cqm-reports 2.0.0 → 2.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: 9f52ee70f2be4c43ccf9c3d918ed805a323d942d1768d5621967c9232ea303c5
-  data.tar.gz: c866224aca04b6760a35a3fd0f8d78e03c5fe85d9bff0a4d41a8af907eebf995
+SHA1:
+  metadata.gz: dd0b9911f4358fceaa323afe6557281f181c2357
+  data.tar.gz: 2c2ba002d028ff2870fb7d6622231984611d0b9d
 SHA512:
-  metadata.gz: 42797a2e8c76511344a48f803034e6d5bc4bf1468b5fcd8853f53a10cea295413a96fea7299767dbfcef6b0cf7663e9f9e648715c3f3c7bb412e09391e08bb68
-  data.tar.gz: 94dc517b00e37117d00eea8ca516103bc3fa21af59457c7697e4299a4d2c92d8f46090fca4103cdfdbaede0aa6e130e3a52e3af1395564d447ccff712959cbd7
+  metadata.gz: 7980f689cd77ad9e2ba0869f89abdd1867a065108cbe8b9e534c7547de51fe3ded3169fc67e49826240bfe821e7bba779e0a1dc02a34955505e26afb6197e396
+  data.tar.gz: d37767e44596b127a5ea5197cb9c18dcdb36450661c23817ca84366e9a04ab7eebe4744d4e26e69682c76f4dd82bcd237667d46138cb4ec32f85a2b710b0df83

data/Gemfile

@@ -28,6 +28,6 @@ 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.git', branch: 'master'
+  gem 'cqm-validators'
   gem 'nokogiri-diff'
 end

data/README.md

@@ -4,15 +4,17 @@ A library for import and export of reports for use with electronic Clinical Qual
 Versioning
 ==========
 
-Starting with version **1.0.0.0** released on 5/22/2019, cqm-reports versioning has the format **W.X.Y.Z**, where:
+Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning has the format **X.Y.Z**, where:
 
-* **W** maps to a version of QRDA Category 1 and QRDA Category 3. See the table below to see the existing mapping to QRDA versions.
+* **X** maps to a version of QRDA. See the table below to see the existing mapping to QRDA versions.
 
-  | W | QRDA Cat 1 | QRDA Cat 3 |
+  | X | QRDA Cat 1 | QRDA Cat 3 |
   | --- | --- | --- |
-  | 1 | R1 STU5.1 | R1 STU2.1 |
+  | 2 | R1 STU5.1 | R1 STU2.1 |
 
-* **X.Y.Z** uses [SemVer](http://semver.org/) for versioning. **X.Y.Z** starts at 0.0.0 when **W** is incremented.
+* **Y** indicates major changes (incompatible API changes)
+
+* **Z** indicates minor changes (added functionality in a backwards-compatible manner) and patch changes (backwards-compatible bug fixes)
 
 For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-validators/tags).
 
@@ -24,4 +26,4 @@ Licensed under the Apache License, Version 2.0 (the "License"); you may not use
 
 http://www.apache.org/licenses/LICENSE-2.0
 
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

data/lib/cqm_report.rb

@@ -72,6 +72,4 @@ require_relative 'qrda-import/data-element-importers/substance_administered_impo
 require_relative 'qrda-import/data-element-importers/substance_order_importer.rb'
 require_relative 'qrda-import/data-element-importers/substance_recommended_importer.rb'
 require_relative 'qrda-import/data-element-importers/symptom_importer.rb'
-require_relative 'qrda-import/patient_importer.rb'
-require_relative 'ext/data_element.rb'
-require_relative 'ext/code.rb'
+require_relative 'qrda-import/patient_importer.rb'

data/lib/qrda-export/catI-r5/qrda_templates/allergy_intolerance.mustache

@@ -6,13 +6,8 @@
     <templateId root="2.16.840.1.113883.10.20.24.3.147" extension="2017-08-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>
-    {{#prevalencePeriod}}
-    {{#completed_prevalence_period}}
     <statusCode code="completed" />
-    {{/completed_prevalence_period}}
-    {{^completed_prevalence_period}}
-    <statusCode code="active" />
-    {{/completed_prevalence_period}}
+    {{#prevalencePeriod}}
     <!-- QDM Attribute: Prevalence Period -->
     {{{prevalence_period}}}
     {{/prevalencePeriod}}

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

@@ -6,6 +6,10 @@
           <!-- QDM Attribute: Category -->
           <code {{> _code}}/>
         {{/category}}
+        {{^category}}
+          <!-- QDM Attribute: Category -->
+          <code nullFlavor="NA"/>
+        {{/category}}
         <statusCode code="completed"/>
         {{#relevantPeriod}}
           <!-- QDM Attribute: Relevant Period -->
@@ -42,10 +46,9 @@
           <!-- QDM Attribute: Negation Rationale -->
           {{> qrda_templates/template_partials/_reason}}
         {{/negationRationale}}
-        {{^negationRationale}}
-        <entryRelationship typeCode="RSON">
+        <entryRelationship typeCode="REFR">
           <observation classCode="OBS" moodCode="EVN">
-            <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
+            <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"/>
@@ -53,7 +56,6 @@
             {{> qrda_templates/template_partials/_data_element_codes_as_values}}
           </observation>
         </entryRelationship>
-        {{/negationRationale}}
         {{#relatedTo}}
           <!-- QDM Attribute: relatedTo -->
           {{> qrda_templates/template_partials/_related_to}}

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

@@ -28,11 +28,11 @@
           <!-- QDM Attribute: Reason -->
           {{> qrda_templates/template_partials/_reason}}
         {{/reason}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </supply>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/device_recommended.mustache

@@ -27,11 +27,11 @@
           <!-- QDM Attribute: Reason -->
           {{> qrda_templates/template_partials/_reason}}
         {{/reason}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </supply>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/diagnosis.mustache

@@ -25,13 +25,8 @@
         <code code="29308-4" codeSystem="2.16.840.1.113883.6.1">
           <translation code="282291009" codeSystem="2.16.840.1.113883.6.96"/>
         </code>
-        {{#prevalencePeriod}}
-        {{#completed_prevalence_period}}
         <statusCode code="completed" />
-        {{/completed_prevalence_period}}
-        {{^completed_prevalence_period}}
-        <statusCode code="active" />
-        {{/completed_prevalence_period}}
+        {{#prevalencePeriod}}
         <!-- QDM Attribute: Prevalence Period -->
         {{{prevalence_period}}}
         {{/prevalencePeriod}}

data/lib/qrda-export/catI-r5/qrda_templates/encounter_order.mustache

@@ -25,11 +25,11 @@
           <!-- QDM Attribute: Reason -->
           {{> qrda_templates/template_partials/_reason}}
         {{/reason}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </encounter>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/encounter_performed.mustache

@@ -42,11 +42,11 @@
           <!-- QDM Attribute: Diagnoses -->
           {{> qrda_templates/template_partials/_encounter_diagnosis}}
         {{/diagnoses}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </encounter>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

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

@@ -27,11 +27,11 @@
           <!-- QDM Attribute: Reason -->
           {{> qrda_templates/template_partials/_reason}}
         {{/reason}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </encounter>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/immunization_administered.mustache

@@ -1,7 +1,7 @@
 <entry>
   <substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
     <!-- C-CDA R2 Immunization Activity -->
-    <templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2014-06-09"/>
+    <templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2015-08-01"/>
     <!-- Immunization Administered -->
     <templateId root="2.16.840.1.113883.10.20.24.3.140" extension="2017-08-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>

data/lib/qrda-export/catI-r5/qrda_templates/medication_discharge.mustache

@@ -35,9 +35,6 @@
         {{#authorDatetime}}
           {{> qrda_templates/template_partials/_author_participation}}
         {{/authorDatetime}}
-        {{#negationRationale}}
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}} 
       </substanceAdministration>
     </entryRelationship>
     {{#reason}}

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

@@ -60,11 +60,11 @@
               {{> qrda_templates/template_partials/_medication_supply_request}}
           </entryRelationship>
         {{/supply}}
-        {{#negationRationale}}
-          <!-- QDM Attribute: Negation Rationale -->
-          {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </supply>
     </entryRelationship>
+    {{#negationRationale}}
+      <!-- QDM Attribute: Negation Rationale -->
+      {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

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

@@ -17,6 +17,10 @@
     <!-- QDM Attribute: Result -->
     {{{result_value}}}
     {{/result}}
+    {{^result}}
+    <!-- QDM Attribute: Result -->
+    <value xsi:type="CD" nullFlavor="UNK"/>
+    {{/result}}
     {{#method}}
       <!-- QDM Attribute: Method -->
       {{> qrda_templates/template_partials/_method}}

data/lib/qrda-export/catI-r5/qrda_templates/symptom.mustache

@@ -25,13 +25,8 @@
         <code code="75325-1" codeSystem="2.16.840.1.113883.6.1">
           <translation code="418799008" displayName="Symptom" codeSystem="2.16.840.1.113883.6.96"/>
         </code>
-        {{#prevalencePeriod}}
-        {{#completed_prevalence_period}}
         <statusCode code="completed" />
-        {{/completed_prevalence_period}}
-        {{^completed_prevalence_period}}
-        <statusCode code="active" />
-        {{/completed_prevalence_period}}
+        {{#prevalencePeriod}}
         <!-- QDM Attribute: Prevalence Period -->
         {{{prevalence_period}}}
         {{/prevalencePeriod}}

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

@@ -8,7 +8,7 @@
 {{/negated}}
 {{^negated}}
 {{#dosage}}
-<!--  QDM Attribute: Dosage -->
-<doseQuantity value="{{value}}" unit="{{unit}}"/>
+  <!--  QDM Attribute: Dosage -->
+  {{{dose_quantity_value}}}
 {{/dosage}}
 {{/negated}}

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

@@ -30,7 +30,11 @@
 {{/negated}}
 {{^negated}}
 {{#dosage}}
+  <!--  QDM Attribute: Dosage -->
+  {{{dose_quantity_value}}}
+{{/dosage}}
+{{^dosage}}
 <!--  QDM Attribute: Dosage -->
-<doseQuantity value="{{value}}" unit="{{unit}}"/>
+<doseQuantity nullFlavor="UNK"/>
 {{/dosage}}
 {{/negated}}

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

@@ -13,5 +13,5 @@
     {{{author_effective_time}}}
     {{/authorDatetime}}
   {{/relevantPeriod}}
-  <quantity value="{{value}}"/>
+  <quantity value="{{{value_as_float}}}"/>
 </supply>

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

@@ -5,19 +5,7 @@
     <id root="1.3.6.1.4.1.115" extension="{{random_id}}"/>
     {{> _codes}}
     <statusCode code="completed"/>
-    {{#resultDatetime}}
     {{{result_date_time}}}
-    {{/resultDatetime}}
-    {{^resultDatetime}}
-      {{#relevantPeriod}}
-      {{{relevant_period_as_value}}}
-      {{/relevantPeriod}}
-      {{^relevantPeriod}}
-        {{#authorDatetime}}
-        {{{author_effective_time}}}
-        {{/authorDatetime}}
-      {{/relevantPeriod}}
-    {{/resultDatetime}}
     {{{result_value}}}
  </observation>
 </entryRelationship>

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

@@ -120,7 +120,7 @@ module Qrda
             end
             entry_populations << population if population
           end
-          return if population_groups.find {|pg| pg.populations.collect(&:id).sort == entry_populations.collect(&:id).sort }
+          return if population_groups.find {|pg| pg.populations.collect(&:id).compact.sort == entry_populations.collect(&:id).compact.sort }
 
           pg = PopulationGroup.new
           pg.populations = entry_populations

data/lib/qrda-export/helper/cat1_view_helper.rb

@@ -51,6 +51,15 @@ module Qrda
           translation_list
         end
 
+        def value_as_float
+          self['value'].to_f
+        end
+
+        def dose_quantity_value
+          return "<doseQuantity value=\"#{value_as_float}\" unit=\"#{self['unit']}\"/>" if self['unit']
+          "<doseQuantity value=\"#{value_as_float}\" />"
+        end
+
         def result_value
           return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless self['result']
 

data/lib/qrda-import/base-importers/section_importer.rb

@@ -49,7 +49,7 @@ module QRDA
         if @result_xpath
           entry.result = extract_result_values(entry_element)
         end
-        extract_reason_or_negation(entry_element, entry)
+        extract_negation(entry_element, entry)
         entry
       end
 
@@ -95,13 +95,13 @@ module QRDA
           high_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
         end
         if parent_element.at_xpath("#{interval_xpath}/cda:low")
-          low_time = DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:low")['value'])
+          low_time = if parent_element.at_xpath("#{interval_xpath}/cda:low")['value']
+                       DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:low")['value'])
+                     end
         end
         if parent_element.at_xpath("#{interval_xpath}/cda:high")
           high_time = if parent_element.at_xpath("#{interval_xpath}/cda:high")['value']
                         DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:high")['value'])
-                      else
-                        DateTime.new(9999,1,1)
                       end
         end
         if parent_element.at_xpath("#{interval_xpath}/cda:center")
@@ -125,8 +125,7 @@ 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
-        oid = value[:codeSystem] || value[:codeSystemOid]
-        QDM::Code.new(key, oid)
+        QDM::Code.new(key, value[:code_system])
       end
 
       def extract_frequency_in_hours(parent_element, frequency_xpath)
@@ -140,7 +139,8 @@ module QRDA
         # Expected units are H (hours) and D (days)
         if unit && unit.upcase == 'D'
           low = low * 24 if low
-          high = high * 34 if high
+          high = high * 24 if high
+          unit = 'h'
         end
         { low: low, high: high, unit: unit, institution_specified: institution_specified }
       end
@@ -158,32 +158,36 @@ module QRDA
 
         value = value_element['value']
         if value.present?
-          return value.strip.to_i if (value_element['unit'] == "1" || value_element['unit'].nil?)
+          return value.strip.to_f if (value_element['unit'] == "1" || value_element['unit'].nil?)
 
-          return QDM::Quantity.new(value.strip.to_i, value_element['unit'])
+          return QDM::Quantity.new(value.strip.to_f, value_element['unit'])
         elsif value_element['code'].present?
           return code_if_present(value_element)
         end
       end
 
-      # extracts the reason or negation data. if an element is negated and the code has a null flavor, a random code is assigned for calculation
-      # coded_parent_element is the 'parent' element when the coded is nested (e.g., medication order)
-      def extract_reason_or_negation(parent_element, entry, coded_parent_element = nil)
-        coded_parent_element ||= parent_element
-        reason_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 | .//cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code")
+      def extract_reason(parent_element)
+        return unless @reason_xpath
+        reason_element = parent_element.xpath(@reason_xpath)
         negation_indicator = parent_element['negationInd']
-        unless reason_element.blank?
-          if negation_indicator.eql?('true')
-            entry.negationRationale = code_if_present(reason_element.first)
-          else
-            entry.reason = code_if_present(reason_element.first) unless @entry_does_not_have_reason
-          end
-        end
-        extract_negated_code(coded_parent_element, entry)
+        # 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) 
+      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') 
+        
+        entry.negationRationale = code_if_present(negation_element.first) unless negation_element.blank?
+        extract_negated_code(parent_element, entry)
       end
 
-      def extract_negated_code(coded_parent_element, entry)
-        code_elements = coded_parent_element.xpath(@code_xpath)
+      def extract_negated_code(parent_element, entry)
+        code_elements = parent_element.xpath(@code_xpath)
         code_elements.each do |code_element|
           if code_element['nullFlavor'] == 'NA' && code_element['sdtc:valueSet']
             entry.dataElementCodes = [{ code: code_element['sdtc:valueSet'], codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
@@ -193,9 +197,9 @@ module QRDA
 
       def extract_scalar(parent_element, scalar_xpath)
         scalar_element = parent_element.at_xpath(scalar_xpath)
-        return unless scalar_element
+        return unless scalar_element && scalar_element['value'].present?
 
-        QDM::Quantity.new(scalar_element['value'].to_i, scalar_element['unit'])
+        QDM::Quantity.new(scalar_element['value'].to_f, scalar_element['unit'])
       end
 
       def extract_components(parent_element)