cqm-reports 2.0.0 → 2.0.5

data/lib/qrda-import/data-element-importers/substance_order_importer.rb

@@ -11,6 +11,7 @@ module QRDA
         @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
         @refills_xpath = "./cda:repeatNumber"
         @route_xpath = "./cda:routeCode"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::SubstanceOrder
       end
 
@@ -21,6 +22,7 @@ module QRDA
         substance_order.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
         substance_order.refills = extract_scalar(entry_element, @refills_xpath)&.value
         substance_order.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        substance_order.reason = extract_reason(entry_element)
         substance_order
       end
 

data/lib/qrda-import/data-element-importers/substance_recommended_importer.rb

@@ -10,6 +10,7 @@ module QRDA
         @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
         @refills_xpath = "./cda:repeatNumber"
         @route_xpath = "./cda:routeCode"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::SubstanceRecommended
       end
 
@@ -19,6 +20,7 @@ module QRDA
         substance_recommended.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
         substance_recommended.refills = extract_scalar(entry_element, @refills_xpath)&.value
         substance_recommended.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        substance_recommended.reason = extract_reason(entry_element)
         substance_recommended
       end
 

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?
@@ -109,7 +130,7 @@ module QRDA
 
           relations_to_add = []
           data_element.relatedTo.each do |related_to|
-            relations_to_add << entry_id_map[related_to.value]
+            relations_to_add << entry_id_map["#{related_to.value}_#{related_to.namingSystem}"]
           end
           data_element.relatedTo.destroy
           relations_to_add.each do |relation_to_add|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.5
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-20 00:00:00.000000000 Z
+date: 2019-10-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -44,56 +44,56 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: '2.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: '2.7'
 - !ruby/object:Gem::Dependency
   name: mongoid-tree
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '2.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '2.1'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.10.3
+        version: '1.10'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.10.3
+        version: '1.10'
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.3.7
+        version: '2.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.3.7
+        version: '2.3'
 - !ruby/object:Gem::Dependency
   name: zip-zip
   requirement: !ruby/object:Gem::Requirement
@@ -114,28 +114,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.10
+        version: '1.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.10
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: memoist
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.1
+        version: '0.9'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.1
+        version: '0.9'
 description: A library for import and export of reports for use with electronic Clinical
   Quality Measures (eCQMs).
 email: tacoma-list@lists.mitre.org
@@ -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