RubyGems - cqm-reports - Versions diffs - 3.0.0 → 3.1.3 - Mend

cqm-reports 3.0.0 → 3.1.3

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 (34) hide show

checksums.yaml CHANGED

@@ -1,7 +1,7 @@
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-SHA1:
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-  data.tar.gz: 906d1984866e314876ca0d713f6b08a01a6ab8f5
+SHA256:
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+  data.tar.gz: ff99962ce100bd5f73bb5bc73299d55bd4b2ed1185de971996292b713baf8060
 SHA512:
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-  data.tar.gz: 9f4fa410245d83fbd1beb11183461a4cd8442859bfc391b7bffd90c5d9afeb2c91cd3ca83d54e9bc7c6a49f8ad9b6c9fe55230167161fd03cc4fc188066aec95
+  metadata.gz: b2b306d0fc7131de73ebad247d9bdb6d1032fb18d25397e55ddf0926c53002f141bed46facc8e37926b38b27a57f3d2e8d11d6071403502a4eeca751e2839e20
+  data.tar.gz: 27b7e2a699c9f3c897ecbeda9a06cba45dd21e87fc5ddb5315fa07acddd659e6ef9654d9fc4bdf89d28d784ffdecfb1cc907902c228635ffcd94a1971b499acc

data/Gemfile CHANGED

@@ -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', '~> 3.0.3'
   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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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/assessment_performed.mustache CHANGED

@@ -6,16 +6,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#result}}
     <!-- QDM Attribute: Result -->
     {{{result_value}}}

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

@@ -8,16 +8,7 @@
     <code code="360030002" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="application of device"/>
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#anatomicalLocationSite}}
       <!-- QDM Attribute: Anatomical Location Site -->
       {{> qrda_templates/template_partials/_anatomical_location_site}}

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

@@ -1,7 +1,6 @@
 <entry>
   <act classCode="ACT" moodCode="RQO" {{{negation_ind}}}>
     <templateId root="2.16.840.1.113883.10.20.24.3.130" extension="2019-12-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="SPLY" codeSystem="2.16.840.1.113883.5.6" displayName="Supply" codeSystemName="ActClass"/>
     <entryRelationship typeCode="SUBJ">
       <supply classCode="SPLY" moodCode="RQO">

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

@@ -9,16 +9,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     <value nullFlavor="NA" xsi:type="CD" />
     {{#method}}
       <!-- QDM Attribute: Method -->

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

@@ -2,7 +2,6 @@
   <act classCode="ACT" moodCode="INT" {{{negation_ind}}}>
     <!--Encounter Recommended Act (V2) -->
     <templateId root="2.16.840.1.113883.10.20.24.3.134" extension="2019-12-01"/>
-    <id extension="{{object_id}}" root="1.3.6.1.4.1.115"/>
     <code code="ENC" codeSystem="2.16.840.1.113883.5.6" codeSystemName="ActClass" displayName="Encounter"/>
     <entryRelationship typeCode="SUBJ">
       <encounter classCode="ENC" moodCode="INT">

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

@@ -8,16 +8,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#authorDatetime}}
       <!-- QDM Attribute: Author dateTime -->
       {{> qrda_templates/template_partials/_author}}

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

@@ -6,16 +6,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#method}}
       <!-- QDM Attribute: Method -->
       {{> qrda_templates/template_partials/_method}}
@@ -50,5 +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/medication_discharge.mustache CHANGED

@@ -2,7 +2,6 @@
   <act classCode="ACT" moodCode="RQO" {{{negation_ind}}}>
     <!-- Discharge Medication Entry -->
     <templateId root="2.16.840.1.113883.10.20.24.3.105" extension="2019-12-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="75311-1" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Discharge medications"/>
     <statusCode code="active"/>
     {{#prescriber}}

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

@@ -2,7 +2,6 @@
   <act classCode="ACT" moodCode="EVN" {{{negation_ind}}}>
     <!-- Medication Dispensed Act -->
     <templateId root="2.16.840.1.113883.10.20.24.3.139" extension="2019-12-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="SPLY" codeSystem="2.16.840.1.113883.5.6" displayName="supply" codeSystemName="ActClass"/>
     <entryRelationship typeCode="SUBJ">
       <!--Medication dispensed -->
@@ -23,6 +22,9 @@
             <!-- QDM Attribute: Relevant Period -->
             {{{medication_duration_effective_time}}}
           {{/relevantPeriod}}
+          {{^relevantPeriod}}
+            <effectiveTime xsi:type="IVL_TS" nullFlavor="UNK"/>
+          {{/relevantPeriod}}
         {{/relevantDatetime}}
         <product>
           <manufacturedProduct classCode="MANU">

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

@@ -9,16 +9,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#result}}
     <!-- QDM Attribute: Result -->
     {{{result_value}}}
@@ -57,5 +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/procedure_performed.mustache CHANGED

@@ -8,16 +8,7 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="completed"/>
-    {{#relevantDatetime}}
-      <!-- QDM Attribute: Relevant dateTime -->
-      {{{relevant_date_time_value}}}
-    {{/relevantDatetime}}
-    {{^relevantDatetime}}
-      {{#relevantPeriod}}
-        <!-- QDM Attribute: Relevant Period -->
-        {{{relevant_period}}}
-      {{/relevantPeriod}}
-    {{/relevantDatetime}}
+    {{{relevant_date_period_or_null_flavor}}}
     {{#method}}
       <!-- QDM Attribute: Method -->
       {{> qrda_templates/template_partials/_method}}

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

@@ -6,6 +6,9 @@
     <templateId root="2.16.840.1.113883.10.20.24.3.75" extension="2019-12-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <statusCode code="active"/>
+    <effectiveTime xsi:type="IVL_TS">
+      <low nullFlavor="NA"/>
+    </effectiveTime>
     {{> qrda_templates/template_partials/_medication_details}}
     <consumable>
       <manufacturedProduct classCode="MANU">

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

@@ -3,7 +3,6 @@
     <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"/>
-    <statusCode code="completed"/>
     {{#relevantPeriod}}
     {{{relevant_period}}}
     {{/relevantPeriod}}

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

@@ -4,7 +4,7 @@
 <!-- US Realm Header Template Id -->
 <templateId root="2.16.840.1.113883.10.20.27.1.1" extension="2017-06-01"/>
 <!-- QRDA Category III Report - CMS (V4) -->
-<templateId root="2.16.840.1.113883.10.20.27.1.2" extension="2019-05-01"/>
+<templateId root="2.16.840.1.113883.10.20.27.1.2" extension="2020-05-01"/>
 <!-- This is the globally unique identifier for this QRDA document -->
 <id root="{{random_id}}"/>
 <!-- QRDA III document type code -->

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

@@ -96,20 +96,16 @@ module Qrda
           "</effectiveTime>"
         end
-        def relevant_period_as_value
-          "<effectiveTime #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"
-        end
-        def relevant_date_time_low
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['relevantDatetime'])}/>"\
-          "</effectiveTime>"
-        end
         def relevant_date_time_value
           "<effectiveTime #{value_or_null_flavor(self['relevantDatetime'])}/>"
         end
+        def relevant_date_period_or_null_flavor
+          return relevant_period if self['relevantPeriod']
+          return relevant_date_time_value if self['relevantDatetime']
+          "<effectiveTime nullFlavor='UNK'/>"
+        end
         def medication_duration_effective_time
           "<effectiveTime xsi:type=\"IVL_TS\">"\
           "<low #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"\

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

@@ -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

@@ -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

@@ -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
@@ -93,6 +97,9 @@ module QRDA
       end
       def extract_interval(parent_element, 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'])
@@ -111,9 +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
@@ -128,6 +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
@@ -153,7 +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)
@@ -166,6 +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
@@ -176,16 +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
@@ -193,8 +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
@@ -226,7 +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/diagnostic_study_performed_importer.rb CHANGED

@@ -21,7 +21,7 @@ module QRDA
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         diagnostic_study_performed = super
         diagnostic_study_performed.resultDatetime = extract_time(entry_element, @result_datetime_xpath)
-        diagnostic_study_performed.resultDatetime ||= extract_interval(entry_element, @result_datetime_xpath).low
+        diagnostic_study_performed.resultDatetime ||= extract_interval(entry_element, @result_datetime_xpath)&.low
         diagnostic_study_performed.status = code_if_present(entry_element.at_xpath(@status_xpath))
         diagnostic_study_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         diagnostic_study_performed.facilityLocation = extract_facility_locations(entry_element)[0]

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

@@ -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/data-element-importers/encounter_recommended_importer.rb CHANGED

@@ -3,7 +3,7 @@ module QRDA
     class EncounterRecommendedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.134']"))
         super(entry_finder)
-        @id_xpath = './cda:id'
+        @id_xpath = './cda:entryRelationship/cda:encounter/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.24']/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.24']/cda:author/cda:time"
         @facility_locations_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.24']/cda:participant[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.100']"

data/lib/qrda-import/data-element-importers/medication_discharge_importer.rb CHANGED

@@ -3,7 +3,7 @@ module QRDA
     class MedicationDischargeImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.105']"))
         super(entry_finder)
-        @id_xpath = './cda:id'
+        @id_xpath = './cda:entryRelationship/cda:substanceAdministration/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.16']/cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.16']/cda:author/cda:time"
         @refills_xpath = "./cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.16']/cda:repeatNumber"

data/lib/qrda-import/data-element-importers/medication_dispensed_importer.rb CHANGED

@@ -3,7 +3,7 @@ module QRDA
     class MedicationDispensedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.139']"))
         super(entry_finder)
-        @id_xpath = './cda:id'
+        @id_xpath = './cda:entryRelationship/cda:supply/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:product/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
         @relevant_period_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:effectiveTime"
         @relevant_date_time_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:effectiveTime"

data/lib/qrda-import/patient_importer.rb CHANGED

@@ -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
@@ -107,13 +110,20 @@ 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
       def key_elements_for_determining_encounter_uniqueness(encounter)
         codes = encounter.codes.collect { |dec| "#{dec.code}_#{dec.system}" }.sort.to_s
-        admission_date_time = encounter.relevantPeriod.low.to_s
-        discharge_date_time = encounter.relevantPeriod.high.to_s
+        admission_date_time = encounter&.relevantPeriod&.low.to_s
+        discharge_date_time = encounter&.relevantPeriod&.high.to_s
         "#{codes}#{admission_date_time}#{discharge_date_time}"
       end
@@ -131,17 +141,11 @@ module QRDA
           relations_to_add = []
           data_element.relatedTo.each do |related_to|
-            relations_to_add += entry_id_map["#{related_to.value}_#{related_to.namingSystem}"]
+            relations_to_add += entry_id_map["#{related_to['value']}_#{related_to['namingSystem']}"]
           end
           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

@@ -1,17 +1,31 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 3.0.0
+  version: 3.1.3
 platform: ruby
 authors:
 - The MITRE Corporation
-autorequire:
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-05-11 00:00:00.000000000 Z
+date: 2020-10-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.3
+- !ruby/object:Gem::Dependency
+  name: cqm-validators
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -314,7 +328,6 @@ files:
 - lib/qrda-import/data-element-importers/substance_recommended_importer.rb
 - lib/qrda-import/data-element-importers/symptom_importer.rb
 - lib/qrda-import/entry_finder.rb
-- lib/qrda-import/entry_package.rb
 - lib/qrda-import/narrative_reference_handler.rb
 - lib/qrda-import/patient_importer.rb
 - lib/util/code_system_helper.rb
@@ -330,7 +343,7 @@ 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 +358,8 @@ 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

@@ -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