caruby-scat 1.2.1

data/.gitignore

@@ -0,0 +1,17 @@
+.DS_Store
+**~
+cruft
+ext
+.project
+.idea
+.loadpath
+.yardoc
+.*/
+redis.pid
+**redis-server
+*.gem
+*.pdf
+*.tar*
+**log
+/doc/api
+/test/results

data/Gemfile

@@ -0,0 +1,25 @@
+source :rubygems
+gemspec
+
+group :development do
+  gem 'ruby-debug'
+  # Uncomment the following lines if there are local gem changes. Change the path option
+  # to your workspace location. Commit the changed Gemfile and Gemfile.lock to a git branch
+  # named 'local' rather than to the master branch. Do not check in the local change.
+  gem 'caruby-core', :path => File.dirname(__FILE__) + '/../core'
+  gem 'caruby-tissue', :path => File.dirname(__FILE__) + '/../tissue'
+  gem 'caruby-small', :path => File.dirname(__FILE__) + '/../small'
+  gem 'jinx', :path => File.dirname(__FILE__) + '/../../jinx/core'
+  gem 'jinx-json', :path => File.dirname(__FILE__) + '/../../jinx/json'
+  gem 'caruby-scat', :path => File.dirname(__FILE__), :require => 'scat'
+end
+
+group :test do
+  gem 'rspec', '>= 2.6'
+  gem 'sinatra', '=1.2.6' # TODO - retry with 1.3 when it is available
+  gem 'shotgun'
+  gem 'cucumber'
+  gem 'capybara'
+  gem 'launchy'
+  gem 'rack-test', :require => 'rack/test'
+end

data/Gemfile.lock

@@ -0,0 +1,158 @@
+PATH
+  remote: .
+  specs:
+    caruby-scat (1.1.1)
+      bundler
+      caruby-tissue (>= 2.1.4)
+      haml
+      jruby-openssl
+      rack
+      redis
+      redis-store
+      sinatra
+      sinatra-authorization
+
+PATH
+  remote: /Users/loneyf/workspace/caruby/core
+  specs:
+    caruby-core (2.1.3)
+      bundler
+      jinx (~> 2.1.1)
+      jinx-json (~> 2.1.1)
+      jinx-migrate (>= 2.1.1)
+      rdbi
+
+PATH
+  remote: /Users/loneyf/workspace/caruby/tissue
+  specs:
+    caruby-tissue (2.1.5)
+      bundler
+      caruby-core (>= 2.1.1)
+      uom (>= 1.2.2)
+
+PATH
+  remote: /Users/loneyf/workspace/jinx/core
+  specs:
+    jinx (2.1.3)
+      bundler
+
+PATH
+  remote: /Users/loneyf/workspace/jinx/json
+  specs:
+    jinx-json (2.1.2)
+      bundler
+      jinx
+      json_pure
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    addressable (2.2.8)
+    bouncy-castle-java (1.5.0146.1)
+    builder (3.0.0)
+    capybara (1.1.2)
+      mime-types (>= 1.16)
+      nokogiri (>= 1.3.3)
+      rack (>= 1.0.0)
+      rack-test (>= 0.5.4)
+      selenium-webdriver (~> 2.0)
+      xpath (~> 0.1.4)
+    childprocess (0.3.2)
+      ffi (~> 1.0.6)
+    columnize (0.3.6)
+    cucumber (1.2.1)
+      builder (>= 2.1.2)
+      diff-lcs (>= 1.1.3)
+      gherkin (~> 2.11.0)
+      json (>= 1.4.6)
+    diff-lcs (1.1.3)
+    epoxy (0.3.1)
+    extensional (1.3.1)
+    fastercsv (1.5.5)
+    ffi (1.0.11-java)
+    gherkin (2.11.0-java)
+      json (>= 1.4.6)
+    haml (3.1.6)
+    jinx-migrate (2.1.2)
+      bundler
+      fastercsv
+      rack
+    jruby-openssl (0.7.7)
+      bouncy-castle-java (>= 1.5.0146.1)
+    json (1.7.3-java)
+    json_pure (1.7.3)
+    launchy (2.1.0-java)
+      addressable (~> 2.2.6)
+      ffi (~> 1.0.9)
+      spoon (~> 0.0.1)
+    libwebsocket (0.1.3)
+      addressable
+    methlab (0.1.0)
+    mime-types (1.18)
+    multi_json (1.3.6)
+    nokogiri (1.5.4-java)
+    rack (1.4.1)
+    rack-test (0.6.1)
+      rack (>= 1.0)
+    rake (0.9.2.2)
+    rdbi (0.9.1)
+      epoxy (>= 0.3.1)
+      methlab (>= 0.0.9)
+      typelib
+    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)
+      diff-lcs (~> 1.1.3)
+    rspec-mocks (2.10.1)
+    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)
+      childprocess (>= 0.2.5)
+      ffi (~> 1.0)
+      libwebsocket (~> 0.1.3)
+      multi_json (~> 1.0)
+      rubyzip
+    shotgun (0.9)
+      rack (>= 1.0)
+    sinatra (1.2.6)
+      rack (~> 1.1)
+      tilt (>= 1.2.2, < 2.0)
+    sinatra-authorization (1.0.0)
+      sinatra (>= 0.9.1.1)
+    spoon (0.0.1)
+    tilt (1.3.3)
+    typelib (0.1.0)
+    uom (1.2.2)
+      extensional
+    xpath (0.1.4)
+      nokogiri (~> 1.3)
+    yard (0.8.2.1)
+
+PLATFORMS
+  java
+
+DEPENDENCIES
+  capybara
+  caruby-core!
+  caruby-scat!
+  caruby-tissue!
+  cucumber
+  jinx!
+  jinx-json!
+  launchy
+  rack-test
+  rake
+  rspec (>= 2.6)
+  ruby-debug
+  shotgun
+  sinatra (= 1.2.6)
+  yard

data/History.md

@@ -0,0 +1,9 @@
+This history lists major release themes. See the git commits for change details.
+
+1.2.1 / 2012-06-18
+------------------
+* Preserve fields.
+
+1.1.1 / 2012-04-24
+------------------
+* Initial release.

data/LEGAL

@@ -0,0 +1,4 @@
+LEGAL NOTICE INFORMATION
+------------------------
+All the files in this distribution are covered under either the MIT
+license (see the file LICENSE).

data/LICENSE

@@ -0,0 +1,22 @@
+Copyright (c) 2012 Oregon Health & Science University
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,131 @@
+Scat: a _S_imple _caT_issue application 
+=============================================
+**Git**:          [http://github.com/caruby/scat](http://github.com/caruby/scat)       
+**Author**:       OHSU Knight Cancer Institute    
+**Copyright**:    2012    
+**License**:      MIT License    
+
+Synopsis
+--------
+Scat is a light-weight [caRuby Tissue](http://caruby.rubyforge.org/tissue.html) web application.
+
+Features
+--------
+1. Create tissue specimens in caTissue.
+
+2. Create the specimen subject, registration and collection group as necessary.
+
+3. Auto-complete the diagnosis and tissue site.
+
+4. Authorize the user.
+
+5. One small edit page to rule them all.
+
+6. Dynamically responds to tablet and even smartphone devices.
+
+7. Simple edit form configuration.
+
+8. Leverage the [caRuby](http://caruby.rubyforge.org) declarative API.
+
+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                                     
+
+Installation
+------------
+Scat is installed on a caTissue server as a JRuby gem:
+
+   sudo jgem install caruby-scat
+
+The log file is +/var/log/scat.log+. Ensure that the +/var/log+ directory is writable.
+
+Usage
+-----
+1. Execute +crtscat+ to start Scat.
+
+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.
+
+4. Enter five or more letters in the Diagnosis or Tissue Site and wait briefly to
+   bring up a list of matching caTissue values.
+
+5. Press the Submit button to create a new specimen.
+
+The Diagnosis and Tissue Site term => controlled value matches are cached locally and
+persistently. Subsequent term auto-completion is very fast.
+
+Within a session, the first save takes a while to find the Collection Protocol, Site and
+other information. Subsequent saves are faster. Successive creation of new specimens
+for the same patient and pathology report are considerably faster. 
+
+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:
+
+1. Install [git](http://git-scm.com/) on your workstation if necessary.
+
+2. Install Scat as described in the Installation section above. 
+
+3. Make a workspace directory on your workstation.
+
+4. From that directory, execute +git clone git://github.com/caruby/scat.git+
+
+5. 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.
+
+7. 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:
+
+      rackup
+
+9. 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+
+
+10. Package your changes by executing the following:
+
+      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
+
+You can make your changes public by forking the Scat repository:
+
+1. Register for a [GitHub](https://github.com) account, if you don't already have one.
+
+2. Navigate to the Scat [repository](https://github.com/caruby/scat).
+
+3. Press the Fork button in the upper right.
+
+4. Fork the repository to your GitHub account.
+
+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
+
+6. Commit the changes to your local git repository.
+
+7. Push the changes to your fork with the command:
+
+    git push origin master
+
+Your GitHub fork is publicly visible. You can see other Scat forks by searching on the
+term +scat+ in GitHub.
+
+
+

data/Rakefile

@@ -0,0 +1,41 @@
+require 'fileutils'
+require File.expand_path('version', File.dirname(__FILE__) + '/lib/scat')
+
+desc "Default: run all tests"
+task :default => :test
+
+desc "Launch Scat"
+task :launch do
+  jruby "bin/scat"
+end
+
+# the gem name
+GEM = 'caruby-scat'
+GEM_VERSION = Scat::VERSION
+
+WINDOWS = (Config::CONFIG['host_os'] =~ /mingw|win32|cygwin/ ? true : false) rescue false
+SUDO = WINDOWS ? '' : 'sudo'
+
+desc 'Builds the gem'
+task :gem do
+  sh "jgem build #{GEM}.gemspec"
+end
+
+desc 'Installs the gem'
+task :install => :gem do
+  sh "#{SUDO} jgem install #{GEM}-#{GEM_VERSION}.gem"
+end
+
+desc 'Documents the API'
+task :doc do
+  FileUtils.rm_rf 'doc/api'
+  sh "yardoc"
+end
+
+desc 'Runs the specs'
+task :spec do
+  Dir['spec/**/*_spec.rb'].each { |f| sh "rspec #{f}" rescue nil }
+end
+
+desc 'Runs the tests'
+task :test => :spec

data/bin/scat

@@ -0,0 +1,7 @@
+#!/usr/bin/env jruby
+#
+# scat: Start the Scat web application
+#
+
+require 'scat'
+rackup --env production File.dirname(__FILE__) + '../config.ru'

data/bin/scatseed

@@ -0,0 +1,10 @@
+#!/usr/bin/env jruby
+#
+# scatseed: Create a sample Scat protocol
+#
+
+require 'catissue'
+require File.dirname(__FILE__) + '/../test/fixtures/seed'
+
+Jinx.logger(:app => 'Scat', :debug => true)
+Scat::Seed.protocol_for('Scat').find(:create)

data/caruby-scat.gemspec

@@ -0,0 +1,30 @@
+require 'date'
+require File.dirname(__FILE__) + '/lib/scat/version'
+
+Gem::Specification.new do |s|
+  s.name          = 'caruby-scat'
+  s.summary       = 'Simple caTissue web application'
+  s.description   = s.summary + '. See the home page for more information.'
+  s.version       = Scat::VERSION
+  s.date          = Date.today
+  s.author        = "OHSU"
+  s.email         = 'caruby.org@gmail.com'
+  s.homepage      = 'https://github.com/caruby/scat'
+  s.require_path  = 'lib'
+  s.bindir        = 'bin'
+  s.files         = `git ls-files`.split("\n") << 'ext/redis-server'
+  s.test_files    = `git ls-files features spec test`.split("\n")
+  s.executables   = `git ls-files bin`.split("\n").map { |f| File.basename(f) }
+  s.add_runtime_dependency     'bundler'
+  s.add_runtime_dependency     'rack'
+  s.add_runtime_dependency     'sinatra'
+  s.add_runtime_dependency     'haml'
+  s.add_runtime_dependency     'redis'
+  s.add_runtime_dependency     'redis-store'
+  s.add_runtime_dependency     'jruby-openssl'
+  s.add_runtime_dependency     'caruby-small'
+  s.add_development_dependency 'yard'
+  s.add_development_dependency 'rake'
+  s.has_rdoc      = 'yard'
+  s.license       = 'MIT'
+end