actually work:
>> f = @posts.first
=> #<Post:0x13630c4 @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>
>> f.
Display all 152 possibilities? (y or n)
Finally, when you’re ready to resume execution, you can enter “cont”.
The console is a Ruby shell, which allows you to interact with your application’s domain model. Here you’ll have all parts of the application configured, just like it is when the application is running. You can inspect domain models, change values, and save to the database. Starting the script without arguments will launch it in the development environment.
To start the console, run rails console from the application directory.
Options:
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Passing the
-s, --sandboxargument will rollback any modifications made to the database. -
Passing an environment name as an argument will load the corresponding environment. Example:
rails console production.
To reload your controllers and models after launching the console run reload!
More information about irb can be found at: http://www.rubycentral.org/pickaxe/irb.html
You can go to the command line of your database directly through rails dbconsole. You would be connected to the database with the credentials defined in database.yml. Starting the script without arguments will connect you to the development database. Passing an argument will connect you to a different database, like rails dbconsole production. Currently works for MySQL, PostgreSQL and SQLite 3.
The default directory structure of a generated Ruby on Rails application:
|-- app
| |-- assets
| |-- images
| |-- javascripts
| `-- stylesheets
| |-- controllers
| |-- helpers
| |-- mailers
| |-- models
| `-- views
| `-- layouts
|-- config
| |-- environments
| |-- initializers
| `-- locales
|-- db
|-- doc
|-- lib
| `-- tasks
|-- log
|-- public
|-- script
|-- test
| |-- fixtures
| |-- functional
| |-- integration
| |-- performance
| `-- unit
|-- tmp
| |-- cache
| |-- pids
| |-- sessions
| `-- sockets
`-- vendor
|-- assets
`-- stylesheets
`-- plugins
app
Holds all the code that's specific to this particular application.
app/assets
Contains subdirectories for images, stylesheets, and JavaScript files.
app/controllers
Holds controllers that should be named like weblogs_controller.rb for automated URL mapping. All controllers should descend from ApplicationController which itself descends from ActionController::Base.
app/models
Holds models that should be named like post.rb. Models descend from ActiveRecord::Base by default.
app/views
Holds the template files for the view that should be named like weblogs/index.html.erb for the WeblogsController#index action. All views use eRuby syntax by default.
app/views/layouts
Holds the template files for layouts to be used with views. This models the common header/footer method of wrapping views. In your views, define a layout using the <tt>layout :default</tt> and create a file named default.html.erb. Inside default.html.erb, call <% yield %> to render the view using this layout.
app/helpers
Holds view helpers that should be named like weblogs_helper.rb. These are generated for you automatically when using generators for controllers. Helpers can be used to wrap functionality for your views into methods.
config
Configuration files for the Rails environment, the routing map, the database, and other dependencies.
db
Contains the database schema in schema.rb. db/migrate contains all the sequence of Migrations for your schema.
doc
This directory is where your application documentation will be stored when generated using <tt>rake doc:app</tt>
lib
Application specific libraries. Basically, any kind of custom code that doesn't belong under controllers, models, or helpers. This directory is in the load path.
public
The directory available for the web server. Also contains the dispatchers and the default HTML files. This should be set as the DOCUMENT_ROOT of your web server.
script
Helper scripts for automation and generation.
test
Unit and functional tests along with fixtures. When using the rails generate command, template test files will be generated for you and placed in this directory.
vendor
External libraries that the application depends on. Also includes the plugins subdirectory. If the app has frozen rails, those gems also go here, under vendor/rails/. This directory is in the load path.