# Install instructions from a SuSE 10.1 development environment == Install required packages == wget http://superb-west.dl.sourceforge.net/sourceforge/crfpp/CRF++-0.47.tar.gz tar xvzf CRF++-0.47.tar.gz cd CRF++-0.47 ./configure && make && sudo make install cd CRF++-0.47/ruby ruby extconf.rb make sudo make install If you are running fedora, you will have to take these additional steps: su echo "/usr/local/lib" > /etc/ld.so.conf.d/default-i386.conf ldconfig sudo gem install -v=2.1 rails gem install ruby-postgres == Configure Postgres == sudo gem install ruby-postgres # as postgres initdb pg_ctl -D /var/lib/pgsql/data -l logfile start /sbin/chkconfig postgresql on # create user, answer no to all questions createuser freecite psql ALTER USER freecite PASSWORD 'changemetosomethingmoresecure'; CREATE DATABASE freecite_development; CREATE DATABASE freecite_production; CREATE DATABASE freecite_test; GRANT ALL ON DATABASE "freecite_development" TO freecite; GRANT ALL ON DATABASE "freecite_production" TO freecite; GRANT ALL ON DATABASE "freecite_test" TO freecite; \q == Train the model == # A trained model is checked in to the repo, so this step is not necessary # unless you are making local changes. > rake crfparser:train_model == Using the API == http://0.0.0.0:3000/citations/create * (required argument) citation or citation[] - a citation or array of citations to parse * Accept: text/xml or text/html If accepting xml, returns the parsed citation string and resulting context object in xml format. If accepting html returns the parsed citation string as spans. examples: # in ruby: require 'net/http' Net::HTTP.start('localhost', 3000) do |http| response = http.post('/citations/create', 'citation=A. Bookstein and S. T. Klein, Detecting content-bearing words by serial clustering, Proceedings of the Nineteenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, pp. 319327, 1995.', 'Accept' => 'text/xml') puts "Code: #{response.code}" puts "Message: #{response.message}" puts "Body:\n #{response.body}" end # with curl curl -H 'Accept: text/xml' -d "citation[]=Fielderman, A., Silvester, G., Gatsonis, C.A., Hoenig, J., Flynn, S. Prognostic significance of flow cytometric DNA analysis and proliferative index in stage I non-small cell lung cancer. American Review of Respiratory Disease, 1992; 146:707-710.&citation[]=Udvarhelyi, I.S., Gatsonis, C.A., Epstein, A.M., Pashos, C.L., Newhouse, J.P. and McNeil, B.J. Acute Myocardial Infarction in the Medicare population: process of care and clinical outcomes. Journal of the American Medical Association, 1992; 18:2530-2536. " http://0.0.0.0:3000/citations/create == Using the Web App == http://0.0.0.0:3000/citations/create Enter a citation, or a list of citations separated by newlines. Should be self-explanitory. == Welcome to Rails Rails is a web-application and persistence framework that includes everything needed to create database-backed web-applications according to the Model-View-Control pattern of separation. This pattern splits the view (also called the presentation) into "dumb" templates that are primarily responsible for inserting pre-built data in between HTML tags. The model contains the "smart" domain objects (such as Account, Product, Person, Post) that holds all the business logic and knows how to persist themselves to a database. The controller handles the incoming requests (such as Save New Account, Update Product, Show Post) by manipulating the model and directing data to the view. In Rails, the model is handled by what's called an object-relational mapping layer entitled Active Record. This layer allows you to present the data from database rows as objects and embellish these data objects with business logic methods. You can read more about Active Record in link:files/vendor/rails/activerecord/README.html. The controller and view are handled by the Action Pack, which handles both layers by its two parts: Action View and Action Controller. These two layers are bundled in a single package due to their heavy interdependence. This is unlike the relationship between the Active Record and Action Pack that is much more separate. Each of these packages can be used independently outside of Rails. You can read more about Action Pack in link:files/vendor/rails/actionpack/README.html. == Getting started 1. Start the web server: <tt>ruby script/server</tt> (run with --help for options) 2. Go to http://localhost:3000/ and get "Welcome aboard: You’re riding the Rails!" 3. Follow the guidelines to start developing your application == Web servers Rails uses the built-in web server in Ruby called WEBrick by default, so you don't have to install or configure anything to play around. If you have lighttpd installed, though, it'll be used instead when running script/server. It's considerably faster than WEBrick and suited for production use, but requires additional installation and currently only works well on OS X/Unix (Windows users are encouraged to start with WEBrick). We recommend version 1.4.11 and higher. You can download it from http://www.lighttpd.net. If you want something that's halfway between WEBrick and lighttpd, we heartily recommend Mongrel. It's a Ruby-based web server with a C-component (so it requires compilation) that also works very well with Windows. See more at http://mongrel.rubyforge.org/. But of course its also possible to run Rails with the premiere open source web server Apache. To get decent performance, though, you'll need to install FastCGI. For Apache 1.3, you want to use mod_fastcgi. For Apache 2.0+, you want to use mod_fcgid. See http://wiki.rubyonrails.com/rails/pages/FastCGI for more information on FastCGI. == Example for Apache conf <VirtualHost *:80> ServerName rails DocumentRoot /path/application/public/ ErrorLog /path/application/log/server.log <Directory /path/application/public/> Options ExecCGI FollowSymLinks AllowOverride all Allow from all Order allow,deny </Directory> </VirtualHost> NOTE: Be sure that CGIs can be executed in that directory as well. So ExecCGI should be on and ".cgi" should respond. All requests from 127.0.0.1 go through CGI, so no Apache restart is necessary for changes. All other requests go through FCGI (or mod_ruby), which requires a restart to show changes. == Debugging Rails Have "tail -f" commands running on both the server.log, production.log, and test.log files. 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. == Breakpoints Breakpoint support is available through the script/breakpointer client. This means that you can break out of execution at any point in the code, investigate and change the model, AND then resume execution! Example: class WeblogController < ActionController::Base def index @posts = Post.find_all breakpoint "Breaking out from the list" end end So the controller will accept the action, run the first line, then present you with a IRB prompt in the breakpointer window. Here you can do things like: Executing breakpoint "Breaking out from the list" at .../webrick_server.rb:16 in 'breakpoint' >> @posts.inspect => "[#<Post:0x14a6be8 @attributes={\"title\"=>nil, \"body\"=>nil, \"id\"=>\"1\"}>, #<Post:0x14a6620 @attributes={\"title\"=>\"Rails you know!\", \"body\"=>\"Only ten..\", \"id\"=>\"2\"}>]" >> @posts.first.title = "hello from a breakpoint" => "hello from a breakpoint" ...and even better is that 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 press CTRL-D == Console You can interact with the domain model by starting the console through script/console. 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. Passing an argument will specify a different environment, like <tt>script/console production</tt>. To reload your controllers and models after launching the console run <tt>reload!</tt> == Description of contents app Holds all the code that's specific to this particular application. app/controllers Holds controllers that should be named like weblog_controller.rb for automated URL mapping. All controllers should descend from ActionController::Base. app/models Holds models that should be named like post.rb. Most models will descend from ActiveRecord::Base. app/views Holds the template files for the view that should be named like weblog/index.rhtml for the WeblogController#index action. All views use eRuby syntax. This directory can also be used to keep stylesheets, images, and so on that can be symlinked to public. app/helpers Holds view helpers that should be named like weblog_helper.rb. app/apis Holds API classes for web services. config Configuration files for the Rails environment, the routing map, the database, and other dependencies. components Self-contained mini-applications that can bundle together controllers, models, and views. db Contains the database schema in schema.rb. db/migrate contains all the sequence of Migrations for your schema. 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. Contains subdirectories for images, stylesheets, and javascripts. Also contains the dispatchers and the default HTML files. script Helper scripts for automation and generation. test Unit and functional tests along with fixtures. vendor External libraries that the application depends on. Also includes the plugins subdirectory. This directory is in the load path.