cqm-reports 3.0.1 → 3.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 62734f201648d065ea3bec1903f34d1c7005443b
+  metadata.gz: f221e687f62214c36812fd10c6f805bd4c8318d0
+  data.tar.gz: 8ced778300575e57e368770bc705f8e5cc4f4d3d
 SHA512:
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+  metadata.gz: d4056e6d8f4e26ad6247fa558511d5ce0aad9bc61ca0ecd7c31ec69f160b4c555ced11b5fdfc3ce0e518165de92b2efbd2538bde2d73128035a84e7fa06ddc8e
+  data.tar.gz: 33d50e677dcb99de986b9d0a9e4423530fdbed178b99bb0a6512eedf41d4bcf0e8a0eeeb9a936a6035419914f0089fa7de8c1435bdd40971bdbc6861666bcd32

data/Gemfile

@@ -27,6 +27,5 @@ group :test do
   gem 'minitest', '~> 5.3'
   gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
-  gem 'cqm-validators', git: 'https://github.com/projecttacoma/cqm-validators', branch: 'master'
   gem 'nokogiri-diff'
 end

data/README.md

@@ -24,7 +24,7 @@ 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 = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
+        patient, warnings = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
 
 Exporting QRDA Category I
 ==========

data/lib/cqm-reports.rb

@@ -19,7 +19,6 @@ 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/html-export/qdm-patient/qdm_patient.mustache

@@ -24,7 +24,7 @@
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Date of birth</span></div>
           <div class="div-table-head">{{{birthdate}}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Date of expiration</span></div>
-          <div class="div-table-head"></div>
+          <div class="div-table-head">{{{expiration}}}</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">Race</span></div>
@@ -39,8 +39,10 @@
           <div class="div-table-head">{{{mrn}}} Cypress</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">Contact info</span></div>
-          <div class="div-table-head"></div>
+          <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Address</span></div>
+          <div class="div-table-head">{{{patient_addresses}}}</div>
+          <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Telecom</span></div>
+          <div class="div-table-head">{{{patient_telecoms}}}</div>
         </div>
       </div>
     </div>

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

@@ -9,6 +9,36 @@ class QdmPatient < Mustache
     @include_style = include_style
     @patient = patient
     @qdmPatient = patient.qdmPatient
+    @patient_addresses = patient['addresses']
+    @patient_telecoms = patient['telecoms']
+  end
+
+  def patient_addresses
+    @patient_addresses ||= [CQM::Address.new(
+      use: 'HP',
+      street: ['202 Burlington Rd.'],
+      city: 'Bedford',
+      state: 'MA',
+      zip: '01730',
+      country: 'US'
+    )]
+    address_str = ""
+    @patient_addresses.each do |address|
+      # create formatted address
+      address_str += "<address>"
+      address['street'].each { |street| address_str += "#{street}<br>" }
+      address_str += "#{address['city']}, #{address['state']} #{address['zip']}<br> #{address['country']} </address>"
+    end
+    address_str
+  end
+
+  def patient_telecoms
+    @patient_telecoms ||= [CQM::Telecom.new(
+      use: 'HP',
+      value: '555-555-2003'
+    )]
+    # create formatted telecoms
+    @patient_telecoms.map { |telecom| "(#{telecom['use']}) #{telecom['value']}" }.join("<br>")
   end
 
   def include_style?
@@ -25,7 +55,7 @@ class QdmPatient < Mustache
   end
 
   def unit_string
-    return "#{self['value']} " unless self['unit']
+    return "#{self['value']} " if !self['unit'] || self['unit'] == '1'
     "#{self['value']} #{self['unit']}"
   end
 

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

@@ -16,16 +16,19 @@ module Qrda
 
         def provider_npi
           return nil unless self['ids']
+
           self['ids'].map { |id| id if id['namingSystem'] == '2.16.840.1.113883.4.6' }.compact
         end
 
         def provider_tin
           return nil unless self['ids']
+
           self['ids'].map { |id| id if id['namingSystem'] == '2.16.840.1.113883.4.2' }.compact
         end
 
         def provider_ccn
           return nil unless self['ids']
+
           self['ids'].map { |id| id if id['namingSystem'] == '2.16.840.1.113883.4.336' }.compact
         end
 
@@ -40,6 +43,42 @@ module Qrda
         def given_name
           self['givenNames'].join(' ')
         end
+
+        def gender
+          gender_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicSex" }
+          return if gender_elements.empty?
+          gender_elements.first.dataElementCodes.first['code']
+        end
+
+        def birthdate
+          birthdate_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicBirthdate" }
+          return "None" if birthdate_elements.empty?
+          birthdate_elements.first['birthDatetime']
+        end
+
+        def expiration
+          expired_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicExpired" }
+          return "None" if expired_elements.empty?
+          expired_elements.first['expiredDatetime']
+        end
+
+        def race
+          race_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicRace" }
+          return if race_elements.empty?
+          race_elements.first.dataElementCodes.first['code']
+        end
+
+        def ethnic_group
+          ethnic_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicEthnicity" }
+          return if ethnic_elements.empty?
+          ethnic_elements.first.dataElementCodes.first['code']
+        end
+
+        def payer
+          payer_elements = @qdmPatient.dataElements.select { |de| de._type == "QDM::PatientCharacteristicPayer" }
+          return if payer_elements.empty?
+          payer_elements.first.dataElementCodes.first['code']
+        end
       end
     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
+      attr_accessor :check_for_usable, :status_xpath, :code_xpath, :warnings
 
       def initialize(entry_finder)
         @entry_finder = entry_finder
@@ -9,6 +9,7 @@ module QRDA
         @entry_id_map = {}
         @check_for_usable = true
         @entry_class = QDM::DataElement
+        @warnings = []
       end
 
       # Traverses an HL7 CDA document passed in and creates an Array of Entry
@@ -112,6 +113,19 @@ 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
+          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} and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension).",
+                                           location: parent_element.path)
+        end
+        if low_time.nil? && high_time.nil?
+          id_attr = parent_element.at_xpath(".//cda:id").attributes
+          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} and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value if id_attr['extension']}(extension).",
+                                           location: parent_element.path)
+        end
         QDM::Interval.new(low_time, high_time).shift_dates(0)
       end
 
@@ -167,6 +181,10 @@ 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
+          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} and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension).",
+                                           location: value_element.path)
           return value_element.text
         end
       end
@@ -194,8 +212,17 @@ 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'], system: '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'], system: '1.2.3.4.5.6.7.8.9.10' }]
+            else
+              # negated code is nullFlavored with no valueset
+              entry.dataElementCodes = [{ code: "NA", system: '1.2.3.4.5.6.7.8.9.10' }]
+              id_attr = parent_element.at_xpath(".//cda:id").attributes
+              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} and id: #{id_attr['root']&.value}(root), #{id_attr['extension']&.value}(extension).",
+                                               location: parent_element.path)
+            end
           end
         end
       end

data/lib/qrda-import/patient_importer.rb

@@ -12,70 +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(ProgramParticipationImporter)
-        @data_element_importers << generate_importer(ProviderCareExperienceImporter)
-        @data_element_importers << generate_importer(RelatedPersonImporter)
-        @data_element_importers << generate_importer(SubstanceAdministeredImporter)
-        @data_element_importers << generate_importer(SubstanceOrderImporter)
-        @data_element_importers << generate_importer(SubstanceRecommendedImporter)
-        @data_element_importers << generate_importer(SymptomImporter)
-      end 
+        @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 << ProgramParticipationImporter.new
+        @data_element_importers << ProviderCareExperienceImporter.new
+        @data_element_importers << RelatedPersonImporter.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 = []
         entry_id_map = {}
-        import_data_elements(patient, doc, entry_id_map)
+        import_data_elements(patient, doc, entry_id_map, warnings)
         normalize_references(patient, entry_id_map)
         get_demographics(patient, doc)
-        patient
+        [patient, warnings]
       end
 
-      def import_data_elements(patient, doc, entry_id_map)
+      def import_data_elements(patient, doc, entry_id_map, 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|
@@ -92,7 +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
@@ -107,6 +108,9 @@ 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
+          importer.warnings = []
         end
       end
 
@@ -136,12 +140,6 @@ module QRDA
           data_element.relatedTo = relations_to_add.map(&:to_s)
         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: 3.0.1
+  version: 3.1.0
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-09 00:00:00.000000000 Z
+date: 2020-07-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -24,6 +24,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 3.0.0
+- !ruby/object:Gem::Dependency
+  name: cqm-validators
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -314,7 +328,6 @@ 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