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

cqm-reports 3.0.1 → 3.1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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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-  data.tar.gz: 13c9d7aca7e2497f47e66919b54926f33bd6fd4d2714aadbde204d24072f23e95aa0fbad63458572e4c776c0dac9caa67fae2dc3efa063d7f340d618eea4cd3f
+  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