cqm-reports 2.0.8 → 2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8d2524cbacaae3fea93a3dca5545a113a25f1454
-  data.tar.gz: 77634976e41228b7dbdf43293f0596b481ed9eba
+  metadata.gz: e8ef5e1f1c6d14646a8d523109b41d9d9609503c
+  data.tar.gz: 1ccc64f200b387965a3271501cb933e795435cba
 SHA512:
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-  data.tar.gz: 7030f81b37ddd6362c967a16fa166a6f2fac407dcc084ee2be739eade82ae2b54947bf3edc792fefeafd886b7fbd02ca9be8497edc6cef49951382cda984ec40
+  metadata.gz: 62af1b280c4701bed265910f768bb6d19be6f087bd028b022b9cdfbd4b02fae834252fc1ed0798e6555b4e978962f9e4d237d27c9528523cc5c6ba89d8ace2e1
+  data.tar.gz: 71cc7d395c9af17f8d946e28ac108f25142c9d2e4e6028e4799e8297fb8a5fc47f1b898939554cbd7616494320ec9d79c8caa489fc8bda0b60f3eb4050f8d69f

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-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 +92,7 @@ module QRDA
       end
 
       def extract_interval(parent_element, interval_xpath)
+        return nil unless parent_element.at_xpath(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'])
@@ -108,6 +111,21 @@ 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
 
@@ -150,7 +168,7 @@ 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)
@@ -163,6 +181,11 @@ module QRDA
         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
@@ -173,16 +196,16 @@ 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
@@ -190,8 +213,18 @@ 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: 2.0.8
+  version: 2.1.0
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-08 00:00:00.000000000 Z
+date: 2020-09-02 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