health-data-standards 3.5.3 → 3.6.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 758234c177f32a11c9606258a38bf83387fe2fb9
+  metadata.gz: 59b91fc289603c22a9152c776bebee15f193f70e
+  data.tar.gz: cde5d51f408a2eb237bd1ed632a2383936bc5631
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+  data.tar.gz: 9df5f732d24fc1f85232e13debff907f2afb82d41850301d865279b3a185bd984cc0806b1673005e4a0fd16705b3d96b2080921c4dadcd4bb3ecf3443c0268b1

data/Gemfile

@@ -1,12 +1,11 @@
-source "http://rubygems.org"
+source "https://rubygems.org"
 
 gemspec :development_group => :test
 
 group :development do
   gem 'rake'
   gem 'pry', '~> 0.9.10'
-  gem 'pry-nav', '~> 0.2.2'
-
+  gem 'pry-nav', '~> 0.2.2', platforms: [:ruby_21, :ruby_22]
 end
 
 group :test do

data/README.md

@@ -1,11 +1,11 @@
-This is a project to generate and consume HITSP C32, ASTM CCR, QRDA Category I, QRDA Category III and PQRI.
+This is a project to generate and consume HITSP C32, QRDA Category I, and QRDA Category III.
 
 In addition this project also contains libraries for parsing HQMF documents and for dealing with NLM valuesets.
 
 Environment
 ===========
 
-This project currently uses Ruby 1.9.3, Ruby 2.0.0, Ruby 2.1.1 and JRuby 1.7.11 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
+This project currently uses Ruby 2.0.0, Ruby 2.1.1, Ruby 2.2.1, and JRuby 1.7.11 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
 
     gem install bundler
 
@@ -29,6 +29,14 @@ Change Log
 
 * Upgrading to mongoid 4
 
+* 3.6.0
+
+* Support for QRDA Cat I R3
+* Additional validators for QRDA Cat I/III
+* Removed GC32 & CCR code
+* Support latest QDM changes
+* Additional support for running in JRuby
+
 3.5.3 - January 20, 2015
 
 * Support for 2014 QRDA Errata Release

data/lib/health-data-standards.rb

@@ -26,15 +26,9 @@ require_relative 'health-data-standards/export/view_helper'
 require_relative 'health-data-standards/export/rendering_context'
 require_relative 'health-data-standards/export/c32'
 require_relative 'health-data-standards/export/ccda'
-require_relative 'health-data-standards/export/ccr'
 require_relative 'health-data-standards/export/csv'
 require_relative 'health-data-standards/export/hdata/metadata'
 
-require_relative 'health-data-standards/export/helper/gc32_view_helper'
-require_relative 'health-data-standards/export/green_c32/record'
-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'
 
@@ -43,6 +37,7 @@ require_relative 'health-data-standards/models/result_value'
 require_relative 'health-data-standards/models/coded_result_value'
 require_relative 'health-data-standards/models/physical_quantity_result_value'
 require_relative 'health-data-standards/models/cda_identifier'
+require_relative 'health-data-standards/models/reference'
 require_relative 'health-data-standards/models/entry'
 require_relative 'health-data-standards/models/allergy'
 require_relative 'health-data-standards/models/encounter'
@@ -99,6 +94,7 @@ require_relative 'health-data-standards/export/helper/html_view_helper'
 require_relative 'health-data-standards/export/html'
 require_relative 'health-data-standards/export/helper/cat1_view_helper'
 require_relative 'health-data-standards/export/cat_1'
+require_relative 'health-data-standards/export/cat_1_r2'
 require_relative 'health-data-standards/export/cat_3'
 
 require_relative 'health-data-standards/import/cda/narrative_reference_handler'
@@ -122,13 +118,6 @@ require_relative 'health-data-standards/import/c32/patient_importer'
 require_relative 'health-data-standards/import/c32/insurance_provider_importer'
 require_relative 'health-data-standards/import/c32/care_goal_importer'
 
-require_relative 'health-data-standards/import/ccr/patient_importer'
-require_relative 'health-data-standards/import/ccr/provider_importer'
-require_relative 'health-data-standards/import/ccr/section_importer'
-require_relative 'health-data-standards/import/ccr/result_importer'
-require_relative 'health-data-standards/import/ccr/simple_importer'
-require_relative 'health-data-standards/import/ccr/product_importer'
-
 require_relative 'health-data-standards/import/ccda/patient_importer'
 require_relative 'health-data-standards/import/ccda/allergy_importer'
 require_relative 'health-data-standards/import/ccda/condition_importer'
@@ -142,21 +131,6 @@ require_relative 'health-data-standards/import/ccda/care_goal_importer'
 require_relative 'health-data-standards/import/ccda/medical_equipment_importer'
 require_relative 'health-data-standards/import/ccda/insurance_provider_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'
-require_relative 'health-data-standards/import/green_c32/support_importer'
-require_relative 'health-data-standards/import/green_c32/advance_directive_importer'
-require_relative 'health-data-standards/import/green_c32/medical_equipment_importer'
-require_relative 'health-data-standards/import/green_c32/care_goal_importer'
-
 require_relative 'health-data-standards/import/cat1/gestational_age_importer'
 require_relative 'health-data-standards/import/cat1/procedure_intolerance_importer'
 require_relative 'health-data-standards/import/cat1/procedure_performed_importer'
@@ -176,11 +150,14 @@ require_relative 'health-data-standards/import/cat1/lab_result_importer'
 require_relative 'health-data-standards/import/cat1/ecog_status_importer'
 require_relative 'health-data-standards/import/cat1/symptom_active_importer'
 require_relative 'health-data-standards/import/cat1/insurance_provider_importer'
+require_relative 'health-data-standards/import/cat1/procedure_importer'
 
 require_relative 'health-data-standards/import/bundle/importer'
 
 require_relative 'health-data-standards/import/bulk_record_importer'
 
+require_relative 'health-data-standards/validate/validators'
+
 module HealthDataStandards
   class << self
     attr_accessor :logger

data/lib/health-data-standards/export/cat_1.rb

@@ -9,9 +9,10 @@ module HealthDataStandards
       end
 
       @@vs_map = nil
-      def export(patient, measures, start_date, end_date, header=nil)
+      def export(patient, measures, start_date, end_date, header=nil, r2_compatibility=false)
         @rendering_context.render(:template => 'show', :locals => {:patient => patient, :measures => measures,
-                                                :start_date => start_date, :end_date => end_date, :header => header})
+						:start_date => start_date, :end_date => end_date, :header => header,
+						:r2_compatibility => r2_compatibility})
       end
     end
   end

data/lib/health-data-standards/export/cat_1_r2.rb

@@ -0,0 +1,11 @@
+# require_relative 'cat_1'
+
+module HealthDataStandards
+  module Export
+    class Cat1R2 < Cat1
+      def export(patient, measures, start_date, end_date, header=nil, r2_compatibiliy=true)
+        super(patient, measures, start_date, end_date, header, r2_compatibiliy)
+      end
+    end
+  end
+end

data/lib/health-data-standards/ext/node.rb

@@ -10,7 +10,6 @@ if RUBY_PLATFORM.include?('java')
       NAMESPACES = {'cda' => 'urn:hl7-org:v3',
                 'sdtc' => 'urn:hl7-org:sdtc',
                 'gc32' => 'urn:hl7-org:greencda:c32',
-                'ccr' => 'urn:astm-org:CCR',
                 'vs' => 'urn:ihe:iti:svs:2008',
                 'xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
                 'hrf-md' => 'http://www.hl7.org/schemas/hdata/2009/11/metadata',
@@ -43,4 +42,4 @@ if RUBY_PLATFORM.include?('java')
       end
     end
   end
-end
+end

data/lib/health-data-standards/import/bulk_record_importer.rb

@@ -7,7 +7,7 @@ module HealthDataStandards
         failed_dir ||= File.join(source_dir, '../', 'failed_imports')
         files = Dir.glob(File.join(source_dir, '*.*'))
         files.each do |file|
-           BulkRecordImporter.import_file(file,File.new(file).read,failed_dir)
+	   self.import_file(file,File.new(file).read,failed_dir)
         end
       end
 
@@ -27,7 +27,7 @@ module HealthDataStandards
             end
             next if entry.directory?
             data = zipfile.read(entry.name)
-            BulkRecordImporter.import_file(entry.name,data,failed_dir)
+	    self.import_file(entry.name,data,failed_dir)
           end
         end
 
@@ -60,9 +60,9 @@ module HealthDataStandards
         begin
           ext = File.extname(name)
           if ext == ".json"
-            BulkRecordImporter.import_json(data)
+	    self.import_json(data)
           else
-            BulkRecordImporter.import(data)
+	    self.import(data)
           end
         rescue
           FileUtils.mkdir_p(File.dirname(File.join(failed_dir,name)))

data/lib/health-data-standards/import/bundle/importer.rb

@@ -132,12 +132,74 @@ module HealthDataStandards
           entries.each_with_index do |entry, index|
             patient = Record.new(unpack_json(entry))
             patient['bundle_id'] = bundle.id
+
+            #index
+            source_data_with_references = Array.new
+            source_data_reference_id_hash = Hash.new
+            source_data_id_hash = Hash.new
+            index = 0
+            #loops through source data criteria, if there are references adds ids to hash
+            patient['source_data_criteria'].each do |data_criteria|
+              source_data_id_hash[data_criteria['criteria_id']] = index
+              if data_criteria['references'] != nil
+                source_data_with_references.push(index)
+                reference_ids = Array.new
+                data_criteria['references'].each do |reference|
+                  reference_ids.push(reference['reference_id'])
+                end
+                source_data_reference_id_hash[data_criteria['criteria_id']] = reference_ids
+              end
+              index = index + 1
+            end
+            #if there are references, id references are reestablished
+            if source_data_with_references.size > 0
+              reconnect_references(patient, source_data_with_references, source_data_reference_id_hash, source_data_id_hash)
+            end
             patient.save
             report_progress('patients', (index*100/entries.length)) if index%10 == 0
           end
           puts "\rLoading: Patients Complete          "
         end
 
+        #bit of a hack here, equality is made by date and codes
+        def self.compare_and_update_entries(patient, reference_id, start_date, end_date, codes)
+          patient.entries.each do |entry|
+            # if dates and codes match then replace id with original
+            if compare_dates(entry, start_date, end_date)
+              if entry.codes == codes
+                entry._id = BSON::ObjectId.from_string(reference_id)
+              end
+            end
+          end
+        end
+
+        def self.compare_dates(entry, start_date, end_date)
+          if entry.start_time * 1000 ==  start_date
+            if entry.end_time == nil 
+              if end_date == nil
+                return true
+              else 
+                return false
+              end
+            else entry.end_time * 1000 == end_date
+              return true   
+            end
+          end
+          return false
+        end
+
+        def self.reconnect_references(patient, source_data_with_references, source_data_reference_id_hash, source_data_id_hash)
+
+          source_data_with_references.each do |source_data_with_reference|
+            #only do this with the references
+            sdc = patient['source_data_criteria'][source_data_with_reference]
+            source_data_reference_id_hash[sdc['criteria_id']].each do |ref_criteria_id|
+              ref_sdc = patient['source_data_criteria'][source_data_id_hash[ref_criteria_id]]
+              compare_and_update_entries(patient, ref_sdc['coded_entry_id'],ref_sdc['start_date'],ref_sdc['end_date'],ref_sdc['codes'])
+            end
+          end
+        end
+
         def self.unpack_and_store_valuesets(zip, bundle)
           entries = zip.glob(SOURCE_ROOTS[:valuesets])
           entries.each_with_index do |entry, index|

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

@@ -2,13 +2,13 @@ module HealthDataStandards
   module Import
     module C32
       class InsuranceProviderImporter < CDA::SectionImporter
-        
+
         def initialize(entry_finder=CDA::EntryFinder.new("//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.26']"))
           super(entry_finder)
           @check_for_usable = false # needs to be this way becase InsuranceProvider does not respond
                                     # to usable?
         end
-        
+
         def create_entry(payer_element, nrh = CDA::NarrativeReferenceHandler.new)
           ip = InsuranceProvider.new
           type = extract_code(payer_element, "./cda:code")
@@ -21,25 +21,27 @@ module HealthDataStandards
           name = payer_element.at_xpath("./cda:entryRelationship[@typeCode='REFR']/cda:act[@classCode='ACT' and @moodCode='DEF']/cda:text")
           ip.name = name.try(:text)
           patient_element = member_info_element.at_xpath("./cda:participantRole[@classCode='PAT']")
-          ip.member_id = patient_element.at_xpath("./cda:id")
-          ip.relationship = extract_code(patient_element, "./cda:code")
+          if patient_element
+            ip.member_id = patient_element.at_xpath("./cda:id")
+            ip.relationship = extract_code(patient_element, "./cda:code")
+          end
           ip.financial_responsibility_type = extract_code(payer_element, "./cda:performer/cda:assignedEntity/cda:code")
           ip
         end
-        
+
         def extract_guarantors(guarantor_elements)
           guarantor_elements.map do |guarantor_element|
             guarantor = Guarantor.new
-            extract_dates(guarantor_element, guarantor, element_name="time")
+            extract_dates(guarantor_element, guarantor, "time")
             guarantor_entity = guarantor_element.at_xpath("./cda:assignedEntity")
             guarantor.person = import_person(guarantor_entity.at_xpath("./cda:assignedPerson"))
             guarantor.organization = import_organization(guarantor_entity.at_xpath("./cda:representedOrganization"))
             guarantor
           end
         end
-        
+
       end
     end
   end
-  
+
 end

data/lib/health-data-standards/import/cat1/patient_importer.rb

@@ -35,7 +35,7 @@ module HealthDataStandards
                                              generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']", '2.16.840.1.113883.3.560.1.45', 'ordered'), #intervention ordered
                                              generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']", '2.16.840.1.113883.3.560.1.46', 'performed'), #intervention performed
                                              generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
-                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']", '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
+                                             generate_importer(Cat1::ProcedureImporter, nil, '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
                                              generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']", '2.16.840.1.113883.3.560.1.30'), #comm from patient to provider
                                              generate_importer(ProcedureOrderImporter, nil, '2.16.840.1.113883.3.560.1.62', 'ordered'),
                                              generate_importer(ProcedurePerformedImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
@@ -56,7 +56,8 @@ module HealthDataStandards
                                           generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']", '2.16.840.1.113883.3.560.1.5', 'performed'), #lab performed
                                           generate_importer(CDA::ResultImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
                                           generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.57']", '2.16.840.1.113883.3.560.1.18'), #physical exam finding
-                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result    
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result  
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.26']", '2.16.840.1.113883.3.560.1.85'),  #functional status, performed
                                           generate_importer(LabResultImporter, nil, '2.16.840.1.113883.3.560.1.12')] #lab result
 
           @section_importers[:encounters] = [generate_importer(EncounterPerformedImporter, "./cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']", '2.16.840.1.113883.3.560.1.79', 'performed'), #encounter performed
@@ -85,7 +86,6 @@ module HealthDataStandards
           nrh.build_id_map(doc)
           @section_importers.each do |section, entry_packages|
             entry_packages.each do |entry_package|
-              # binding.pry if section == :results
               record.send(section) << entry_package.package_entries(context, nrh)
             end
           end

data/lib/health-data-standards/import/cat1/procedure_importer.rb

@@ -0,0 +1,42 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class ProcedureImporter < CDA::ProcedureImporter
+
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']"))
+          super(entry_finder)
+          @reference_xpath = "./sdtc:inFulfillmentOf1"
+        end
+
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          procedure = super
+          extract_references(entry_element, procedure)
+          procedure
+        end
+
+        private
+
+        def extract_references(parent_element, entry)
+          parent_element.xpath(@reference_xpath).each do |ref_xml|
+            ref = Reference.new
+            ref.type = case ref_xml.at_xpath("./@typeCode").value
+            when "FLFS"
+              "fulfills"
+            end
+            ref.referenced_type = case ref_xml.at_xpath("./sdtc:actReference/@classCode").value
+            when "ACT"
+              "Procedure"
+            end
+            id_element = ref_xml.at_xpath("./sdtc:actReference/sdtc:id")
+            identifier = CDAIdentifier.new
+            identifier.root = id_element['root']
+            identifier.extension = id_element['extension']
+            ref.referenced_id = identifier
+            entry.references << ref
+          end
+        end
+
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cda/medication_importer.rb

@@ -1,7 +1,7 @@
 module HealthDataStandards
   module Import
     module CDA
-      
+
       # TODO: Coded Product Name, Free Text Product Name, Coded Brand Name and Free Text Brand name need to be pulled out separatelty
       #       This would mean overriding extract_codes
       # TODO: Patient Instructions needs to be implemented. Will likely be a reference to the narrative section
@@ -24,26 +24,26 @@ module HealthDataStandards
 
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           medication = super
-          
+
           extract_administration_timing(entry_element, medication)
-          
+
           medication.route = extract_code(entry_element, "./cda:routeCode")
           medication.dose = extract_scalar(entry_element, "./cda:doseQuantity")
           medication.site = extract_code(entry_element, "./cda:approachSiteCode", 'SNOMED-CT')
-          
+
           extract_dose_restriction(entry_element, medication)
-          
+
           medication.product_form = extract_code(entry_element, "./cda:administrationUnitCode", 'NCI Thesaurus')
           medication.delivery_method = extract_code(entry_element, "./cda:code", 'SNOMED-CT')
           medication.type_of_medication = extract_code(entry_element, @type_of_med_xpath, 'SNOMED-CT') if @type_of_med_xpath
           medication.indication = extract_code(entry_element, @indication_xpath, 'SNOMED-CT')
           medication.vehicle = extract_code(entry_element, @vehicle_xpath, 'SNOMED-CT')
-          
+
           extract_order_information(entry_element, medication)
-          
+
           extract_fulfillment_history(entry_element, medication)
           extract_negation(entry_element, medication)
-          
+
           medication
         end
 
@@ -68,20 +68,20 @@ module HealthDataStandards
             end
           end
         end
-    
+
         def extract_order_information(parent_element, medication)
           order_elements = parent_element.xpath("./cda:entryRelationship[@typeCode='REFR']/cda:supply[@moodCode='INT']")
           if order_elements
             order_elements.each do |order_element|
               order_information = OrderInformation.new
               actor_element = order_element.at_xpath('./cda:author')
-              if actor_element
+              if actor_element && Mongoid.configured? # Also make sure we can look up providers
                 order_information.provider = ProviderImporter.instance.extract_provider(actor_element, "assignedAuthor")
               end
               order_information.order_number = order_element.at_xpath('./cda:id').try(:[], 'root')
               order_information.fills = order_element.at_xpath('./cda:repeatNumber').try(:[], 'value').try(:to_i)
               order_information.quantity_ordered = extract_scalar(order_element, "./cda:quantity")
-          
+
               medication.orderInformation << order_information
             end
           end