cqm-reports 1.0.0.0 → 2.0.4

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

@@ -10,6 +10,7 @@ module QRDA
         @dosage_xpath = "./cda:doseQuantity"
         @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
         @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::MedicationAdministered
       end
 
@@ -18,6 +19,7 @@ module QRDA
         medication_administered.dosage = extract_scalar(entry_element, @dosage_xpath)
         medication_administered.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
         medication_administered.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        medication_administered.reason = extract_reason(entry_element)
         medication_administered
       end
 

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

@@ -3,7 +3,6 @@ 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)
-        @entry_does_not_have_reason = true
         @id_xpath = './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"

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

@@ -15,6 +15,7 @@ module QRDA
         @setting_xpath = "./cda:participant/cda:participantRole/cda:code"
         @prescriber_id_xpath = "./cda:author/cda:assignedAuthor/cda:id"
         @days_supplied_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.157']/cda:quantity"
+        @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::MedicationOrder
       end
 
@@ -28,6 +29,7 @@ module QRDA
         medication_order.setting = code_if_present(entry_element.at_xpath(@setting_xpath))
         medication_order.prescriberId = extract_id(entry_element, @prescriber_id_xpath)
         medication_order.daysSupplied = extract_scalar(entry_element, @days_supplied_xpath)&.value
+        medication_order.reason = extract_reason(entry_element)
         medication_order
       end
 

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

@@ -6,11 +6,13 @@ module QRDA
         @id_xpath = './cda:id'
         @code_xpath = './cda:value'
         @relevant_period_xpath = "./cda:effectiveTime"
+        @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::PatientCharacteristicClinicalTrialParticipant
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         patient_characteristic_clinical_trial_participant = super
+        patient_characteristic_clinical_trial_participant.reason = extract_reason(entry_element)
         patient_characteristic_clinical_trial_participant
       end
 

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

@@ -7,12 +7,14 @@ module QRDA
         @code_xpath = "./cda:value"
         @author_datetime_xpath = "./cda:author/cda:time"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
+        @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::PhysicalExamOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         physical_exam_order = super
         physical_exam_order.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
+        physical_exam_order.reason = extract_reason(entry_element)
         physical_exam_order
       end
 

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

@@ -11,6 +11,7 @@ module QRDA
         @result_xpath = "./cda:value"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @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::PhysicalExamPerformed
       end
 
@@ -19,6 +20,7 @@ module QRDA
         physical_exam_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         physical_exam_performed.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         physical_exam_performed.components = extract_components(entry_element)
+        physical_exam_performed.reason = extract_reason(entry_element)
         physical_exam_performed
       end
 

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

@@ -7,12 +7,14 @@ module QRDA
         @code_xpath = "./cda:value"
         @author_datetime_xpath = "./cda:author/cda:time"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
+        @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::PhysicalExamRecommended
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         physical_exam_recommended = super
         physical_exam_recommended.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
+        physical_exam_recommended.reason = extract_reason(entry_element)
         physical_exam_recommended
       end
 

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

@@ -8,6 +8,7 @@ module QRDA
         @author_datetime_xpath = "./cda:author/cda:time"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @ordinality_xpath = "./cda:priorityCode"
+        @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::ProcedureOrder
       end
 
@@ -15,6 +16,7 @@ module QRDA
         procedure_order = super
         procedure_order.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         procedure_order.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
+        procedure_order.reason = extract_reason(entry_element)
         procedure_order
       end
 

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

@@ -14,6 +14,7 @@ module QRDA
         @ordinality_xpath = "./cda:priorityCode"
         @incision_datetime_xpath = "./cda:entryRelationship/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.89']/cda:effectiveTime"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @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::ProcedurePerformed
       end
 
@@ -25,6 +26,7 @@ module QRDA
         procedure_performed.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
         procedure_performed.incisionDatetime = extract_time(entry_element, @incision_datetime_xpath)
         procedure_performed.components = extract_components(entry_element)
+        procedure_performed.reason = extract_reason(entry_element)
         procedure_performed
       end
 

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

@@ -8,6 +8,7 @@ module QRDA
         @author_datetime_xpath = "./cda:author/cda:time"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @ordinality_xpath = "./cda:priorityCode"
+        @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::ProcedureRecommended
       end
 
@@ -15,6 +16,7 @@ module QRDA
         procedure_recommended = super
         procedure_recommended.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         procedure_recommended.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
+        procedure_recommended.reason = extract_reason(entry_element)
         procedure_recommended
       end
 

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

@@ -3,7 +3,6 @@ module QRDA
     class SubstanceAdministeredImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']"))
         super(entry_finder)
-        @entry_does_not_have_reason = true
         @id_xpath = './cda:id'
         @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -109,7 +109,7 @@ 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|

data/lib/util/code_system_helper.rb

@@ -6,7 +6,6 @@ module HQMF
         '2.16.840.1.113883.6.1' =>    'LOINC',
         '2.16.840.1.113883.6.96' =>   'SNOMEDCT',
         '2.16.840.1.113883.6.12' =>   'CPT',
-        #'2.16.840.1.113883.3.88.12.80.32' => 'CPT', # Encounter Type from C32, a subset of CPT
         '2.16.840.1.113883.6.88' =>   'RXNORM',
         '2.16.840.1.113883.6.103' =>  'ICD9CM',
         '2.16.840.1.113883.6.104' =>  'ICD9CM',
@@ -35,37 +34,17 @@ module HQMF
         '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
         '2.16.840.1.113883.6.13' => 'CDT',
         '2.16.840.1.113883.18.2' => 'AdministrativeSex',
-        '2.16.840.1.113883.5.1' => 'AdministrativeGender'
-      }
-
-      CODE_SYSTEM_ALIASES = {
-        'FDA SPL' => 'NCI Thesaurus',
-        'HSLOC' => 'HL7 Healthcare Service Location',
-        'SOP' => "Source of Payment Typology"
-      }
-
-      # Some old OID are still around in data, this hash maps retired OID values to
-      # the new value
-      OID_ALIASES = {
-        '2.16.840.1.113883.6.59' => '2.16.840.1.113883.12.292' # CVX
-      }
+        '2.16.840.1.113883.5.1' => 'AdministrativeGender',
+        '1.2.3.4.5.6.7.8.9.10' => 'NA_VALUESET'
+      }.freeze
 
       # Returns the name of a code system given an oid
       # @param [String] oid of a code system
       # @return [String] the name of the code system as described in the measure definition JSON
       def self.code_system_for(oid)
-        oid = OID_ALIASES[oid] if OID_ALIASES[oid]
         CODE_SYSTEMS[oid] || "Unknown"
       end
 
-      # Returns the oid for a code system given a codesystem name
-      # @param [String] the name of the code system
-      # @return [String] the oid of the code system
-      def self.oid_for_code_system(code_system)
-        code_system = CODE_SYSTEM_ALIASES[code_system] if CODE_SYSTEM_ALIASES[code_system]
-        CODE_SYSTEMS.invert[code_system]
-      end
-
       # Returns the whole map of OIDs to code systems
       # @terurn [Hash] oids as keys, code system names as values
       def self.code_systems

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 1.0.0.0
+  version: 2.0.4
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-22 00:00:00.000000000 Z
+date: 2019-08-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.1.0
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.1.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -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
@@ -248,7 +248,10 @@ files:
 - lib/qrda-export/catIII-r2-1/qrda_header/_author.mustache
 - lib/qrda-export/catIII-r2-1/qrda_header/_custodian.mustache
 - lib/qrda-export/catIII-r2-1/qrda_header/_documentation_of_service_event.mustache
+- lib/qrda-export/catIII-r2-1/qrda_header/_information_recipient.mustache
 - lib/qrda-export/catIII-r2-1/qrda_header/_legal_authenticator.mustache
+- lib/qrda-export/catIII-r2-1/qrda_header/_participant_ehr.mustache
+- lib/qrda-export/catIII-r2-1/qrda_header/_participant_location.mustache
 - lib/qrda-export/helper/aggregate_object_helper.rb
 - lib/qrda-export/helper/cat1_view_helper.rb
 - lib/qrda-export/helper/date_helper.rb
@@ -335,8 +338,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: A library for import and export of reports for use with electronic Clinical