fhir_scorecard 1.0

data/lib/rubrics/rxnorm_meds.rb

@@ -0,0 +1,73 @@
+module FHIR
+  class RxNormMeds < FHIR::Rubrics
+
+    # Medications should be coded with RxNorm
+    rubric :rxnorm_meds do |record|
+      results = {
+        :eligible_fields => 0,
+        :validated_fields => 0
+      }
+      # Medication.code (CodeableConcept)
+      # MedicationAdministration.medicationCodeableConcept / medicationReference
+      # MedicationDispense.medicationCodeableConcept / medicationReference
+      # MedicationOrder.medicationCodeableConcept / medicationReference
+      # MedicationStatement.medicationCodeableConcept / medicationReference
+
+      resources = record.entry.map{|e|e.resource}
+      resources.each do |resource|
+        if resource.is_a?(FHIR::Medication)
+            results[:eligible_fields] += 1
+            results[:validated_fields] += 1 if rxnorm?(resource.code)        
+        elsif (
+            resource.is_a?(FHIR::MedicationOrder) ||
+            resource.is_a?(FHIR::MedicationDispense) ||
+            resource.is_a?(FHIR::MedicationAdministration) ||
+            resource.is_a?(FHIR::MedicationStatement) )
+          if resource.medicationCodeableConcept
+            results[:eligible_fields] += 1
+            results[:validated_fields] += 1 if rxnorm?(resource.medicationCodeableConcept)
+          elsif resource.medicationReference
+            results[:eligible_fields] += 1
+            results[:validated_fields] += 1 if local_rxnorm_reference?(resource.medicationReference,record,resource.contained)            
+          end
+        end
+      end
+
+      percentage = results[:validated_fields].to_f / results[:eligible_fields].to_f
+      percentage = 0.0 if percentage.nan?
+      points = 10.0 * percentage
+      message = "#{(100 * percentage).to_i}% (#{results[:validated_fields]}/#{results[:eligible_fields]}) of Medication[x] Resource codes use RxNorm. Maximum of 10 points."
+      response(points.to_i,message)
+    end
+
+    def self.rxnorm?(codeableconcept)
+      return false if codeableconcept.nil? || codeableconcept.coding.nil?
+      codeableconcept.coding.any?{|x| x.system=='http://www.nlm.nih.gov/research/umls/rxnorm' && FHIR::Terminology.get_description('RXNORM',x.code)}
+    end
+
+    def self.local_rxnorm_reference?(reference,record,contained)
+      if contained && reference.reference && reference.reference.start_with?('#')
+        contained.each do |resource|
+          return true if resource.is_a?(FHIR::Medication) && reference.reference[1..-1]==resource.id
+        end
+      end
+      record.entry.each do |entry|
+        if entry.resource.is_a?(FHIR::Medication) && reference_matchs?(reference,entry)
+          return true
+        end
+      end
+      false    
+    end
+
+    def self.reference_matchs?(reference,entry)
+      if reference.reference.start_with?('urn:uuid:')
+        (reference.reference == entry.fullUrl)
+      elsif reference.reference.include?('Medication/')
+        (reference.reference.split('Medication/').last.split('/').first == entry.id)
+      else 
+        false # unable to verify reference points to RXNORM
+      end
+    end
+
+  end
+end

data/lib/rubrics/smoking_status.rb

@@ -0,0 +1,48 @@
+module FHIR
+  class SmokingStatus < FHIR::Rubrics
+
+    SMOKING_CODES = [
+      '449868002', #Current every day smoker  
+      '428041000124106', #Current some day smoker 
+      '8517006', #Former smoker 
+      '266919005', #Never smoker  
+      '77176002', #Smoker, current status unknown  
+      '266927001', #Unknown if ever smoked  
+      '428071000124103', #Current Heavy tobacco smoker  
+      '428061000124105' #Current Light tobacco smoker
+    ]
+
+    # The Patient Record should include Smoking Status
+    rubric :smoking_status do |record|
+      
+      resources = record.entry.map{|e|e.resource}
+      has_smoking_status = resources.any? do |resource|
+        resource.is_a?(FHIR::Observation) && smoking_observation?(resource)
+      end
+
+      if has_smoking_status
+        points = 10
+      else
+        points = 0
+      end
+
+      message = "The Patient Record should include Smoking Status (DAF-core-smokingstatus profile on Observation)."
+      response(points.to_i,message)
+    end
+
+    def self.smoking_observation?(resource)
+      smoking_code?(resource.code) && smoking_value?(resource.valueCodeableConcept)
+    end
+
+    def self.smoking_code?(codeableconcept)
+      return false if codeableconcept.nil? || codeableconcept.coding.nil?
+      codeableconcept.coding.any?{|x| x.system=='http://loinc.org' && x.code=='72166-2'}
+    end
+
+    def self.smoking_value?(codeableconcept)
+      return false if codeableconcept.nil? || codeableconcept.coding.nil?
+      codeableconcept.coding.any?{|x| x.system=='http://snomed.info/sct' && SMOKING_CODES.include?(x.code)}
+    end
+
+  end
+end

data/lib/rubrics/snomed_conditions.rb

@@ -0,0 +1,32 @@
+module FHIR
+  class SnomedConditions < FHIR::Rubrics
+
+    # Conditions should be coded with the SNOMED Core Subset
+    rubric :snomed_core do |record|
+      results = {
+        :eligible_fields => 0,
+        :validated_fields => 0
+      }
+
+      resources = record.entry.map{|e|e.resource}
+      resources.each do |resource|
+        if resource.is_a?(FHIR::Condition)
+          results[:eligible_fields] += 1
+          results[:validated_fields] += 1 if snomed_core?(resource.code)
+        end
+      end
+
+      percentage = results[:validated_fields].to_f / results[:eligible_fields].to_f
+      percentage = 0.0 if percentage.nan?
+      points = 10.0 * percentage
+      message = "#{(100 * percentage).to_i}% (#{results[:validated_fields]}/#{results[:eligible_fields]}) of Condition Resource codes use the SNOMED Core Subset. Maximum of 10 points."
+      response(points.to_i,message)
+    end
+
+    def self.snomed_core?(codeableconcept)
+      return false if codeableconcept.nil? || codeableconcept.coding.nil?
+      codeableconcept.coding.any?{|x| x.system=='http://snomed.info/sct' && FHIR::Terminology.is_core_snomed?(x.code)}
+    end
+
+  end
+end

data/lib/rubrics/vital_signs.rb

@@ -0,0 +1,64 @@
+module FHIR
+  class VitalSigns < FHIR::Rubrics
+
+    # http://hl7.org/fhir/2016Sep/observation-vitalsigns.html
+    VITAL_SIGNS = {
+      # '8716-3' => '', # vital signs group
+      '9279-1' => [], #'/min', # respitory rate
+      '8867-4' => [], #'/min', # heart rate
+      '59408-5' => [], #'%', # Oxygen saturation  
+      '8310-5' => [], #'Cel', # Body temperature
+      '8302-2' => [], #'cm', # Body height
+      '9843-4' => [], #'cm', # Head circumference
+      '29463-7' => [], #'kg', # Body weight
+      '39156-5' => [], #'kg/m2', # Body mass index 
+      '55284-4' => ['8480-6','8462-4'] # Blood pressure systolic and diastolic group
+      # '8480-6' => 'mm[Hg]', # Systolic blood pressure
+      # '8462-4' => 'mm[Hg]', # Diastolic blood pressure
+      # '8478-0' => 'mm[Hg]' # Mean blood pressure  
+    }
+
+    # Vital Signs should be present with specific LOINC codes
+    rubric :vital_signs do |record|
+      
+      not_found = VITAL_SIGNS.clone
+
+      resources = record.entry.map{|e|e.resource}
+      resources.each do |resource|
+        if resource.is_a?(FHIR::Observation)
+          found_code = get_vital_code(resource.code)
+          components = not_found[ found_code ]
+          if components.nil?
+            components = []
+          else
+            components = components.clone
+          end
+          if components.empty?
+            not_found.delete(found_code)
+          elsif resource.component
+            resource.component.each do |component|
+              sub_code = get_vital_code(component.code)
+              components.delete(sub_code)         
+            end
+            not_found.delete(found_code) if components.empty?
+          end
+        end
+      end
+
+      percentage = ( (VITAL_SIGNS.length.to_f - not_found.length.to_f) / (VITAL_SIGNS.length.to_f) )
+      percentage = 0.0 if percentage.nan?
+      points = 10.0 * percentage
+      message = "#{(100 * percentage).to_i}% (#{VITAL_SIGNS.length - not_found.length}/#{VITAL_SIGNS.length}) of Vital Signs had at least one recorded Observation. Maximum of 10 points."
+      response(points.to_i,message)
+    end
+
+    def self.get_vital_code(codeableconcept)
+      return nil if codeableconcept.nil? || codeableconcept.coding.nil?
+
+      coding = codeableconcept.coding.find{|x| x.system=='http://loinc.org' && VITAL_SIGNS.has_key?(x.code)}
+      code = coding.code if coding
+      code
+    end
+
+  end
+end

data/lib/rubrics.rb

@@ -0,0 +1,23 @@
+module FHIR
+  class Rubrics
+
+    @@rubrics = {}
+
+    def self.apply(record)
+      report = {}
+      @@rubrics.each do |key,rubric| 
+        report[key] = rubric.call(record)
+      end
+      report
+    end
+
+    def self.rubric(key,&block)
+      @@rubrics[key] = block
+    end
+
+    def self.response(points,message)
+      {:points=>points,:message=>message}
+    end
+
+  end
+end

data/lib/scorecard.rb

@@ -0,0 +1,46 @@
+module FHIR
+  class Scorecard
+
+    attr_accessor :report
+    attr_accessor :points
+
+    def score(bundle_raw)
+      @report = {}
+      @points = 0
+
+      # Check that the patient record is a FHIR Bundle.
+      bundle = FHIR.from_contents(bundle_raw)
+      if bundle.is_a?(FHIR::Bundle)
+        @points += 10
+        @report[:bundle] = { :points=>10, :message=>'Patient Record is a FHIR Bundle.'}
+      else
+        @report[:bundle] = { :points=>0, :message=>'Patient Record must be a FHIR Bundle.'}
+      end
+
+      if bundle.is_a?(FHIR::Bundle)
+
+        # Check that the patient record contains a FHIR Patient.
+        @patient = nil
+        count = 0
+        bundle.entry.each do |entry|
+          if entry.resource && entry.resource.is_a?(FHIR::Patient)
+            @patient = entry.resource
+            count += 1
+          end
+        end
+        if @patient && count==1
+          @points += 10
+          @report[:patient] = { :points=>10, :message=>'Patient Record contains one FHIR Patient.'}
+        else
+          @report[:patient] = { :points=>0, :message=>'Patient Record must contain one FHIR Patient.'}
+        end
+
+        report.merge!(FHIR::Rubrics.apply(bundle))
+      end
+
+      @report[:points] = @report.values.inject(0){|sum,section| sum+=section[:points]}
+      @report
+    end
+
+  end
+end

data/lib/tasks/tasks.rake

@@ -0,0 +1,207 @@
+namespace :fhir do
+
+  desc 'console'
+  task :console, [] do |t, args|
+    binding.pry
+  end
+
+  desc 'score a FHIR Bundle'
+  task :score, [:bundle_path] do |t, args|
+    bundle_path = args[:bundle_path]
+    if bundle_path.nil?
+      puts 'A path to FHIR Bundle is required!'
+    else
+      contents = File.open(bundle_path,'r:UTF-8',&:read)
+      scorecard = FHIR::Scorecard.new
+      report = scorecard.score(contents)
+      puts 
+      puts "  POINTS            CATEGORY   MESSAGE"
+      puts "  ------            --------   -------"
+      report.each do |key,value|
+        next if key==:points
+        printf("   %3d  %20s   %s\n", value[:points], key, value[:message])
+      end
+      puts "  ------"
+      printf("   %3d  %20s\n", report[:points], 'TOTAL')
+      puts
+    end
+  end
+
+  desc 'post-process LOINC Top 2000 common lab results CSV'
+  task :process_loinc, [] do |t, args|
+    require 'find'
+    require 'csv'
+    puts 'Looking for `./terminology/LOINC*.csv`...'
+    loinc_file = Find.find('terminology').find{|f| /LOINC.*\.csv$/ =~f }
+    if loinc_file
+      output_filename = 'terminology/scorecard_loinc_2000.txt'
+      puts "Writing to #{output_filename}..."
+      output = File.open(output_filename,'w:UTF-8')
+      line = 0
+      begin
+        CSV.foreach(loinc_file, encoding: 'iso-8859-1:utf-8', headers: true) do |row|
+          line += 1
+          next if row.length <=1 || row[1].nil? # skip the categories
+          #              CODE    | DESC    | UCUM UNITS
+          output.write("#{row[1]}|#{row[2]}|#{row[6]}\n")
+        end
+      rescue Exception => e
+        puts "Error at line #{line}"
+        puts e.message
+      end
+      output.close
+      puts 'Done.'
+    else
+      puts 'LOINC file not found.'
+      puts 'Download the LOINC Top 2000 Common Lab Results file'
+      puts '  -> http://loinc.org/usage/obs/loinc-top-2000-plus-loinc-lab-observations-us.csv'
+      puts 'copy it into your `./terminology` folder, and rerun this task.'
+    end
+  end
+
+  desc 'post-process SNOMED Core Subset file'
+  task :process_snomed, [] do |t, args|
+    require 'find'
+    puts 'Looking for `./terminology/SNOMEDCT_CORE_SUBSET*.txt`...'
+    snomed_file = Find.find('terminology').find{|f| /SNOMEDCT_CORE_SUBSET.*\.txt$/ =~f }
+    if snomed_file
+      output_filename = 'terminology/scorecard_snomed_core.txt'
+      output = File.open(output_filename,'w:UTF-8')
+      line = 0
+      begin
+        entire_file = File.read(snomed_file)
+        puts "Writing to #{output_filename}..."
+        entire_file.split("\n").each do |l|
+          row = l.split('|')
+          line += 1
+          next if line==1 # skip the headers
+          #              CODE    | DESC    
+          output.write("#{row[0]}|#{row[1]}\n")
+        end
+      rescue Exception => e
+        puts "Error at line #{line}"
+        puts e.message
+      end
+      output.close
+      puts 'Done.'
+    else
+      puts 'SNOMEDCT file not found.'
+      puts 'Download the SNOMEDCT Core Subset file'
+      puts '  -> https://www.nlm.nih.gov/research/umls/Snomed/core_subset.html'
+      puts 'copy it into your `./terminology` folder, and rerun this task.'
+    end
+  end
+
+  desc 'post-process common UCUM codes'
+  task :process_ucum, [] do |t, args|
+    require 'find'
+    puts 'Looking for `./terminology/concepts.tsv`...'
+    ucum_file = Find.find('terminology').find{|f| /concepts.tsv$/ =~f }
+    if ucum_file
+      output_filename = 'terminology/scorecard_ucum.txt'
+      output = File.open(output_filename,'w:UTF-8')
+      line = 0
+      begin
+        entire_file = File.read(ucum_file)
+        puts "Writing to #{output_filename}..."
+        entire_file.split("\n").each do |l|
+          row = l.split("\t")
+          line += 1
+          next if line==1 # skip the headers
+          output.write("#{row[0]}\n") # code
+          output.write("#{row[5]}\n") if row[0]!=row[5] # synonym
+        end
+      rescue Exception => e
+        puts "Error at line #{line}"
+        puts e.message
+      end
+      output.close
+      puts 'Done.'
+    else
+      puts 'UCUM concepts file not found.'
+      puts 'Download the UCUM concepts file'
+      puts '  -> http://download.hl7.de/documents/ucum/concepts.tsv'
+      puts 'copy it into your `./terminology` folder, and rerun this task.'
+    end
+  end
+
+  desc 'post-process UMLS terminology file'
+  task :process_umls, [] do |t, args|
+    require 'find'
+    puts 'Looking for `./terminology/MRCONSO.RRF`...'
+    input_file = Find.find('terminology').find{|f| f=='terminology/MRCONSO.RRF' }
+    if input_file
+      start = Time.now
+      output_filename = 'terminology/scorecard_umls.txt'
+      output = File.open(output_filename,'w:UTF-8')
+      line = 0
+      excluded = 0
+      excluded_systems = Hash.new(0)
+      begin
+        entire_file = File.read(input_file)
+        puts "Writing to #{output_filename}..."
+        entire_file.split("\n").each do |l|
+          row = l.split('|')
+          line += 1
+          include_code = false
+          codeSystem = row[11]
+          code = row[13]
+          description = row[14]
+          case codeSystem
+          when 'SNOMEDCT_US'
+            codeSystem = 'SNOMED'
+            include_code = (row[4]=='PF' && ['FN','OAF'].include?(row[12]))
+          when 'LNC'
+            codeSystem = 'LOINC'
+            include_code = true
+          when 'ICD10CM'
+            codeSystem = 'ICD10'
+            include_code = (row[12]=='PT')
+          when 'ICD10PCS'
+            codeSystem = 'ICD10'
+            include_code = (row[12]=='PT')            
+          when 'ICD9CM'
+            codeSystem = 'ICD9'
+            include_code = (row[12]=='PT')
+          when 'MTHICD9'
+            codeSystem = 'ICD9'
+            include_code = true
+          when 'RXNORM'
+            include_code = true
+          when 'CVX'
+            include_code = (['PT','OP'].include?(row[12]))
+          when 'SRC'
+            # 'SRC' rows define the data sources in the file
+            include_code = false
+          else
+            include_code = false
+            excluded_systems[codeSystem] += 1
+          end
+          if include_code
+            output.write("#{codeSystem}|#{code}|#{description}\n")             
+          else
+            excluded += 1
+          end
+        end
+      rescue Exception => e
+        puts "Error at line #{line}"
+        puts e.message
+      end
+      output.close
+      puts "Processed #{line} lines, excluding #{excluded} redundant entries."
+      puts "Excluded code systems: #{excluded_systems}" if !excluded_systems.empty?
+      finish = Time.now
+      minutes = ((finish-start)/60)
+      seconds = (minutes - minutes.floor) * 60
+      puts "Completed in #{minutes.floor} minute(s) #{seconds.floor} second(s)."
+      puts 'Done.'
+    else
+      puts 'UMLS file not found.'
+      puts 'Download the US National Library of Medicine (NLM) Unified Medical Language System (UMLS) Full Release files'
+      puts '  -> https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html'
+      puts 'Install the metathesaurus with the following data sources:'
+      puts '  CVX|CVX;ICD10CM|ICD10CM;ICD10PCS|ICD10PCS;ICD9CM|ICD9CM;LNC|LNC;MTHICD9|ICD9CM;RXNORM|RXNORM;SNOMEDCT_US|SNOMEDCT'
+      puts 'After installation, copy `{install path}/META/MRCONSO.RRF` into your `./terminology` folder, and rerun this task.'
+    end
+  end
+end

data/lib/terminology.rb

@@ -0,0 +1,135 @@
+module FHIR
+  class Terminology
+
+    CODE_SYSTEMS = {
+      'http://snomed.info/sct'=>'SNOMED',
+      'http://loinc.org'=>'LOINC',
+      'http://www.nlm.nih.gov/research/umls/rxnorm'=>'RXNORM',
+      'http://hl7.org/fhir/sid/icd-10'=>'ICD10',
+      'http://hl7.org/fhir/sid/icd-10-de'=>'ICD10',
+      'http://hl7.org/fhir/sid/icd-10-nl'=>'ICD10',
+      'http://hl7.org/fhir/sid/icd-10-us'=>'ICD10',
+      'http://www.icd10data.com/icd10pcs'=>'ICD10',
+      'http://hl7.org/fhir/sid/icd-9-cm'=>'ICD9',
+      'http://hl7.org/fhir/sid/icd-9-cm/diagnosis'=>'ICD9',
+      'http://hl7.org/fhir/sid/icd-9-cm/procedure'=>'ICD9',
+      'http://hl7.org/fhir/sid/cvx'=>'CVX'
+    }
+    
+    @@term_root = File.expand_path '../terminology',File.dirname(File.absolute_path(__FILE__))
+
+    @@loaded = false
+    @@top_lab_code_units = {}
+    @@top_lab_code_descriptions = {}
+    @@known_codes = {}
+    @@core_snomed = {}
+    @@common_ucum = []
+
+    def self.set_terminology_root(root)
+      @@term_root = root
+    end
+
+    def self.load_terminology
+      if !@@loaded
+        begin
+          # load the top lab codes
+          filename = File.join(@@term_root,'scorecard_loinc_2000.txt')
+          raw = File.open(filename,'r:UTF-8',&:read)
+          raw.split("\n").each do |line|
+            row = line.split('|')
+            @@top_lab_code_descriptions[row[0]] = row[1] if !row[1].nil?
+            @@top_lab_code_units[row[0]] = row[2] if !row[2].nil?
+          end
+        rescue Exception => error
+          FHIR.logger.error error
+        end
+
+        begin
+          # load the known codes
+          filename = File.join(@@term_root,'scorecard_umls.txt')
+          raw = File.open(filename,'r:UTF-8',&:read)
+          raw.split("\n").each do |line|
+            row = line.split('|')
+            codeSystem = row[0]
+            code = row[1]
+            description = row[2]
+            if @@known_codes[codeSystem]
+              codeSystemHash = @@known_codes[codeSystem]
+            else
+              codeSystemHash = {}
+              @@known_codes[codeSystem] = codeSystemHash
+            end
+            codeSystemHash[code] = description
+          end
+        rescue Exception => error
+          FHIR.logger.error error
+        end
+
+        begin
+          # load the core snomed codes
+          @@known_codes['SNOMED'] = {} if @@known_codes['SNOMED'].nil?
+          codeSystemHash = @@known_codes['SNOMED']
+          filename = File.join(@@term_root,'scorecard_snomed_core.txt')
+          raw = File.open(filename,'r:UTF-8',&:read)
+          raw.split("\n").each do |line|
+            row = line.split('|')
+            code = row[0]
+            description = row[1]
+            codeSystemHash[code] = description if codeSystemHash[code].nil?
+            @@core_snomed[code] = description
+          end   
+        rescue Exception => error
+          FHIR.logger.error error
+        end
+
+        begin
+          # load common UCUM codes
+          filename = File.join(@@term_root,'scorecard_ucum.txt')
+          raw = File.open(filename,'r:UTF-8',&:read)
+          raw.split("\n").each do |code|
+            @@common_ucum << code
+          end
+          @@common_ucum.uniq!
+        rescue Exception => error
+          FHIR.logger.error error
+        end
+
+        @@loaded = true
+      end
+    end
+
+    def self.get_description(system,code)
+      load_terminology
+      if @@known_codes[system]
+        @@known_codes[system][code]
+      else
+        nil
+      end
+    end
+
+    def self.is_core_snomed?(code)
+      load_terminology
+      !@@core_snomed[code].nil?
+    end
+
+    def self.is_top_lab_code?(code)
+      load_terminology
+      !@@top_lab_code_units[code].nil?
+    end
+
+    def self.lab_units(code)
+      load_terminology
+      @@top_lab_code_units[code]
+    end
+
+    def self.is_known_ucum?(units)
+      load_terminology
+      @@top_lab_code_units.values.include?(units) || @@common_ucum.include?(units)
+    end
+
+    def self.lab_description(code)
+      load_terminology
+      @@top_lab_code_descriptions[code]
+    end
+  end
+end

data/test/test_helper.rb

@@ -0,0 +1,9 @@
+require 'simplecov'
+require_relative '../lib/fhir_scorecard'
+
+require 'fhir_models'
+require 'fileutils'
+require 'pry'
+require 'minitest'
+require 'minitest/autorun'
+require 'bundler/setup'