caruby-scat 1.2.1 → 1.2.2

data/Gemfile.lock

@@ -1,16 +1,15 @@
 PATH
   remote: .
   specs:
-    caruby-scat (1.1.1)
+    caruby-scat (1.2.1)
       bundler
-      caruby-tissue (>= 2.1.4)
+      caruby-small
       haml
       jruby-openssl
       rack
       redis
       redis-store
       sinatra
-      sinatra-authorization
 
 PATH
   remote: /Users/loneyf/workspace/caruby/core
@@ -22,6 +21,17 @@ PATH
       jinx-migrate (>= 2.1.1)
       rdbi
 
+PATH
+  remote: /Users/loneyf/workspace/caruby/small
+  specs:
+    caruby-small (1.1.2)
+      bundler
+      caruby-tissue (>= 2.1.5)
+      jruby-openssl
+      rack
+      sinatra
+      sinatra-authorization
+
 PATH
   remote: /Users/loneyf/workspace/caruby/tissue
   specs:
@@ -39,7 +49,7 @@ PATH
 PATH
   remote: /Users/loneyf/workspace/jinx/json
   specs:
-    jinx-json (2.1.2)
+    jinx-json (2.1.3)
       bundler
       jinx
       json_pure
@@ -57,7 +67,7 @@ GEM
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.3.2)
+    childprocess (0.3.3)
       ffi (~> 1.0.6)
     columnize (0.3.6)
     cucumber (1.2.1)
@@ -70,7 +80,7 @@ GEM
     extensional (1.3.1)
     fastercsv (1.5.5)
     ffi (1.0.11-java)
-    gherkin (2.11.0-java)
+    gherkin (2.11.1-java)
       json (>= 1.4.6)
     haml (3.1.6)
     jinx-migrate (2.1.2)
@@ -85,12 +95,12 @@ GEM
       addressable (~> 2.2.6)
       ffi (~> 1.0.9)
       spoon (~> 0.0.1)
-    libwebsocket (0.1.3)
+    libwebsocket (0.1.4)
       addressable
     methlab (0.1.0)
-    mime-types (1.18)
+    mime-types (1.19)
     multi_json (1.3.6)
-    nokogiri (1.5.4-java)
+    nokogiri (1.5.5-java)
     rack (1.4.1)
     rack-test (0.6.1)
       rack (>= 1.0)
@@ -102,22 +112,21 @@ GEM
     redis (3.0.1)
     redis-store (1.1.1)
       redis (>= 2.2.0)
-    rspec (2.10.0)
-      rspec-core (~> 2.10.0)
-      rspec-expectations (~> 2.10.0)
-      rspec-mocks (~> 2.10.0)
-    rspec-core (2.10.1)
-    rspec-expectations (2.10.0)
+    rspec (2.11.0)
+      rspec-core (~> 2.11.0)
+      rspec-expectations (~> 2.11.0)
+      rspec-mocks (~> 2.11.0)
+    rspec-core (2.11.0)
+    rspec-expectations (2.11.1)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.10.1)
+    rspec-mocks (2.11.1)
     ruby-debug (0.10.4)
       columnize (>= 0.1)
       ruby-debug-base (~> 0.10.4.0)
     ruby-debug-base (0.10.4-java)
     rubyzip (0.9.9)
-    selenium-webdriver (2.22.2)
+    selenium-webdriver (2.24.0)
       childprocess (>= 0.2.5)
-      ffi (~> 1.0)
       libwebsocket (~> 0.1.3)
       multi_json (~> 1.0)
       rubyzip
@@ -144,6 +153,7 @@ DEPENDENCIES
   capybara
   caruby-core!
   caruby-scat!
+  caruby-small!
   caruby-tissue!
   cucumber
   jinx!

data/History.md

@@ -1,5 +1,9 @@
 This history lists major release themes. See the git commits for change details.
 
+1.2.2 / 2012-07-18
+------------------
+* Add scat executable.
+
 1.2.1 / 2012-06-18
 ------------------
 * Preserve fields.

data/README.md

@@ -1,5 +1,5 @@
-Scat: a _S_imple _caT_issue application 
-=============================================
+Scat: a <em>S</em>imple <em>caT</em>issue application 
+===========================================
 **Git**:          [http://github.com/caruby/scat](http://github.com/caruby/scat)       
 **Author**:       OHSU Knight Cancer Institute    
 **Copyright**:    2012    
@@ -29,28 +29,28 @@ Features
 
 Requirements
 ------------
-The current Scat release requires the caTissue API client and Linux.
-
-After installation, the supported caTissue versions are listed by the following command:
-
-    crtsmoke --version                                     
+The current Scat release only runs on Linux.
 
 Installation
 ------------
 Scat is installed on a caTissue server as a JRuby gem:
 
-   sudo jgem install caruby-scat
+   `sudo jgem install caruby-scat`
+   
+See the caRuby Tissue [FAQ](http://caruby.tenderapp.com/kb) for configuring the caTissue API client.
 
-The log file is +/var/log/scat.log+. Ensure that the +/var/log+ directory is writable.
+The log file is `/var/log/scat.log`. Ensure that the `/var/log` directory is writable
+by the Linux user which starts Scat. The preferred Linux way to do this is to make `/var/log`
+owned and writable by the `adm` group and add the user to that group.
 
 Usage
 -----
-1. Execute +crtscat+ to start Scat.
+1. Execute `scat` in a console to start Scat.
 
-2. Open a web browser on +http:://+_server_+:4567/+, where _server_ is the name of your server.
+2. Open a web browser on `http:://server:4567/`, where _server_ is the name of your server.
 
-3. Scat starts on the specimen edit page. Hover over the edit form entry question mark to
-   describe the field. Enter values for each field.
+3. Scat starts on the specimen edit page (see the screen shot below). Hover over the edit form
+   entry question mark to describe the field. Enter values for each field.
 
 4. Enter five or more letters in the Diagnosis or Tissue Site and wait briefly to
    bring up a list of matching caTissue values.
@@ -64,47 +64,63 @@ Within a session, the first save takes a while to find the Collection Protocol,
 other information. Subsequent saves are faster. Successive creation of new specimens
 for the same patient and pathology report are considerably faster. 
 
+Screen Shot:
+
+![alt text](https://github.com/caruby/scat/blob/master/doc/Scat.tiff?raw=true "The Scat display")
+
 Customization
 -------------
 Scat is a reference implementation which captures minimal specimen information. Adding
 edit fields is done in a single simple text configuration file.
 
-Enhance Scat for your own site as follows:
+There are two ways to enhance Scat for your own site:
+
+The quick-and-dirty approach:
+
+1. Edit the following file:
+
+  <pre>`jgem environment gemdir`/gems/caruby-scat*/conf/fields.yaml</pre>
+
+2. Add or remove fields to display.
+
+3. Refresh the Scat edit page.
+
+The safe-and-sane approach:
 
 1. Install [git](http://git-scm.com/) on your workstation if necessary.
 
-2. Install Scat as described in the Installation section above. 
+2. Make a workspace directory on your workstation.
 
-3. Make a workspace directory on your workstation.
+3. From that directory, execute the following:
 
-4. From that directory, execute +git clone git://github.com/caruby/scat.git+
+   `git clone git://github.com/caruby/scat.git`
 
-5. Modify the +conf/fields.yaml+ configuration file to add edit fields.
+4. Modify the `conf/fields.yaml` configuration file to add edit fields.
 
-6. Modify the +scat/public/stylesheets/scat.css+ file to change the web display.
+5. Modify the `scat/public/stylesheets/scat.css` file to change the web display.
 
-7. Add views and routes to this [Sinatra](http://www.sinatrarb.com/) application as you see fit.
+6. Add views and routes to this [Sinatra](http://www.sinatrarb.com/) application as you see fit.
 
-8. Run Scat with your changes by executing the following in the workspace +scat+ directory:
+7. Run Scat with your changes by executing the following in the workspace `scat` directory:
 
-      rackup
+   `rackup`
 
-9. See your changes by opening a web browser on +http://localhost:4567/+.
+8. See your changes by opening a web browser on `http://localhost:4567/`.
 
-11. Change the version number in the +lib/scat/version.rb+ file by appending a branch number,
-    e.g. change the base version +1.2.2+ to +1.2.2.1+
+9. When you are satisfied with the changes, bump the version number in the `lib/scat/version.rb`
+   file by appending a branch number, e.g. change the base version `1.2.2` to `1.2.2.1`.
 
 10. Package your changes by executing the following:
 
-      rake gem
+    `rake gem`
       
 11. Copy the resulting gem file to your server.
 
 12. On the server, install the new gem, e.g.:
 
-      gem install caruby-scat-1.2.2.1.gem
+    `gem install caruby-scat-1.2.2.1.gem`
 
-You can make your changes public by forking the Scat repository:
+You can proudly share your changes with the world by forking the Scat repository:
 
 1. Register for a [GitHub](https://github.com) account, if you don't already have one.
 
@@ -114,18 +130,18 @@ You can make your changes public by forking the Scat repository:
 
 4. Fork the repository to your GitHub account.
 
-5. Set the git origin in your workstation +scat+ directory, e.g.:
+5. Set the git origin in your workstation `scat` directory, e.g.:
 
-      git config --replace-all remote.origin.url git@github.com:mygitaccount/scat.git
+   `git config --replace-all remote.origin.url git@github.com:mygitaccount/scat.git`
 
 6. Commit the changes to your local git repository.
 
 7. Push the changes to your fork with the command:
 
-    git push origin master
+   `git push origin master`
 
 Your GitHub fork is publicly visible. You can see other Scat forks by searching on the
-term +scat+ in GitHub.
+term `scat` in GitHub.
 
 
 

data/bin/scat

@@ -4,4 +4,5 @@
 #
 
 require 'scat'
-rackup --env production File.dirname(__FILE__) + '../config.ru'
+
+`rackup --env production #{File.dirname(__FILE__) + '/../config.ru'}`

data/lib/scat/authorization.rb

@@ -0,0 +1,88 @@
+require 'sinatra/authorization'
+
+module Scat
+  module Authorization
+    include Sinatra::Authorization
+    # Runs the given block in an HTTP basic authorization context.
+    # The session status is set to the result of performing the given block.
+    #
+    # @yield perform the caTissue operation and return a status message
+    def protect!(&block)
+      login_required
+      session[:status] = perform!(session[:email], session[:password], &block)
+    end
+
+    # @return [CaTissue::User] the user who is submitting this edit
+    # @raise [ArgumentError] if there is no such caTissue user
+    def current_user
+      # The caTissue login name is the user's email address.
+      email = session[:email]
+      raise ScatError.new("The caTissue login is not available in this web session.") unless email
+      # the current caTissue User
+      user = CaTissue::User.new(:email_address => email)
+      # the cached caTissue User id
+      user_id = session[:user_id]
+      if user_id then
+        user.identifier = user_id
+      else
+        # Fetch the User and cache the id.
+        raise ScatError.new("User not found: #{user.email_address}") unless user.find
+        session[:user_id] = user.identifier
+      end
+      user
+    end
+      
+    # Fix +Sinatra::Authorization.authorization_realm+ per the
+    # (https://github.com/sr/sinatra-authorization)[https://github.com/sr/sinatra-authorization]
+    # patch.
+    def authorization_realm
+      settings.authorization_realm
+    end
+    
+    private
+    
+    # Obtains the HTML Basic authorization username and password.
+    # Formats the caTissue login name as _username_+@+_domain_,
+    # where _domain_ is the domain portion of the system +hostname+.
+    #
+    # @param [String] the caTissue login name, with or without the +@+_domain_ suffix
+    # @param [String] the caTissue password
+    # @return [Boolean] the authorization result
+    def authorize(username, password)
+      email = session[:email] = infer_email_address(username)
+      session[:password] = password
+      # Try to start a session.
+      begin
+        CaTissue::Database.current.open(email, password) {}
+        logger.debug { "Scat captured the caTissue login name #{email} and password." }
+        true
+      rescue Exception => e
+        logger.debug { "Scat caTissue login #{email.qp} with password #{password.qp} is invalid." }
+        session[:status] = "caTissue login was unsuccessful - #{e.message}"
+        false 
+      end
+    end
+    
+    # Runs the given caTissue operation block with the given caTissue credentials.
+    #
+    # @yield (see #protect!)
+    # @return [String, nil] the status message
+    def perform!(email, password, &block)
+      login_required
+      CaTissue::Database.current.open(email, password, &block)
+    end
+    
+    # @param [String] the username, with or without the +@+_domain_ suffix
+    # @param [String] the email address
+    def infer_email_address(username)
+      if username.index('@') then
+        username
+      else
+        # The email domain is the last two components of the hostname, e.g.
+        # the prod01.cluster.galena.edu domain is galena.edu. 
+        domain = `hostname`.chomp[/[^.]+\.[^.]+$/]
+        domain.empty? ? username : [username, domain].join('@')
+      end
+    end
+  end
+end

data/lib/scat/version.rb

@@ -1,3 +1,3 @@
 module Scat
-  VERSION = '1.2.1'
+  VERSION = '1.2.2'
 end

data/spec/edit_spec.rb

@@ -18,7 +18,7 @@ describe Scat do
         :malignant => 'Malignant',
         :quantity => '4'
       }
-      @spc = Scat::Edit.instance.save(@params)
+      @spc = Scat::Edit.instance.save(@params, {})
     end
     
     subject { @spc }
@@ -39,7 +39,7 @@ describe Scat do
       before(:all) do
         oparams = @params.delete_if { |k, v| k == :malignant }
         oparams[:quantity] = '5'
-        @other = Scat::Edit.instance.save(oparams)
+        @other = Scat::Edit.instance.save(oparams, {})
       end  
       
       it "should save the additional specimen" do 

metadata

@@ -2,7 +2,7 @@
 name: caruby-scat
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 1.2.1
+  version: 1.2.2
 platform: ruby
 authors: 
   - OHSU
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-07-17 00:00:00 Z
+date: 2012-07-18 00:00:00 Z
 dependencies: 
   - !ruby/object:Gem::Dependency 
     name: bundler
@@ -146,12 +146,14 @@ files:
   - conf/fields.yaml
   - conf/redis.conf
   - config.ru
+  - doc/Scat.tiff
   - ext/README.txt
   - features/edit.feature
   - features/step_definitions/scat_steps.rb
   - features/support/env.rb
   - features/support/seed.rb
   - lib/scat.rb
+  - lib/scat/authorization.rb
   - lib/scat/autocomplete.rb
   - lib/scat/cache.rb
   - lib/scat/configuration.rb