health-data-standards 0.7.1 → 0.8.0

data/Gemfile

@@ -5,5 +5,13 @@ gemspec :development_group => :test
 group :development do
   gem 'rake'
   gem 'pry'
-  gem 'cover_me'
+  gem 'pry-nav'
+
+end
+
+group :test do
+  gem 'factory_girl'
+  gem "tailor"
+  gem "cane"
+  gem 'simplecov', :require => false
 end

data/Rakefile

@@ -1,4 +1,6 @@
 require 'rake/testtask'
+require 'cane/rake_task'
+require "simplecov"
 
 Rake::TestTask.new(:test_unit) do |t|
   t.libs << "test"
@@ -6,7 +8,15 @@ Rake::TestTask.new(:test_unit) do |t|
   t.verbose = true
 end
 
-task :test => [:test_unit] do
-  require 'cover_me'
-  CoverMe.complete!
-end
+Cane::RakeTask.new(:quality) do |cane|
+  cane.abc_max = 45
+  cane.add_threshold 'coverage/covered_percent', :>=, 97
+  cane.style_measure = 120
+  cane.no_style = true
+  cane.no_doc = true
+end
+
+task :test => [:test_unit, :quality] do
+
+  system("open coverage/index.html")
+end

data/lib/health-data-standards.rb

@@ -19,10 +19,14 @@ require_relative 'health-data-standards/export/rendering_context'
 require_relative 'health-data-standards/export/c32'
 require_relative 'health-data-standards/export/ccr'
 require_relative 'health-data-standards/export/csv'
+require_relative 'health-data-standards/export/html'
+require_relative 'health-data-standards/export/hdata/metadata'
 
 require_relative 'health-data-standards/export/green_c32/entry'
 require_relative 'health-data-standards/export/green_c32/export_generator'
 
+require_relative 'health-data-standards/import/provider_import_utils'
+require_relative 'health-data-standards/import/hdata/metadata_importer'
 
 require_relative 'health-data-standards/models/entry'
 require_relative 'health-data-standards/models/allergy'
@@ -37,10 +41,21 @@ require_relative 'health-data-standards/models/lab_result'
 require_relative 'health-data-standards/models/record'
 require_relative 'health-data-standards/models/provider'
 require_relative 'health-data-standards/models/provider_performance'
+require_relative 'health-data-standards/models/social_history'
+require_relative 'health-data-standards/models/vital_sign'
+require_relative 'health-data-standards/models/organization'
+require_relative 'health-data-standards/models/address'
+require_relative 'health-data-standards/models/telecom'
+require_relative 'health-data-standards/models/metadata/base'
+require_relative 'health-data-standards/models/metadata/author'
+require_relative 'health-data-standards/models/metadata/change_info'
+require_relative 'health-data-standards/models/metadata/link_info'
+require_relative 'health-data-standards/models/metadata/pedigree'
 
 require_relative 'health-data-standards/import/c32/section_importer'
 require_relative 'health-data-standards/import/c32/allergy_importer'
 require_relative 'health-data-standards/import/c32/encounter_importer'
+require_relative 'health-data-standards/import/c32/condition_importer'
 require_relative 'health-data-standards/import/c32/immunization_importer'
 require_relative 'health-data-standards/import/c32/medication_importer'
 require_relative 'health-data-standards/import/c32/procedure_importer'
@@ -48,6 +63,7 @@ require_relative 'health-data-standards/import/c32/result_importer'
 require_relative 'health-data-standards/import/c32/vital_sign_importer'
 require_relative 'health-data-standards/import/c32/patient_importer'
 require_relative 'health-data-standards/import/c32/provider_importer'
+require_relative 'health-data-standards/import/c32/organization_importer'
 
 require_relative 'health-data-standards/import/ccr/patient_importer'
 require_relative 'health-data-standards/import/ccr/provider_importer'
@@ -59,3 +75,10 @@ require_relative 'health-data-standards/import/ccr/product_importer'
 require_relative 'health-data-standards/import/green_c32/section_importer'
 require_relative 'health-data-standards/import/green_c32/result_importer'
 require_relative 'health-data-standards/import/green_c32/condition_importer'
+require_relative 'health-data-standards/import/green_c32/vital_sign_importer'
+require_relative 'health-data-standards/import/green_c32/procedure_importer'
+require_relative 'health-data-standards/import/green_c32/encounter_importer'
+require_relative 'health-data-standards/import/green_c32/medication_importer'
+require_relative 'health-data-standards/import/green_c32/allergy_importer'
+require_relative 'health-data-standards/import/green_c32/social_history_importer'
+require_relative 'health-data-standards/import/green_c32/immunization_importer'

data/lib/health-data-standards/export/ccr.rb

@@ -28,16 +28,17 @@ module HealthDataStandards
           end
           to_ccr_purpose(xml)
           xml.Body do
+            
             to_ccr_problems(xml, patient)
+            to_ccr_socialhistory(xml, patient)
             to_ccr_allergies(xml, patient)
+            
             to_ccr_medications(xml, patient)
             to_ccr_immunizations(xml, patient)
             to_ccr_vitals(xml, patient)
             to_ccr_results(xml, patient) 
             to_ccr_procedures(xml, patient)
-            to_ccr_encounters(xml, patient)
-            to_ccr_socialhistory(xml, patient)
-            
+            to_ccr_encounters(xml, patient)   
           end
           to_ccr_actors(xml, patient)
         end
@@ -83,13 +84,7 @@ module HealthDataStandards
             patient.conditions.each_with_index do |condition, index|
               xml.Problem do
                 xml.CCRDataObjectID("PR000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Start date")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(condition.time))
-                end
+                to_ccr_date(xml, condition.as_point_in_time, "Start date")
                 xml.Type do
                   #TODO: Need to fix this and not be a hard-coded value
                   xml.Text("Diagnosis")
@@ -114,13 +109,7 @@ module HealthDataStandards
             patient.encounters.each_with_index do |encounter, index|
               xml.Encounter do
                 xml.CCRDataObjectID("EN000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Encounter Date")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(encounter.time))
-                end
+                to_ccr_date(xml, encounter.as_point_in_time, "Encounter Date")
                 xml.Description do
                   xml.Text(encounter.description)
                   code_section(xml, encounter.codes)
@@ -163,14 +152,7 @@ module HealthDataStandards
      def to_result(xml, res, ccr_id )
        xml.Result do
          xml.CCRDataObjectID(ccr_id)
-         xml.DateTime do
-           xml.Type do
-             xml.Text("Start date")
-           end
-           #time
-           xml.ExactDateTime(convert_to_ccr_time_string(res.time))
-         end
-                 
+         to_ccr_date(xml, res.as_point_in_time, "Start date")       
          xml.Source
          xml.Test do
            xml.CCRDataObjectID("#{ccr_id}TestResult")
@@ -200,13 +182,7 @@ module HealthDataStandards
             patient.medications.each_with_index do |medication, index|
               xml.Medication do
                 xml.CCRDataObjectID("MD000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Prescription Date")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(medication.time))
-                end
+                to_ccr_date(xml, medication.as_point_in_time, "Prescription Date")  
                 xml.Type do
                   xml.Text("Medication")
                 end
@@ -235,13 +211,7 @@ module HealthDataStandards
             patient.immunizations.each_with_index do |immunization, index|
               xml.Immunization do
                 xml.CCRDataObjectID("IM000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Prescription Date")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(immunization.time))
-                end
+                to_ccr_date(xml, immunization.as_point_in_time, "Prescription Date")  
                 xml.Type do
                   xml.Text("Immunization")
                 end
@@ -272,13 +242,7 @@ module HealthDataStandards
             patient.procedures.each_with_index do |procedure, index|
               xml.Procedure do
                 xml.CCRDataObjectID("PR000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Service date")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(procedure.time))
-                end
+                to_ccr_date(xml, procedure.as_point_in_time, "Service date")  
                 xml.Description do
                   xml.Text(procedure.description)
                   code_section(xml, procedure.codes)
@@ -299,13 +263,7 @@ module HealthDataStandards
             patient.allergies.each_with_index do |allergy, index|
               xml.Alert do
                 xml.CCRDataObjectID("AL000#{index + 1}")
-                xml.DateTime do
-                  xml.Type do
-                    xml.Text("Initial Occurrence")
-                  end
-                  #time
-                  xml.ExactDateTime(convert_to_ccr_time_string(allergy.time))
-                end
+                to_ccr_date(xml, allergy.as_point_in_time, "Initial Occurrence")  
                 xml.Type do
                   xml.Text("Allergy")
                 end
@@ -339,9 +297,38 @@ module HealthDataStandards
                     code_section(xml, history.codes)
                   end
                 
-               
+                xml.Source
               end
             end
+            
+              if patient.race
+                xml.SocialHistoryElement do
+                  xml.CCRDataObjectID("SH000RACE")
+                   xml.Type do 
+                      xml.Text("Race")
+                    end       
+                    xml.Description do
+                   
+                      code_section(xml, {"2.16.840.1.113883.6.238"=>[patient.race["code"]]})
+                    end   
+                  xml.Source
+                end
+             end
+          
+             if patient.ethnicity
+                xml.SocialHistoryElement do
+                  xml.CCRDataObjectID("SH000ETHICITY")   
+                    xml.Type do 
+                      xml.Text("Ethnicity")  
+                    end                          
+                    xml.Description do
+                    
+                      code_section(xml, {"2.16.840.1.113883.6.238" => [patient.ethnicity["code"]]})
+                    end            
+                  xml.Source
+                end
+             end
+             
           end
         end
       end
@@ -404,8 +391,20 @@ module HealthDataStandards
       end
 
       def convert_to_ccr_time_string(time)
-        converted_time = Time.at(time)
-        converted_time.strftime("%Y-%m-%dT%H:%M:%SZ")
+          converted_time = Time.at(time)
+          converted_time.strftime("%Y-%m-%dT%H:%M:%SZ")
+      end
+
+      def to_ccr_date(xml, time, type)
+        if time
+          xml.DateTime do
+            xml.Type do
+              xml.Text(type)
+            end
+            #time
+            xml.ExactDateTime(convert_to_ccr_time_string(time))
+          end
+        end
       end
 
     end

data/lib/health-data-standards/export/hdata/metadata.rb

@@ -0,0 +1,16 @@
+module HealthDataStandards
+  module Export
+    module Hdata
+      module Metadata
+        include TemplateHelper
+
+        def export(entry, metadata)
+          self.template_format = "hdata"
+          render(:template => 'metadata', :locals => {entry: entry, metadata: metadata})
+        end
+        
+        extend self
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/html.rb

@@ -0,0 +1,21 @@
+module HealthDataStandards
+  module Export
+    module HTML
+      include TemplateHelper
+
+       def export(patient)
+        self.template_format = "html"
+        render(:template => 'show', :locals => {:patient => patient})
+      end
+
+      extend self
+
+
+     
+
+
+
+
+    end
+  end
+end

data/lib/health-data-standards/export/template_helper.rb

@@ -14,6 +14,8 @@ module HealthDataStandards
       def partial(partial_name)
         template("_#{partial_name}")
       end
+      
+
 
       def render(params)
         erb = nil
@@ -22,6 +24,7 @@ module HealthDataStandards
         elsif params[:partial]
           erb = partial(params[:partial])
         end
+        
         locals = params[:locals]
         locals ||= {}
         rendering_context = RenderingContext.new(locals)

data/lib/health-data-standards/export/view_helper.rb

@@ -3,24 +3,30 @@ module HealthDataStandards
     module ViewHelper
       def code_display(entry, options={})
         options['tag_name'] ||= 'code'
+        options['attribute'] ||= :codes
         code_string = nil
-        preferred_code = entry.preferred_code(options['preferred_code_sets'])
+        preferred_code = entry.preferred_code(options['preferred_code_sets'], options['attribute'])
         if preferred_code
           code_system_oid = HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(preferred_code['code_set'])
           code_string = "<#{options['tag_name']} code=\"#{preferred_code['code']}\" codeSystem=\"#{code_system_oid}\" #{options['extra_content']}>"
         else
           code_string = "<#{options['tag_name']} nullFlavor=\"UNK\" #{options['extra_content']}>"
         end
-        code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>"
-        entry.translation_codes(options['preferred_code_sets']).each do |translation|
-          code_string += "<translation code=\"#{translation['code']}\" codeSystem=\"#{HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(translation['code_set'])}\"/>\n"
+        
+        code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>" if entry.respond_to?(:description)
+        
+        if entry.respond_to?(:translation_codes)
+          entry.translation_codes(options['preferred_code_sets']).each do |translation|
+            code_string += "<translation code=\"#{translation['code']}\" codeSystem=\"#{HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(translation['code_set'])}\"/>\n"
+          end
         end
+        
         code_string += "</#{options['tag_name']}>"
         code_string
       end
       
       def status_code_for(entry)
-        case entry.status.to_s
+        case entry.status.to_s.downcase
         when 'active'
           '55561003'
         when 'inactive'
@@ -29,6 +35,24 @@ module HealthDataStandards
           '413322009'
         end
       end
+      
+      def value_or_null_flavor(time)
+        if time 
+          return "value='#{Time.at(time).utc.to_formatted_s(:number)}'"
+        else 
+         return "nullFlavor='UNK'"
+       end
+      end
+
+      
+      def quantity_display(value, tag_name="value")
+        return unless value
+        "<#{tag_name} value=\"#{value['value']}\" units=\"#{value['unit']}\" />"
+      end
+
+      def time_if_not_nil(*args)
+        args.compact.map {|t| Time.at(t)}.first
+      end
     end
   end
 end

data/lib/health-data-standards/import/c32/condition_importer.rb

@@ -4,9 +4,10 @@ module HealthDataStandards
       class ConditionImporter < SectionImporter
         
         def initialize
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.11']"
-          @code_xpath = "./cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
+          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.103']/cda:entry/cda:act/cda:entryRelationship/cda:observation"
+          @code_xpath = "./cda:value"
+          @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.50']/cda:value"
+          @description_xpath = "./cda:text/cda:reference[@value]"
         end
         
         def create_entries(doc, id_map = {})
@@ -19,47 +20,44 @@ module HealthDataStandards
             
             extract_codes(entry_element, condition)
             extract_dates(entry_element, condition)
+            extract_status(entry_element, condition)
             extract_description(entry_element, condition, id_map)
-            
-            condition.diagnosis_priority = extract_code(entry_element, "???")
-            
-            condition.problem_date = extract_code(entry_element, 
-              "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[@classCode='OBS']/cda.effectiveTime")
-              
-            condition.problem_type = extract_code(entry_element, 
-              "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[@classCode='OBS']")
-              
-            condition.problem_name = extract_code(entry_element, "./cda:text")
-
-            condition.problem_code = extract_code(entry_element, 
-              "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[@classCode='OBS']/cda:code[@code='11450-4']/cda:value[@codeSystem='2.16.840.1.113883.96']")
-            
-            condition.age_at_onset = extract_code(entry_element, "???")
-            
             extract_cause_of_death(entry_element, condition)
-            
-            condition.problem_status = extract_code(entry_element,
-              "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[@classCode='OBS']/cda:statusCode[@code='completed']")
+            extract_type(entry_element, condition)
+
+            entry_element.xpath("./cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:performer").each do |provider_element|
+              condition.treating_provider < import_actor(provider_element)
+            end
 
             condition_list << condition
           end
           
           condition_list
         end
-        
+
         private
-        
-        def extract_cause_of_death(parent_element, condition)
-          cause_of_death_element = parent_element.at_xpath("???")
-          
-          if cause_of_death_element
-            condition.cause_of_death = {}
-            
-            condition.cause_of_death[:time_of_death] = cause_of_death_element.xpath("???")
-            condition.cause_of_death[:age_at_death] = cause_of_death_element.xpath("???")
+
+        def extract_cause_of_death(entry_element, condition)
+          cod = entry_element.at_xpath("./cda:entryRelationship[@typeCode='CAUS']/cda:observation/cda:code[@code='419620001']")
+          condition.cause_of_death = cod.present?
+        end
+
+        def extract_type(entry_element, condition)
+          code_element = entry_element.at_xpath('./cda:code')
+          if code_element
+            condition.type = case code_element['code']
+                               when '404684003'  then 'Finding'
+                               when '418799008'  then 'Symptom'
+                               when '55607006'   then 'Problem'
+                               when '409586006'  then 'Complaint'
+                               when '64572001'   then 'Condition'
+                               when '282291009'  then 'Diagnosis'
+                               when '248536006'  then 'Functional limitation'
+                               else nil
+                             end
           end
         end
-        
+
       end
     end
   end