cqm-reports 2.0.4 → 2.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: ad6bc7084fe1a758d982a929b4175c5ffecc3c3ec1f070bd8ff4944539f469da
-  data.tar.gz: fb3c251103f1d3e6dae7f138ba9e6f72f261e43650aaada83895eeaca6e1a64b
+SHA1:
+  metadata.gz: dd0b9911f4358fceaa323afe6557281f181c2357
+  data.tar.gz: 2c2ba002d028ff2870fb7d6622231984611d0b9d
 SHA512:
-  metadata.gz: 643b2cc26827bf8507df366ee0354dd2ef6a9b9039be532a289cdebc4178e05edb894bf2eaa4c3fc9b1f3ff8c8d6516c6d82fdc4bdf68189b759d0b83cb9bf13
-  data.tar.gz: d968b34bdc0e4f0e07ac4a52a403fd494ac1e23dd540fa6557b42a055e2c2ff20782db2d80d11e5ce1695c3be467a1a22795d832dc27165c38178770d19ad09c
+  metadata.gz: 7980f689cd77ad9e2ba0869f89abdd1867a065108cbe8b9e534c7547de51fe3ded3169fc67e49826240bfe821e7bba779e0a1dc02a34955505e26afb6197e396
+  data.tar.gz: d37767e44596b127a5ea5197cb9c18dcdb36450661c23817ca84366e9a04ab7eebe4744d4e26e69682c76f4dd82bcd237667d46138cb4ec32f85a2b710b0df83

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

@@ -8,7 +8,7 @@
         {{/category}}
         {{^category}}
           <!-- QDM Attribute: Category -->
-          <code nullFlavor="UNK"/>
+          <code nullFlavor="NA"/>
         {{/category}}
         <statusCode code="completed"/>
         {{#relevantPeriod}}
@@ -48,7 +48,7 @@
         {{/negationRationale}}
         <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"/>

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/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/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-import/patient_importer.rb

@@ -78,16 +78,30 @@ module QRDA
           new_data_elements = []
 
           id_map.each_value do |elem_ids|
-            
             elem_id = elem_ids.first
             data_element = data_elements.find { |de| de.id == elem_id }
+            # Keep the first element with a shared ID
+            new_data_elements << data_element
 
-            elem_ids[1,elem_ids.length].each do |merge_id|
-              merge_element = data_elements.find { |de| de.id == merge_id }
-              data_element.merge!(merge_element)
-            end
+            # Encounters require elements beyond id for uniqueness
+            next unless data_element._type == 'QDM::EncounterPerformed'
+            unique_element_keys = []
+            # Add key_elements_for_determining_encounter_uniqueness to array, this is used to determine if other
+            # elements with the same ID should be considered as unique
+            unique_element_keys << key_elements_for_determining_encounter_uniqueness(data_element)
 
-            new_data_elements << data_element
+            # Loop through all other data elements with the same 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
+              # If all key fields match, move on.
+              next if unique_element_keys.include?(dup_element_keys)
+              # If all key fields don't match, keep element
+              new_data_elements << dup_element
+              # Add to list of unique element keys
+              unique_element_keys << dup_element_keys
+            end
           end
 
           patient.qdmPatient.dataElements << new_data_elements
@@ -95,6 +109,13 @@ module QRDA
         end
       end
 
+      def key_elements_for_determining_encounter_uniqueness(encounter)
+        codes = encounter.codes.collect { |dec| "#{dec.code}_#{dec.codeSystemOid}" }.sort.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
+
       def get_patient_expired(record, doc)
         entry_elements = 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']/cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
         return unless entry_elements.empty?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 2.0.4
+  version: 2.0.5
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-28 00:00:00.000000000 Z
+date: 2019-10-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -147,8 +147,6 @@ files:
 - README.md
 - Rakefile
 - lib/cqm_report.rb
-- lib/ext/code.rb
-- lib/ext/data_element.rb
 - lib/html-export/qdm-patient/_header_css.mustache
 - lib/html-export/qdm-patient/_javascript.mustache
 - lib/html-export/qdm-patient/data_element/_data_element.mustache
@@ -338,7 +336,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubyforge_project: 
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: A library for import and export of reports for use with electronic Clinical

data/lib/ext/code.rb

@@ -1,11 +0,0 @@
-module QDM
-  class Code    
-    def ==(other)
-      return false unless other.is_a? QDM::Code
-
-      (code == other.code) && (codeSystem == other.codeSystem) && (codeSystemOid == other.codeSystemOid) && (version == other.version)
-    end
-
-    alias eql? ==
-  end
-end

data/lib/ext/data_element.rb

@@ -1,24 +0,0 @@
-module QDM
-  class DataElement
-    def merge!(other)
-      # ensure they're the same category (e.g. 'encounter')
-      return unless qdmCategory == other.qdmCategory
-
-      # ensure they're the same status (e.g. 'performed'), and that they both have a status set (or that they both don't)
-      return if respond_to?(:qdmStatus) && !other.respond_to?(:qdmStatus)
-      return if !respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus)
-      return if respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus) && qdmStatus != other.qdmStatus
-      
-      # iterate over non-code fields
-      fields.each_key do |field|
-        next if field[0] == '_' || %w[dataElementCodes qdmCategory qdmVersion qdmStatus].include?(field)
-        
-        if send(field).nil?
-          send(field + '=', other.send(field))
-        end
-      end
-
-      self.dataElementCodes = dataElementCodes.concat(other.dataElementCodes).uniq
-    end
-  end
-end