RubyGems - cqm-reports - Versions diffs - 3.0.1 → 3.1.4 - Mend

cqm-reports 3.0.1 → 3.1.4

Files changed (26) hide show

checksums.yaml CHANGED Viewed

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 62734f201648d065ea3bec1903f34d1c7005443b
+SHA256:
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+  data.tar.gz: c969fcf65e9f7f8efabb02c636aad2bef9659d2221c0e72a94afe9ec993c8e16
 SHA512:
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+  metadata.gz: aa75bf444859f1fdff85ae788fa277f0acb8f75e4d6e036717a0545f7af2a19800f446500101f36f9773bff9eb815b3cf4601bf1694d26af2468f04ffa3cc5cc
+  data.tar.gz: 78fe7570a996c1cd80517e74a856c2149a5cb351b933dccda3870f8b6781f707cd0c957b343421a0b54a5d8205c3bcfe96d535f4fe2fc53658c2cd0db8e2ba95

data/Gemfile CHANGED Viewed

@@ -17,7 +17,7 @@ group :development do
 end
 group :test do
-  gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models', branch: 'master'
+  gem 'cqm-models', '~> 3.0'
   gem 'factory_girl', '~> 4.1.0'
   gem 'tailor', '~> 1.1.2'
   gem 'cane', '~> 2.3.0'
@@ -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 CHANGED Viewed

@@ -11,6 +11,7 @@ Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning ha
   | X | QRDA Cat 1 | QRDA Cat 3 |
   | --- | --- | --- |
   | 2 | R1 STU5.1 | R1 STU2.1 |
+  | 3 | R1 STU5.2 | R1 STU2.1 |
 * **Y** indicates major changes (incompatible API changes)
@@ -24,7 +25,7 @@ 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 CHANGED Viewed

@@ -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/data_element/_data_element_codes.mustache CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -3,7 +3,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
     {{#patient}}
-    <title>Cypress Certification Patient Test Record: {{{given_name}}} {{familyName}}</title>
+    <title>Cypress Certification Patient Test Record: {{given_name}} {{familyName}}</title>
     {{/patient}}
     {{#include_style?}}
       {{> _header_css}}
@@ -11,36 +11,38 @@
   </head>
   <body>
     {{#patient}}
-    <h1 class="h1center">Cypress Certification Patient Test Record: {{{given_name}}} {{familyName}}</h1>
+    <h1 class="h1center">Cypress Certification Patient Test Record: {{given_name}} {{familyName}}</h1>
     <div class="div-table">
       <div class="div-table-body">
         <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">Patient</span></div>
-          <div class="div-table-head">{{{given_name}}} {{familyName}}</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>
           <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>
-          <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>
+          <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>
         <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 CHANGED Viewed

@@ -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
@@ -61,13 +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_header/_record_target.mustache CHANGED Viewed

@@ -18,7 +18,7 @@
     <patient>
       {{#patient}}
         <name>
-          <given>{{{given_name}}}</given>
+          <given>{{given_name}}</given>
           <family>{{familyName}}</family>
         </name>
       {{/patient}}

data/lib/qrda-export/catI-r5/qrda_templates/communication_performed.mustache CHANGED Viewed

@@ -48,7 +48,6 @@
         <entryRelationship typeCode="REFR">
           <observation classCode="OBS" moodCode="EVN">
             <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2017-08-01"/>
-            <id root="1.3.6.1.4.1.115" extension="{{object_id}}" />
             <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
             <statusCode code="completed"/>
             <!-- QDM Attribute: Code -->

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

@@ -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 CHANGED Viewed

@@ -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-export/catI-r5/qrda_templates/template_partials/_reaction_observation.mustache CHANGED Viewed

@@ -4,6 +4,6 @@
       <id root="4adc1020-7b14-11db-9fe1-0800200c9a64" />
       <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4" />
       <statusCode code="completed" />
-      {{> qrda_templates/template_partials/_data_element_codes_as_values}}
+      <value xsi:type="CD" {{> _code}}/>
     </observation>
   </entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_reason.mustache CHANGED Viewed

@@ -1,7 +1,6 @@
 <entryRelationship typeCode="RSON">
   <observation classCode="OBS" moodCode="EVN">
     <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2017-08-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{random_id}}" />
     <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
     {{#relevantPeriod}}
     {{{relevant_period}}}

data/lib/qrda-export/catIII-r2-1/_continuous_variable_value.mustache CHANGED Viewed

@@ -2,16 +2,16 @@
   <observation classCode="OBS" moodCode="EVN">
     <templateId root="2.16.840.1.113883.10.20.27.3.2"/>
     <code nullFlavor="OTH">
-      <originalText>Time Difference</originalText>
+      <originalText>Other</originalText>
     </code>
     <statusCode code="completed"/>
-    <value xsi:type="PQ" value="{{value}}" unit="min"/>
-    <methodCode code="MEDIAN" displayName="Median" codeSystem="2.16.840.1.113883.5.84" codeSystemName="ObservationMethod"/>
+    <value xsi:type="REAL" value="{{value}}"/>
+    <methodCode code="{{method}}" displayName="{{method}}" codeSystem="2.16.840.1.113883.5.84" codeSystemName="ObservationMethod"/>
     <reference typeCode="REFR">
       <!-- reference to the relevant measure observation in the eMeasure -->
       <externalObservation classCode="OBS" moodCode="EVN">
-        <id root="{{id}}"/>
+        <id root="{{hqmf_id}}"/>
       </externalObservation>
     </reference>
   </observation>
-</entryRelationship>
+</entryRelationship>

data/lib/qrda-export/catIII-r2-1/_measure_data.mustache CHANGED Viewed

@@ -27,11 +27,9 @@
         {{> _supplemental_data}}
       {{/population_supplemental_data}}
     {{/supplemental_data}}
-    {{#msrpopl?}}
       {{#population_observation}}
         {{> _continuous_variable_value}}
       {{/population_observation}}
-    {{/msrpopl?}}
     <reference typeCode="REFR">
        <externalObservation classCode="OBS" moodCode="EVN">
           <id root="{{id}}"/>

data/lib/qrda-export/catIII-r2-1/_stratification.mustache CHANGED Viewed

@@ -15,11 +15,9 @@
         <methodCode code="COUNT" displayName="Count" codeSystem="2.16.840.1.113883.5.84" codeSystemName="ObservationMethod"/>
       </observation>
     </entryRelationship>
-    {{#msrpopl?}}
-      {{#stratification_observation}}
-        {{> _continuous_variable_value}}
-      {{/stratification_observation}}
-    {{/msrpopl?}}
+    {{#stratification_observation}}
+      {{> _continuous_variable_value}}
+    {{/stratification_observation}}
     <reference typeCode="REFR">
       <externalObservation classCode="OBS" moodCode="EVN">
         <id root="{{id}}"/>

data/lib/qrda-export/catIII-r2-1/qrda3_r21.rb CHANGED Viewed

@@ -58,14 +58,11 @@ class Qrda3R21 < Mustache
   end
   def stratification_observation
-    observation = @measure_result_hash[self['measure_id']].aggregate_count.populations.find {|p| p.type == "OBSERV"}
-    stratification_observation = @measure_result_hash[self['measure_id']].aggregate_count.populations.find {|p| p.type == "OBSERV"}.stratifications.find {|s| s.id == self['id'] }
-    stratification_observation.id = observation.id
-    stratification_observation
+    self['observation']
   end
   def population_observation
-    @measure_result_hash[self['measure_id']].aggregate_count.populations.find {|p| p.type == "OBSERV"}
+    self['observation']
   end
   def supplemental_template_ids

data/lib/qrda-export/helper/aggregate_object_helper.rb CHANGED Viewed

@@ -57,23 +57,24 @@ module Qrda
         end
       end
       class Population
-        attr_accessor :type, :value, :id, :stratifications, :supplemental_data
+        attr_accessor :type, :value, :id, :stratifications, :supplemental_data, :observation
         def initialize
           @stratifications = []
         end
-        def add_stratification(id,value)
-          stratifications << Stratification.new(id,value) unless stratifications.find {|st| st.id == id}
+        def add_stratification(id,value,observation)
+          stratifications << Stratification.new(id,value,observation) unless stratifications.find {|st| st.id == id}
         end
       end
       class Stratification
-        attr_accessor :id, :value
-        def initialize(id,value)
+        attr_accessor :id, :value, :observation
+        def initialize(id,value, observation)
           @id = id
           @value = value
+          @observation = observation
         end
       end
@@ -107,15 +108,17 @@ module Qrda
         def add_entry(cache_entry, population_sets)
           population_set = population_sets.where(population_set_id: cache_entry.pop_set_hash[:population_set_id]).first
           entry_populations = []
-          %w[IPP DENOM NUMER NUMEX DENEX DENEXCEP MSRPOPL MSRPOPLEX OBSERV].each do |pop_code|
-            next unless population_set.populations[pop_code] || pop_code == 'OBSERV'
+          %w[IPP DENOM NUMER NUMEX DENEX DENEXCEP MSRPOPL MSRPOPLEX].each do |pop_code|
+            next unless population_set.populations[pop_code]
             population = create_population_from_population_set(pop_code, population_set, cache_entry)
             if cache_entry.pop_set_hash[:stratification_id]
               strat_id = population_set.stratifications.where(stratification_id: cache_entry.pop_set_hash[:stratification_id]).first&.hqmf_id
-              population.add_stratification(strat_id,cache_entry[pop_code])
+              observation = cache_entry['observations'][pop_code] if cache_entry['observations'] && cache_entry['observations'][pop_code]
+              population.add_stratification(strat_id,cache_entry[pop_code], observation)
             else
               population.value = cache_entry[pop_code]
+              population.observation = cache_entry['observations'][pop_code] if cache_entry['observations'] && cache_entry['observations'][pop_code]
               population.supplemental_data = cache_entry.supplemental_data[pop_code]
             end
             entry_populations << population if population
@@ -128,19 +131,12 @@ module Qrda
         end
         def create_population_from_population_set(pop_code, population_set, cache_entry)
-          population = if pop_code == 'OBSERV'
-                         populations.find { |pop| pop.id == population_set.observations&.first&.hqmf_id }
-                       elsif pop_code != 'STRAT'
-                         populations.find { |pop| pop.id == population_set.populations[pop_code]&.hqmf_id }
-                       end
+          population = populations.find { |pop| pop.id == population_set.populations[pop_code]&.hqmf_id } if pop_code != 'STRAT'
           return population unless population.nil? && !cache_entry.pop_set_hash[:stratification_id]
           population = Population.new
           population.type = pop_code
-          population.id = if pop_code == 'OBSERV'
-                            population_set.observations&.first&.hqmf_id
-                          else
-                            population_set.populations[pop_code]&.hqmf_id
-                          end
+          population.id = population_set.populations[pop_code]&.hqmf_id
           populations << population
           population
         end

data/lib/qrda-export/helper/date_helper.rb CHANGED Viewed

@@ -101,7 +101,7 @@ module Qrda
         end
         def relevant_date_period_or_null_flavor
-          return relevant_period if self['relevantPeriod']
+          return relevant_period if self['relevantPeriod'] && (self['relevantPeriod']['low'] || self['relevantPeriod']['high'])
           return relevant_date_time_value if self['relevantDatetime']
           "<effectiveTime nullFlavor='UNK'/>"
         end
@@ -128,4 +128,4 @@ module Qrda
       end
     end
   end
-end
+end

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

@@ -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/demographics_importer.rb CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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, :codes_modifiers
       def initialize(entry_finder)
         @entry_finder = entry_finder
@@ -9,6 +9,9 @@ module QRDA
         @entry_id_map = {}
         @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
@@ -41,7 +44,7 @@ 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)
@@ -80,6 +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
@@ -93,7 +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'])
@@ -112,9 +118,32 @@ 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
@@ -129,6 +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
@@ -154,7 +184,7 @@ 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)
@@ -167,6 +197,11 @@ 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
@@ -177,16 +212,16 @@ 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
@@ -194,8 +229,18 @@ 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'], 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
+              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
@@ -227,7 +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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -12,70 +12,73 @@ 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)
+        @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 = []
+        codes = Set.new
+        codes_modifiers = {}
         entry_id_map = {}
-        import_data_elements(patient, doc, entry_id_map)
+        import_data_elements(patient, doc, entry_id_map, codes, codes_modifiers, warnings)
         normalize_references(patient, entry_id_map)
-        get_demographics(patient, doc)
-        patient
+        get_demographics(patient, doc, codes)
+        [patient, warnings, codes, codes_modifiers]
       end
-      def import_data_elements(patient, doc, entry_id_map)
+      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)
-        @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 +95,7 @@ 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 +110,13 @@ module QRDA
           patient.qdmPatient.dataElements << new_data_elements
           entry_id_map.merge!(id_map)
+          warnings.concat(importer.warnings)
+          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
@@ -136,12 +146,6 @@ 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 CHANGED Viewed

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.1.4
 platform: ruby
 authors:
 - The MITRE Corporation
-autorequire:
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-07-09 00:00:00.000000000 Z
+date: 2021-06-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -16,14 +16,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: cqm-validators
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -70,16 +84,22 @@ dependencies:
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: 1.8.5
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 1.12.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.5
+    - - "<"
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: 1.12.0
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement
@@ -314,7 +334,6 @@ 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
@@ -330,7 +349,7 @@ homepage: https://github.com/projecttacoma/cqm-reports
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -345,9 +364,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.6.14
-signing_key:
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: A library for import and export of reports for use with electronic Clinical
   Quality Measures (eCQMs).

data/lib/qrda-import/entry_package.rb DELETED Viewed

@@ -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