health-data-standards 3.3.0 → 3.4.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
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+  data.tar.gz: 93fc2151c1654a38fb0fbb0d550cddde76773079
+SHA512:
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data/README.md

@@ -25,6 +25,22 @@ Please try to follow the [GitHub Coding Style Guides](https://github.com/stylegu
 Change Log
 ==========
 
+3.4.0 - January 23, 2014
+
+* _New Feature_ - BulkRecordImporter class now available that provides the ability to import QRDA Cat I, Consolidated CDA and HITSP C32 
+* TemplateHelper now properly accepts a different directory for templates
+* QRDA Cat I importer now extracts negation on procedures
+* Implemented support to encounter transfers in QRDA Cat I import and export
+* Fixed bug where clinical trial participant would always return true on Record
+* QRDA Cat I importer now extracts ordinality and values from procedures
+* Better de-duplicating of data elements imported from QRDA Cat I
+* CDA importers now handle removal time on medical equipment
+* QRDA Cat I exporter now handles 38 week gestational period
+* Stratification fixes for QRDA Cat III export
+* QRDA Cat I importer now extracts incision date/time from procedure performed templates
+* CDA importers set admit times on encounters
+* QRDA Cat I diagnostic study order  and procedure order importer now better handles order time for CQM calculation
+
 3.3.0 - November 7, 2013
 
 * Removing hardcoded headers in QRDA documents and replacing them with templates populated by Ruby objects

data/lib/health-data-standards.rb

@@ -65,6 +65,7 @@ require_relative 'health-data-standards/models/person'
 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/transfer'
 require_relative 'health-data-standards/models/svs/value_set'
 require_relative 'health-data-standards/models/svs/concept'
 require_relative 'health-data-standards/models/facility'
@@ -164,6 +165,7 @@ require_relative 'health-data-standards/import/cat1/lab_order_importer'
 require_relative 'health-data-standards/import/cat1/medication_active_importer'
 require_relative 'health-data-standards/import/cat1/medication_dispensed_importer'
 require_relative 'health-data-standards/import/cat1/encounter_order_importer'
+require_relative 'health-data-standards/import/cat1/encounter_performed_importer'
 require_relative 'health-data-standards/import/cat1/diagnostic_study_order_importer'
 require_relative 'health-data-standards/import/cat1/tobacco_use_importer'
 require_relative 'health-data-standards/import/cat1/entry_package'
@@ -174,6 +176,7 @@ require_relative 'health-data-standards/import/cat1/insurance_provider_importer'
 
 require_relative 'health-data-standards/import/bundle/importer'
 
+require_relative 'health-data-standards/import/bulk_record_importer'
 
 module HealthDataStandards
   class << self

data/lib/health-data-standards/export/helper/cat1_view_helper.rb

@@ -41,7 +41,7 @@ module HealthDataStandards
           return nil if codedValue.nil?
           valueset_oids ||=[]
           code = codedValue["code"]
-          code_system = codedValue["code_set"]
+          code_system = codedValue["code_set"] || codedValue["code_system"]
           vs_map = (value_set_map(bundle_id) || {})
           valueset_oids.each do |vs_oid|
             oid_list = (vs_map[vs_oid] || [])

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

@@ -1,5 +1,6 @@
 module HealthDataStandards
   module Export
+
     # Used to actually render stuff. A RenderingContext needs to be set up with
     # a template helper and may be provided with extensions.
     #
@@ -51,8 +52,9 @@ module HealthDataStandards
               rendering_context.extend(extension)
             end
           end
-          eruby = Erubis::EscapedEruby.new(erb) # TODO: cache these
-          eruby.result(rendering_context.my_binding)
+            eruby = Erubis::EscapedEruby.new(erb) # TODO: cache these
+            eruby.filename=  @template_helper.template_file((params[:template] || params[:partial]), params[:partial]).path
+            eruby.result(rendering_context.my_binding)
         end.join
       end
     end

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

@@ -17,12 +17,12 @@ module HealthDataStandards
       end
 
       def template_root
-        @template_directory ||= File.dirname(__FILE__)
+        @template_directory ||= File.join(File.dirname(__FILE__), '..', '..', '..', 'templates')
 
         if @template_subdir
-          return File.join(@template_directory, '..', '..', '..', 'templates', @template_subdir)
+          return File.join(@template_directory, @template_subdir)
         else
-          return File.join(@template_directory, '..', '..', '..', 'templates')
+          return @template_directory
         end
       end
 
@@ -37,6 +37,12 @@ module HealthDataStandards
       def partial(partial_name)
         template("_#{partial_name}")
       end
+
+      def template_file(file,partial=false)
+        file = partial ? "_#{file}" : file
+        File.new(File.join(template_root, "#{file}.#{@template_format}.erb"))
+      end
+
     end
   end
 end

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

@@ -0,0 +1,88 @@
+require 'fileutils'
+module HealthDataStandards
+  module Import
+    class BulkRecordImporter
+
+      def self.import_directory(source_dir)
+
+        xml_files = Dir.glob(File.join(source_dir, '*.*'))
+        xml_files.each do |file|
+          begin
+            
+            result = RecordImporter.import(File.new(file).read, provider_map)
+            
+            if (result[:status] == 'success') 
+              record = result[:record]
+              record.save
+            else 
+              assert result[:message]
+            end
+            
+          rescue Exception => e
+            failed_dir = File.join(source_dir, '../', 'failed_imports')
+            unless(Dir.exists?(failed_dir))
+              Dir.mkdir(failed_dir)
+            end
+            FileUtils.cp(file, failed_dir)
+          end
+        end
+      end
+      
+      def self.import_archive(file) 
+        Zip::ZipFile.open(file.path) do |zipfile|
+          zipfile.entries.each do |entry|
+            next if entry.directory?
+            xml = zipfile.read(entry.name)
+            begin
+              BulkRecordImporter.import(xml)
+            rescue Exception => e
+              failed_dir = File.join(file.dirname, 'failed_imports')
+              unless(Dir.exists?(failed_dir))
+                Dir.mkdir(failed_dir)
+              end
+              FileUtils.cp(file, failed_dir)
+            end
+          end
+        end
+      end
+      
+      def self.import(xml_data, provider_map = {})
+        doc = Nokogiri::XML(xml_data)
+        
+        providers = []
+        root_element_name = doc.root.name
+        
+        if root_element_name == 'ClinicalDocument'
+          doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
+          doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
+
+          if doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.3.88.11.32.1']")
+            patient_data = C32::PatientImporter.instance.parse_c32(doc)
+          elsif doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.10.20.22.1.2']")
+            patient_data = CCDA::PatientImporter.instance.parse_ccda(doc)
+          elsif doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.10.20.24.1.2']")
+            patient_data = Cat1::PatientImporter.instance.parse_cat1(doc)
+          else
+            STDERR.puts("Unable to determinate document template/type of CDA document")
+            return {status: 'error', message: "Document templateId does not identify it as a C32 or CCDA", status_code: 400}
+          end
+          
+          begin
+            providers = CDA::ProviderImporter.instance.extract_providers(doc)
+          rescue Exception => e
+            STDERR.puts "error extracting providers"
+          end
+        else
+          return {status: 'error', message: 'Unknown XML Format', status_code: 400}
+        end
+
+        record = Record.update_or_create(patient_data)
+        record.provider_performances = providers
+        record.save
+        
+        {status: 'success', message: 'patient imported', status_code: 201, record: record}
+
+      end
+    end
+  end
+end

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

@@ -11,7 +11,7 @@ module HealthDataStandards
 
         def extract_dates(parent_element, entry, element_name="author")
           if parent_element.at_xpath("cda:#{element_name}/cda:time/@value")
-            entry.start_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
+            entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
           end
         end
       end

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

@@ -0,0 +1,38 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class EncounterPerformedImporter < CDA::EncounterImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']"))
+          super(entry_finder)
+          @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation"
+        end
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          encounter = super
+          extract_admit_time(entry_element, encounter)
+          extract_reason(entry_element, encounter, nrh)
+          encounter
+        end
+
+        private
+
+        def extract_reason(parent_element, encounter, nrh)
+          reason_element = parent_element.at_xpath(@reason_xpath)
+          if reason_element
+            reason = Entry.new
+            extract_codes(reason_element, reason)
+            extract_reason_description(reason_element, reason, nrh)
+            extract_status(reason_element, reason)
+            extract_dates(reason_element, reason)
+            encounter.reason = reason
+          end
+        end
+
+        def extract_admit_time(parent_element, encounter)
+          encounter.admit_time = encounter.start_time
+        end
+
+      end
+    end
+  end
+end

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

@@ -38,7 +38,7 @@ module HealthDataStandards
                                              generate_importer(CDA::ProcedureImporter, "//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(CDA::ProcedureImporter, "//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(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
+                                             generate_importer(ProcedurePerformedImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
                                              generate_importer(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
                                              generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'),
                                              generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
@@ -59,7 +59,7 @@ module HealthDataStandards
                                           generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.20']", '2.16.840.1.113883.3.560.1.111'), #diagnostic study result not done
                                           generate_importer(LabResultImporter, nil, '2.16.840.1.113883.3.560.1.12')] #lab result
 
-          @section_importers[:encounters] = [generate_importer(CDA::EncounterImporter, "//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
+          @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
                                              generate_importer(EncounterOrderImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered')]
 
           @section_importers[:social_history] = [generate_importer(TobaccoUseImporter, nil, '2.16.840.1.113883.3.560.1.1001', 'completed')]
@@ -90,7 +90,7 @@ module HealthDataStandards
 
         def get_clinical_trial_participant(record, doc)
           entry_elements = doc.xpath("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.51']")
-          record.clinicalTrialParticipant = true unless entry_elements.nil? 
+          record.clinicalTrialParticipant = true unless entry_elements.blank?
         end
 
         def get_patient_expired(record, doc)
@@ -111,4 +111,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

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

@@ -6,7 +6,7 @@ module HealthDataStandards
           super(entry_finder)
           @entry_class = Procedure
         end
-        
+
         def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
           procedure = super
           procedure.status_code = {'HL7 ActStatus' => ['ordered']}
@@ -20,7 +20,7 @@ module HealthDataStandards
 
         def extract_dates(parent_element, entry, element_name="author")
           if parent_element.at_xpath("cda:#{element_name}/cda:time/@value")
-            entry.start_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
+            entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
           end
         end
 

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

@@ -13,6 +13,7 @@ module HealthDataStandards
           procedure = super
           extract_ordinality(entry_element, procedure)
           extract_incision_date_time(entry_element,procedure)
+          extract_negation(entry_element, procedure)
           procedure
         end
 

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

@@ -8,7 +8,6 @@ module HealthDataStandards
           @code_xpath = "./cda:participant/cda:participantRole/cda:playingEntity/cda:code"
           @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
           @type_xpath = "./cda:code"
-          @free_text_xpath= "./cda:participant/cda:participantRole/cda:playingEntity/cda:name"
           @reaction_xpath = "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.54']/cda:value"
           @severity_xpath = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.55']/cda:value"
           @status_xpath   = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.39']/cda:value"
@@ -17,7 +16,6 @@ module HealthDataStandards
     
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           allergy = super
-          allergy.free_text = entry_element.at_xpath(@free_text_xpath).try(:text)
           extract_negation(entry_element, allergy)
           allergy.type = extract_code(entry_element, @type_xpath)
           allergy.reaction = extract_code(entry_element, @reaction_xpath)

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

@@ -18,6 +18,7 @@ module HealthDataStandards
           extract_negation(entry_element, encounter)
           extract_admission(entry_element, encounter)
           extract_discharge_disposition(entry_element, encounter)
+          extract_transfers(entry_element, encounter)
           encounter
         end
     
@@ -45,7 +46,7 @@ module HealthDataStandards
           if reason_element
             reason = Entry.new
             extract_codes(reason_element, reason)
-            extract_description(reason_element, reason, nrh)
+            extract_reason_description(reason_element, reason, nrh)
             extract_status(reason_element, reason)
             extract_dates(reason_element, reason)
             encounter.reason = reason
@@ -60,6 +61,28 @@ module HealthDataStandards
           encounter.discharge_time = encounter.end_time
           encounter.discharge_disposition = extract_code(parent_element, "./sdtc:dischargeDispositionCode")
         end
+
+        def extract_transfers(parent_element, encounter)
+          transfer_from_element = parent_element.at_xpath("./cda:participant[@typeCode='ORG']")
+          if (transfer_from_element)
+            transfer_from = Transfer.new(time: transfer_from_element.at_xpath("./cda:time")['value'])
+            transfer_from_subelement = transfer_from_element.at_xpath("./cda:participantRole[@classCode='LOCE']")
+            raw_tf_code = extract_code(transfer_from_subelement, './cda:code')
+            code_hash = {CodeSystemHelper.code_system_for(raw_tf_code["codeSystemOid"]) => [raw_tf_code["code"]]}
+            transfer_from.codes = code_hash
+            encounter.transfer_from = transfer_from
+          end
+
+          transfer_to_element = parent_element.at_xpath("./cda:participant[@typeCode='DST']")
+          if (transfer_to_element)
+            transfer_to = Transfer.new(time: transfer_to_element.at_xpath("./cda:time")['value'])
+            transfer_to_subelement = transfer_to_element.at_xpath("./cda:participantRole[@classCode='LOCE']")
+            raw_tt_code = extract_code(transfer_to_subelement, './cda:code')
+            code_hash = {CodeSystemHelper.code_system_for(raw_tt_code["codeSystemOid"]) => [raw_tt_code["code"]]}
+            transfer_to.codes = code_hash
+            encounter.transfer_to = transfer_to
+          end
+        end
       end
     end
   end

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

@@ -13,6 +13,7 @@ module HealthDataStandards
           medical_equipment = super
           extract_manufacturer(entry_element, medical_equipment)
           extract_anatomical_structure(entry_element, medical_equipment)
+          extract_removal_time(entry_element, medical_equipment)
           medical_equipment
         end
 
@@ -21,7 +22,13 @@ module HealthDataStandards
           entry.manufacturer = manufacturer.strip if manufacturer
         end
 
-        def extract_anatomical_structure(entry_element, entry) 
+        def extract_removal_time(entry_element, entry)
+          if entry_element.at_xpath("cda:effectiveTime/cda:high")
+            entry.removal_time = HL7Helper.timestamp_to_integer(entry_element.at_xpath("cda:effectiveTime/cda:high")['value'])
+          end
+        end
+
+        def extract_anatomical_structure(entry_element, entry)
           site = entry_element.at_xpath(@anatomical_xpath)
           if site
             entry.anatomical_structure = {CodeSystemHelper.code_system_for(site['codeSystem']) => [site['code']]}

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

@@ -25,10 +25,6 @@ module HealthDataStandards
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           medication = super
           
-          if medication.description.present?
-            medication.free_text = medication.description
-          end
-          
           extract_administration_timing(entry_element, medication)
           
           medication.route = extract_code(entry_element, "./cda:routeCode")

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

@@ -8,19 +8,29 @@ module HealthDataStandards
         def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root!='2.16.840.1.113883.3.88.11.83.124']//cda:procedure"))
           super(entry_finder)
           @entry_class = Procedure
-          @value_xpath = nil
+          @value_xpath = ".//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.87']/cda:value"
+          @ordinality_xpath = "./cda:priorityCode"
         end
-        
+
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           procedure = super
+          extract_ordinality(entry_element, procedure)
           extract_performer(entry_element, procedure)
           extract_site(entry_element, procedure)
           extract_negation(entry_element, procedure)
+          extract_scalar(entry_element, procedure)
           procedure
         end
 
         private
 
+        def extract_ordinality(parent_element, procedure)
+          ordinality_element = parent_element.at_xpath(@ordinality_xpath)
+          if ordinality_element
+            procedure.ordinality = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
+          end
+        end
+
         def extract_performer(parent_element, procedure)
           performer_element = parent_element.at_xpath("./cda:performer")
           procedure.performer = import_actor(performer_element) if performer_element
@@ -30,6 +40,17 @@ module HealthDataStandards
           procedure.site = extract_code(parent_element, "./cda:targetSiteCode")
         end
 
+        def extract_scalar(parent_element, procedure)
+          return unless scalar_element = parent_element.at_xpath("./cda:value")
+          case scalar_element["xsi:type"]
+          when "PQ"
+            procedure.set_value scalar_element['value'].to_i, scalar_element['unit']
+          when "BL"
+            procedure.set_value scalar_element['value']
+          when "ST"
+            procedure.set_value scalar_element.content
+          end
+        end
       end
     end
   end