cqm-reports 3.1.2 → 3.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9d999a13b64a6a37c2ad61c53c5325162a31eb948e95556a421474eb22cca735
-  data.tar.gz: f4d69a6e256859b77ea3da62a332f48e358ca4a3589d1d08bbf57889b6977f20
+  metadata.gz: b9895c3e39093e4e3b01d4ab490bd91db2b881b5ff9870b8de0c6369fc792601
+  data.tar.gz: ff99962ce100bd5f73bb5bc73299d55bd4b2ed1185de971996292b713baf8060
 SHA512:
-  metadata.gz: 99e4bb97fe1ecbcb0a4f336b0e2e6d0f5d6d85dd05f539a4ea71ad28fbb091b9cf78c2c23605f0e1344c736b4fdc38e0cda8bc12efb2ca52f4f393f158f979c6
-  data.tar.gz: 5c0b2e94fa51e623b071aecfc34537bc16efed7069d1bac433b178491462679fde863b24b6ee7cce9191b27e320d24fdfa004b0077f6e5be8492524f23cc89e5
+  metadata.gz: b2b306d0fc7131de73ebad247d9bdb6d1032fb18d25397e55ddf0926c53002f141bed46facc8e37926b38b27a57f3d2e8d11d6071403502a4eeca751e2839e20
+  data.tar.gz: 27b7e2a699c9f3c897ecbeda9a06cba45dd21e87fc5ddb5315fa07acddd659e6ef9654d9fc4bdf89d28d784ffdecfb1cc907902c228635ffcd94a1971b499acc

data/lib/html-export/qdm-patient/data_element/_data_element_codes.mustache

@@ -2,7 +2,7 @@
 <div class="div-table-body">
 {{#dataElementCodes}}
 <div class="div-head-row">
-	<div class="div-table-head--no-border"><span class="criteria-heading">{{{code_system_name}}}:</span>  {{code}}</div>
+	<div class="div-table-head--no-border"><span class="criteria-heading">{{{code_system_name}}}:</span>  {{code}}{{{code_description}}}</div>
 </div>
 {{/dataElementCodes}}
 </div>

data/lib/html-export/qdm-patient/qdm_patient.mustache

@@ -18,7 +18,7 @@
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Patient</span></div>
           <div class="div-table-head">{{given_name}} {{familyName}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Sex</span></div>
-          <div class="div-table-head">{{{gender}}}</div>
+          <div class="div-table-head">{{{gender}}}{{#demographic_code_description}}gender{{/demographic_code_description}}</div>
         </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Date of birth</span></div>
@@ -28,13 +28,13 @@
         </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Race</span></div>
-          <div class="div-table-head">{{{race}}}</div>
+          <div class="div-table-head">{{{race}}}{{#demographic_code_description}}race{{/demographic_code_description}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Ethnicity</span></div>
-          <div class="div-table-head">{{{ethnic_group}}}</div>
+          <div class="div-table-head">{{{ethnic_group}}}{{#demographic_code_description}}ethnic_group{{/demographic_code_description}}</div>
         </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Insurance Providers</span></div>
-          <div class="div-table-head">{{{payer}}}</div>
+          <div class="div-table-head">{{{payer}}}{{#demographic_code_description}}payer{{/demographic_code_description}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Patient IDs</span></div>
           <div class="div-table-head">{{{mrn}}} Cypress</div>
         </div>

data/lib/html-export/qdm-patient/qdm_patient.rb

@@ -91,13 +91,31 @@ class QdmPatient < Mustache
   end
 
   def code_for_element(element)
-    "#{element['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(element['system'])})"
+    "#{element['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(element['system'])})#{code_description(element)}"
   end
 
   def code_system_name
     HQMF::Util::CodeSystemHelper.code_system_for(self['system'])
   end
 
+  def code_description(element = self)
+    has_descriptions = @patient.respond_to?(:code_description_hash) && !@patient.code_description_hash.empty?
+    # mongo keys cannot contain '.', so replace all '.', key example: '21112-8:2_16_840_1_113883_6_1'
+    return " - #{@patient.code_description_hash["#{element['code']}:#{element['system']}".tr('.', '_')]}" if has_descriptions
+    # no code description available
+    ""
+  end
+
+  def demographic_code_description(code)
+    # only have code, don't need code system
+    has_descriptions = code && @patient.respond_to?(:code_description_hash) && !@patient.code_description_hash.empty?
+    if has_descriptions
+      key = @patient.code_description_hash.keys.detect { |k| k.starts_with?("#{send(code)}:") }
+      return " - #{@patient.code_description_hash[key]}"
+    end
+    ""
+  end
+
   def result_string
     return unit_string if self['value']
     return code_code_system_string if self['code']

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

@@ -41,5 +41,9 @@
       <!-- QDM Attribute: Components -->
       {{> qrda_templates/template_partials/_component}}
     {{/components}}
+    {{#encounter_id}}
+      <!-- QDM Attribute: relatedTo -->
+      {{> qrda_templates/template_partials/_related_to}}
+    {{/encounter_id}}
     </observation>
 </entry>

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

@@ -48,5 +48,9 @@
       <!-- QDM Attribute: Components -->
       {{> qrda_templates/template_partials/_component}}
     {{/components}}
+    {{#encounter_id}}
+      <!-- QDM Attribute: relatedTo -->
+      {{> qrda_templates/template_partials/_related_to}}
+    {{/encounter_id}}
   </observation>
 </entry>

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

@@ -1,7 +1,7 @@
 module QRDA
   module Cat1
     module DemographicsImporter
-      def get_demographics(patient, doc)
+      def get_demographics(patient, doc, codes)
         patient_role_element = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole')
         patient_element = patient_role_element.at_xpath('./cda:patient')
         patient.givenNames = [patient_element.at_xpath('cda:name/cda:given').text]
@@ -9,28 +9,29 @@ module QRDA
         patient.qdmPatient.birthDatetime = DateTime.parse(patient_element.at_xpath('cda:birthTime')['value'])
         pcbd = QDM::PatientCharacteristicBirthdate.new
         pcbd.birthDatetime = patient.qdmPatient.birthDatetime
-        pcbd.dataElementCodes = [{ code: '21112-8', system: '2.16.840.1.113883.6.1' }]
+        pcbd.dataElementCodes = [QDM::Code.new('21112-8', '2.16.840.1.113883.6.1')]
+        codes.add("21112-8:2.16.840.1.113883.6.1")
         patient.qdmPatient.dataElements << pcbd
 
         pcs = QDM::PatientCharacteristicSex.new
         code_element = patient_element.at_xpath('cda:administrativeGenderCode')
-        pcs.dataElementCodes = [code_if_present(code_element)]
+        pcs.dataElementCodes = [code_if_present(code_element, codes)]
         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)]
+        pcr.dataElementCodes = [code_if_present(code_element, codes)]
         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)]
+        pce.dataElementCodes = [code_if_present(code_element, codes)]
         patient.qdmPatient.dataElements << pce unless pce.dataElementCodes.compact.blank?
       end
 
-      def code_if_present(code_element)
+      def code_if_present(code_element, codes)
         return unless code_element && code_element['code'] && code_element['codeSystem']
-
+        codes.add("#{code_element['code']}:#{code_element['codeSystem']}")
         QDM::Code.new(code_element['code'], code_element['codeSystem'])
       end
     end

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, :warnings
+      attr_accessor :check_for_usable, :status_xpath, :code_xpath, :warnings, :codes, :codes_modifiers
 
       def initialize(entry_finder)
         @entry_finder = entry_finder
@@ -10,6 +10,8 @@ module QRDA
         @check_for_usable = true
         @entry_class = QDM::DataElement
         @warnings = []
+        @codes = Set.new
+        @codes_modifiers = {}
       end
 
       # Traverses an HL7 CDA document passed in and creates an Array of Entry
@@ -81,6 +83,7 @@ module QRDA
 
       def code_if_present(code_element)
         return unless code_element && code_element['code'] && code_element['codeSystem']
+        @codes.add("#{code_element['code']}:#{code_element['codeSystem']}")
         QDM::Code.new(code_element['code'], code_element['codeSystem'])
       end
 
@@ -94,7 +97,9 @@ module QRDA
       end
 
       def extract_interval(parent_element, interval_xpath)
-        return nil unless parent_element.at_xpath(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'])
@@ -131,6 +136,14 @@ module QRDA
         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
@@ -145,6 +158,7 @@ module QRDA
         # If a Direct Reference Code isn't found, return nil
         return nil unless key
         # If a Direct Reference Code is found, return that code
+        @codes.add("#{key}:#{value[:code_system]}")
         QDM::Code.new(key, value[:code_system])
       end
 
@@ -258,7 +272,7 @@ module QRDA
           participant_element = facility_location_element.at_xpath("./cda:participantRole[@classCode='SDLOC']/cda:code")
           facility_location.code = code_if_present(participant_element)
           facility_location.locationPeriod = extract_interval(facility_location_element, './cda:time')
-          facility_locations << facility_location
+          facility_locations << facility_location if facility_location.code
         end
         facility_locations
       end

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

@@ -21,15 +21,25 @@ module QRDA
         encounter_performed.facilityLocations = extract_facility_locations(entry_element)
         encounter_performed.diagnoses = extract_diagnoses(entry_element)
         if encounter_performed&.relevantPeriod&.low && encounter_performed&.relevantPeriod&.high
-          los = encounter_performed.relevantPeriod.high - encounter_performed.relevantPeriod.low
+          los = encounter_performed.relevantPeriod.high.to_date - encounter_performed.relevantPeriod.low.to_date
           encounter_performed.lengthOfStay = QDM::Quantity.new(los.to_i, 'd')
         end
         encounter_performed.participant = extract_entity(entry_element, "./cda:entryRelationship/cda:encounter//cda:participant[@typeCode='PRF']")
+        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/patient_importer.rb

@@ -59,19 +59,21 @@ module QRDA
         @data_element_importers << SubstanceOrderImporter.new
         @data_element_importers << SubstanceRecommendedImporter.new
         @data_element_importers << SymptomImporter.new
-      end
+      end 
 
       def parse_cat1(doc)
         patient = CQM::Patient.new
         warnings = []
+        codes = Set.new
+        codes_modifiers = {}
         entry_id_map = {}
-        import_data_elements(patient, doc, entry_id_map, warnings)
+        import_data_elements(patient, doc, entry_id_map, codes, codes_modifiers, warnings)
         normalize_references(patient, entry_id_map)
-        get_demographics(patient, doc)
-        [patient, warnings]
+        get_demographics(patient, doc, codes)
+        [patient, warnings, codes, codes_modifiers]
       end
 
-      def import_data_elements(patient, doc, entry_id_map, warnings = [])
+      def import_data_elements(patient, doc, entry_id_map, codes = Set.new, 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)
@@ -109,8 +111,12 @@ module QRDA
           patient.qdmPatient.dataElements << new_data_elements
           entry_id_map.merge!(id_map)
           warnings.concat(importer.warnings)
-          # reset warnings after they're captured so that the importer can be re-used
+          codes.merge(importer.codes)
+          codes_modifiers.merge!(importer.codes_modifiers)
+          # reset warnings and codes after they're captured so that the importer can be re-used
           importer.warnings = []
+          importer.codes_modifiers = {}
+          importer.codes = Set.new
         end
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 3.1.2
+  version: 3.1.3
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-08-24 00:00:00.000000000 Z
+date: 2020-10-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -358,7 +358,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.4
 signing_key:
 specification_version: 4
 summary: A library for import and export of reports for use with electronic Clinical