fhir_scorecard 1.0

data/test/unit/basic_test.rb

@@ -0,0 +1,52 @@
+require_relative '../test_helper'
+
+class BasicTest < Minitest::Test
+
+  # turn off the ridiculous warnings
+  $VERBOSE=nil
+
+  def test_bundle
+    bundle = FHIR::Bundle.new
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:points]==10), 'Scorecard points incorrect.'
+    assert (report[:bundle][:points]), 'Bundle section should report points.'
+    assert (report[:bundle][:points]==10), 'Bundle section points incorrect.'
+    assert (report[:patient][:points]), 'Patient section should report points.'
+    assert (report[:patient][:points]==0), 'Patient section points incorrect.'
+  end
+
+  def test_not_bundle
+    basic = FHIR::Basic.new
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(basic.to_json)
+
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:points]==0), 'Scorecard points incorrect.'
+    assert (report[:bundle][:points]), 'Bundle section should report points.'
+    assert (report[:bundle][:points]==0), 'Bundle section points incorrect.'
+  end
+
+  def test_bundle_with_patient
+    patient = FHIR::Patient.new
+    bundle = FHIR::Bundle.new({'entry'=>[ {} ]})
+    bundle.entry.first.resource = patient
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:points]==20), 'Scorecard points incorrect.'
+    assert (report[:bundle][:points]), 'Bundle section should report points.'
+    assert (report[:bundle][:points]==10), 'Bundle section points incorrect.'
+    assert (report[:patient][:points]), 'Patient section should report points.'
+    assert (report[:patient][:points]==10), 'Patient section points incorrect.'
+  end
+
+end

data/test/unit/codes_exist_test.rb

@@ -0,0 +1,169 @@
+require_relative '../test_helper'
+
+class CodesExistTest < Minitest::Test
+
+  # turn off the ridiculous warnings
+  $VERBOSE=nil
+
+  def test_codes_exist_none
+    patient = FHIR::Patient.new
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==0), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=0)."
+  end
+
+  def test_codes_exist_1of3
+    patient = FHIR::Patient.new({ 'gender'=>'male' })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==3), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=3)."
+  end
+
+  def test_codes_exist_1of3_wrongtype
+    patient = FHIR::Patient.new({ 'gender'=>0 })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==0), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=0)."
+  end
+
+  def test_codes_exist_2of3
+    patient = FHIR::Patient.new({ 
+      'gender'=>'male', 
+      'maritalStatus'=> { 
+        'coding'=>[ {'code'=>'S','system'=>'http://hl7.org/fhir/v3/MaritalStatus'} ]
+      } 
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==6), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=6)."
+  end
+
+  def test_codes_exist_2of3_textonly
+    patient = FHIR::Patient.new({ 
+      'gender'=>'male', 
+      'maritalStatus'=> { 
+        'text'=>'Single'
+      } 
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==3), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=3)."
+  end
+
+  def test_codes_exist_3of3
+    patient = FHIR::Patient.new({ 
+      'language'=>'en-US',
+      'gender'=>'male', 
+      'maritalStatus'=> { 
+        'coding'=>[ {'code'=>'S','system'=>'http://hl7.org/fhir/v3/MaritalStatus'} ]
+      } 
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==10), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=10)."
+  end
+
+  def test_codes_exist_with_backbone_elements
+    patient = FHIR::Patient.new({ 
+      'language'=>'en-US',
+      'gender'=>'male', 
+      'maritalStatus'=> { 
+        'coding'=>[ {'code'=>'S','system'=>'http://hl7.org/fhir/v3/MaritalStatus'} ]
+      },
+      'communication'=> [
+        { 'language'=> { 
+            'coding'=>[ {'code'=>'en-US','system'=>'urn:ietf:bcp:47'} ]
+          }, 
+          'preferred'=> true },
+        { 'language'=> { 
+            'coding'=>[ {'code'=>'es','system'=>'urn:ietf:bcp:47'} ]
+          }
+        }
+      ]
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==10), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=10)."
+  end
+
+  def test_codes_exist_with_backbone_elements_and_array
+    patient = FHIR::Patient.new({ 
+      'language'=>'en-US',
+      'gender'=>'male', 
+      'maritalStatus'=> { 
+        'coding'=>[ {'code'=>'S','system'=>'http://hl7.org/fhir/v3/MaritalStatus'} ]
+      },
+      'contact'=> [
+        { 'gender'=>'male',
+          'relationship'=> [
+            {  'coding'=>[ {'code'=>'c','system'=>'http://hl7.org/fhir/v2/0131'} ] }
+          ]
+        },{ 'gender'=>'female',
+          'relationship'=> [
+            {  'coding'=>[ {'code'=>'n','system'=>'http://hl7.org/fhir/v2/0131'} ] }
+          ]
+        }
+      ] 
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => patient.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==10), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=10)."
+  end
+
+  def test_codes_exist_with_coding
+    encounter = FHIR::Encounter.new({ 
+      'language'=>'en-US',
+      'status'=>'planned',
+      'class'=>{'code'=>'AMB','system'=>'http://hl7.org/fhir/v3/ActCode'}
+    })
+    bundle = FHIR::Bundle.new({ 'entry'=>[ { 'resource' => encounter.to_hash } ] })
+    scorecard = FHIR::Scorecard.new
+    report = scorecard.score(bundle.to_json)
+    assert (report[:points]), 'Scorecard should report points.'
+    assert (report[:bundle]), 'Scorecard should report Bundle section.'
+    assert (report[:patient]), 'Scorecard should report Patient section.'
+    assert (report[:codes_exist]), 'Scorecard should report Codes Exist section.'
+    assert (report[:codes_exist][:points]==5), "Codes Exist section points incorrect (#{report[:codes_exist][:points]}!=5)."
+  end
+
+end

data/test/unit/terminology_test.rb

@@ -0,0 +1,91 @@
+require_relative '../test_helper'
+
+class TerminologyTest < Minitest::Test
+
+  # turn off the ridiculous warnings
+  $VERBOSE=nil
+
+  @@term_root = File.expand_path '../../terminology',File.dirname(File.absolute_path(__FILE__))
+
+  def setup
+    loinc_file = File.join(@@term_root,'scorecard_loinc_2000.txt')
+    umls_file = File.join(@@term_root,'scorecard_umls.txt')
+    snomed_file = File.join(@@term_root,'scorecard_snomed_core.txt')
+    FileUtils.mv(loinc_file, "#{loinc_file}.bak", :force=>true)
+    FileUtils.mv(umls_file, "#{umls_file}.bak", :force=>true)
+    FileUtils.mv(snomed_file, "#{snomed_file}.bak", :force=>true)
+    file = File.open(loinc_file,'w:UTF-8')
+    file.write('foo|Foo Description|mg')
+    file.close
+    file = File.open(umls_file,'w:UTF-8')
+    file.write("LOINC|foo|Foo Description\n")
+    file.write("RXNORM|placebo|Placebo Description\n")
+    file.write("LOINC|bar|Bar Description\n")
+    file.close
+    file = File.open(snomed_file,'w:UTF-8')
+    file.write("baz|Baz Description\n")
+    file.close
+  end
+
+  def teardown
+    loinc_file = File.join(@@term_root,'scorecard_loinc_2000.txt')
+    umls_file = File.join(@@term_root,'scorecard_umls.txt')
+    snomed_file = File.join(@@term_root,'scorecard_snomed_core.txt')
+    FileUtils.rm(loinc_file, :force=>true)
+    FileUtils.rm(umls_file, :force=>true)
+    FileUtils.rm(snomed_file, :force=>true)
+    FileUtils.mv("#{loinc_file}.bak",loinc_file, :force=>true)
+    FileUtils.mv("#{umls_file}.bak",umls_file, :force=>true)
+    FileUtils.mv("#{snomed_file}.bak",snomed_file, :force=>true)    
+  end
+
+  def test_get_description_foo
+    description = FHIR::Terminology.get_description('LOINC','foo')
+    assert description=='Foo Description', "Incorrect description: #{description}"
+  end
+
+  def test_get_description_placebo
+    description = FHIR::Terminology.get_description('RXNORM','placebo')
+    assert description=='Placebo Description', "Incorrect description: #{description}"
+  end
+
+  def test_get_description_bar
+    description = FHIR::Terminology.get_description('LOINC','bar')
+    assert description=='Bar Description', "Incorrect description: #{description}"
+  end
+
+  def test_get_description_negative
+    description = FHIR::Terminology.get_description('LOINC','baz')
+    assert description.nil?, 'Expected nil description.'
+  end
+
+  def test_get_description_negative_unknown_system
+    description = FHIR::Terminology.get_description('FAKE','fake')
+    assert description.nil?, 'Expected nil description.'
+  end
+
+  def test_is_top_lab_code_true
+    assert FHIR::Terminology.is_top_lab_code?('foo'), 'Top lab code not found.'
+  end
+
+  def test_is_top_lab_code_false
+    assert !FHIR::Terminology.is_top_lab_code?('bar'), 'Lab code should not have been found.'
+  end
+
+  def test_lab_units_foo
+    assert FHIR::Terminology.lab_units('foo')=='mg', 'Incorrect units returned.'
+  end
+
+  def test_lab_units_bar
+    assert FHIR::Terminology.lab_units('bar').nil?, 'Units were unexpectedly returned (should be nil).'
+  end
+
+  def test_lab_description_foo
+    assert FHIR::Terminology.lab_description('foo')=='Foo Description', 'Incorrect description returned.'
+  end
+
+  def test_lab_description_bar
+    assert FHIR::Terminology.lab_description('bar').nil?, 'Description was unexpectedly returned (should be nil).'
+  end
+
+end

metadata

@@ -0,0 +1,90 @@
+--- !ruby/object:Gem::Specification
+name: fhir_scorecard
+version: !ruby/object:Gem::Version
+  version: '1.0'
+platform: ruby
+authors:
+- Jason Walonoski
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-11-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: fhir_models
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A Gem for scoring FHIR Patient Records (as Bundles)
+email: jwalonoski@mitre.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".simplecov"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- Rakefile
+- fhir_scorecard.gemspec
+- lib/fhir_scorecard.rb
+- lib/rubrics.rb
+- lib/rubrics/codes_exist.rb
+- lib/rubrics/codes_umls.rb
+- lib/rubrics/codes_umls_preferred_descriptions.rb
+- lib/rubrics/completeness.rb
+- lib/rubrics/cvx_immunizations.rb
+- lib/rubrics/cvx_meds.rb
+- lib/rubrics/datetimes_iso8601.rb
+- lib/rubrics/labs_loinc.rb
+- lib/rubrics/quantities_ucum.rb
+- lib/rubrics/references_resolve.rb
+- lib/rubrics/rxnorm_meds.rb
+- lib/rubrics/smoking_status.rb
+- lib/rubrics/snomed_conditions.rb
+- lib/rubrics/vital_signs.rb
+- lib/scorecard.rb
+- lib/tasks/tasks.rake
+- lib/terminology.rb
+- logs/.keep
+- terminology/.keep
+- test/test_helper.rb
+- test/unit/basic_test.rb
+- test/unit/codes_exist_test.rb
+- test/unit/terminology_test.rb
+homepage: https://github.com/fhir-crucible/fhir_scorecard
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.7
+signing_key: 
+specification_version: 4
+summary: Scorecard for a FHIR Patient Record (as Bundle)
+test_files: []