fhir_scorecard 1.8.0 → 3.0.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: dc1534f80e10d27ea0541aff94ebf5211a32daf1
+  metadata.gz: 33e738412732ba23a26dac7ff0482beeb3adf674
+  data.tar.gz: 7e19bfd199b23c73148768329bb4d76579bd5e69
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data/.travis.yml

@@ -1,5 +1,6 @@
 language: ruby
 rvm:
-  - "2.0.0"
+  - "2.3.3"
+  - "2.4.0"
 script:
   - bundle exec rake test

data/Gemfile

@@ -4,6 +4,9 @@ gemspec
 gem 'rake'
 gem 'pry'
 
+# gem 'fhir_models', :path => '../fhir_models'
+# gem 'fhir_models', :git => 'https://github.com/fhir-crucible/fhir_models.git', :branch => '3.0.0-release'
+
 group :test do
   gem 'simplecov', :require => false
   gem 'minitest', '~> 5.3'

data/Gemfile.lock

@@ -1,8 +1,8 @@
 PATH
   remote: .
   specs:
-    fhir_scorecard (1.8.0)
-      fhir_models (~> 1.8)
+    fhir_scorecard (3.0.1)
+      fhir_models (>= 3.0.0)
 
 GEM
   remote: https://rubygems.org/
@@ -11,35 +11,35 @@ GEM
     awesome_print (1.7.0)
     bcp47 (0.3.3)
       i18n
-    builder (3.2.2)
+    builder (3.2.3)
     coderay (1.1.1)
     date_time_precision (0.8.1)
     docile (1.1.5)
-    fhir_models (1.8.1)
+    fhir_models (3.0.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 1.16, < 3)
       nokogiri (>= 1.6)
-    i18n (0.7.0)
-    json (2.0.2)
+    i18n (0.8.1)
+    json (2.0.3)
     method_source (0.8.2)
     mime-types (2.99.3)
     mini_portile2 (2.1.0)
-    minitest (5.9.1)
-    minitest-reporters (1.1.12)
+    minitest (5.10.1)
+    minitest-reporters (1.1.14)
       ansi
       builder
       minitest (>= 5.0)
       ruby-progressbar
-    nokogiri (1.6.8.1)
+    nokogiri (1.7.1)
       mini_portile2 (~> 2.1.0)
     pry (0.10.4)
       coderay (~> 1.1.0)
       method_source (~> 0.8.1)
       slop (~> 3.4)
-    rake (11.3.0)
+    rake (12.0.0)
     ruby-progressbar (1.8.1)
-    simplecov (0.12.0)
+    simplecov (0.14.1)
       docile (~> 1.1.0)
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
@@ -59,4 +59,4 @@ DEPENDENCIES
   simplecov
 
 BUNDLED WITH
-   1.13.6
+   1.14.6

data/fhir_scorecard.gemspec

@@ -7,9 +7,9 @@ Gem::Specification.new do |s|
   s.email = "jwalonoski@mitre.org"
   s.homepage = "https://github.com/fhir-crucible/fhir_scorecard"
   s.authors = ["Jason Walonoski"]
-  s.version = '1.8.0'
+  s.version = '3.0.1'
 
   s.files = s.files = `git ls-files`.split("\n")
 
-  s.add_runtime_dependency 'fhir_models', '~> 1.8'
+  s.add_runtime_dependency 'fhir_models', '>= 3.0.0'
 end

data/lib/fhir_scorecard.rb

@@ -6,6 +6,7 @@ root = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
 
 require File.join(root,'lib','scorecard.rb')
 require File.join(root,'lib','terminology.rb')
+require File.join(root,'lib','implementation_guides.rb')
 require File.join(root,'lib','rubrics.rb')
 
 Dir.glob(File.join(root, 'lib','rubrics','**','*.rb')).each do |file|

data/lib/implementation_guides.rb

@@ -0,0 +1,184 @@
+module FHIR
+  class ImplementationGuideLookup
+
+    @@resources = File.expand_path './resources', File.dirname(File.absolute_path(__FILE__))
+    @@loaded = false
+
+    @@us_core = {}
+    @@standard_health_record = {}
+    @@shr_indicators = {}
+
+    @@shr_defaults = {
+      'Practitioner' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-Practitioner',
+      'Organization' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-Organization',
+      'RelatedPerson' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-RelatedPerson',
+      'AllergyIntolerance' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-AllergyIntolerance',
+      'BodySite' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-core-BodySite',
+      'Patient' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-demographics-PersonOfRecord',
+      'Coverage' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-demographics-HealthInsurance',
+      'Device' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-device-Device',
+      'DeviceUseStatement' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-device-DeviceUse',
+      'Encounter' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-encounter-Encounter',
+      'Immunization' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-immunization-Immunization',
+      'Medication' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-medication-Medication',
+      'MedicationStatement' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-medication-MedicationUse',
+      'MedicationRequest' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-medication-MedicationPrescription',
+      'DiagnosticReport' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-Panel',
+      'Observation' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-Observation',
+      'Condition' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-problem-Problem',
+      'Procedure' => 'http://standardhealthrecord.org/fhir/StructureDefinition/shr-procedure-Procedure'
+    }
+
+    def self.guess_shr_profile(resource)
+      load_guides
+      if resource && !@@shr_indicators.nil? && !@@shr_indicators.empty?
+        # if the profile is given, we don't need to guess
+        if resource.meta && resource.meta.profile && !resource.meta.profile.empty?
+          resource.meta.profile.each do |uri|
+            return @@standard_health_record[uri] if @@standard_health_record[uri]
+          end
+        end
+        # if the profile is not named, then we need to guess using some heuristic indicators
+        @@shr_indicators.each do |url, data|
+          if data['resource'] == resource.resourceType
+            indicators = true
+            resource_hash = resource.to_hash
+            data['fixedValues'].each do |requirement|
+              # indicators = false if requirement not met
+              steps = requirement['path'].split('.')
+              steps.delete(data['resource'])
+              actual_values = select(steps, resource_hash)
+              expected_value = requirement['value']
+              if actual_values.nil? || (actual_values.is_a?(Array) && actual_values.empty?)
+                indicators = false
+              elsif actual_values.is_a?(Array)
+                actual_values.each do |onevalue|
+                  if onevalue.is_a?(Hash)
+                    if onevalue['coding']
+                      actual_code = onevalue['coding'].map{|x|x['code']}
+                      expected_code = expected_value['coding'].map{|x|x['code']}
+                      any_match = false
+                      actual_code.each do |x|
+                        any_match = true if expected_code.include?(x)
+                      end
+                      indicators = false unless any_match
+                    else
+                      expected_value.each do |key, value|
+                        indicators = false unless onevalue[key] == value
+                      end
+                    end
+                  end
+                end
+              elsif actual_values.is_a?(Hash)
+                if actual_values['coding']
+                  actual_code = actual_values['coding'].map{|x|x['code']}
+                  expected_code = expected_value['coding'].map{|x|x['code']}
+                  any_match = false
+                  actual_code.each do |x|
+                    any_match = true if expected_code.include?(x)
+                  end
+                  indicators = false unless any_match
+                else
+                  expected_value.each do |key, value|
+                    indicators = false unless actual_values[key] == value
+                  end
+                end
+              elsif actual_values.is_a?(TrueClass) || actual_values.is_a?(FalseClass)
+                indicators = false unless actual_values == expected_value
+              end
+            end
+            return @@standard_health_record[uri] if indicators
+          end
+        end
+        # if the heuristics do not help, use a default if possible
+        default = @@shr_defaults[resource.resourceType]
+        return @@standard_health_record[default] if default
+      end
+      nil
+    end
+
+    def self.select(steps=[], obj)
+      return obj if steps.nil? || steps.empty?
+      copysteps = steps.clone
+      if obj.is_a?(Hash)
+        step = copysteps.delete_at(0)
+        obj = obj[step]
+        select(copysteps, obj)
+      elsif obj.is_a?(Array)
+        obj.map do |x|
+          select(copysteps, x)
+        end
+      end
+    end
+
+    def self.guess_uscore_profile(resource)
+      load_guides
+       if resource
+        # if the profile is given, we don't need to guess
+        if resource.meta && resource.meta.profile && !resource.meta.profile.empty?
+          resource.meta.profile.each do |uri|
+            return @@us_core[uri] if @@us_core[uri]
+          end
+        end
+        # TODO consider VitalSigns/Observations
+        # Otherwise, guess the first profile that matches on resource type
+        @@us_core.each do |url, thing|
+          if thing.is_a?(FHIR::StructureDefinition)
+            return thing if thing.type == resource.resourceType
+          end
+        end
+      end
+      nil
+    end
+
+    def self.lookup(url)
+      load_guides
+      @@us_core[url] || @@standard_health_record[url] || nil
+    end
+
+    def self.load_guides
+      if !@@loaded
+        begin
+          # load all the FHIR resources in the US Core Implementation Guide
+          Dir.glob(File.join(@@resources,'us_core','**','*.json')).each do |filename|
+            raw = File.open(filename,'r:UTF-8',&:read)
+            resource = FHIR.from_contents(raw)
+            if resource
+              @@us_core[resource.id] = resource if resource.id
+              @@us_core[resource.url] = resource if resource.url
+            end
+          end
+        rescue => error
+          FHIR.logger.error error
+        end
+
+        begin
+          # load all the FHIR resources in the Standard Health Record Implementation Guide
+          Dir.glob(File.join(@@resources,'standard_health_record','**','*.json')).each do |filename|
+            raw = File.open(filename,'r:UTF-8',&:read)
+            resource = FHIR.from_contents(raw)
+            if resource
+              @@standard_health_record[resource.id] = resource if resource.id
+              @@standard_health_record[resource.url] = resource if resource.url
+            end
+          end
+        rescue => error
+          FHIR.logger.error error
+        end
+
+        begin
+          # load some indicators to help guess which SHR profile to use
+          filename = File.join(@@resources,'profile_indicators.json')
+          raw = File.open(filename,'r:UTF-8',&:read)
+          @@shr_indicators = JSON.parse(raw)
+        rescue => error
+          @@shr_indicators = {}
+          FHIR.logger.error error
+        end        
+
+        @@loaded = true
+      end
+    end
+
+  end
+end

data/lib/resources/profile_indicators.json

@@ -0,0 +1,1633 @@
+{
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-EmergencyContact": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-EmergencyContact",
+    "resource": "CareTeam",
+    "fixedValues": [
+      {
+        "path": "CareTeam.participant.role",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C1552023"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-PrimaryCareProvider": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-PrimaryCareProvider",
+    "resource": "CareTeam",
+    "fixedValues": [
+      {
+        "path": "CareTeam.participant.role",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2735026"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-NoPrimaryCareProvider": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-NoPrimaryCareProvider",
+    "resource": "CareTeam",
+    "fixedValues": [
+      {
+        "path": "CareTeam.participant.role",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2735026"
+            }
+          ]
+        }
+      },
+      {
+        "path": "CareTeam.modifierExtension.extension.valueBoolean",
+        "value": true
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-problem-Asplenia": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-problem-Asplenia",
+    "resource": "Condition",
+    "fixedValues": [
+      {
+        "path": "Condition.code",
+        "value": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "93030006"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-adverse-AdverseReaction": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-adverse-AdverseReaction",
+    "resource": "Condition",
+    "fixedValues": [
+      {
+        "path": "Condition.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://standardhealthrecord.org/fhir/CodeSystem/shr-problem-ProblemCategoryVS",
+              "code": "adverse_reaction"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-DrugAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-DrugAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "drug"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-FoodAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-FoodAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "food"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "food"
+      },
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "medication"
+      },
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "biologic"
+      },
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "environment"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      },
+      {
+        "path": "AllergyIntolerance.verificationStatus",
+        "value": "unconfirmed"
+      },
+      {
+        "path": "AllergyIntolerance.modifierExtension.extension.valueBoolean",
+        "value": true
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownFoodAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownFoodAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "food"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      },
+      {
+        "path": "AllergyIntolerance.verificationStatus",
+        "value": "unconfirmed"
+      },
+      {
+        "path": "AllergyIntolerance.modifierExtension.extension.valueBoolean",
+        "value": true
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownDrugAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownDrugAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "drug"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      },
+      {
+        "path": "AllergyIntolerance.verificationStatus",
+        "value": "unconfirmed"
+      },
+      {
+        "path": "AllergyIntolerance.modifierExtension.extension.valueBoolean",
+        "value": true
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownEnvironmentalAllergy": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-allergy-NoKnownEnvironmentalAllergy",
+    "resource": "AllergyIntolerance",
+    "fixedValues": [
+      {
+        "path": "AllergyIntolerance.category",
+        "value": "environment"
+      },
+      {
+        "path": "AllergyIntolerance.type",
+        "value": "allergy"
+      },
+      {
+        "path": "AllergyIntolerance.verificationStatus",
+        "value": "unconfirmed"
+      },
+      {
+        "path": "AllergyIntolerance.modifierExtension.extension.valueBoolean",
+        "value": true
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-HistoryObservation": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-HistoryObservation",
+    "resource": "Observation",
+    "fixedValues": [
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2004062"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-SocialHistory": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-observation-SocialHistory",
+    "resource": "Observation",
+    "fixedValues": [
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2004062"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "social-history"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-BehavioralObservation": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-BehavioralObservation",
+    "resource": "Observation",
+    "fixedValues": [
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "54511-1"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-SubstanceUse": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-SubstanceUse",
+    "resource": "Observation",
+    "fixedValues": [
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2004062"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C0332157"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C024251"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-IntravenousDrugUse": {
+    "profile": "http://standardhealthrecord.org/fhir/StructureDefinition/shr-behavior-IntravenousDrugUse",
+    "resource": "Observation",
+    "fixedValues": [
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C2004062"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C0332157"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.category",
+        "value": {
+          "coding": [
+            {
+              "system": "http://ncimeta.nci.nih.gov",
+              "code": "C024251"
+            }
+          ]
+        }
+      },
+      {
+        "path": "Observation.code",
+        "value": {
+          "coding": [
+            {
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+          "code": "mm[Hg]"
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+      }
+    ]
+  }
+}