gcig_ca125 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d133224038fb6ef26a93a6f8e32585f222e74ca3
-  data.tar.gz: 592cec79d5630e8841308510953eb38215462c7c
+  metadata.gz: 76fa91bd39d34feb8ae7b5521132c18beb344e3d
+  data.tar.gz: c87cff8d12dbae562b935d983bc8c84a49988748
 SHA512:
-  metadata.gz: 28daead6112db7d7aaa2b3885012f03c852e471e16bcca2053b778a7bb36afa9f826a1e05b2db665c2bbb595976edbfe8d87a24b9993255602e9708d9de0ba83
-  data.tar.gz: 26174659d1b40019e22fd9de89b26ef87243594b69405221962c7f954c41df657c97f53e152d6b07da1ae6968fa84bc92962ef1677428dbcbde837ff4ddcdba7
+  metadata.gz: 91620c11a1bb806f70c8f8f7a49ccf0efe84a28d5f71d7c82ee8c7a80ab78c0bb6e0814b1e9343e3d7a9656b3be1262ac95c6e2aab910372a963932dba8ce659
+  data.tar.gz: 218edbbc82098ae824811291f5853d91e3641dd149976f606b8972401261b92f316649d8af3cd4c5193b87614d23c3721c70d8f7b4d3d1bc9f3827cbca94810a

data/.travis.yml

@@ -0,0 +1,8 @@
+language: ruby
+rvm:
+  - 2.1.0
+  - jruby-19mode
+  - ruby-head
+addons:
+  code_climate:
+    repo_token: 936ba787c4e63cb58c1de8ba0cdd098ad7f6a5611ad8830ea133744b5c7ee065

data/Gemfile

@@ -6,9 +6,9 @@ source "http://rubygems.org"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
+  gem "codeclimate-test-reporter", group: :test, require: nil
   gem "rspec", "~> 3.2"
   gem "rdoc", "~> 4.2"
   gem "bundler", "~> 1.7"
   gem "jeweler", "~> 2.0"
-  gem "simplecov", "~> 0.9"
 end

data/Gemfile.lock

@@ -3,6 +3,8 @@ GEM
   specs:
     addressable (2.3.7)
     builder (3.2.2)
+    codeclimate-test-reporter (0.4.7)
+      simplecov (>= 0.7.1, < 1.0.0)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     diff-lcs (1.2.5)
@@ -72,7 +74,7 @@ PLATFORMS
 
 DEPENDENCIES
   bundler (~> 1.7)
+  codeclimate-test-reporter
   jeweler (~> 2.0)
   rdoc (~> 4.2)
   rspec (~> 3.2)
-  simplecov (~> 0.9)

data/README.rdoc

@@ -1,6 +1,10 @@
+{<img src="https://travis-ci.org/yatsura/gcig_ca125.svg?branch=master" alt="Build Status" />}[https://travis-ci.org/yatsura/gcig_ca125]
+{<img src="https://codeclimate.com/github/yatsura/gcig_ca125.png" />}[https://codeclimate.com/github/yatsura/gcig_ca125]
+{<img src="https://codeclimate.com/github/yatsura/gcig_ca125/coverage.png" />}[https://codeclimate.com/github/yatsura/gcig_ca125]
+
 = gcig_ca125
 
-Description goes here.
+http://www.gcig.igcs.org/CA-125.html
 
 == Contributing to gcig_ca125
  

data/Rakefile

@@ -33,12 +33,6 @@ RSpec::Core::RakeTask.new(:spec) do |spec|
   spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-desc "Code coverage detail"
-task :simplecov do
-  ENV['COVERAGE'] = "true"
-  Rake::Task['spec'].execute
-end
-
 task :default => :spec
 
 require 'rdoc/task'

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/gcig_ca125.gemspec

@@ -0,0 +1,71 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: gcig_ca125 0.2.0 ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "gcig_ca125"
+  s.version = "0.2.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
+  s.authors = ["Paul D Mitchell"]
+  s.date = "2015-03-09"
+  s.description = " A Ruby gem of calculating the response of Ovarian cancer patient\naccording to levels of CA 125 as defined by the GCIG"
+  s.email = "paul.d.mitchell@ed.ac.uk"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    ".travis.yml",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "gcig_ca125.gemspec",
+    "lib/gcig_ca125.rb",
+    "lib/gcig_ca125/calculator.rb",
+    "lib/gcig_ca125/result.rb",
+    "lib/gcig_ca125/version.rb",
+    "spec/data/gcig_test_data.csv",
+    "spec/gcig_ca125_spec.rb",
+    "spec/lib/gcig_ca125/calculator_spec.rb",
+    "spec/spec_helper.rb",
+    "spec/support/test_data_reader.rb"
+  ]
+  s.homepage = "http://github.com/yatsura/gcig_ca125"
+  s.licenses = ["MIT"]
+  s.rubygems_version = "2.4.2"
+  s.summary = "Response and progression of ovarian cancer according to serum CA 125 levels"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<codeclimate-test-reporter>, [">= 0"])
+      s.add_development_dependency(%q<rspec>, ["~> 3.2"])
+      s.add_development_dependency(%q<rdoc>, ["~> 4.2"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.7"])
+      s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
+    else
+      s.add_dependency(%q<codeclimate-test-reporter>, [">= 0"])
+      s.add_dependency(%q<rspec>, ["~> 3.2"])
+      s.add_dependency(%q<rdoc>, ["~> 4.2"])
+      s.add_dependency(%q<bundler>, ["~> 1.7"])
+      s.add_dependency(%q<jeweler>, ["~> 2.0"])
+    end
+  else
+    s.add_dependency(%q<codeclimate-test-reporter>, [">= 0"])
+    s.add_dependency(%q<rspec>, ["~> 3.2"])
+    s.add_dependency(%q<rdoc>, ["~> 4.2"])
+    s.add_dependency(%q<bundler>, ["~> 1.7"])
+    s.add_dependency(%q<jeweler>, ["~> 2.0"])
+  end
+end
+

data/lib/gcig_ca125/calculator.rb

@@ -9,7 +9,7 @@ module GcigCa125
     end
 
     def result
-      Result.new is_evaluable?, is_response?, is_normalised?
+      Result.new self
     end
 
     def add_ca125_test(date, value)
@@ -18,21 +18,53 @@ module GcigCa125
     end
 
     def is_evaluable?
-      @evaluable = (@tests.first[0] <= @rx_date) && (@tests.first[0] >= (@rx_date - 9))
-      @evaluable = (@tests.first[1] > @normal_range.max * 2) if @evaluable
+      sample_before_rx? && sample_within_a_week_of_rx? && first_twice_uln?
     end
 
     def is_response?
       if is_evaluable?
-        @tests.select { |test| (test[0] > date_of_fall + 28 ) && test[1] < half_of_first }.any?
+        @tests.select { |test| (test[0] > day_28_after_fall ) && test[1] < half_of_first }.any?
       else
-        @response = false
+        false
       end
     end
 
     def is_normalised?
-      @normalised = find_normalised
-      @normalised.any?
+      find_normalised().any?
+    end
+
+    def samples_28days_after_fall?
+      test = Proc.new do |item|
+        item[0] > day_28_after_fall
+      end
+      @tests.select(&test).any?
+    end
+
+    def reduced_by_half?
+      (@tests.last[1].to_f / @tests.first[1].to_f ) <= 0.5
+    end
+
+    def first_twice_uln?
+      @tests.first[1] > @normal_range.max * 2
+    end
+
+    def test_pre_rx?
+      sample_before_rx? && sample_within_a_week_of_rx?
+    end
+
+    def sample_before_rx?
+      @tests.first[0] <= @rx_date
+    end
+
+    def sample_within_a_week_of_rx?
+      @tests.first[0] >= (@rx_date - 9)
+    end
+
+    def reduction_maintained?
+      test =  Proc.new do |item|
+        item[0] > day_28_after_fall && item[1] > (value_at_fall+15)
+      end
+      @tests.select(&test).empty?
     end
 
     def sort_tests
@@ -40,17 +72,29 @@ module GcigCa125
     end
 
     private
+    def day_28_after_fall
+      date_of_fall + 28
+    end
+
     def date_of_fall
-      valid_response = Proc.new do |test|
-        #(test[1] < half_of_first) && (test[0] > (@rx_date + 28))
-        (test[1] < half_of_first) && (test[0] > (@tests.first[0]))
-      end
-      if @tests.select(&valid_response).any?
-        @tests.select(&valid_response).first[0]
+      if tests_after_fall.any?
+        tests_after_fall.first[0]
       else
         Date.parse('2999-01-01')
       end
     end
+
+    def value_at_fall
+      tests_after_fall.first[1] if tests_after_fall.any?
+    end
+
+    def tests_after_fall
+      valid_response = Proc.new do |test|
+        (test[1] < half_of_first) && (test[0] > (@tests.first[0]))
+      end
+      @tests.select(&valid_response)
+    end
+
     def half_of_first
       @tests.first[1] / 2.0
     end

data/lib/gcig_ca125/result.rb

@@ -1,12 +1,50 @@
 module GcigCa125
   class Result
-    def initialize(eva, res, norm)
-      @evaluable = eva
-      @response  = res
-      @normalised = norm
+    def initialize(calculator)
+      @calculator = calculator
     end
+
     def to_s
-      "Not evaluable"
+      result_string = if @calculator.is_evaluable?
+        if @calculator.is_normalised?
+          if @calculator.is_response?
+            "Confirmed response"
+          else
+            "Not confirmed"
+          end
+        else
+          if @calculator.is_response?
+            "Confirmed response"
+          else
+            "No response"
+          end
+        end
+      else
+        "Not evaluable"
+      end
+      if !@calculator.samples_28days_after_fall?
+        result_string = "Not confirmed: no sample > 28 days after fall"
+      end
+      if !@calculator.reduced_by_half?
+        result_string = "No response: no 50% reduction"
+      end
+      if !@calculator.first_twice_uln?
+        result_string = "Not evaluable: 1st sample < 2.ULN"
+      end
+      if !@calculator.reduction_maintained?
+        result_string = "Not confirmed: reduction not maintained"
+      end
+      if !@calculator.test_pre_rx?
+        result_string = "Not evaluable: no sample pre-Rx"
+      end
+      if !@calculator.sample_within_a_week_of_rx?
+        result_string = "Not evaluable: no sample within 1 week of Rx"
+        if !@calculator.first_twice_uln?
+          result_string = "Not evaluable: 1st sample < 2.ULN"
+        end
+
+      end
+      result_string
     end
 
     def message
@@ -14,16 +52,15 @@ module GcigCa125
     end
 
     def evaluable?
-      @evaluable
+      @calculator.is_evaluable?
     end
 
     def response?
-      @response
+      @calculator.is_response?
     end
 
     def normalised?
-      @normalised
+      @calculator.is_normalised?
     end
-
   end
 end

data/lib/gcig_ca125/version.rb

@@ -1,7 +1,7 @@
 module GcigCa125
   class Version
     MAJOR = 0
-    MINOR = 1
+    MINOR = 2
     PATCH = 0
     BUILD = nil
 

data/spec/data/gcig_test_data.csv

@@ -80,11 +80,11 @@
 ,,1994-12-28,500,,,,
 ,,1995-01-17,74,,,,
 ,,1995-02-14,8,,,1,
-17,1994-07-28,1994-07-25,75,YES,YES,YES,Confirmed response.
+17,1994-07-28,1994-07-25,75,YES,YES,YES,Confirmed response
 ,,1994-08-07,25,,1,1,
 ,,1994-09-20,13,,2,2,
 ,,1994-10-18,11,,,,
-18,1994-11-16,1994-11-10,8384,YES,YES,NO,Confirmed response.
+18,1994-11-16,1994-11-10,8384,YES,YES,NO,Confirmed response
 ,,1994-12-06,1030,,1,,
 ,,1994-12-27,818,,2,,
 ,,1995-01-17,155,,,,

data/spec/lib/gcig_ca125/calculator_spec.rb

@@ -1,8 +1,7 @@
-require 'pry'
 require 'spec_helper'
 
 # Test data from GCIG RESP SET
-#
+# This is an integration test
 
 describe "GcigCa125::Calculator" do
   before(:all) do
@@ -44,6 +43,11 @@ describe "GcigCa125::Calculator" do
             expect(@calculator.result).not_to be_normalised
           end
         end
+
+        it "message" do
+          start_of_message = @data[:note].strip
+          expect(@calculator.result.message).to eq(start_of_message)
+        end
       end
     end
   end

data/spec/spec_helper.rb

@@ -1,19 +1,6 @@
-require 'simplecov'
+require "codeclimate-test-reporter"
+CodeClimate::TestReporter.start
 
-module SimpleCov::Configuration
-  def clean_filters
-    @filters = []
-  end
-end
-
-SimpleCov.configure do
-  clean_filters
-  load_adapter 'test_frameworks'
-end
-
-ENV["COVERAGE"] && SimpleCov.start do
-  add_filter "/.rvm/"
-end
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 
@@ -25,5 +12,7 @@ require 'gcig_ca125'
 Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
 
 RSpec.configure do |config|
-
+  config.mock_with :rspec do |mocks|
+    mocks.verify_doubled_constant_names = true
+  end
 end

metadata

@@ -1,15 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: gcig_ca125
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Paul D Mitchell
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-06 00:00:00.000000000 Z
+date: 2015-03-09 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: codeclimate-test-reporter
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -66,20 +80,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-- !ruby/object:Gem::Dependency
-  name: simplecov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.9'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.9'
 description: |2-
    A Ruby gem of calculating the response of Ovarian cancer patient
   according to levels of CA 125 as defined by the GCIG
@@ -92,12 +92,14 @@ extra_rdoc_files:
 files:
 - ".document"
 - ".rspec"
+- ".travis.yml"
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
 - README.rdoc
 - Rakefile
 - VERSION
+- gcig_ca125.gemspec
 - lib/gcig_ca125.rb
 - lib/gcig_ca125/calculator.rb
 - lib/gcig_ca125/result.rb
@@ -105,7 +107,6 @@ files:
 - spec/data/gcig_test_data.csv
 - spec/gcig_ca125_spec.rb
 - spec/lib/gcig_ca125/calculator_spec.rb
-- spec/lib/gcig_ca125/result_spec.rb
 - spec/spec_helper.rb
 - spec/support/test_data_reader.rb
 homepage: http://github.com/yatsura/gcig_ca125

data/spec/lib/gcig_ca125/result_spec.rb

@@ -1,37 +0,0 @@
-require 'spec_helper'
-
-describe "GcigCa125::Result" do
-  it "response to message" do
-    expect(GcigCa125::Result.instance_methods).to include(:message)
-  end
-
-  it "response to evaluable" do
-    expect(GcigCa125::Result.instance_methods).to include(:evaluable?)
-  end
-
-  it "response to response" do
-    expect(GcigCa125::Result.instance_methods).to include(:response?)
-  end
-
-  it "response to normalised" do
-    expect(GcigCa125::Result.instance_methods).to include(:normalised?)
-  end
-
-  context "#message" do
-    it "starts with 'No response' if evaluable but no response and has not normalised" do
-      skip
-    end
-
-    it "starts with 'Not evaluable' if not evaluable" do
-      skip
-    end
-
-    it "starts with 'Not confirmed' if evaluable and normalised but not response" do
-      skip
-    end
-
-    it "starts with 'Confirmed response' if evaluable, normalised and is a response" do
-      skip
-    end
-  end
-end