cqm-reports 2.0.5 → 2.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: dd0b9911f4358fceaa323afe6557281f181c2357
-  data.tar.gz: 2c2ba002d028ff2870fb7d6622231984611d0b9d
+  metadata.gz: 6af15ff075a9533c61c844f95c5adc741e999dec
+  data.tar.gz: 2cf3f0aeb6c3e1744e5e2f8a45a8d0e90a1ab5a1
 SHA512:
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-  data.tar.gz: d37767e44596b127a5ea5197cb9c18dcdb36450661c23817ca84366e9a04ab7eebe4744d4e26e69682c76f4dd82bcd237667d46138cb4ec32f85a2b710b0df83
+  metadata.gz: a4ab0c6c763b00dfa1c7985110969e6262ecc977d9a6509ca64c82e3979e6fd6e27f1bd888ae05ac5eaeecf600645a7cfea95d7013f8a5b01d1b85e865d80f52
+  data.tar.gz: fdfe64bbfb95f37e11dae78380147076daeb9b155a05eadb663c063191ffb9155390af0ae32a6f9643d87d852d605a87cb6fd48c4dc1cf0c9f631a7f929c4538

data/Gemfile

@@ -28,6 +28,5 @@ group :test do
   gem 'minitest', '~> 5.3'
   gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
-  gem 'cqm-validators'
   gem 'nokogiri-diff'
 end

data/README.md

@@ -18,6 +18,33 @@ Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning ha
 
 For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-validators/tags).
 
+=======
+Importing QRDA
+==========
+
+A QRDA document can be imported into a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following commands.
+
+        doc = Nokogiri::XML(file)
+        patient, warnings = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
+
+Exporting QRDA Category I
+==========
+
+Exporting a QRDA document from a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following command.
+
+        Qrda1R5.new(patient, measures, options).render
+* patient is a [CQM::Patient](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/patient.rb)
+* measures is an array of [CQM::Measure](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/measure.rb)
+* options is a hash that can be used to pass in:
+  * provider
+  * patient_addresses
+  * patient_telecoms
+  * start_time
+  * end_time
+  * submission_program 
+
+QRDA export requires the [mustache](https://github.com/mustache/mustache) gem 
+
 ## License
 
 Copyright 2019 The MITRE Corporation

data/lib/cqm_report.rb

@@ -18,7 +18,6 @@ require_relative 'html-export/qdm-patient/qdm_patient.rb'
 require_relative 'qrda-export/catI-r5/qrda1_r5.rb'
 require_relative 'qrda-export/catIII-r2-1/qrda3_r21.rb'
 
-require_relative 'qrda-import/entry_package.rb'
 require_relative 'qrda-import/cda_identifier.rb'
 require_relative 'qrda-import/narrative_reference_handler.rb'
 require_relative 'qrda-import/entry_finder.rb'

data/lib/qrda-export/catI-r5/_header.mustache

@@ -6,9 +6,9 @@
 <!-- QRDA templateId -->
 <templateId root="2.16.840.1.113883.10.20.24.1.1" extension="2017-08-01"/>
 <!-- QDM-based QRDA templateId -->
-<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="2017-08-01"/>
+<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="2018-10-01"/>
 <!-- CMS QRDA templateId -->
-<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="2018-02-01"/>
+<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="2019-02-01"/>
 <!-- This is the globally unique identifier for this QRDA document -->
 <id root="{{random_id}}"/>
 <!-- QRDA document type code -->

data/lib/qrda-export/catI-r5/qrda1_r5.mustache

@@ -12,8 +12,8 @@
           <!-- This is the templateId for Patient Data section -->
           <templateId root="2.16.840.1.113883.10.20.17.2.4"/>
           <!-- This is the templateId for Patient Data QDM section -->
-          <templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.2.1"/>
-          <templateId extension="2018-02-01" root="2.16.840.1.113883.10.20.24.2.1.1"/>
+          <templateId extension="2018-10-01" root="2.16.840.1.113883.10.20.24.2.1"/>
+          <templateId extension="2019-02-01" root="2.16.840.1.113883.10.20.24.2.1.1"/>
           <code code="55188-7" codeSystem="2.16.840.1.113883.6.1"/>
           <title>Patient Data</title>
           <text/>

data/lib/qrda-export/catI-r5/qrda1_r5.rb

@@ -13,11 +13,33 @@ class Qrda1R5 < Mustache
     @qdmPatient = patient.qdmPatient
     @measures = measures
     @provider = options[:provider]
+    @patient_address_option = options[:patient_addresses]
+    @patient_telecom_option = options[:patient_telecoms]
     @performance_period_start = options[:start_time]
     @performance_period_end = options[:end_time]
     @submission_program = options[:submission_program]
   end
 
+  def patient_addresses
+    @patient_address_option ||= [CQM::Address.new(
+      use: 'HP',
+      street: ['202 Burlington Rd.'],
+      city: 'Bedford',
+      state: 'MA',
+      zip: '01730',
+      country: 'US'
+    )]
+    JSON.parse(@patient_address_option.to_json)
+  end
+
+  def patient_telecoms
+    @patient_telecom_option ||= [CQM::Telecom.new(
+      use: 'HP',
+      value: '555-555-2003'
+    )]
+    JSON.parse(@patient_telecom_option.to_json)
+  end
+
   def patient_characteristic_payer
     JSON.parse(@qdmPatient.get_data_elements('patient_characteristic', 'payer').to_json)
   end
@@ -173,7 +195,7 @@ class Qrda1R5 < Mustache
   def physical_exam_order
     JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'order').to_json)
   end
-  
+
   def physical_exam_performed
     JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'performed').to_json)
   end
@@ -213,7 +235,7 @@ class Qrda1R5 < Mustache
   def substance_recommended
     JSON.parse(@qdmPatient.get_data_elements('substance', 'recommended').to_json)
   end
-  
+
   def symptom
     JSON.parse(@qdmPatient.get_data_elements('symptom', nil).to_json)
   end

data/lib/qrda-export/catI-r5/qrda_header/_record_target.mustache

@@ -1,14 +1,20 @@
 <recordTarget>
   <patientRole>
     <id extension="{{mrn}}" root="1.3.6.1.4.1.115" />
-    <addr use="HP">
-      <streetAddressLine>202 Burlington Rd.</streetAddressLine>
-      <city>Bedford</city>
-      <state>MA</state>
-      <postalCode>01730</postalCode>
-      <country>US</country>
-    </addr>
-    <telecom use="WP" value="tel:+1-781-271-3000"/>
+    {{#patient_addresses}}
+      <addr use="{{use}}">
+        {{#street}}
+          <streetAddressLine>{{.}}</streetAddressLine>
+        {{/street}}
+        <city>{{city}}</city>
+        <state>{{state}}</state>
+        <postalCode>{{zip}}</postalCode>
+        <country>{{country}}</country>
+      </addr>
+    {{/patient_addresses}}
+    {{#patient_telecoms}}
+      <telecom use="{{use}}" value="tel:{{value}}"/>
+    {{/patient_telecoms}}
     <patient>
       {{#patient}}
         <name>
@@ -21,6 +27,9 @@
           <administrativeGenderCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_sex}}
+      {{^patient_characteristic_sex}}
+          <administrativeGenderCode nullFlavor="UNK"/>
+      {{/patient_characteristic_sex}}
       {{#patient_characteristic_birthdate}}
         {{{birth_date_time}}}
       {{/patient_characteristic_birthdate}}
@@ -29,16 +38,20 @@
           <raceCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_race}}
+      {{^patient_characteristic_race}}
+          <raceCode nullFlavor="UNK"/>
+      {{/patient_characteristic_race}}
       {{#patient_characteristic_ethnicity}}
         {{#dataElementCodes}}
           <ethnicGroupCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_ethnicity}}
+      {{^patient_characteristic_ethnicity}}
+          <ethnicGroupCode nullFlavor="UNK"/>
+      {{/patient_characteristic_ethnicity}}
       <languageCommunication>
-        <templateId root="2.16.840.1.113883.3.88.11.83.2" assigningAuthorityName="HITSP/C83"/>
-        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.2.1" assigningAuthorityName="IHE/PCC"/>
         <languageCode code="eng"/>
       </languageCommunication>
     </patient>
   </patientRole>
-</recordTarget>
+</recordTarget>

data/lib/qrda-export/catI-r5/qrda_templates/immunization_administered.mustache

@@ -1,5 +1,10 @@
 <entry>
-  <substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
+    {{#negated}}
+      <substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
+    {{/negated}}
+    {{^negated}}
+      <substanceAdministration classCode="SBADM" moodCode="EVN" negationInd="false">
+    {{/negated}}
     <!-- C-CDA R2 Immunization Activity -->
     <templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2015-08-01"/>
     <!-- Immunization Administered -->

data/lib/qrda-export/catI-r5/qrda_templates/medication_discharge.mustache

@@ -9,8 +9,6 @@
       <substanceAdministration moodCode="EVN" classCode="SBADM">
         <!-- Medication Activity (consolidation) template -->
         <templateId root="2.16.840.1.113883.10.20.22.4.16" extension="2014-06-09"/> 
-        <!-- Medication, Active template -->
-        <templateId root="2.16.840.1.113883.10.20.24.3.41" extension="2016-02-01"/>
         <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
         <text>{{description}}</text>
         <statusCode code="active"/> 

data/lib/qrda-export/catI-r5/qrda_templates/substance_recommended.mustache

@@ -6,6 +6,7 @@
     <templateId root="2.16.840.1.113883.10.20.24.3.75" extension="2017-08-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <statusCode code="active"/>
+    {{{author_effective_time}}}
     {{> qrda_templates/template_partials/_medication_details}}
     <consumable>
       <manufacturedProduct classCode="MANU">

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_medication_supply_request.mustache

@@ -1,6 +1,6 @@
 <supply classCode="SPLY" moodCode="RQO">
  <!-- Medication Supply Request (V2) template -->
-  <templateId root="2.16.840.1.113883.10.20.24.3.99" extension="2014-04-05"/>
+  <templateId root="2.16.840.1.113883.10.20.24.3.99" extension="2015-04-05"/>
   <!-- Conforms to C-CDA R2 Planned Supply (V2) template-->
   <templateId root="2.16.840.1.113883.10.20.22.4.43" extension="2014-06-09" />
   <id root="{{random_id}}"/>

data/lib/qrda-export/helper/cat1_view_helper.rb

@@ -67,6 +67,8 @@ module Qrda
                             result_value_as_string(self['result'][0])
                           elsif self['result'].is_a? Hash
                             result_value_as_string(self['result'])
+                          elsif self['result'].is_a? String
+                            "<value xsi:type=\"ST\">#{self['result']}</value>"
                           elsif !self['result'].nil?
                             "<value xsi:type=\"PQ\" value=\"#{self['result']}\" unit=\"1\"/>"
                           end

data/lib/qrda-import/base-importers/demographics_importer.rb

@@ -15,17 +15,17 @@ module QRDA
         pcs = QDM::PatientCharacteristicSex.new
         code_element = patient_element.at_xpath('cda:administrativeGenderCode')
         pcs.dataElementCodes = [code_if_present(code_element)]
-        patient.qdmPatient.dataElements << pcs
+        patient.qdmPatient.dataElements << pcs unless pcs.dataElementCodes.compact.blank?
 
         pcr = QDM::PatientCharacteristicRace.new
         code_element = patient_element.at_xpath('cda:raceCode')
         pcr.dataElementCodes = [code_if_present(code_element)]
-        patient.qdmPatient.dataElements << pcr
+        patient.qdmPatient.dataElements << pcr unless pcr.dataElementCodes.compact.blank?
 
         pce = QDM::PatientCharacteristicEthnicity.new
         code_element = patient_element.at_xpath('cda:ethnicGroupCode')
         pce.dataElementCodes = [code_if_present(code_element)]
-        patient.qdmPatient.dataElements << pce
+        patient.qdmPatient.dataElements << pce unless pce.dataElementCodes.compact.blank?
       end
 
       def code_if_present(code_element)

data/lib/qrda-import/base-importers/section_importer.rb

@@ -1,7 +1,7 @@
 module QRDA
   module Cat1
     class SectionImporter
-      attr_accessor :check_for_usable, :status_xpath, :code_xpath
+      attr_accessor :check_for_usable, :status_xpath, :code_xpath, :warnings, :codes_modifiers
 
       def initialize(entry_finder)
         @entry_finder = entry_finder
@@ -9,6 +9,8 @@ module QRDA
         @entry_id_map = {}
         @check_for_usable = true
         @entry_class = QDM::DataElement
+        @warnings = []
+        @codes_modifiers = {}
       end
 
       # Traverses an HL7 CDA document passed in and creates an Array of Entry
@@ -41,7 +43,7 @@ module QRDA
         # This is the id found in the QRDA file
         entry_qrda_id = extract_id(entry_element, @id_xpath)
         # Create a hash to map all of entry.ids to the same QRDA ids. This will be used to merge QRDA entries
-        # that represent the same event. 
+        # that represent the same event.
         @entry_id_map["#{entry_qrda_id.value}_#{entry_qrda_id.namingSystem}"] ||= []
         @entry_id_map["#{entry_qrda_id.value}_#{entry_qrda_id.namingSystem}"] << entry.id
         entry.dataElementCodes = extract_codes(entry_element, @code_xpath)
@@ -90,6 +92,9 @@ module QRDA
       end
 
       def extract_interval(parent_element, interval_xpath)
+        # nil if the time interval does not exist
+        return nil unless time_interval_exists(parent_element, interval_xpath)
+
         if parent_element.at_xpath("#{interval_xpath}/@value")
           low_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
           high_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
@@ -108,9 +113,32 @@ module QRDA
           low_time = Time.parse(parent_element.at_xpath("#{interval_xpath}/cda:center")['value'])
           high_time = Time.parse(parent_element.at_xpath("#{interval_xpath}/cda:center")['value'])
         end
+        if low_time && high_time && low_time > high_time
+          # pass warning: current code continues as expected, but adds warning
+          id_attr = parent_element.at_xpath(".//cda:id")&.attributes
+          id_str = id_attr ? "and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension)" : ""
+          qrda_type = @entry_class.to_s.split("::")[1]
+          @warnings << ValidationError.new(message: "Interval with low time after high time. Located in element with QRDA type: #{qrda_type} #{id_str}",
+                                           location: parent_element.path)
+        end
+        if low_time.nil? && high_time.nil?
+          id_attr = parent_element.at_xpath(".//cda:id")&.attributes
+          id_str = id_attr ? "and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension)" : ""
+          qrda_type = @entry_class.to_s.split("::")[1]
+          @warnings << ValidationError.new(message: "Interval with nullFlavor low time and nullFlavor high time. Located in element with QRDA type: #{qrda_type} #{id_str}",
+                                           location: parent_element.path)
+        end
         QDM::Interval.new(low_time, high_time).shift_dates(0)
       end
 
+      def time_interval_exists(parent_element, interval_xpath)
+        # false if the time interval does not exist
+        return false unless parent_element.at_xpath(interval_xpath)
+        # false if the time element exists but has a null Flavor
+        return false if parent_element.at_xpath(interval_xpath)['nullFlavor']
+        true
+      end
+
       def extract_time(parent_element, datetime_xpath)
         DateTime.parse(parent_element.at_xpath(datetime_xpath)['value']) if parent_element.at_xpath("#{datetime_xpath}/@value")
       end
@@ -150,12 +178,11 @@ module QRDA
         parent_element.xpath(@result_xpath).each do |elem|
           result << extract_result_value(elem)
         end
-        result.size > 1 ? result : result.first 
+        result.size > 1 ? result : result.first
       end
 
       def extract_result_value(value_element)
         return unless value_element && !value_element['nullFlavor']
-
         value = value_element['value']
         if value.present?
           return value.strip.to_f if (value_element['unit'] == "1" || value_element['unit'].nil?)
@@ -163,6 +190,13 @@ module QRDA
           return QDM::Quantity.new(value.strip.to_f, value_element['unit'])
         elsif value_element['code'].present?
           return code_if_present(value_element)
+        elsif value_element.text.present?
+          id_attr = value_element.parent.at_xpath(".//cda:id")&.attributes
+          id_str = id_attr ? "and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension)" : ""
+          qrda_type = @entry_class.to_s.split("::")[1]
+          @warnings << ValidationError.new(message: "Value with string type found. When possible, it's best practice to use a coded value or scalar. Located in element with QRDA type: #{qrda_type} #{id_str}",
+                                           location: value_element.path)
+          return value_element.text
         end
       end
 
@@ -172,16 +206,16 @@ module QRDA
         negation_indicator = parent_element['negationInd']
         # Return and do not set reason attribute if the entry is negated
         return nil if negation_indicator.eql?('true')
-        
-        reason_element.blank? ? nil : code_if_present(reason_element.first) 
+
+        reason_element.blank? ? nil : code_if_present(reason_element.first)
       end
 
       def extract_negation(parent_element, entry)
         negation_element = parent_element.xpath("./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value")
         negation_indicator = parent_element['negationInd']
         # Return and do not set negationRationale attribute if the entry is not negated
-        return unless negation_indicator.eql?('true') 
-        
+        return unless negation_indicator.eql?('true')
+
         entry.negationRationale = code_if_present(negation_element.first) unless negation_element.blank?
         extract_negated_code(parent_element, entry)
       end
@@ -189,8 +223,18 @@ module QRDA
       def extract_negated_code(parent_element, entry)
         code_elements = parent_element.xpath(@code_xpath)
         code_elements.each do |code_element|
-          if code_element['nullFlavor'] == 'NA' && code_element['sdtc:valueSet']
-            entry.dataElementCodes = [{ code: code_element['sdtc:valueSet'], codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
+          if code_element['nullFlavor'] == 'NA'
+            if code_element['sdtc:valueSet']
+              entry.dataElementCodes = [{ code: code_element['sdtc:valueSet'], codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
+            else
+              # negated code is nullFlavored with no valueset
+              entry.dataElementCodes = [{ code: "NA", codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
+              id_attr = parent_element.at_xpath(".//cda:id")&.attributes
+              id_str = id_attr ? "and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension)" : ""
+              qrda_type = @entry_class.to_s.split("::")[1]
+              @warnings << ValidationError.new(message: "Negated code element contains nullFlavor code but no valueset. Located in element with QRDA type: #{qrda_type} #{id_str}.",
+                                               location: parent_element.path)
+            end
           end
         end
       end

data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb

@@ -20,7 +20,7 @@ module QRDA
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         diagnostic_study_performed = super
         diagnostic_study_performed.resultDatetime = extract_time(entry_element, @result_datetime_xpath)
-        diagnostic_study_performed.resultDatetime ||= extract_interval(entry_element, @result_datetime_xpath).low
+        diagnostic_study_performed.resultDatetime ||= extract_interval(entry_element, @result_datetime_xpath)&.low
         diagnostic_study_performed.status = code_if_present(entry_element.at_xpath(@status_xpath))
         diagnostic_study_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         diagnostic_study_performed.facilityLocation = extract_facility_locations(entry_element)[0]

data/lib/qrda-import/data-element-importers/encounter_performed_importer.rb

@@ -26,11 +26,21 @@ module QRDA
           los = encounter_performed.relevantPeriod.high - encounter_performed.relevantPeriod.low
           encounter_performed.lengthOfStay = QDM::Quantity.new(los.to_i, 'd')
         end
+        extract_modifier_code(encounter_performed, entry_element)
         encounter_performed
       end
 
       private
 
+      def extract_modifier_code(encounter_performed, entry_element)
+        code_element = entry_element.at_xpath(@code_xpath)
+        return unless code_element
+
+        qualifier_name = code_element.at_xpath('./cda:qualifier/cda:name')
+        qualifier_value = code_element.at_xpath('./cda:qualifier/cda:value')
+        codes_modifiers[encounter_performed.id] = { name: code_if_present(qualifier_name), value: code_if_present(qualifier_value), xpath_location: entry_element.path } if qualifier_value || qualifier_name
+      end
+
       def extract_diagnoses(parent_element)
         diagnosis_elements = parent_element.xpath(@diagnosis_xpath)
         diagnosis_list = []

data/lib/qrda-import/data-element-importers/immunization_order_importer.rb

@@ -16,7 +16,7 @@ module QRDA
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         immunization_order = super
-        immunization_order.activeDatetime = extract_interval(entry_element, @active_datetime_xpath).low
+        immunization_order.activeDatetime = extract_interval(entry_element, @active_datetime_xpath)&.low
         immunization_order.dosage = extract_scalar(entry_element, @dosage_xpath)
         immunization_order.supply = extract_scalar(entry_element, @supply_xpath)
         immunization_order.route = code_if_present(entry_element.at_xpath(@route_xpath))

data/lib/qrda-import/patient_importer.rb

@@ -12,69 +12,71 @@ module QRDA
       def initialize
         # This differs from other HDS patient importers in that sections can have multiple importers
         @data_element_importers = []
-        @data_element_importers << generate_importer(AdverseEventImporter)
-        @data_element_importers << generate_importer(AllergyIntoleranceImporter)
-        @data_element_importers << generate_importer(AssessmentOrderImporter)
-        @data_element_importers << generate_importer(AssessmentPerformedImporter)
-        @data_element_importers << generate_importer(AssessmentRecommendedImporter)
-        @data_element_importers << generate_importer(CommunicationPerformedImporter)
-        @data_element_importers << generate_importer(DeviceAppliedImporter)
-        @data_element_importers << generate_importer(DeviceOrderImporter)
-        @data_element_importers << generate_importer(DeviceRecommendedImporter)
-        @data_element_importers << generate_importer(DiagnosisImporter)
-        @data_element_importers << generate_importer(DiagnosticStudyOrderImporter)
-        @data_element_importers << generate_importer(DiagnosticStudyPerformedImporter)
-        @data_element_importers << generate_importer(DiagnosticStudyRecommendedImporter)
-        @data_element_importers << generate_importer(EncounterOrderImporter)
-        @data_element_importers << generate_importer(EncounterPerformedImporter)
-        @data_element_importers << generate_importer(EncounterRecommendedImporter)
-        @data_element_importers << generate_importer(FamilyHistoryImporter)
-        @data_element_importers << generate_importer(ImmunizationAdministeredImporter)
-        @data_element_importers << generate_importer(ImmunizationOrderImporter)
-        @data_element_importers << generate_importer(InterventionOrderImporter)
-        @data_element_importers << generate_importer(InterventionPerformedImporter)
-        @data_element_importers << generate_importer(InterventionRecommendedImporter)
-        @data_element_importers << generate_importer(LaboratoryTestOrderImporter)
-        @data_element_importers << generate_importer(LaboratoryTestPerformedImporter)
-        @data_element_importers << generate_importer(LaboratoryTestRecommendedImporter)
-        @data_element_importers << generate_importer(MedicationActiveImporter)
-        @data_element_importers << generate_importer(MedicationAdministeredImporter)
-        @data_element_importers << generate_importer(MedicationDischargeImporter)
-        @data_element_importers << generate_importer(MedicationDispensedImporter)
-        @data_element_importers << generate_importer(MedicationOrderImporter)
-        @data_element_importers << generate_importer(PatientCareExperienceImporter)
-        @data_element_importers << generate_importer(PatientCharacteristicClinicalTrialParticipantImporter)
-        @data_element_importers << generate_importer(PatientCharacteristicExpiredImporter)
-        @data_element_importers << generate_importer(PatientCharacteristicPayerImporter)
-        @data_element_importers << generate_importer(PhysicalExamOrderImporter)
-        @data_element_importers << generate_importer(PhysicalExamPerformedImporter)
-        @data_element_importers << generate_importer(PhysicalExamRecommendedImporter)
-        @data_element_importers << generate_importer(ProcedureOrderImporter)
-        @data_element_importers << generate_importer(ProcedurePerformedImporter)
-        @data_element_importers << generate_importer(ProcedureRecommendedImporter)
-        @data_element_importers << generate_importer(ProviderCareExperienceImporter)
-        @data_element_importers << generate_importer(ProviderCharacteristicImporter)
-        @data_element_importers << generate_importer(SubstanceAdministeredImporter)
-        @data_element_importers << generate_importer(SubstanceOrderImporter)
-        @data_element_importers << generate_importer(SubstanceRecommendedImporter)
-        @data_element_importers << generate_importer(SymptomImporter)
+        @data_element_importers << AdverseEventImporter.new
+        @data_element_importers << AllergyIntoleranceImporter.new
+        @data_element_importers << AssessmentOrderImporter.new
+        @data_element_importers << AssessmentPerformedImporter.new
+        @data_element_importers << AssessmentRecommendedImporter.new
+        @data_element_importers << CommunicationPerformedImporter.new
+        @data_element_importers << DeviceAppliedImporter.new
+        @data_element_importers << DeviceOrderImporter.new
+        @data_element_importers << DeviceRecommendedImporter.new
+        @data_element_importers << DiagnosisImporter.new
+        @data_element_importers << DiagnosticStudyOrderImporter.new
+        @data_element_importers << DiagnosticStudyPerformedImporter.new
+        @data_element_importers << DiagnosticStudyRecommendedImporter.new
+        @data_element_importers << EncounterOrderImporter.new
+        @data_element_importers << EncounterPerformedImporter.new
+        @data_element_importers << EncounterRecommendedImporter.new
+        @data_element_importers << FamilyHistoryImporter.new
+        @data_element_importers << ImmunizationAdministeredImporter.new
+        @data_element_importers << ImmunizationOrderImporter.new
+        @data_element_importers << InterventionOrderImporter.new
+        @data_element_importers << InterventionPerformedImporter.new
+        @data_element_importers << InterventionRecommendedImporter.new
+        @data_element_importers << LaboratoryTestOrderImporter.new
+        @data_element_importers << LaboratoryTestPerformedImporter.new
+        @data_element_importers << LaboratoryTestRecommendedImporter.new
+        @data_element_importers << MedicationActiveImporter.new
+        @data_element_importers << MedicationAdministeredImporter.new
+        @data_element_importers << MedicationDischargeImporter.new
+        @data_element_importers << MedicationDispensedImporter.new
+        @data_element_importers << MedicationOrderImporter.new
+        @data_element_importers << PatientCareExperienceImporter.new
+        @data_element_importers << PatientCharacteristicClinicalTrialParticipantImporter.new
+        @data_element_importers << PatientCharacteristicExpiredImporter.new
+        @data_element_importers << PatientCharacteristicPayerImporter.new
+        @data_element_importers << PhysicalExamOrderImporter.new
+        @data_element_importers << PhysicalExamPerformedImporter.new
+        @data_element_importers << PhysicalExamRecommendedImporter.new
+        @data_element_importers << ProcedureOrderImporter.new
+        @data_element_importers << ProcedurePerformedImporter.new
+        @data_element_importers << ProcedureRecommendedImporter.new
+        @data_element_importers << ProviderCareExperienceImporter.new
+        @data_element_importers << ProviderCharacteristicImporter.new
+        @data_element_importers << SubstanceAdministeredImporter.new
+        @data_element_importers << SubstanceOrderImporter.new
+        @data_element_importers << SubstanceRecommendedImporter.new
+        @data_element_importers << SymptomImporter.new
       end 
 
       def parse_cat1(doc)
         patient = CQM::Patient.new
+        warnings = []
+        codes_modifiers = {}
         entry_id_map = {}
-        import_data_elements(patient, doc, entry_id_map)
+        import_data_elements(patient, doc, entry_id_map, codes_modifiers, warnings)
         normalize_references(patient, entry_id_map)
         get_demographics(patient, doc)
-        patient
+        [patient, warnings, codes_modifiers]
       end
 
-      def import_data_elements(patient, doc, entry_id_map)
+      def import_data_elements(patient, doc, entry_id_map, codes_modifiers, warnings = [])
         context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
         nrh = NarrativeReferenceHandler.new
         nrh.build_id_map(doc)
-        @data_element_importers.each do |entry_package|
-          data_elements, id_map = entry_package.package_entries(context, nrh)
+        @data_element_importers.each do |importer|
+          data_elements, id_map = importer.create_entries(context, nrh)
           new_data_elements = []
 
           id_map.each_value do |elem_ids|
@@ -91,7 +93,7 @@ module QRDA
             unique_element_keys << key_elements_for_determining_encounter_uniqueness(data_element)
 
             # Loop through all other data elements with the same id
-            elem_ids[1,elem_ids.length].each do |dup_id|                
+            elem_ids[1,elem_ids.length].each do |dup_id|
               dup_element = data_elements.find { |de| de.id == dup_id }
               dup_element_keys = key_elements_for_determining_encounter_uniqueness(dup_element)
               # See if a previously selected data element shared all of the keys files
@@ -106,13 +108,18 @@ module QRDA
 
           patient.qdmPatient.dataElements << new_data_elements
           entry_id_map.merge!(id_map)
+          warnings.concat(importer.warnings)
+          codes_modifiers.merge!(importer.codes_modifiers)
+          # reset warnings after they're captured so that the importer can be re-used
+          importer.warnings = []
+          importer.codes_modifiers = {}
         end
       end
 
       def key_elements_for_determining_encounter_uniqueness(encounter)
         codes = encounter.codes.collect { |dec| "#{dec.code}_#{dec.codeSystemOid}" }.sort.to_s
-        admission_date_time = encounter.relevantPeriod.low.to_s
-        discharge_date_time = encounter.relevantPeriod.high.to_s
+        admission_date_time = encounter&.relevantPeriod&.low.to_s
+        discharge_date_time = encounter&.relevantPeriod&.high.to_s
         "#{codes}#{admission_date_time}#{discharge_date_time}"
       end
 
@@ -138,12 +145,6 @@ module QRDA
           end
         end
       end
-
-      private
-
-      def generate_importer(importer_class)
-        EntryPackage.new(importer_class.new)
-      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 2.0.5
+  version: 2.1.1
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-25 00:00:00.000000000 Z
+date: 2020-09-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -24,6 +24,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: cqm-validators
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -306,7 +320,6 @@ files:
 - lib/qrda-import/data-element-importers/substance_recommended_importer.rb
 - lib/qrda-import/data-element-importers/symptom_importer.rb
 - lib/qrda-import/entry_finder.rb
-- lib/qrda-import/entry_package.rb
 - lib/qrda-import/narrative_reference_handler.rb
 - lib/qrda-import/patient_importer.rb
 - lib/util/code_system_helper.rb

data/lib/qrda-import/entry_package.rb

@@ -1,16 +0,0 @@
-module QRDA
-  module Cat1
-    class EntryPackage
-
-      attr_accessor :importer_type
-
-      def initialize(type)
-        self.importer_type = type
-      end  
-
-      def package_entries(doc, nrh)
-        importer_type.create_entries(doc, nrh)
-      end
-    end
-  end
-end